From ecfc03c4ed025a92b9d795b8d6e26619202539aa Mon Sep 17 00:00:00 2001
From: alex-l-kong <alkong@ucdavis.edu>
Date: Thu, 22 Aug 2024 12:10:48 -0700
Subject: [PATCH 01/58] Enforce exact_match=True for get_estimated_time

---
 src/toffy/mph_comp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toffy/mph_comp.py b/src/toffy/mph_comp.py
index 92bd0d3d..d93f0814 100644
--- a/src/toffy/mph_comp.py
+++ b/src/toffy/mph_comp.py
@@ -24,7 +24,7 @@ def get_estimated_time(bin_file_dir, fov):
     io_utils.validate_paths(bin_file_dir)
 
     # get fov json file in bin_file_path
-    json_file = io_utils.list_files(bin_file_dir, fov + ".json")
+    json_file = io_utils.list_files(bin_file_dir, fov + ".json", exact_match=True)
     if len(json_file) == 0:
         raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")
 

From 221bcdd1b5826cb828a7c4c9cee69ca8f9803c7c Mon Sep 17 00:00:00 2001
From: alex-l-kong <alkong@ucdavis.edu>
Date: Wed, 11 Sep 2024 15:51:33 -0700
Subject: [PATCH 02/58] Ensure we're not searching for the actual extension

---
 src/toffy/mph_comp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toffy/mph_comp.py b/src/toffy/mph_comp.py
index d93f0814..c5ee1b4a 100644
--- a/src/toffy/mph_comp.py
+++ b/src/toffy/mph_comp.py
@@ -24,7 +24,7 @@ def get_estimated_time(bin_file_dir, fov):
     io_utils.validate_paths(bin_file_dir)
 
     # get fov json file in bin_file_path
-    json_file = io_utils.list_files(bin_file_dir, fov + ".json", exact_match=True)
+    json_file = io_utils.list_files(bin_file_dir, fov, exact_match=True)
     if len(json_file) == 0:
         raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")
 

From fb2f4c002e47b3355e235f3f6dda801236030765 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Thu, 12 Sep 2024 08:55:56 -0700
Subject: [PATCH 03/58] Modify list_files to use "correct" syntax for
 exact_match=True and filter out non-.json

---
 src/toffy/mph_comp.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/toffy/mph_comp.py b/src/toffy/mph_comp.py
index c5ee1b4a..78e46ed5 100644
--- a/src/toffy/mph_comp.py
+++ b/src/toffy/mph_comp.py
@@ -24,7 +24,8 @@ def get_estimated_time(bin_file_dir, fov):
     io_utils.validate_paths(bin_file_dir)
 
     # get fov json file in bin_file_path
-    json_file = io_utils.list_files(bin_file_dir, fov, exact_match=True)
+    json_file = sorted(io_utils.list_files(bin_file_dir, fov, exact_match=True))
+    json_file = list(filter(lambda f: ".json" in f, json_file))
     if len(json_file) == 0:
         raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")
 

From 0f4e63f8f0bd46bba3436ea364e6a1d94502f1af Mon Sep 17 00:00:00 2001
From: alex-l-kong <alkong@ucdavis.edu>
Date: Thu, 12 Sep 2024 14:26:59 -0700
Subject: [PATCH 04/58] Make workflow of getting bin file easier

---
 src/toffy/mph_comp.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/toffy/mph_comp.py b/src/toffy/mph_comp.py
index 78e46ed5..19dc7835 100644
--- a/src/toffy/mph_comp.py
+++ b/src/toffy/mph_comp.py
@@ -24,13 +24,12 @@ def get_estimated_time(bin_file_dir, fov):
     io_utils.validate_paths(bin_file_dir)
 
     # get fov json file in bin_file_path
-    json_file = sorted(io_utils.list_files(bin_file_dir, fov, exact_match=True))
-    json_file = list(filter(lambda f: ".json" in f, json_file))
-    if len(json_file) == 0:
+    json_file = os.path.join(bin_file_dir, f"{fov}.json")
+    if not os.path.exists(json_file) == 0:
         raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")
 
     # retrieve estimated time (frame dimensions x pixel dwell time)
-    run_metadata = read_json_file(os.path.join(bin_file_dir, json_file[0]), encoding="utf-8")
+    run_metadata = read_json_file(json_file, encoding="utf-8")
     try:
         size = run_metadata.get("frameSize")
         time = run_metadata.get("dwellTimeMillis")

From 553d4cc2433a3d30252c923ab6e559a10428b4a3 Mon Sep 17 00:00:00 2001
From: alex-l-kong <alkong@ucdavis.edu>
Date: Thu, 12 Sep 2024 14:33:12 -0700
Subject: [PATCH 05/58] Remove the == 0

---
 src/toffy/mph_comp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toffy/mph_comp.py b/src/toffy/mph_comp.py
index 19dc7835..1020a8f4 100644
--- a/src/toffy/mph_comp.py
+++ b/src/toffy/mph_comp.py
@@ -25,7 +25,7 @@ def get_estimated_time(bin_file_dir, fov):
 
     # get fov json file in bin_file_path
     json_file = os.path.join(bin_file_dir, f"{fov}.json")
-    if not os.path.exists(json_file) == 0:
+    if not os.path.exists(json_file):
         raise FileNotFoundError(f"The FOV name supplied doesn't have a JSON file: {fov}")
 
     # retrieve estimated time (frame dimensions x pixel dwell time)

From 326e9c25d25ad6a75d364ff6dab4554ca76b3167 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Fri, 13 Sep 2024 11:50:11 -0700
Subject: [PATCH 06/58] Add processing.json files to test

---
 data/combined/fov-1-scan-1_processing.json | 0
 data/combined/fov-2-scan-1_processing.json | 0
 data/combined/fov-3-scan-1_processing.json | 0
 data/combined/fov-4-scan-1_processing.json | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 data/combined/fov-1-scan-1_processing.json
 create mode 100644 data/combined/fov-2-scan-1_processing.json
 create mode 100644 data/combined/fov-3-scan-1_processing.json
 create mode 100644 data/combined/fov-4-scan-1_processing.json

diff --git a/data/combined/fov-1-scan-1_processing.json b/data/combined/fov-1-scan-1_processing.json
new file mode 100644
index 00000000..e69de29b
diff --git a/data/combined/fov-2-scan-1_processing.json b/data/combined/fov-2-scan-1_processing.json
new file mode 100644
index 00000000..e69de29b
diff --git a/data/combined/fov-3-scan-1_processing.json b/data/combined/fov-3-scan-1_processing.json
new file mode 100644
index 00000000..e69de29b
diff --git a/data/combined/fov-4-scan-1_processing.json b/data/combined/fov-4-scan-1_processing.json
new file mode 100644
index 00000000..e69de29b

From a529f537b6af26822cfbd40ef4b02d22cc9138fa Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 14:23:36 -0700
Subject: [PATCH 07/58] Fix bin file generation by simulating update only after
 .json file written (not immediately after .bin file written)

---
 tests/fov_watcher_test.py | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index df50326f..d354de1a 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -50,6 +50,7 @@ def _slow_copy_sample_tissue_data(
         temp_bin (bool):
             Use initial temp bin file paths or not
     """
+    num_bin_files = 0
     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
         time.sleep(delta)
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
@@ -69,20 +70,22 @@ def _slow_copy_sample_tissue_data(
                 time.sleep(delta)
                 copied_tissue_path = os.path.join(dest, "." + tissue_file + ".aBcDeF")
                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
+
             else:
                 shutil.copy(tissue_path, dest)
 
-    # get all .bin files
-    bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
-
-    # simulate updating the creation time for some .bin files, this tests _check_bin_updates
-    for i, bfile in enumerate(bin_files):
-        if i % 2 == 0:
-            shutil.copy(
-                os.path.join(COMBINED_DATA_PATH, bfile), os.path.join(dest, bfile + ".temp")
-            )
-            os.remove(os.path.join(dest, bfile))
-            os.rename(os.path.join(dest, bfile + ".temp"), os.path.join(dest, bfile))
+            # simulate a timestamp update if .bin file has been extracted
+            # NOTE: this assumes .json file always copies after the .bin, which does happen on Ionpath
+            tissue_data = os.path.splitext(tissue_file)
+            if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
+                if num_bin_files % 2 == 0:
+                    bin_file_name = tissue_data[0] + ".bin"
+                    shutil.copy(
+                        os.path.join(COMBINED_DATA_PATH, bin_file_name), os.path.join(dest, bin_file_name + ".temp")
+                    )
+                    os.remove(os.path.join(dest, bin_file_name))
+                    os.rename(os.path.join(dest, bin_file_name + ".temp"), os.path.join(dest, bin_file_name))
+                num_bin_files += 1
 
 
 COMBINED_RUN_JSON_SPOOF = {
@@ -255,7 +258,6 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
-    print("The watcher start lag is: %d" % watcher_start_lag)
     try:
         with tempfile.TemporaryDirectory() as tmpdir:
             tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)

From 875da781d4bade04198d942b72d817f500081462 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 14:26:44 -0700
Subject: [PATCH 08/58] Formatting to avoid going over 100 characters per line

---
 tests/fov_watcher_test.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index d354de1a..ba54e2c4 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -81,10 +81,14 @@ def _slow_copy_sample_tissue_data(
                 if num_bin_files % 2 == 0:
                     bin_file_name = tissue_data[0] + ".bin"
                     shutil.copy(
-                        os.path.join(COMBINED_DATA_PATH, bin_file_name), os.path.join(dest, bin_file_name + ".temp")
+                        os.path.join(COMBINED_DATA_PATH, bin_file_name),
+                        os.path.join(dest, bin_file_name + ".temp")
                     )
                     os.remove(os.path.join(dest, bin_file_name))
-                    os.rename(os.path.join(dest, bin_file_name + ".temp"), os.path.join(dest, bin_file_name))
+                    os.rename(
+                        os.path.join(dest, bin_file_name + ".temp"),
+                        os.path.join(dest, bin_file_name)
+                    )
                 num_bin_files += 1
 
 

From 673cd5352f774b3ddb810bc916de1ca3f714893a Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 14:29:03 -0700
Subject: [PATCH 09/58] Add trailing comma to please black linter

---
 tests/fov_watcher_test.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index ba54e2c4..8d220cae 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -82,12 +82,12 @@ def _slow_copy_sample_tissue_data(
                     bin_file_name = tissue_data[0] + ".bin"
                     shutil.copy(
                         os.path.join(COMBINED_DATA_PATH, bin_file_name),
-                        os.path.join(dest, bin_file_name + ".temp")
+                        os.path.join(dest, bin_file_name + ".temp"),
                     )
                     os.remove(os.path.join(dest, bin_file_name))
                     os.rename(
                         os.path.join(dest, bin_file_name + ".temp"),
-                        os.path.join(dest, bin_file_name)
+                        os.path.join(dest, bin_file_name),
                     )
                 num_bin_files += 1
 

From 77c7cb6b02194028a3ba1ba80a49fd296a62e623 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 20:56:23 -0700
Subject: [PATCH 10/58] Print statement debugging

---
 tests/fov_watcher_test.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 8d220cae..1de4d39a 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -80,15 +80,19 @@ def _slow_copy_sample_tissue_data(
             if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
                 if num_bin_files % 2 == 0:
                     bin_file_name = tissue_data[0] + ".bin"
+                    print(f"Simulating .bin file update on {bin_file_name}")
                     shutil.copy(
                         os.path.join(COMBINED_DATA_PATH, bin_file_name),
                         os.path.join(dest, bin_file_name + ".temp"),
                     )
+                    print("Renamed bin file to temp")
                     os.remove(os.path.join(dest, bin_file_name))
+                    print("Removed old bin file")
                     os.rename(
                         os.path.join(dest, bin_file_name + ".temp"),
                         os.path.join(dest, bin_file_name),
                     )
+                    print("Renamed temp bin file back to orig")
                 num_bin_files += 1
 
 

From 4392878fe16950d3dcb15eaf703e47075564d50f Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 23:10:29 -0700
Subject: [PATCH 11/58] See if an OSError is being thrown

---
 tests/fov_watcher_test.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 1de4d39a..a7ba08da 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -427,8 +427,9 @@ def test_watcher(
             # pulse heights check
             validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
 
-    except OSError:
-        warnings.warn("Temporary file cleanup was incomplete.")
+    except OSError as ose:
+        print(ose)
+        # warnings.warn("Temporary file cleanup was incomplete.")
 
 
 def test_watcher_missing_fovs():

From 660ec0ae9de2dff0f6e34975227be43d10362fae Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 23:26:13 -0700
Subject: [PATCH 12/58] More debugging statements: need to see the MPH process

---
 src/toffy/normalize.py         | 3 +++
 src/toffy/watcher_callbacks.py | 1 +
 2 files changed, 4 insertions(+)

diff --git a/src/toffy/normalize.py b/src/toffy/normalize.py
index 956352f8..6d7694e9 100644
--- a/src/toffy/normalize.py
+++ b/src/toffy/normalize.py
@@ -65,14 +65,17 @@ def write_mph_per_mass(
         proficient (bool): whether proficient MPH data is written or not
     """
     # compute pulse heights
+    print("Inside writing MPH per mass")
     panel = make_panel(
         mass=masses, target_name=masses, low_range=start_offset, high_range=stop_offset
     )
 
     # generate the MPH values for each mass
+    print("About to get median pulse height")
     mph_vals = list(
         get_median_pulse_height(data_dir=base_dir, fov=fov, channels=masses, panel=panel).values()
     )
+    print("Computed median pulse height")
 
     fovs = np.repeat(fov, len(masses))
     out_df = pd.DataFrame({"mass": masses, "fov": fovs, "pulse_height": mph_vals})
diff --git a/src/toffy/watcher_callbacks.py b/src/toffy/watcher_callbacks.py
index 14dbfaf0..f69da667 100644
--- a/src/toffy/watcher_callbacks.py
+++ b/src/toffy/watcher_callbacks.py
@@ -369,6 +369,7 @@ def generate_pulse_heights(self, pulse_out_dir: str, panel: pd.DataFrame = None,
              - start_offset
              - stop_offset
         """
+        print("Inside computing pulse heights")
         if not os.path.exists(pulse_out_dir):
             os.makedirs(pulse_out_dir)
 

From 6dea20b136add907a1c996c74f813aed9eb5eaee Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 23:35:27 -0700
Subject: [PATCH 13/58] Test the presence and contents of log_out

---
 tests/fov_watcher_test.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index a7ba08da..3a87fec0 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -381,6 +381,9 @@ def test_watcher(
 
                     res_scan.get()
 
+            print("Testing log out status")
+            print(log_out)
+            print(os.listdir(log_out))
             with open(os.path.join(log_out, "test_run_log.txt")) as f:
                 logtxt = f.read()
                 assert add_blank == ("non-zero file size..." in logtxt)

From 517687a6e4e1fa736d4e4bd6fdad20a87008e11e Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 23:45:16 -0700
Subject: [PATCH 14/58] See what the actual log path is being set to

---
 src/toffy/fov_watcher.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 85f6104b..54ab4d62 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -216,6 +216,7 @@ def __init__(
         self.log_path = os.path.join(log_folder, f"{Path(run_folder).parts[-1]}_log.txt")
         if not os.path.exists(log_folder):
             os.makedirs(log_folder)
+        print(f"Setting log path to {self.log_path}")
         logging.basicConfig(
             level=logging.INFO,
             filename=self.log_path,

From 9737c5c7261448be3182f5920620952785c38916 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Mon, 7 Oct 2024 23:54:03 -0700
Subject: [PATCH 15/58] Try adding a simple logging statement at the beginning
 to force

---
 src/toffy/fov_watcher.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 54ab4d62..b381688f 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -223,6 +223,7 @@ def __init__(
             filemode="a",
             format="%(name)s - %(levelname)s - %(message)s",
         )
+        logging.info(f"Starting run on {run_folder}\n")
 
         # create run structure
         self.run_structure = RunStructure(run_folder, fov_timeout=fov_timeout)

From db326a6c24a947162226e7b33c265b9799236c02 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 8 Oct 2024 11:54:11 -0700
Subject: [PATCH 16/58] Try to set logging propagation to be False

---
 src/toffy/fov_watcher.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index b381688f..4820472e 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -224,6 +224,8 @@ def __init__(
             format="%(name)s - %(levelname)s - %(message)s",
         )
         logging.info(f"Starting run on {run_folder}\n")
+        logger = logging.getLogger()
+        logger.propagate = False
 
         # create run structure
         self.run_structure = RunStructure(run_folder, fov_timeout=fov_timeout)

From 57421cfb7a8bcb758ab6c6520c05fb4e7a83a7ce Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 8 Oct 2024 12:14:06 -0700
Subject: [PATCH 17/58] Fix pyproject.toml logging

---
 pyproject.toml           | 4 ++++
 src/toffy/fov_watcher.py | 2 --
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4bc35847..718e4431 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -128,3 +128,7 @@ filterwarnings = [
 ]
 testpaths = ["tests"]
 norecursedirs = ["tests/utilities"]
+log_cli = True
+log_level = "INFO"
+log_file = "pytest.log"
+log_file_level = "INFO"
diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 4820472e..b381688f 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -224,8 +224,6 @@ def __init__(
             format="%(name)s - %(levelname)s - %(message)s",
         )
         logging.info(f"Starting run on {run_folder}\n")
-        logger = logging.getLogger()
-        logger.propagate = False
 
         # create run structure
         self.run_structure = RunStructure(run_folder, fov_timeout=fov_timeout)

From 53f18fae0535c16374f7108318ab6a0dd62265a3 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 8 Oct 2024 12:20:51 -0700
Subject: [PATCH 18/58] Additional changes to pytest pyproject.toml

---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 718e4431..f68f56eb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -128,7 +128,10 @@ filterwarnings = [
 ]
 testpaths = ["tests"]
 norecursedirs = ["tests/utilities"]
+
 log_cli = True
 log_level = "INFO"
 log_file = "pytest.log"
 log_file_level = "INFO"
+log_format = "%(asctime)s %(levelname)s %(message)s"
+log_date_format = "%Y-%m-%d %H:%M:%S"

From 7e6ef2ce27a067332cf99f663c6cd6ea780daff2 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 8 Oct 2024 12:25:21 -0700
Subject: [PATCH 19/58] Lowercase true for pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f68f56eb..c6e78a3a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -129,7 +129,7 @@ filterwarnings = [
 testpaths = ["tests"]
 norecursedirs = ["tests/utilities"]
 
-log_cli = True
+log_cli = true
 log_level = "INFO"
 log_file = "pytest.log"
 log_file_level = "INFO"

From fd021c6f51e4184a82b6539832958639e2b501c9 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 12:42:57 -0700
Subject: [PATCH 20/58] Attempt to force pytest fixture to write to log file

---
 tests/fov_watcher_test.py | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 3a87fec0..29c53fed 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -35,6 +35,23 @@
 SLOW_COPY_INTERVAL_S = 1
 
 
+@pytest.fixture
+def configure_logging():
+    log_file = "test_log_file.log"
+    
+    # Ensure any existing log file is removed
+    if os.path.exists(log_file):
+        os.remove(log_file)
+    
+    # Set up logging to write to the file
+    logging.basicConfig(filename=log_file, level=logging.INFO)
+    
+    yield log_file
+    
+    # Optionally flush the logs to ensure file is written
+    logging.shutdown()
+
+
 def _slow_copy_sample_tissue_data(
     dest: str, delta: int = 10, one_blank: bool = False, temp_bin: bool = False
 ):
@@ -384,7 +401,8 @@ def test_watcher(
             print("Testing log out status")
             print(log_out)
             print(os.listdir(log_out))
-            with open(os.path.join(log_out, "test_run_log.txt")) as f:
+            # with open(os.path.join(log_out, "test_run_log.txt")) as f:
+            with open("test_log_file.txt") as f:
                 logtxt = f.read()
                 assert add_blank == ("non-zero file size..." in logtxt)
 

From 58f915afbff1443c5d3ed1bd070fd684889aac45 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 12:45:50 -0700
Subject: [PATCH 21/58] Add logging import

---
 tests/fov_watcher_test.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 29c53fed..07442795 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -1,3 +1,4 @@
+import logging
 import os
 import shutil
 import tempfile

From 63f7388d48ba7790de897c504f4da7dc0de41ac8 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 12:51:08 -0700
Subject: [PATCH 22/58] Remove whitespace

---
 tests/fov_watcher_test.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 07442795..9caf541b 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -39,16 +39,16 @@
 @pytest.fixture
 def configure_logging():
     log_file = "test_log_file.log"
-    
+
     # Ensure any existing log file is removed
     if os.path.exists(log_file):
         os.remove(log_file)
-    
+
     # Set up logging to write to the file
     logging.basicConfig(filename=log_file, level=logging.INFO)
-    
+
     yield log_file
-    
+
     # Optionally flush the logs to ensure file is written
     logging.shutdown()
 

From 170ab4d6abaea69e5fdaad469779d5af071892fb Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 13:27:17 -0700
Subject: [PATCH 23/58] Try to fix logging issue

---
 pyproject.toml            |  2 +-
 tests/fov_watcher_test.py | 30 ++++++++++++------------------
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c6e78a3a..2ceab615 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -131,7 +131,7 @@ norecursedirs = ["tests/utilities"]
 
 log_cli = true
 log_level = "INFO"
-log_file = "pytest.log"
+log_file = "pytest.txt"
 log_file_level = "INFO"
 log_format = "%(asctime)s %(levelname)s %(message)s"
 log_date_format = "%Y-%m-%d %H:%M:%S"
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 9caf541b..e42eac48 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -36,21 +36,11 @@
 SLOW_COPY_INTERVAL_S = 1
 
 
-@pytest.fixture
+@pytest.fixture(scope="session", autouse=True)
 def configure_logging():
-    log_file = "test_log_file.log"
-
-    # Ensure any existing log file is removed
-    if os.path.exists(log_file):
-        os.remove(log_file)
-
-    # Set up logging to write to the file
-    logging.basicConfig(filename=log_file, level=logging.INFO)
-
-    yield log_file
-
-    # Optionally flush the logs to ensure file is written
-    logging.shutdown()
+    logging.basicConfig(filename="pytest.txt", level=logging.INFO)
+    yield
+    logging.shutdown()  # Ensure all log messages are flushed to the file
 
 
 def _slow_copy_sample_tissue_data(
@@ -74,7 +64,6 @@ def _slow_copy_sample_tissue_data(
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
             # create blank (0 size) file
             open(os.path.join(dest, tissue_file), "w").close()
-            one_blank = False
         else:
             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
             if temp_bin and ".bin" in tissue_file:
@@ -92,11 +81,14 @@ def _slow_copy_sample_tissue_data(
             else:
                 shutil.copy(tissue_path, dest)
 
-            # simulate a timestamp update if .bin file has been extracted
+            # simulate a timestamp update if .bin file has been extracted AND not blank
             # NOTE: this assumes .json file always copies after the .bin, which does happen on Ionpath
             tissue_data = os.path.splitext(tissue_file)
             if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
-                if num_bin_files % 2 == 0:
+                if one_blank:
+                    one_blank = False
+                    continue
+                elif num_bin_files % 2 == 0:
                     bin_file_name = tissue_data[0] + ".bin"
                     print(f"Simulating .bin file update on {bin_file_name}")
                     shutil.copy(
@@ -284,6 +276,8 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
+    if add_blank:
+        print("Add blank is True, testing")
     try:
         with tempfile.TemporaryDirectory() as tmpdir:
             tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)
@@ -403,7 +397,7 @@ def test_watcher(
             print(log_out)
             print(os.listdir(log_out))
             # with open(os.path.join(log_out, "test_run_log.txt")) as f:
-            with open("test_log_file.txt") as f:
+            with open("pytest.txt") as f:
                 logtxt = f.read()
                 assert add_blank == ("non-zero file size..." in logtxt)
 

From 93735fc2eacae820e9691f9eb949e4c565a05c51 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 13:34:28 -0700
Subject: [PATCH 24/58] Overwrite pytest.txt with blank stuff

---
 tests/fov_watcher_test.py | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index e42eac48..b1ab4317 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -36,11 +36,11 @@
 SLOW_COPY_INTERVAL_S = 1
 
 
-@pytest.fixture(scope="session", autouse=True)
-def configure_logging():
-    logging.basicConfig(filename="pytest.txt", level=logging.INFO)
-    yield
-    logging.shutdown()  # Ensure all log messages are flushed to the file
+# @pytest.fixture(scope="session", autouse=True)
+# def configure_logging():
+#     logging.basicConfig(filename="pytest.txt", level=logging.INFO)
+#     yield
+#     logging.shutdown()  # Ensure all log messages are flushed to the file
 
 
 def _slow_copy_sample_tissue_data(
@@ -416,6 +416,7 @@ def test_watcher(
                 fovs = fovs[1:]
 
             # extract tiffs check
+            print("TIFF validator check")
             validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
             if kwargs["extract_prof"]:
                 validators[0](
@@ -427,9 +428,11 @@ def test_watcher(
                 )
 
             # qc check
+            print("QC check")
             validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
 
             # mph check
+            print("MPH check")
             validators[2](
                 os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
                 os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
@@ -443,7 +446,11 @@ def test_watcher(
             # pulse heights check
             validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
 
+            with open("pytest.txt", "w") as infile:
+                infile.write("\n")
+
     except OSError as ose:
+        print("There was a failure:")
         print(ose)
         # warnings.warn("Temporary file cleanup was incomplete.")
 

From 3d2832c5122bc2c83e9de6c1853876ecc4e1096a Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 13:43:34 -0700
Subject: [PATCH 25/58] More testing fixes

---
 tests/fov_watcher_test.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index b1ab4317..ed70c9b1 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -397,6 +397,7 @@ def test_watcher(
             print(log_out)
             print(os.listdir(log_out))
             # with open(os.path.join(log_out, "test_run_log.txt")) as f:
+            print(os.listdir("."))
             with open("pytest.txt") as f:
                 logtxt = f.read()
                 assert add_blank == ("non-zero file size..." in logtxt)

From c9b943969cfa5a900dfeca973472d11b723231fa Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 13:50:50 -0700
Subject: [PATCH 26/58] Use the absolute path to the directory for accessing
 hte log

---
 tests/fov_watcher_test.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index ed70c9b1..c1647792 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -395,10 +395,9 @@ def test_watcher(
 
             print("Testing log out status")
             print(log_out)
-            print(os.listdir(log_out))
             # with open(os.path.join(log_out, "test_run_log.txt")) as f:
             print(os.listdir("."))
-            with open("pytest.txt") as f:
+            with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
                 logtxt = f.read()
                 assert add_blank == ("non-zero file size..." in logtxt)
 
@@ -447,7 +446,7 @@ def test_watcher(
             # pulse heights check
             validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
 
-            with open("pytest.txt", "w") as infile:
+            with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:
                 infile.write("\n")
 
     except OSError as ose:

From 4db71a3b9343ded43dcf14d4dd24aac91a75d0dc Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 15:07:31 -0700
Subject: [PATCH 27/58] Adjust error message

---
 tests/fov_watcher_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index c1647792..7f01e259 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -450,7 +450,7 @@ def test_watcher(
                 infile.write("\n")
 
     except OSError as ose:
-        print("There was a failure:")
+        print("Ran into an error:")
         print(ose)
         # warnings.warn("Temporary file cleanup was incomplete.")
 

From a046bc3b44422a39f91335d64111ff543b1d08f8 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 22:00:40 -0700
Subject: [PATCH 28/58] Don't print add_blank

---
 tests/fov_watcher_test.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 7f01e259..6d9ae94d 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -276,8 +276,6 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
-    if add_blank:
-        print("Add blank is True, testing")
     try:
         with tempfile.TemporaryDirectory() as tmpdir:
             tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)

From 98013de7cad3182471a4a434b578d61a975cf9f3 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Thu, 17 Oct 2024 22:30:03 -0700
Subject: [PATCH 29/58] Check if the error is happening during the renaming
 phases

---
 tests/fov_watcher_test.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 6d9ae94d..f76f349d 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -68,13 +68,16 @@ def _slow_copy_sample_tissue_data(
             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
             if temp_bin and ".bin" in tissue_file:
                 # copy to a temporary file with hash extension, then move to dest folder
+                print(f"Copying over a temporary file with hash extension on {tissue_file}")
                 new_tissue_path = os.path.join(COMBINED_DATA_PATH, "." + tissue_file + ".aBcDeF")
                 shutil.copy(tissue_path, new_tissue_path)
                 shutil.copy(new_tissue_path, dest)
+                print(f"Removing the old tissue path at .{tissue_file}.aBcDeF")
                 os.remove(new_tissue_path)
 
                 # simulate a renaming event in dest
                 time.sleep(delta)
+                print(f"Renaming back to {tissue_file}")
                 copied_tissue_path = os.path.join(dest, "." + tissue_file + ".aBcDeF")
                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
 

From 378a82a46c2d988549abe85ae83762a07f305cc8 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 11:55:27 -0800
Subject: [PATCH 30/58] Add some more tests in

---
 src/toffy/image_stitching.py | 8 ++++++++
 tests/fov_watcher_test.py    | 2 +-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/toffy/image_stitching.py b/src/toffy/image_stitching.py
index c41141ff..284ecb92 100644
--- a/src/toffy/image_stitching.py
+++ b/src/toffy/image_stitching.py
@@ -253,6 +253,14 @@ def stitch_images(
             num_cols = math.isqrt(len(folders))
             max_img_size = get_max_img_size(tiff_out_dir, img_sub_folder, run_dir)
 
+            print(tiff_out_dir)
+            print(img_sub_folder)
+            print(os.listdir(tiff_out_dir))
+            directories = os.listdir(tiff_out_dir)
+            subfolder = "" if img_sub_folder is None else img_sub_folder
+            for fov in folders:
+                print(f"Here's what's in fov {fov}")
+                print(os.listdir(os.path.join(tiff_out_dir, fov, subfolder)))
             image_data = load_utils.load_imgs_from_tree(
                 tiff_out_dir,
                 img_sub_folder=img_sub_folder,
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index f76f349d..b8ada8b2 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -448,7 +448,7 @@ def test_watcher(
             validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
 
             with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:
-                infile.write("\n")
+                infile.write("")
 
     except OSError as ose:
         print("Ran into an error:")

From 1fef177187a6651dcb19313cf4d074543b87b0be Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 13:46:02 -0800
Subject: [PATCH 31/58] Actually get image_stitching to print out debug

---
 src/toffy/image_stitching.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/toffy/image_stitching.py b/src/toffy/image_stitching.py
index 284ecb92..d7d30b22 100644
--- a/src/toffy/image_stitching.py
+++ b/src/toffy/image_stitching.py
@@ -256,7 +256,6 @@ def stitch_images(
             print(tiff_out_dir)
             print(img_sub_folder)
             print(os.listdir(tiff_out_dir))
-            directories = os.listdir(tiff_out_dir)
             subfolder = "" if img_sub_folder is None else img_sub_folder
             for fov in folders:
                 print(f"Here's what's in fov {fov}")

From 7b08a84c84d60720fd7491a93d3f308b84eb7450 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 14:25:16 -0800
Subject: [PATCH 32/58] Pin watchdog to version 6

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 2ceab615..48757883 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,7 +44,7 @@ numpy = "1.*"
 natsort = "^8"
 seaborn = "^0.13"
 scikit-learn = "^1"
-watchdog = "^3"
+watchdog = "^6"
 tqdm = "^4"
 scipy = "^1.10.1"
 pandas = "^2"

From e76de609fd7f3202ff55a28c8476a2fcbdb56eb2 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 14:31:07 -0800
Subject: [PATCH 33/58] Update lock file

---
 poetry.lock | 3350 +++++++++++++++++++++++++++------------------------
 1 file changed, 1798 insertions(+), 1552 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 6b9d86eb..6f07c05d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand.
 
 [[package]]
 name = "aiofiles"
@@ -13,28 +13,31 @@ files = [
 
 [[package]]
 name = "aiosqlite"
-version = "0.19.0"
+version = "0.20.0"
 description = "asyncio bridge to the standard sqlite3 module"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "aiosqlite-0.19.0-py3-none-any.whl", hash = "sha256:edba222e03453e094a3ce605db1b970c4b3376264e56f32e2a4959f948d66a96"},
-    {file = "aiosqlite-0.19.0.tar.gz", hash = "sha256:95ee77b91c8d2808bd08a59fbebf66270e9090c3d92ffbf260dc0db0b979577d"},
+    {file = "aiosqlite-0.20.0-py3-none-any.whl", hash = "sha256:36a1deaca0cac40ebe32aac9977a6e2bbc7f5189f23f4a54d5908986729e5bd6"},
+    {file = "aiosqlite-0.20.0.tar.gz", hash = "sha256:6d35c8c256637f4672f843c31021464090805bf925385ac39473fb16eaaca3d7"},
 ]
 
+[package.dependencies]
+typing_extensions = ">=4.0"
+
 [package.extras]
-dev = ["aiounittest (==1.4.1)", "attribution (==1.6.2)", "black (==23.3.0)", "coverage[toml] (==7.2.3)", "flake8 (==5.0.4)", "flake8-bugbear (==23.3.12)", "flit (==3.7.1)", "mypy (==1.2.0)", "ufmt (==2.1.0)", "usort (==1.0.6)"]
-docs = ["sphinx (==6.1.3)", "sphinx-mdinclude (==0.5.3)"]
+dev = ["attribution (==1.7.0)", "black (==24.2.0)", "coverage[toml] (==7.4.1)", "flake8 (==7.0.0)", "flake8-bugbear (==24.2.6)", "flit (==3.9.0)", "mypy (==1.8.0)", "ufmt (==2.3.0)", "usort (==1.0.8.post1)"]
+docs = ["sphinx (==7.2.6)", "sphinx-mdinclude (==0.5.3)"]
 
 [[package]]
 name = "alpineer"
-version = "0.1.11"
+version = "0.1.12"
 description = "Toolbox for Multiplexed Imaging. Contains scripts and little tools which are used throughout ark-analysis, mibi-bin-tools, and toffy."
 optional = false
 python-versions = ">=3.9,<3.13"
 files = [
-    {file = "alpineer-0.1.11-py3-none-any.whl", hash = "sha256:fd70b46b6b18688e3116f597d8f963d71bf38dd2f1b79f5757526e4baa2fb57f"},
-    {file = "alpineer-0.1.11.tar.gz", hash = "sha256:8da224dd0d776f8f34ca050c46c9113300b7bc29196465feb4446cadca39abe7"},
+    {file = "alpineer-0.1.12-py3-none-any.whl", hash = "sha256:4e6a14a2f193d40e2643021bca04d6880655c5162894841b2bebeb36d4b79fec"},
+    {file = "alpineer-0.1.12.tar.gz", hash = "sha256:499cee53ef93ea1fda4ff705e9c0c0ec407b8bf473800f32fbe307ea620f657f"},
 ]
 
 [package.dependencies]
@@ -51,34 +54,35 @@ xmltodict = ">=0.13.0,<0.14.0"
 
 [[package]]
 name = "anyio"
-version = "4.0.0"
+version = "4.6.2.post1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
 exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (>=0.22)"]
+doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"]
+trio = ["trio (>=0.26.1)"]
 
 [[package]]
 name = "appnope"
-version = "0.1.3"
+version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
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+    {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
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 ]
 
 [[package]]
@@ -177,31 +181,32 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
-version = "2.13.1"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [package.extras]
@@ -209,19 +214,22 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
 files = [
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 ]
 
 [package.dependencies]
 soupsieve = ">1.2"
 
 [package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
 html5lib = ["html5lib"]
 lxml = ["lxml"]
 
@@ -262,92 +270,106 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
 name = "cffi"
-version = "1.16.0"
+version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
 python-versions = ">=3.8"
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 docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
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+test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
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+    {file = "fonttools-4.54.1-py3-none-any.whl", hash = "sha256:37cddd62d83dc4f72f7c3f3c2bcf2697e89a30efb152079896544a93907733bd"},
+    {file = "fonttools-4.54.1.tar.gz", hash = "sha256:957f669d4922f92c171ba01bef7f29410668db09f6c02111e22b2bce446f3285"},
+]
+
+[package.extras]
+all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "pycairo", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.1.0)", "xattr", "zopfli (>=0.1.4)"]
 graphite = ["lz4 (>=1.7.4.2)"]
-interpolatable = ["munkres", "scipy"]
-lxml = ["lxml (>=4.0,<5)"]
+interpolatable = ["munkres", "pycairo", "scipy"]
+lxml = ["lxml (>=4.0)"]
 pathops = ["skia-pathops (>=0.5.0)"]
 plot = ["matplotlib"]
 repacker = ["uharfbuzz (>=0.23.0)"]
 symfont = ["sympy"]
 type1 = ["xattr"]
 ufo = ["fs (>=2.2.0,<3)"]
-unicode = ["unicodedata2 (>=15.0.0)"]
+unicode = ["unicodedata2 (>=15.1.0)"]
 woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
@@ -852,24 +907,27 @@ files = [
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
-    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+    {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
+    {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
 ]
 
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "imageio"
-version = "2.31.5"
+version = "2.36.0"
 description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "imageio-2.31.5-py3-none-any.whl", hash = "sha256:97f68e12ba676f2f4b541684ed81f7f3370dc347e8321bc68ee34d37b2dbac9f"},
-    {file = "imageio-2.31.5.tar.gz", hash = "sha256:d8e53f9cd4054880276a3dac0a28c85ba7874084856a55a0294a8ae6ed7f3a8e"},
+    {file = "imageio-2.36.0-py3-none-any.whl", hash = "sha256:471f1eda55618ee44a3c9960911c35e647d9284c68f077e868df633398f137f0"},
+    {file = "imageio-2.36.0.tar.gz", hash = "sha256:1c8f294db862c256e9562354d65aa54725b8dafed7f10f02bb3ec20ec1678850"},
 ]
 
 [package.dependencies]
@@ -877,57 +935,67 @@ numpy = "*"
 pillow = ">=8.3.2"
 
 [package.extras]
-all-plugins = ["astropy", "av", "imageio-ffmpeg", "psutil", "tifffile"]
-all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"]
+all-plugins = ["astropy", "av", "imageio-ffmpeg", "numpy (>2)", "pillow-heif", "psutil", "rawpy", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
 build = ["wheel"]
 dev = ["black", "flake8", "fsspec[github]", "pytest", "pytest-cov"]
 docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
 ffmpeg = ["imageio-ffmpeg", "psutil"]
 fits = ["astropy"]
-full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpy (>2)", "numpydoc", "pillow-heif", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "rawpy", "sphinx (<6)", "tifffile", "wheel"]
 gdal = ["gdal"]
 itk = ["itk"]
 linting = ["black", "flake8"]
+pillow-heif = ["pillow-heif"]
 pyav = ["av"]
+rawpy = ["numpy (>2)", "rawpy"]
 test = ["fsspec[github]", "pytest", "pytest-cov"]
 tifffile = ["tifffile"]
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-6.8.0-py3-none-any.whl", hash = "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb"},
-    {file = "importlib_metadata-6.8.0.tar.gz", hash = "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743"},
+    {file = "importlib_metadata-8.5.0-py3-none-any.whl", hash = "sha256:45e54197d28b7a7f1559e60b95e7c567032b602131fbd588f1497f47880aa68b"},
+    {file = "importlib_metadata-8.5.0.tar.gz", hash = "sha256:71522656f0abace1d072b9e5481a48f07c138e00f079c38c8f883823f9c26bd7"},
 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-perf (>=0.9.2)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.4.5"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.0-py3-none-any.whl", hash = "sha256:aa50258bbfa56d4e33fbd8aa3ef48ded10d1735f11532b8df95388cc6bdb7e83"},
-    {file = "importlib_resources-6.1.0.tar.gz", hash = "sha256:9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9"},
+    {file = "importlib_resources-6.4.5-py3-none-any.whl", hash = "sha256:ac29d5f956f01d5e4bb63102a5a19957f1b9175e45649977264a1416783bb717"},
+    {file = "importlib_resources-6.4.5.tar.gz", hash = "sha256:980862a1d16c9e147a59603677fa2aa5fd82b87f223b6cb870695bcfce830065"},
 ]
 
 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["jaraco.test (>=5.4)", "pytest (>=6,!=8.1.*)", "zipp (>=3.17)"]
+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -942,13 +1010,13 @@ files = [
 
 [[package]]
 name = "ipykernel"
-version = "6.26.0"
+version = "6.29.5"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.26.0-py3-none-any.whl", hash = "sha256:3ba3dc97424b87b31bb46586b5167b3161b32d7820b9201a9e698c71e271602c"},
-    {file = "ipykernel-6.26.0.tar.gz", hash = "sha256:553856658eb8430bbe9653ea041a41bff63e9606fc4628873fc92a6cf3abd404"},
+    {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"},
+    {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"},
 ]
 
 [package.dependencies]
@@ -962,7 +1030,7 @@ matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
 psutil = "*"
-pyzmq = ">=20"
+pyzmq = ">=24"
 tornado = ">=6.1"
 traitlets = ">=5.4.0"
 
@@ -971,45 +1039,44 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
-version = "8.17.1"
+version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "ipython-8.17.1-py3-none-any.whl", hash = "sha256:b4510d0a163c89c78cf81be68acc841dde4a8290b6ee3f3c9578ccdd2574553c"},
-    {file = "ipython-8.17.1.tar.gz", hash = "sha256:9e12020f4bf74f08631c0f033bb580e074fbe36c64903195f3e63b9c0a986cbe"},
+    {file = "ipython-8.18.1-py3-none-any.whl", hash = "sha256:e8267419d72d81955ec1177f8a29aaa90ac80ad647499201119e2f05e99aa397"},
+    {file = "ipython-8.18.1.tar.gz", hash = "sha256:ca6f079bb33457c66e233e4580ebfc4128855b4cf6370dddd73842a9563e8a27"},
 ]
 
 [package.dependencies]
-appnope = {version = "*", markers = "sys_platform == \"darwin\""}
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
 exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
-prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0"
+prompt-toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
 stack-data = "*"
 traitlets = ">=5"
 typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
 
 [package.extras]
-all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
 nbformat = ["nbformat"]
 notebook = ["ipywidgets", "notebook"]
 parallel = ["ipyparallel"]
 qtconsole = ["qtconsole"]
-test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
 
 [[package]]
 name = "ipython-genutils"
@@ -1024,21 +1091,21 @@ files = [
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.1"
+version = "8.1.5"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ipywidgets-8.1.1-py3-none-any.whl", hash = "sha256:2b88d728656aea3bbfd05d32c747cfd0078f9d7e159cf982433b58ad717eed7f"},
-    {file = "ipywidgets-8.1.1.tar.gz", hash = "sha256:40211efb556adec6fa450ccc2a77d59ca44a060f4f9f136833df59c9f538e6e8"},
+    {file = "ipywidgets-8.1.5-py3-none-any.whl", hash = "sha256:3290f526f87ae6e77655555baba4f36681c555b8bdbbff430b70e52c34c86245"},
+    {file = "ipywidgets-8.1.5.tar.gz", hash = "sha256:870e43b1a35656a80c18c9503bbf2d16802db1cb487eec6fab27d683381dde17"},
 ]
 
 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.9,<3.1.0"
+jupyterlab-widgets = ">=3.0.12,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.9,<4.1.0"
+widgetsnbextension = ">=4.0.12,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1059,49 +1126,46 @@ arrow = ">=0.15.0"
 
 [[package]]
 name = "isort"
-version = "5.12.0"
+version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
 optional = false
 python-versions = ">=3.8.0"
 files = [
-    {file = "isort-5.12.0-py3-none-any.whl", hash = "sha256:f84c2818376e66cf843d497486ea8fed8700b340f308f076c6fb1229dff318b6"},
-    {file = "isort-5.12.0.tar.gz", hash = "sha256:8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504"},
+    {file = "isort-5.13.2-py3-none-any.whl", hash = "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"},
+    {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"},
 ]
 
 [package.extras]
-colors = ["colorama (>=0.4.3)"]
-pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"]
-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "jedi-0.19.1-py2.py3-none-any.whl", hash = "sha256:e983c654fe5c02867aef4cdfce5a2fbb4a50adc0af145f70504238f18ef5e7e0"},
-    {file = "jedi-0.19.1.tar.gz", hash = "sha256:cf0496f3651bc65d7174ac1b7d043eff454892c708a87d1b683e57b569927ffd"},
+    {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"},
+    {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"},
 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
 docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -1112,49 +1176,49 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "joblib"
-version = "1.3.2"
+version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "joblib-1.3.2-py3-none-any.whl", hash = "sha256:ef4331c65f239985f3f2220ecc87db222f08fd22097a3dd5698f693875f8cbb9"},
-    {file = "joblib-1.3.2.tar.gz", hash = "sha256:92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1"},
+    {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
+    {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
 ]
 
 [[package]]
 name = "json5"
-version = "0.9.14"
+version = "0.9.28"
 description = "A Python implementation of the JSON5 data format."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8.0"
 files = [
-    {file = "json5-0.9.14-py2.py3-none-any.whl", hash = "sha256:740c7f1b9e584a468dbb2939d8d458db3427f2c93ae2139d05f47e453eae964f"},
-    {file = "json5-0.9.14.tar.gz", hash = "sha256:9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02"},
+    {file = "json5-0.9.28-py3-none-any.whl", hash = "sha256:29c56f1accdd8bc2e037321237662034a7e07921e2b7223281a5ce2c46f0c4df"},
+    {file = "json5-0.9.28.tar.gz", hash = "sha256:1f82f36e615bc5b42f1bbd49dbc94b12563c56408c6ffa06414ea310890e9a6e"},
 ]
 
 [package.extras]
-dev = ["hypothesis"]
+dev = ["build (==1.2.2.post1)", "coverage (==7.5.3)", "mypy (==1.13.0)", "pip (==24.3.1)", "pylint (==3.2.3)", "ruff (==0.7.3)", "twine (==5.1.1)", "uv (==0.5.1)"]
 
 [[package]]
 name = "jsonpointer"
-version = "2.4"
+version = "3.0.0"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+python-versions = ">=3.7"
 files = [
-    {file = "jsonpointer-2.4-py2.py3-none-any.whl", hash = "sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a"},
-    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
+    {file = "jsonpointer-3.0.0-py2.py3-none-any.whl", hash = "sha256:13e088adc14fca8b6aa8177c044e12701e6ad4b28ff10e65f2267a90109c9942"},
+    {file = "jsonpointer-3.0.0.tar.gz", hash = "sha256:2b2d729f2091522d61c3b31f82e11870f60b68f43fbc705cb76bf4b832af59ef"},
 ]
 
 [[package]]
 name = "jsonschema"
-version = "4.19.2"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.2-py3-none-any.whl", hash = "sha256:eee9e502c788e89cb166d4d37f43084e3b64ab405c795c03d343a4dbc2c810fc"},
-    {file = "jsonschema-4.19.2.tar.gz", hash = "sha256:c9ff4d7447eed9592c23a12ccee508baf0dd0d59650615e847feb6cdca74f392"},
+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
@@ -1169,25 +1233,25 @@ rfc3339-validator = {version = "*", optional = true, markers = "extra == \"forma
 rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""}
 rpds-py = ">=0.7.1"
 uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""}
-webcolors = {version = ">=1.11", optional = true, markers = "extra == \"format-nongpl\""}
+webcolors = {version = ">=24.6.0", optional = true, markers = "extra == \"format-nongpl\""}
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
-format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
-    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+    {file = "jsonschema_specifications-2024.10.1-py3-none-any.whl", hash = "sha256:a09a0680616357d9a0ecf05c12ad234479f549239d0f5b55f3deea67475da9bf"},
+    {file = "jsonschema_specifications-2024.10.1.tar.gz", hash = "sha256:0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"},
 ]
 
 [package.dependencies]
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "jupyter-client"
@@ -1260,13 +1324,13 @@ test = ["mock", "nbformat", "nose", "pip", "requests"]
 
 [[package]]
 name = "jupyter-core"
-version = "5.5.0"
+version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_core-5.5.0-py3-none-any.whl", hash = "sha256:e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805"},
-    {file = "jupyter_core-5.5.0.tar.gz", hash = "sha256:880b86053bf298a8724994f95e99b99130659022a4f7f45f563084b6223861d3"},
+    {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"},
+    {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"},
 ]
 
 [package.dependencies]
@@ -1276,17 +1340,17 @@ traitlets = ">=5.3"
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
-test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-events"
-version = "0.8.0"
+version = "0.10.0"
 description = "Jupyter Event System library"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_events-0.8.0-py3-none-any.whl", hash = "sha256:81f07375c7673ff298bfb9302b4a981864ec64edaed75ca0fe6f850b9b045525"},
-    {file = "jupyter_events-0.8.0.tar.gz", hash = "sha256:fda08f0defce5e16930542ce60634ba48e010830d50073c3dfd235759cee77bf"},
+    {file = "jupyter_events-0.10.0-py3-none-any.whl", hash = "sha256:4b72130875e59d57716d327ea70d3ebc3af1944d3717e5a498b8a06c6c159960"},
+    {file = "jupyter_events-0.10.0.tar.gz", hash = "sha256:670b8229d3cc882ec782144ed22e0d29e1c2d639263f92ca8383e66682845e22"},
 ]
 
 [package.dependencies]
@@ -1316,17 +1380,18 @@ files = [
 
 [[package]]
 name = "jupyter-nbextensions-configurator"
-version = "0.6.3"
+version = "0.6.4"
 description = "jupyter serverextension providing configuration interfaces for nbextensions."
 optional = false
 python-versions = "*"
 files = [
-    {file = "jupyter_nbextensions_configurator-0.6.3-py2.py3-none-any.whl", hash = "sha256:cece496f3f62cf80bb0b04867ea463c32ed5db19ff5814fe18a3a7f1bb9da95b"},
+    {file = "jupyter_nbextensions_configurator-0.6.4-py2.py3-none-any.whl", hash = "sha256:fe7a7b0805b5926449692fb077e0e659bab8b27563bc68cba26854532fdf99c7"},
 ]
 
 [package.dependencies]
 jupyter-contrib-core = ">=0.3.3"
 jupyter-core = "*"
+jupyter-server = "*"
 notebook = ">=6.0"
 pyyaml = "*"
 tornado = "*"
@@ -1337,49 +1402,49 @@ test = ["jupyter-contrib-core[testing-utils]", "mock", "nose", "requests", "sele
 
 [[package]]
 name = "jupyter-server"
-version = "2.9.1"
+version = "2.14.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server-2.9.1-py3-none-any.whl", hash = "sha256:21ad1a3d455d5a79ce4bef5201925cd17510c17898cf9d54e3ccfb6b12734948"},
-    {file = "jupyter_server-2.9.1.tar.gz", hash = "sha256:9ba71be4b9c16e479e4c50c929f8ac4b1015baf90237a08681397a98c76c7e5e"},
+    {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"},
+    {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"},
 ]
 
 [package.dependencies]
 anyio = ">=3.1.0"
-argon2-cffi = "*"
-jinja2 = "*"
+argon2-cffi = ">=21.1"
+jinja2 = ">=3.0.3"
 jupyter-client = ">=7.4.4"
 jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
-jupyter-events = ">=0.6.0"
-jupyter-server-terminals = "*"
+jupyter-events = ">=0.9.0"
+jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
 nbformat = ">=5.3.0"
-overrides = "*"
-packaging = "*"
-prometheus-client = "*"
-pywinpty = {version = "*", markers = "os_name == \"nt\""}
+overrides = ">=5.0"
+packaging = ">=22.0"
+prometheus-client = ">=0.9"
+pywinpty = {version = ">=2.0.1", markers = "os_name == \"nt\""}
 pyzmq = ">=24"
 send2trash = ">=1.8.2"
 terminado = ">=0.8.3"
 tornado = ">=6.2.0"
 traitlets = ">=5.6.0"
-websocket-client = "*"
+websocket-client = ">=1.7"
 
 [package.extras]
-docs = ["ipykernel", "jinja2", "jupyter-client", "jupyter-server", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
-test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.4)", "pytest-timeout", "requests"]
+docs = ["ipykernel", "jinja2", "jupyter-client", "myst-parser", "nbformat", "prometheus-client", "pydata-sphinx-theme", "send2trash", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-openapi (>=0.8.0)", "sphinxcontrib-spelling", "sphinxemoji", "tornado", "typing-extensions"]
+test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0,<9)", "pytest-console-scripts", "pytest-jupyter[server] (>=0.7)", "pytest-timeout", "requests"]
 
 [[package]]
 name = "jupyter-server-fileid"
-version = "0.9.0"
-description = ""
+version = "0.9.3"
+description = "Jupyter Server extension providing an implementation of the File ID service."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyter_server_fileid-0.9.0-py3-none-any.whl", hash = "sha256:5b489c6fe6783c41174a728c7b81099608518387e53c3d53451a67f46a0cb7b0"},
-    {file = "jupyter_server_fileid-0.9.0.tar.gz", hash = "sha256:171538b7c7d08d11dbc57d4e6da196e0c258e4c2cd29249ef1e032bb423677f8"},
+    {file = "jupyter_server_fileid-0.9.3-py3-none-any.whl", hash = "sha256:f73c01c19f90005d3fff93607b91b4955ba4e1dccdde9bfe8026646f94053791"},
+    {file = "jupyter_server_fileid-0.9.3.tar.gz", hash = "sha256:521608bb87f606a8637fcbdce2f3d24a8b3cc89d2eef61751cb40e468d4e54be"},
 ]
 
 [package.dependencies]
@@ -1388,17 +1453,17 @@ jupyter-server = ">=1.15,<3"
 
 [package.extras]
 cli = ["click"]
-test = ["jupyter-server[test] (>=1.15,<3)", "pytest", "pytest-cov"]
+test = ["jupyter-server[test] (>=1.15,<3)", "pytest", "pytest-cov", "pytest-jupyter"]
 
 [[package]]
 name = "jupyter-server-terminals"
-version = "0.4.4"
+version = "0.5.3"
 description = "A Jupyter Server Extension Providing Terminals."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jupyter_server_terminals-0.4.4-py3-none-any.whl", hash = "sha256:75779164661cec02a8758a5311e18bb8eb70c4e86c6b699403100f1585a12a36"},
-    {file = "jupyter_server_terminals-0.4.4.tar.gz", hash = "sha256:57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d"},
+    {file = "jupyter_server_terminals-0.5.3-py3-none-any.whl", hash = "sha256:41ee0d7dc0ebf2809c668e0fc726dfaf258fcd3e769568996ca731b6194ae9aa"},
+    {file = "jupyter_server_terminals-0.5.3.tar.gz", hash = "sha256:5ae0295167220e9ace0edcfdb212afd2b01ee8d179fe6f23c899590e9b8a5269"},
 ]
 
 [package.dependencies]
@@ -1406,8 +1471,8 @@ pywinpty = {version = ">=2.0.3", markers = "os_name == \"nt\""}
 terminado = ">=0.8.3"
 
 [package.extras]
-docs = ["jinja2", "jupyter-server", "mistune (<3.0)", "myst-parser", "nbformat", "packaging", "pydata-sphinx-theme", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado"]
-test = ["coverage", "jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-cov", "pytest-jupyter[server] (>=0.5.3)", "pytest-timeout"]
+docs = ["jinja2", "jupyter-server", "mistune (<4.0)", "myst-parser", "nbformat", "packaging", "pydata-sphinx-theme", "sphinxcontrib-github-alt", "sphinxcontrib-openapi", "sphinxcontrib-spelling", "sphinxemoji", "tornado"]
+test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>=0.5.3)", "pytest-timeout"]
 
 [[package]]
 name = "jupyter-server-ydoc"
@@ -1449,13 +1514,13 @@ test = ["pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)", "ypy-we
 
 [[package]]
 name = "jupyterlab"
-version = "3.6.6"
+version = "3.6.8"
 description = "JupyterLab computational environment"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "jupyterlab-3.6.6-py3-none-any.whl", hash = "sha256:2c1309e77135670233f1146aef88e2101002ff0dc5b9147c2b987807efbbca07"},
-    {file = "jupyterlab-3.6.6.tar.gz", hash = "sha256:0a47d7adb28bd5659d727783f4113537e54f8c66e0d6322d1d8f9edb081dc926"},
+    {file = "jupyterlab-3.6.8-py3-none-any.whl", hash = "sha256:891284e75158998e23eb7a23ecc4caaf27b365e41adca374109b1305b9f769db"},
+    {file = "jupyterlab-3.6.8.tar.gz", hash = "sha256:a2477383e23f20009188bd9dac7e6e38dbc54307bc36d716bea6ced450647c97"},
 ]
 
 [package.dependencies]
@@ -1473,28 +1538,29 @@ tomli = {version = "*", markers = "python_version < \"3.11\""}
 tornado = ">=6.1.0"
 
 [package.extras]
+docs = ["jsx-lexer", "myst-parser", "pytest", "pytest-check-links", "pytest-tornasync", "sphinx (>=1.8)", "sphinx-copybutton", "sphinx-rtd-theme"]
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+    {file = "matplotlib-3.9.2.tar.gz", hash = "sha256:96ab43906269ca64a6366934106fa01534454a69e471b7bf3d79083981aaab92"},
 ]
 
 [package.dependencies]
@@ -1877,23 +2038,25 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
-numpy = ">=1.21,<2"
+kiwisolver = ">=1.3.1"
+numpy = ">=1.23"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
+
+[package.extras]
+dev = ["meson-python (>=0.13.1)", "numpy (>=1.25)", "pybind11 (>=2.6)", "setuptools (>=64)", "setuptools_scm (>=7)"]
 
 [[package]]
 name = "matplotlib-inline"
-version = "0.1.6"
+version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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-    {file = "matplotlib_inline-0.1.6-py3-none-any.whl", hash = "sha256:f1f41aab5328aa5aaea9b16d083b128102f8712542f819fe7e6a420ff581b311"},
+    {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"},
+    {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"},
 ]
 
 [package.dependencies]
@@ -2003,33 +2166,20 @@ icu = ["PyICU (>=1.0.0)"]
 
 [[package]]
 name = "nbclassic"
-version = "1.0.0"
+version = "1.1.0"
 description = "Jupyter Notebook as a Jupyter Server extension."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "nbclassic-1.0.0-py3-none-any.whl", hash = "sha256:f99e4769b4750076cd4235c044b61232110733322384a94a63791d2e7beacc66"},
-    {file = "nbclassic-1.0.0.tar.gz", hash = "sha256:0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3"},
+    {file = "nbclassic-1.1.0-py3-none-any.whl", hash = "sha256:8c0fd6e36e320a18657ff44ed96c3a400f17a903a3744fc322303a515778f2ba"},
+    {file = "nbclassic-1.1.0.tar.gz", hash = "sha256:77b77ba85f9e988f9bad85df345b514e9e64c7f0e822992ab1df4a78ac64fc1e"},
 ]
 
 [package.dependencies]
-argon2-cffi = "*"
 ipykernel = "*"
 ipython-genutils = "*"
-jinja2 = "*"
-jupyter-client = ">=6.1.1"
-jupyter-core = ">=4.6.1"
-jupyter-server = ">=1.8"
-nbconvert = ">=5"
-nbformat = "*"
 nest-asyncio = ">=1.5"
 notebook-shim = ">=0.2.3"
-prometheus-client = "*"
-pyzmq = ">=17"
-Send2Trash = ">=1.8.0"
-terminado = ">=0.8.3"
-tornado = ">=6.1"
-traitlets = ">=4.2.1"
 
 [package.extras]
 docs = ["myst-parser", "nbsphinx", "sphinx", "sphinx-rtd-theme", "sphinxcontrib-github-alt"]
@@ -2038,13 +2188,13 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-jupyter", "pytest-p
 
 [[package]]
 name = "nbclient"
-version = "0.8.0"
+version = "0.10.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
 optional = false
 python-versions = ">=3.8.0"
 files = [
-    {file = "nbclient-0.8.0-py3-none-any.whl", hash = "sha256:25e861299e5303a0477568557c4045eccc7a34c17fc08e7959558707b9ebe548"},
-    {file = "nbclient-0.8.0.tar.gz", hash = "sha256:f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55"},
+    {file = "nbclient-0.10.0-py3-none-any.whl", hash = "sha256:f13e3529332a1f1f81d82a53210322476a168bb7090a0289c795fe9cc11c9d3f"},
+    {file = "nbclient-0.10.0.tar.gz", hash = "sha256:4b3f1b7dba531e498449c4db4f53da339c91d449dc11e9af3a43b4eb5c5abb09"},
 ]
 
 [package.dependencies]
@@ -2056,17 +2206,17 @@ traitlets = ">=5.4"
 [package.extras]
 dev = ["pre-commit"]
 docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
-test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0,<8)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
 
 [[package]]
 name = "nbconvert"
-version = "7.10.0"
-description = "Converting Jupyter Notebooks"
+version = "7.16.4"
+description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "nbconvert-7.10.0.tar.gz", hash = "sha256:4bedff08848626be544de193b7594d98a048073f392178008ff4f171f5e21d26"},
+    {file = "nbconvert-7.16.4-py3-none-any.whl", hash = "sha256:05873c620fe520b6322bf8a5ad562692343fe3452abda5765c7a34b7d1aa3eb3"},
+    {file = "nbconvert-7.16.4.tar.gz", hash = "sha256:86ca91ba266b0a448dc96fa6c5b9d98affabde2867b363258703536807f9f7f4"},
 ]
 
 [package.dependencies]
@@ -2088,29 +2238,29 @@ tinycss2 = "*"
 traitlets = ">=5.1"
 
 [package.extras]
-all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+all = ["flaky", "ipykernel", "ipython", "ipywidgets (>=7.5)", "myst-parser", "nbsphinx (>=0.2.12)", "playwright", "pydata-sphinx-theme", "pyqtwebengine (>=5.15)", "pytest (>=7)", "sphinx (==5.0.2)", "sphinxcontrib-spelling", "tornado (>=6.1)"]
 docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
-qtpdf = ["nbconvert[qtpng]"]
+qtpdf = ["pyqtwebengine (>=5.15)"]
 qtpng = ["pyqtwebengine (>=5.15)"]
 serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7)", "pytest", "pytest-dependency"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest (>=7)"]
 webpdf = ["playwright"]
 
 [[package]]
 name = "nbformat"
-version = "5.9.2"
+version = "5.10.4"
 description = "The Jupyter Notebook format"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "nbformat-5.10.4-py3-none-any.whl", hash = "sha256:3b48d6c8fbca4b299bf3982ea7db1af21580e4fec269ad087b9e81588891200b"},
+    {file = "nbformat-5.10.4.tar.gz", hash = "sha256:322168b14f937a5d11362988ecac2a4952d3d8e3a2cbeb2319584631226d5b3a"},
 ]
 
 [package.dependencies]
-fastjsonschema = "*"
+fastjsonschema = ">=2.15"
 jsonschema = ">=2.6"
-jupyter-core = "*"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -2119,13 +2269,13 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 
 [[package]]
 name = "nest-asyncio"
-version = "1.5.8"
+version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "nest_asyncio-1.5.8-py3-none-any.whl", hash = "sha256:accda7a339a70599cb08f9dd09a67e0c2ef8d8d6f4c07f96ab203f2ae254e48d"},
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+    {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"},
+    {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"},
 ]
 
 [[package]]
@@ -2148,13 +2298,13 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
 name = "notebook"
-version = "6.5.6"
+version = "6.5.7"
 description = "A web-based notebook environment for interactive computing"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "notebook-6.5.7-py3-none-any.whl", hash = "sha256:a6afa9a4ff4d149a0771ff8b8c881a7a73b3835f9add0606696d6e9d98ac1cd0"},
+    {file = "notebook-6.5.7.tar.gz", hash = "sha256:04eb9011dfac634fbd4442adaf0a8c27cd26beef831fe1d19faf930c327768e4"},
 ]
 
 [package.dependencies]
@@ -2169,7 +2319,7 @@ nbconvert = ">=5"
 nbformat = "*"
 nest-asyncio = ">=1.5"
 prometheus-client = "*"
-pyzmq = ">=17,<25"
+pyzmq = ">=17"
 Send2Trash = ">=1.8.0"
 terminado = ">=0.8.3"
 tornado = ">=6.1"
@@ -2182,13 +2332,13 @@ test = ["coverage", "nbval", "pytest", "pytest-cov", "requests", "requests-unixs
 
 [[package]]
 name = "notebook-shim"
-version = "0.2.3"
+version = "0.2.4"
 description = "A shim layer for notebook traits and config"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "notebook_shim-0.2.4-py3-none-any.whl", hash = "sha256:411a5be4e9dc882a074ccbcae671eda64cceb068767e9a3419096986560e1cef"},
+    {file = "notebook_shim-0.2.4.tar.gz", hash = "sha256:b4b2cfa1b65d98307ca24361f5b30fe785b53c3fd07b7a47e89acb5e6ac638cb"},
 ]
 
 [package.dependencies]
@@ -2199,180 +2349,202 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 
 [[package]]
 name = "numpy"
-version = "1.26.1"
+version = "1.26.4"
 description = "Fundamental package for array computing in Python"
 optional = false
-python-versions = "<3.13,>=3.9"
-files = [
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
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 python-versions = ">=3.6"
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 [package.extras]
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+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
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+version = "0.12.1"
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 [[package]]
 name = "pexpect"
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 description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -2380,95 +2552,121 @@ ptyprocess = ">=0.5"
 
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+
+[package.extras]
+docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+fpx = ["olefile"]
+mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+typing = ["typing-extensions"]
+xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "3.11.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.3.6"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
-version = "1.3.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2477,13 +2675,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prometheus-client"
-version = "0.18.0"
+version = "0.21.0"
 description = "Python client for the Prometheus monitoring system."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "prometheus_client-0.21.0.tar.gz", hash = "sha256:96c83c606b71ff2b0a433c98889d275f51ffec6c5e267de37c7a2b5c9aa9233e"},
 ]
 
 [package.extras]
@@ -2491,13 +2689,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.39"
+version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -2505,31 +2703,33 @@ wcwidth = "*"
 
 [[package]]
 name = "psutil"
-version = "5.9.6"
+version = "6.1.0"
 description = "Cross-platform lib for process and system monitoring in Python."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
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+    {file = "psutil-6.1.0.tar.gz", hash = "sha256:353815f59a7f64cdaca1c0307ee13558a0512f6db064e92fe833784f08539c7a"},
 ]
 
 [package.extras]
-test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
+dev = ["black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pytest-cov", "requests", "rstcheck", "ruff", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "virtualenv", "wheel"]
+test = ["pytest", "pytest-xdist", "setuptools"]
 
 [[package]]
 name = "ptyprocess"
@@ -2544,13 +2744,13 @@ files = [
 
 [[package]]
 name = "pure-eval"
-version = "0.2.2"
+version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.extras]
@@ -2569,49 +2769,49 @@ files = [
 
 [[package]]
 name = "pycodestyle"
-version = "2.11.1"
+version = "2.12.1"
 description = "Python style guide checker"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pycodestyle-2.12.1.tar.gz", hash = "sha256:6838eae08bbce4f6accd5d5572075c63626a15ee3e6f842df996bf62f6d73521"},
 ]
 
 [[package]]
 name = "pycparser"
-version = "2.21"
+version = "2.22"
 description = "C parser in Python"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
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-    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
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+    {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
 ]
 
 [[package]]
 name = "pygments"
-version = "2.16.1"
+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
-plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.1"
+version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -2619,13 +2819,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.3"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
 ]
 
 [package.dependencies]
@@ -2641,13 +2841,13 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 
 [[package]]
 name = "pytest-cases"
-version = "3.8.0"
+version = "3.8.6"
 description = "Separate test code from test cases in pytest."
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -2675,29 +2875,29 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
 name = "pytest-mock"
-version = "3.12.0"
+version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-pytest = ">=5.0"
+pytest = ">=6.2.5"
 
 [package.extras]
 dev = ["pre-commit", "pytest-asyncio", "tox"]
 
 [[package]]
 name = "pytest-pycodestyle"
-version = "2.3.1"
+version = "2.4.1"
 description = "pytest plugin to run pycodestyle"
 optional = false
-python-versions = "~=3.7"
+python-versions = "~=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -2710,28 +2910,28 @@ tests = ["pytest-isort"]
 
 [[package]]
 name = "pytest-randomly"
-version = "3.15.0"
+version = "3.16.0"
 description = "Pytest plugin to randomly order tests and control random.seed."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
-importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
 pytest = "*"
 
 [[package]]
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-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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 [package.dependencies]
@@ -2750,235 +2950,294 @@ files = [
 
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+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
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 [package.dependencies]
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 [package.extras]
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 [[package]]
 name = "seaborn"
-version = "0.13.0"
+version = "0.13.2"
 description = "Statistical data visualization"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
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+matplotlib = ">=3.4,<3.6.1 || >3.6.1"
 numpy = ">=1.20,<1.24.0 || >1.24.0"
 pandas = ">=1.2"
 
@@ -3299,13 +3552,13 @@ stats = ["scipy (>=1.7)", "statsmodels (>=0.12)"]
 
 [[package]]
 name = "send2trash"
-version = "1.8.2"
+version = "1.8.3"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
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 ]
 
 [package.extras]
@@ -3315,41 +3568,23 @@ win32 = ["pywin32"]
 
 [[package]]
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 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
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-
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-python-versions = ">=3.8"
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-[package.dependencies]
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-tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-typing-extensions = "*"
-
 [package.extras]
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-rich = ["rich"]
-test = ["build", "pytest", "rich", "wheel"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"]
+core = ["importlib-metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"]
 
 [[package]]
 name = "six"
@@ -3364,24 +3599,24 @@ files = [
 
 [[package]]
 name = "sniffio"
-version = "1.3.0"
+version = "1.3.1"
 description = "Sniff out which async library your code is running under"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "sniffio-1.3.0-py3-none-any.whl", hash = "sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384"},
-    {file = "sniffio-1.3.0.tar.gz", hash = "sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101"},
+    {file = "sniffio-1.3.1-py3-none-any.whl", hash = "sha256:2f6da418d1f1e0fddd844478f41680e794e6051915791a034ff65e5f100525a2"},
+    {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
 ]
 
 [[package]]
 name = "soupsieve"
-version = "2.5"
+version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "soupsieve-2.5-py3-none-any.whl", hash = "sha256:eaa337ff55a1579b6549dc679565eac1e3d000563bcb1c8ab0d0fefbc0c2cdc7"},
-    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
+    {file = "soupsieve-2.6-py3-none-any.whl", hash = "sha256:e72c4ff06e4fb6e4b5a9f0f55fe6e81514581fca1515028625d0f299c602ccc9"},
+    {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
 ]
 
 [[package]]
@@ -3405,13 +3640,13 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "terminado"
-version = "0.17.1"
+version = "0.18.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "terminado-0.17.1-py3-none-any.whl", hash = "sha256:8650d44334eba354dd591129ca3124a6ba42c3d5b70df5051b6921d506fdaeae"},
-    {file = "terminado-0.17.1.tar.gz", hash = "sha256:6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333"},
+    {file = "terminado-0.18.1-py3-none-any.whl", hash = "sha256:a4468e1b37bb318f8a86514f65814e1afc977cf29b3992a4500d9dd305dcceb0"},
+    {file = "terminado-0.18.1.tar.gz", hash = "sha256:de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e"},
 ]
 
 [package.dependencies]
@@ -3422,27 +3657,28 @@ tornado = ">=6.1.0"
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
+typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "threadpoolctl"
-version = "3.2.0"
+version = "3.5.0"
 description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "threadpoolctl-3.2.0-py3-none-any.whl", hash = "sha256:2b7818516e423bdaebb97c723f86a7c6b0a83d3f3b0970328d66f4d9104dc032"},
-    {file = "threadpoolctl-3.2.0.tar.gz", hash = "sha256:c96a0ba3bdddeaca37dc4cc7344aafad41cdb8c313f74fdfe387a867bba93355"},
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
 ]
 
 [[package]]
 name = "tifffile"
-version = "2023.9.26"
+version = "2024.8.30"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "tifffile-2023.9.26-py3-none-any.whl", hash = "sha256:1de47fa945fddaade256e25ad4f375ae65547f3c1354063aded881c32a64cf89"},
-    {file = "tifffile-2023.9.26.tar.gz", hash = "sha256:67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae"},
+    {file = "tifffile-2024.8.30-py3-none-any.whl", hash = "sha256:8bc59a8f02a2665cd50a910ec64961c5373bee0b8850ec89d3b7b485bf7be7ad"},
+    {file = "tifffile-2024.8.30.tar.gz", hash = "sha256:2c9508fe768962e30f87def61819183fb07692c258cb175b3c114828368485a4"},
 ]
 
 [package.dependencies]
@@ -3450,16 +3686,21 @@ numpy = "*"
 
 [package.extras]
 all = ["defusedxml", "fsspec", "imagecodecs (>=2023.8.12)", "lxml", "matplotlib", "zarr"]
+codecs = ["imagecodecs (>=2023.8.12)"]
+plot = ["matplotlib"]
+test = ["cmapfile", "czifile", "dask", "defusedxml", "fsspec", "imagecodecs", "lfdfiles", "lxml", "ndtiff", "oiffile", "psdtags", "pytest", "roifile", "xarray", "zarr"]
+xml = ["defusedxml", "lxml"]
+zarr = ["fsspec", "zarr"]
 
 [[package]]
 name = "tinycss2"
-version = "1.2.1"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tinycss2-1.2.1-py3-none-any.whl", hash = "sha256:2b80a96d41e7c3914b8cda8bc7f705a4d9c49275616e886103dd839dfc847847"},
-    {file = "tinycss2-1.2.1.tar.gz", hash = "sha256:8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627"},
+    {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"},
+    {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"},
 ]
 
 [package.dependencies]
@@ -3467,48 +3708,48 @@ webencodings = ">=0.4"
 
 [package.extras]
 doc = ["sphinx", "sphinx_rtd_theme"]
-test = ["flake8", "isort", "pytest"]
+test = ["pytest", "ruff"]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.1.0"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+    {file = "tomli-2.1.0-py3-none-any.whl", hash = "sha256:a5c57c3d1c56f5ccdf89f6523458f60ef716e210fc47c4cfb188c5ba473e0391"},
+    {file = "tomli-2.1.0.tar.gz", hash = "sha256:3f646cae2aec94e17d04973e4249548320197cfabdf130015d023de4b74d8ab8"},
 ]
 
 [[package]]
 name = "tornado"
-version = "6.3.3"
+version = "6.4.1"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
-python-versions = ">= 3.8"
+python-versions = ">=3.8"
 files = [
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-    {file = "tornado-6.3.3.tar.gz", hash = "sha256:e7d8db41c0181c80d76c982aacc442c0783a2c54d6400fe028954201a2e032fe"},
+    {file = "tornado-6.4.1-cp38-abi3-macosx_10_9_universal2.whl", hash = "sha256:163b0aafc8e23d8cdc3c9dfb24c5368af84a81e3364745ccb4427669bf84aec8"},
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+    {file = "tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:613bf4ddf5c7a95509218b149b555621497a6cc0d46ac341b30bd9ec19eac7f3"},
+    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:25486eb223babe3eed4b8aecbac33b37e3dd6d776bc730ca14e1bf93888b979f"},
+    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_i686.whl", hash = "sha256:454db8a7ecfcf2ff6042dde58404164d969b6f5d58b926da15e6b23817950fc4"},
+    {file = "tornado-6.4.1-cp38-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:a02a08cc7a9314b006f653ce40483b9b3c12cda222d6a46d4ac63bb6c9057698"},
+    {file = "tornado-6.4.1-cp38-abi3-win32.whl", hash = "sha256:d9a566c40b89757c9aa8e6f032bcdb8ca8795d7c1a9762910c722b1635c9de4d"},
+    {file = "tornado-6.4.1-cp38-abi3-win_amd64.whl", hash = "sha256:b24b8982ed444378d7f21d563f4180a2de31ced9d8d84443907a0a64da2072e7"},
+    {file = "tornado-6.4.1.tar.gz", hash = "sha256:92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9"},
 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.1"
+version = "4.67.0"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
-    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
+    {file = "tqdm-4.67.0-py3-none-any.whl", hash = "sha256:0cd8af9d56911acab92182e88d763100d4788bdf421d251616040cc4d44863be"},
+    {file = "tqdm-4.67.0.tar.gz", hash = "sha256:fe5a6f95e6fe0b9755e9469b77b9c3cf850048224ecaa8293d7d2d31f97d869a"},
 ]
 
 [package.dependencies]
@@ -3516,56 +3757,57 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
 dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.13.0"
+version = "5.14.3"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "traitlets-5.13.0-py3-none-any.whl", hash = "sha256:baf991e61542da48fe8aef8b779a9ea0aa38d8a54166ee250d5af5ecf4486619"},
-    {file = "traitlets-5.13.0.tar.gz", hash = "sha256:9b232b9430c8f57288c1024b34a8f0251ddcc47268927367a0dd3eeaca40deb5"},
+    {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
+    {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=3.0.3)", "mypy (>=1.6.0)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.8.19.14"
+version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "types-python-dateutil-2.8.19.14.tar.gz", hash = "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b"},
-    {file = "types_python_dateutil-2.8.19.14-py3-none-any.whl", hash = "sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9"},
+    {file = "types-python-dateutil-2.9.0.20241003.tar.gz", hash = "sha256:58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446"},
+    {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
-    {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "tzdata"
-version = "2023.3"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
@@ -3584,55 +3826,58 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.0.7"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
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 ]
 
 [package.extras]
@@ -3640,30 +3885,26 @@ watchmedo = ["PyYAML (>=3.10)"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.8"
+version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
 name = "webcolors"
-version = "1.13"
+version = "24.11.1"
 description = "A library for working with the color formats defined by HTML and CSS."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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 ]
 
-[package.extras]
-docs = ["furo", "sphinx", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-notfound-page", "sphinxext-opengraph"]
-tests = ["pytest", "pytest-cov"]
-
 [[package]]
 name = "webencodings"
 version = "0.5.1"
@@ -3677,29 +3918,29 @@ files = [
 
 [[package]]
 name = "websocket-client"
-version = "1.6.4"
+version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
-docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.9"
+version = "4.0.13"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -3718,23 +3959,24 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"]
 
 [[package]]
 name = "xarray"
-version = "2023.10.1"
+version = "2024.7.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
-numpy = ">=1.22"
-packaging = ">=21.3"
-pandas = ">=1.4"
+numpy = ">=1.23"
+packaging = ">=23.1"
+pandas = ">=2.0"
 
 [package.extras]
-accel = ["bottleneck", "flox", "numbagg", "scipy"]
-complete = ["xarray[accel,io,parallel,viz]"]
+accel = ["bottleneck", "flox", "numbagg", "opt-einsum", "scipy"]
+complete = ["xarray[accel,dev,io,parallel,viz]"]
+dev = ["hypothesis", "mypy", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-timeout", "pytest-xdist", "ruff", "xarray[complete]"]
 io = ["cftime", "fsspec", "h5netcdf", "netCDF4", "pooch", "pydap", "scipy", "zarr"]
 parallel = ["dask[complete]"]
 viz = ["matplotlib", "nc-time-axis", "seaborn"]
@@ -3854,20 +4096,24 @@ test = ["mypy", "pre-commit", "pytest", "pytest-asyncio", "websockets (>=10.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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+    {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9,<3.12"
-content-hash = "225e3ed16d8b9412894ee0dac0371c4eaa09a53435deb3b895fee9649ff19fc3"
+content-hash = "281904ab1e52154569944f87cda54331eb6b7cf08598c9fa8bd8449615a156da"

From 8f80979a5cc87a76712c4585808a6d125a71320d Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 15:11:36 -0800
Subject: [PATCH 34/58] Add debug workflow to GitHub PR

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 534c9d21..3337e9e7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -52,6 +52,9 @@ jobs:
         run: |
           poetry install --no-interaction
 
+      - name: Debug
+        uses: lhotari/action-upterm@v1
+
       - name: Run Tests
         run: |
           poetry install --with test --no-interaction --no-root

From 5cb65a9ff5308f7d2f2aa01805de5b42b1310956 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 15:29:36 -0800
Subject: [PATCH 35/58] Remove the lock entirely

---
 src/toffy/fov_watcher.py  | 12 ++++++------
 tests/fov_watcher_test.py |  2 ++
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index b381688f..b844e501 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -489,9 +489,9 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        with self.lock:
-            super().on_created(event)
-            self._run_callbacks(event, check_last_fov)
+        # with self.lock:
+        super().on_created(event)
+        self._run_callbacks(event, check_last_fov)
 
     def file_timer(self, fov_timeout, watcher_timeout):
         """Checks time since last file was generated.
@@ -543,9 +543,9 @@ def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        with self.lock:
-            super().on_moved(event)
-            self._run_callbacks(event, check_last_fov)
+        # with self.lock:
+        super().on_moved(event)
+        self._run_callbacks(event, check_last_fov)
 
     def check_complete(self):
         """Checks run structure fov_progress status.
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index b8ada8b2..96083ab6 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -442,9 +442,11 @@ def test_watcher(
             )
 
             # stitch images check
+            print("Stitch images check")
             validators[3](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched"))
 
             # pulse heights check
+            print("Pulse heights check")
             validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
 
             with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:

From d50c4b4353df887e219b08dc376b415347e467da Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 15:37:06 -0800
Subject: [PATCH 36/58] Nuke file timer functionality

---
 src/toffy/fov_watcher.py | 94 ++++++++++++++++++++--------------------
 1 file changed, 47 insertions(+), 47 deletions(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index b844e501..02a1d018 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -207,11 +207,11 @@ def __init__(
         self.run_folder = run_folder
 
         self.last_event_time = datetime.now()
-        self.timer_thread = threading.Thread(
-            target=self.file_timer, args=(fov_timeout, watcher_timeout)
-        )
-        self.timer_thread.daemon = True
-        self.timer_thread.start()
+        # self.timer_thread = threading.Thread(
+        #     target=self.file_timer, args=(fov_timeout, watcher_timeout)
+        # )
+        # self.timer_thread.daemon = True
+        # self.timer_thread.start()
 
         self.log_path = os.path.join(log_folder, f"{Path(run_folder).parts[-1]}_log.txt")
         if not os.path.exists(log_folder):
@@ -489,45 +489,45 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        # with self.lock:
-        super().on_created(event)
-        self._run_callbacks(event, check_last_fov)
-
-    def file_timer(self, fov_timeout, watcher_timeout):
-        """Checks time since last file was generated.
-
-        Args:
-            fov_timeout (int):
-                how long to wait for fov data to be generated once file detected
-            watcher_timeout (int):
-                length to wait for new file generation before timing out
-        """
-        while True:
-            current_time = datetime.now()
-            time_elapsed = (current_time - self.last_event_time).total_seconds()
-
-            # 3 fov cycles and no new files --> timeout
-            if time_elapsed > watcher_timeout:
-                fov_num = self.last_fov_num_processed
-                fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
-                print(f"Timed out waiting for {fov_name} files to be generated.")
-                logging.info(
-                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
-                    f"waiting for {fov_name} files to be generated.\n"
-                )
-                logging.info(
-                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
-                    f"Running {self.run_func.__name__} on FOVs\n"
-                )
-
-                # mark remaining fovs as completed to exit watcher
-                for fov_name in list(self.run_structure.fov_progress.keys()):
-                    self.run_structure.fov_progress[fov_name] = {"json": True, "bin": True}
-
-                # trigger run callbacks
-                self.run_func(self.run_folder)
-                break
-            time.sleep(fov_timeout)
+        with self.lock:
+            super().on_created(event)
+            self._run_callbacks(event, check_last_fov)
+
+    # def file_timer(self, fov_timeout, watcher_timeout):
+    #     """Checks time since last file was generated.
+
+    #     Args:
+    #         fov_timeout (int):
+    #             how long to wait for fov data to be generated once file detected
+    #         watcher_timeout (int):
+    #             length to wait for new file generation before timing out
+    #     """
+    #     while True:
+    #         current_time = datetime.now()
+    #         time_elapsed = (current_time - self.last_event_time).total_seconds()
+
+    #         # 3 fov cycles and no new files --> timeout
+    #         if time_elapsed > watcher_timeout:
+    #             fov_num = self.last_fov_num_processed
+    #             fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
+    #             print(f"Timed out waiting for {fov_name} files to be generated.")
+    #             logging.info(
+    #                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
+    #                 f"waiting for {fov_name} files to be generated.\n"
+    #             )
+    #             logging.info(
+    #                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
+    #                 f"Running {self.run_func.__name__} on FOVs\n"
+    #             )
+
+    #             # mark remaining fovs as completed to exit watcher
+    #             for fov_name in list(self.run_structure.fov_progress.keys()):
+    #                 self.run_structure.fov_progress[fov_name] = {"json": True, "bin": True}
+
+    #             # trigger run callbacks
+    #             self.run_func(self.run_folder)
+    #             break
+    #         time.sleep(fov_timeout)
 
     def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         """Handles file renaming events.
@@ -543,9 +543,9 @@ def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        # with self.lock:
-        super().on_moved(event)
-        self._run_callbacks(event, check_last_fov)
+        with self.lock:
+            super().on_moved(event)
+            self._run_callbacks(event, check_last_fov)
 
     def check_complete(self):
         """Checks run structure fov_progress status.

From efc3feeb7b1d9d893ef15084b4ff99d499bbf501 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Tue, 12 Nov 2024 15:48:35 -0800
Subject: [PATCH 37/58] Test deleting the lock AND the timer

---
 src/toffy/fov_watcher.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 02a1d018..6b4d5f1b 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -489,9 +489,9 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        with self.lock:
-            super().on_created(event)
-            self._run_callbacks(event, check_last_fov)
+        # with self.lock:
+        super().on_created(event)
+        self._run_callbacks(event, check_last_fov)
 
     # def file_timer(self, fov_timeout, watcher_timeout):
     #     """Checks time since last file was generated.
@@ -543,9 +543,9 @@ def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        with self.lock:
-            super().on_moved(event)
-            self._run_callbacks(event, check_last_fov)
+        # with self.lock:
+        super().on_moved(event)
+        self._run_callbacks(event, check_last_fov)
 
     def check_complete(self):
         """Checks run structure fov_progress status.

From af9369fc355210508dbe55f827eabb96ace6876e Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@stanford.edu>
Date: Wed, 13 Nov 2024 13:24:11 -0800
Subject: [PATCH 38/58] Try pushing old slow copy tissue data

---
 tests/fov_watcher_test.py | 109 ++++++++++++++++++++++++++------------
 1 file changed, 76 insertions(+), 33 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 96083ab6..7bedcac5 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -36,11 +36,70 @@
 SLOW_COPY_INTERVAL_S = 1
 
 
-# @pytest.fixture(scope="session", autouse=True)
-# def configure_logging():
-#     logging.basicConfig(filename="pytest.txt", level=logging.INFO)
-#     yield
-#     logging.shutdown()  # Ensure all log messages are flushed to the file
+# def _slow_copy_sample_tissue_data(
+#     dest: str, delta: int = 10, one_blank: bool = False, temp_bin: bool = False
+# ):
+#     """Slowly copies files from ./data/tissue/.
+
+#     Args:
+#         dest (str):
+#             Where to copy tissue files to
+#         delta (int):
+#             Time (in seconds) between each file copy
+#         one_blank (bool):
+#             Add a blank .bin file or not
+#         temp_bin (bool):
+#             Use initial temp bin file paths or not
+#     """
+#     num_bin_files = 0
+#     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
+#         time.sleep(delta)
+#         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
+#             # create blank (0 size) file
+#             open(os.path.join(dest, tissue_file), "w").close()
+#         else:
+#             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
+#             if temp_bin and ".bin" in tissue_file:
+#                 # copy to a temporary file with hash extension, then move to dest folder
+#                 print(f"Copying over a temporary file with hash extension on {tissue_file}")
+#                 new_tissue_path = os.path.join(COMBINED_DATA_PATH, "." + tissue_file + ".aBcDeF")
+#                 shutil.copy(tissue_path, new_tissue_path)
+#                 shutil.copy(new_tissue_path, dest)
+#                 print(f"Removing the old tissue path at .{tissue_file}.aBcDeF")
+#                 os.remove(new_tissue_path)
+
+#                 # simulate a renaming event in dest
+#                 time.sleep(delta)
+#                 print(f"Renaming back to {tissue_file}")
+#                 copied_tissue_path = os.path.join(dest, "." + tissue_file + ".aBcDeF")
+#                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
+
+#             else:
+#                 shutil.copy(tissue_path, dest)
+
+#             # simulate a timestamp update if .bin file has been extracted AND not blank
+#             # NOTE: this assumes .json file always copies after the .bin, which does happen on Ionpath
+#             tissue_data = os.path.splitext(tissue_file)
+#             if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
+#                 if one_blank:
+#                     one_blank = False
+#                     continue
+#                 elif num_bin_files % 2 == 0:
+#                     bin_file_name = tissue_data[0] + ".bin"
+#                     print(f"Simulating .bin file update on {bin_file_name}")
+#                     shutil.copy(
+#                         os.path.join(COMBINED_DATA_PATH, bin_file_name),
+#                         os.path.join(dest, bin_file_name + ".temp"),
+#                     )
+#                     print("Renamed bin file to temp")
+#                     os.remove(os.path.join(dest, bin_file_name))
+#                     print("Removed old bin file")
+#                     os.rename(
+#                         os.path.join(dest, bin_file_name + ".temp"),
+#                         os.path.join(dest, bin_file_name),
+#                     )
+#                     print("Renamed temp bin file back to orig")
+#                 num_bin_files += 1
 
 
 def _slow_copy_sample_tissue_data(
@@ -58,55 +117,39 @@ def _slow_copy_sample_tissue_data(
         temp_bin (bool):
             Use initial temp bin file paths or not
     """
-    num_bin_files = 0
     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
         time.sleep(delta)
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
             # create blank (0 size) file
             open(os.path.join(dest, tissue_file), "w").close()
+            one_blank = False
         else:
             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
             if temp_bin and ".bin" in tissue_file:
                 # copy to a temporary file with hash extension, then move to dest folder
-                print(f"Copying over a temporary file with hash extension on {tissue_file}")
                 new_tissue_path = os.path.join(COMBINED_DATA_PATH, "." + tissue_file + ".aBcDeF")
                 shutil.copy(tissue_path, new_tissue_path)
                 shutil.copy(new_tissue_path, dest)
-                print(f"Removing the old tissue path at .{tissue_file}.aBcDeF")
                 os.remove(new_tissue_path)
 
                 # simulate a renaming event in dest
                 time.sleep(delta)
-                print(f"Renaming back to {tissue_file}")
                 copied_tissue_path = os.path.join(dest, "." + tissue_file + ".aBcDeF")
                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
-
             else:
                 shutil.copy(tissue_path, dest)
 
-            # simulate a timestamp update if .bin file has been extracted AND not blank
-            # NOTE: this assumes .json file always copies after the .bin, which does happen on Ionpath
-            tissue_data = os.path.splitext(tissue_file)
-            if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
-                if one_blank:
-                    one_blank = False
-                    continue
-                elif num_bin_files % 2 == 0:
-                    bin_file_name = tissue_data[0] + ".bin"
-                    print(f"Simulating .bin file update on {bin_file_name}")
-                    shutil.copy(
-                        os.path.join(COMBINED_DATA_PATH, bin_file_name),
-                        os.path.join(dest, bin_file_name + ".temp"),
-                    )
-                    print("Renamed bin file to temp")
-                    os.remove(os.path.join(dest, bin_file_name))
-                    print("Removed old bin file")
-                    os.rename(
-                        os.path.join(dest, bin_file_name + ".temp"),
-                        os.path.join(dest, bin_file_name),
-                    )
-                    print("Renamed temp bin file back to orig")
-                num_bin_files += 1
+    # get all .bin files
+    bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
+
+    # simulate updating the creation time for some .bin files, this tests _check_bin_updates
+    for i, bfile in enumerate(bin_files):
+        if i % 2 == 0:
+            shutil.copy(
+                os.path.join(COMBINED_DATA_PATH, bfile), os.path.join(dest, bfile + ".temp")
+            )
+            os.remove(os.path.join(dest, bfile))
+            os.rename(os.path.join(dest, bfile + ".temp"), os.path.join(dest, bfile))
 
 
 COMBINED_RUN_JSON_SPOOF = {

From 7aef668e372a17f231a2931ef8594b70fe05e846 Mon Sep 17 00:00:00 2001
From: Sricharan Reddy Varra <sricharanvarra@gmail.com>
Date: Thu, 14 Nov 2024 12:16:42 -0800
Subject: [PATCH 39/58] removed debug

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3337e9e7..aedf2ac7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -52,8 +52,8 @@ jobs:
         run: |
           poetry install --no-interaction
 
-      - name: Debug
-        uses: lhotari/action-upterm@v1
+      # - name: Debug
+      #   uses: lhotari/action-upterm@v1
 
       - name: Run Tests
         run: |

From a7370e752c6016032a1e29c092f219d15be141c1 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 15:58:46 -0800
Subject: [PATCH 40/58] See if sleeping for 2 seconds will prevent the toffy
 segmentation error from popping up

---
 src/toffy/fov_watcher.py  | 100 ++++++++++++++++++++------------------
 tests/fov_watcher_test.py |  44 +++++++++++++----
 2 files changed, 87 insertions(+), 57 deletions(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 6b4d5f1b..953a641e 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -82,6 +82,7 @@ def check_run_condition(self, path: str) -> Tuple[bool, str]:
                 whether or not both json and bin files exist, as well as the name of the point
         """
         filename = Path(path).parts[-1]
+        print(f"The filename to check is: {filename}")
 
         # if filename starts with a '.' (temp file), it should be ignored
         if filename[0] == ".":
@@ -207,11 +208,11 @@ def __init__(
         self.run_folder = run_folder
 
         self.last_event_time = datetime.now()
-        # self.timer_thread = threading.Thread(
-        #     target=self.file_timer, args=(fov_timeout, watcher_timeout)
-        # )
-        # self.timer_thread.daemon = True
-        # self.timer_thread.start()
+        self.timer_thread = threading.Thread(
+            target=self.file_timer, args=(fov_timeout, watcher_timeout)
+        )
+        self.timer_thread.daemon = True
+        self.timer_thread.start()
 
         self.log_path = os.path.join(log_folder, f"{Path(run_folder).parts[-1]}_log.txt")
         if not os.path.exists(log_folder):
@@ -404,6 +405,9 @@ def _check_bin_updates(self):
             fov_bin_path = os.path.join(self.run_folder, fov + ".bin")
             fov_json_path = os.path.join(self.run_folder, fov + ".json")
 
+            print(f"Verifying fov_bin_path: {fov_bin_path}")
+            print(f"Verifying fov_json_path: {fov_json_path}")
+
             # if .bin file ctime > .json file ctime, incomplete extraction, need to re-extract
             fov_bin_create = Path(fov_bin_path).stat().st_ctime
             fov_json_create = Path(fov_json_path).stat().st_ctime
@@ -489,45 +493,45 @@ def on_created(self, event: FileCreatedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        # with self.lock:
-        super().on_created(event)
-        self._run_callbacks(event, check_last_fov)
-
-    # def file_timer(self, fov_timeout, watcher_timeout):
-    #     """Checks time since last file was generated.
-
-    #     Args:
-    #         fov_timeout (int):
-    #             how long to wait for fov data to be generated once file detected
-    #         watcher_timeout (int):
-    #             length to wait for new file generation before timing out
-    #     """
-    #     while True:
-    #         current_time = datetime.now()
-    #         time_elapsed = (current_time - self.last_event_time).total_seconds()
-
-    #         # 3 fov cycles and no new files --> timeout
-    #         if time_elapsed > watcher_timeout:
-    #             fov_num = self.last_fov_num_processed
-    #             fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
-    #             print(f"Timed out waiting for {fov_name} files to be generated.")
-    #             logging.info(
-    #                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
-    #                 f"waiting for {fov_name} files to be generated.\n"
-    #             )
-    #             logging.info(
-    #                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
-    #                 f"Running {self.run_func.__name__} on FOVs\n"
-    #             )
-
-    #             # mark remaining fovs as completed to exit watcher
-    #             for fov_name in list(self.run_structure.fov_progress.keys()):
-    #                 self.run_structure.fov_progress[fov_name] = {"json": True, "bin": True}
-
-    #             # trigger run callbacks
-    #             self.run_func(self.run_folder)
-    #             break
-    #         time.sleep(fov_timeout)
+        with self.lock:
+            super().on_created(event)
+            self._run_callbacks(event, check_last_fov)
+
+    def file_timer(self, fov_timeout, watcher_timeout):
+        """Checks time since last file was generated.
+
+        Args:
+            fov_timeout (int):
+                how long to wait for fov data to be generated once file detected
+            watcher_timeout (int):
+                length to wait for new file generation before timing out
+        """
+        while True:
+            current_time = datetime.now()
+            time_elapsed = (current_time - self.last_event_time).total_seconds()
+
+            # 3 fov cycles and no new files --> timeout
+            if time_elapsed > watcher_timeout:
+                fov_num = self.last_fov_num_processed
+                fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
+                print(f"Timed out waiting for {fov_name} files to be generated.")
+                logging.info(
+                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
+                    f"waiting for {fov_name} files to be generated.\n"
+                )
+                logging.info(
+                    f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
+                    f"Running {self.run_func.__name__} on FOVs\n"
+                )
+
+                # mark remaining fovs as completed to exit watcher
+                for fov_name in list(self.run_structure.fov_progress.keys()):
+                    self.run_structure.fov_progress[fov_name] = {"json": True, "bin": True}
+
+                # trigger run callbacks
+                self.run_func(self.run_folder)
+                break
+            time.sleep(fov_timeout)
 
     def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         """Handles file renaming events.
@@ -543,9 +547,9 @@ def on_moved(self, event: FileMovedEvent, check_last_fov: bool = True):
         if self.last_fov_num_processed == self.run_structure.highest_fov:
             return
 
-        # with self.lock:
-        super().on_moved(event)
-        self._run_callbacks(event, check_last_fov)
+        with self.lock:
+            super().on_moved(event)
+            self._run_callbacks(event, check_last_fov)
 
     def check_complete(self):
         """Checks run structure fov_progress status.
@@ -555,8 +559,10 @@ def check_complete(self):
         NOTE: bin files that had new data written will first need to be re-extracted.
         """
         if all(self.run_structure.check_fov_progress().values()) and not self.all_fovs_complete:
+            print("All FOVs complete, checking for bin updates")
             self.all_fovs_complete = True
             self._check_bin_updates()
+            print("Finished checking for bin updates, starting run callbacks")
             logging.info(f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- All FOVs finished\n')
             logging.info(
                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 7bedcac5..7f0fcc04 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -118,6 +118,7 @@ def _slow_copy_sample_tissue_data(
             Use initial temp bin file paths or not
     """
     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
+        print(f"Copying over file {tissue_file}")
         time.sleep(delta)
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
             # create blank (0 size) file
@@ -138,18 +139,38 @@ def _slow_copy_sample_tissue_data(
                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
             else:
                 shutil.copy(tissue_path, dest)
+                tissue_data = os.path.splitext(tissue_file)
+
+                if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
+                    time.sleep(2)
+                    bin_file_name = tissue_data[0] + ".bin"
+                    print(f"Simulating .bin file update on {bin_file_name}")
+                    shutil.copy(
+                        os.path.join(COMBINED_DATA_PATH, bin_file_name),
+                        os.path.join(dest, bin_file_name + ".temp"),
+                    )
+                    print("Renamed bin file to temp")
+                    os.remove(os.path.join(dest, bin_file_name))
+                    print("Removed old bin file")
+                    os.rename(
+                        os.path.join(dest, bin_file_name + ".temp"),
+                        os.path.join(dest, bin_file_name),
+                    )
+                    print("Renamed temp bin file back to orig")
 
-    # get all .bin files
-    bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
 
-    # simulate updating the creation time for some .bin files, this tests _check_bin_updates
-    for i, bfile in enumerate(bin_files):
-        if i % 2 == 0:
-            shutil.copy(
-                os.path.join(COMBINED_DATA_PATH, bfile), os.path.join(dest, bfile + ".temp")
-            )
-            os.remove(os.path.join(dest, bfile))
-            os.rename(os.path.join(dest, bfile + ".temp"), os.path.join(dest, bfile))
+    # # get all .bin files
+    # bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
+
+    # # simulate updating the creation time for some .bin files, this tests _check_bin_updates
+    # for i, bfile in enumerate(bin_files):
+    #     if i % 2 == 0:
+    #         print(f"Simulating a .bin file update for {bfile}")
+    #         shutil.copy(
+    #             os.path.join(COMBINED_DATA_PATH, bfile), os.path.join(dest, bfile + ".temp")
+    #         )
+    #         os.remove(os.path.join(dest, bfile))
+    #         os.rename(os.path.join(dest, bfile + ".temp"), os.path.join(dest, bfile))
 
 
 COMBINED_RUN_JSON_SPOOF = {
@@ -322,6 +343,9 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
+    print(existing_data)
+    print(add_blank)
+    print(temp_bin)
     try:
         with tempfile.TemporaryDirectory() as tmpdir:
             tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)

From 0eed3804a4a5950f620041b776ddddd9f6ad0f2f Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 16:00:11 -0800
Subject: [PATCH 41/58] black formatting

---
 tests/fov_watcher_test.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 7f0fcc04..433cf39a 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -158,7 +158,6 @@ def _slow_copy_sample_tissue_data(
                     )
                     print("Renamed temp bin file back to orig")
 
-
     # # get all .bin files
     # bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
 

From 510c3981f8003364b25deea5759abbd663386e4c Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 21:36:28 -0800
Subject: [PATCH 42/58] Massive test overhaul: see how many tests pass now

---
 src/toffy/fov_watcher.py       |   9 ---
 src/toffy/image_stitching.py   |   6 --
 src/toffy/normalize.py         |   3 -
 src/toffy/watcher_callbacks.py |   1 -
 tests/fov_watcher_test.py      | 120 ++++++++++++++++++++-------------
 tests/utils/test_utils.py      |   1 -
 6 files changed, 72 insertions(+), 68 deletions(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 953a641e..19004839 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -82,7 +82,6 @@ def check_run_condition(self, path: str) -> Tuple[bool, str]:
                 whether or not both json and bin files exist, as well as the name of the point
         """
         filename = Path(path).parts[-1]
-        print(f"The filename to check is: {filename}")
 
         # if filename starts with a '.' (temp file), it should be ignored
         if filename[0] == ".":
@@ -124,7 +123,6 @@ def check_run_condition(self, path: str) -> Tuple[bool, str]:
 
                     time.sleep(self.timeout / 10)
                     wait_time += self.timeout / 10
-
                 self.fov_progress[fov_name][extension] = True
 
             if all(self.fov_progress[fov_name].values()):
@@ -217,7 +215,6 @@ def __init__(
         self.log_path = os.path.join(log_folder, f"{Path(run_folder).parts[-1]}_log.txt")
         if not os.path.exists(log_folder):
             os.makedirs(log_folder)
-        print(f"Setting log path to {self.log_path}")
         logging.basicConfig(
             level=logging.INFO,
             filename=self.log_path,
@@ -405,9 +402,6 @@ def _check_bin_updates(self):
             fov_bin_path = os.path.join(self.run_folder, fov + ".bin")
             fov_json_path = os.path.join(self.run_folder, fov + ".json")
 
-            print(f"Verifying fov_bin_path: {fov_bin_path}")
-            print(f"Verifying fov_json_path: {fov_json_path}")
-
             # if .bin file ctime > .json file ctime, incomplete extraction, need to re-extract
             fov_bin_create = Path(fov_bin_path).stat().st_ctime
             fov_json_create = Path(fov_json_path).stat().st_ctime
@@ -514,7 +508,6 @@ def file_timer(self, fov_timeout, watcher_timeout):
             if time_elapsed > watcher_timeout:
                 fov_num = self.last_fov_num_processed
                 fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
-                print(f"Timed out waiting for {fov_name} files to be generated.")
                 logging.info(
                     f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
                     f"waiting for {fov_name} files to be generated.\n"
@@ -559,10 +552,8 @@ def check_complete(self):
         NOTE: bin files that had new data written will first need to be re-extracted.
         """
         if all(self.run_structure.check_fov_progress().values()) and not self.all_fovs_complete:
-            print("All FOVs complete, checking for bin updates")
             self.all_fovs_complete = True
             self._check_bin_updates()
-            print("Finished checking for bin updates, starting run callbacks")
             logging.info(f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- All FOVs finished\n')
             logging.info(
                 f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- '
diff --git a/src/toffy/image_stitching.py b/src/toffy/image_stitching.py
index d7d30b22..77b39af1 100644
--- a/src/toffy/image_stitching.py
+++ b/src/toffy/image_stitching.py
@@ -253,13 +253,7 @@ def stitch_images(
             num_cols = math.isqrt(len(folders))
             max_img_size = get_max_img_size(tiff_out_dir, img_sub_folder, run_dir)
 
-            print(tiff_out_dir)
-            print(img_sub_folder)
-            print(os.listdir(tiff_out_dir))
             subfolder = "" if img_sub_folder is None else img_sub_folder
-            for fov in folders:
-                print(f"Here's what's in fov {fov}")
-                print(os.listdir(os.path.join(tiff_out_dir, fov, subfolder)))
             image_data = load_utils.load_imgs_from_tree(
                 tiff_out_dir,
                 img_sub_folder=img_sub_folder,
diff --git a/src/toffy/normalize.py b/src/toffy/normalize.py
index 6d7694e9..956352f8 100644
--- a/src/toffy/normalize.py
+++ b/src/toffy/normalize.py
@@ -65,17 +65,14 @@ def write_mph_per_mass(
         proficient (bool): whether proficient MPH data is written or not
     """
     # compute pulse heights
-    print("Inside writing MPH per mass")
     panel = make_panel(
         mass=masses, target_name=masses, low_range=start_offset, high_range=stop_offset
     )
 
     # generate the MPH values for each mass
-    print("About to get median pulse height")
     mph_vals = list(
         get_median_pulse_height(data_dir=base_dir, fov=fov, channels=masses, panel=panel).values()
     )
-    print("Computed median pulse height")
 
     fovs = np.repeat(fov, len(masses))
     out_df = pd.DataFrame({"mass": masses, "fov": fovs, "pulse_height": mph_vals})
diff --git a/src/toffy/watcher_callbacks.py b/src/toffy/watcher_callbacks.py
index f69da667..14dbfaf0 100644
--- a/src/toffy/watcher_callbacks.py
+++ b/src/toffy/watcher_callbacks.py
@@ -369,7 +369,6 @@ def generate_pulse_heights(self, pulse_out_dir: str, panel: pd.DataFrame = None,
              - start_offset
              - stop_offset
         """
-        print("Inside computing pulse heights")
         if not os.path.exists(pulse_out_dir):
             os.makedirs(pulse_out_dir)
 
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 433cf39a..6e4e07be 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -35,6 +35,10 @@
 
 SLOW_COPY_INTERVAL_S = 1
 
+def _reset_logging_file():
+    with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:
+        pass
+
 
 # def _slow_copy_sample_tissue_data(
 #     dest: str, delta: int = 10, one_blank: bool = False, temp_bin: bool = False
@@ -118,13 +122,14 @@ def _slow_copy_sample_tissue_data(
             Use initial temp bin file paths or not
     """
     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
-        print(f"Copying over file {tissue_file}")
         time.sleep(delta)
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
+            print(f"Creating a blank .bin file at {os.path.join(dest, tissue_file)}")
             # create blank (0 size) file
             open(os.path.join(dest, tissue_file), "w").close()
             one_blank = False
         else:
+            print(f"Copying over file {tissue_file}")
             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
             if temp_bin and ".bin" in tissue_file:
                 # copy to a temporary file with hash extension, then move to dest folder
@@ -141,35 +146,23 @@ def _slow_copy_sample_tissue_data(
                 shutil.copy(tissue_path, dest)
                 tissue_data = os.path.splitext(tissue_file)
 
+                # simulate a .bin file update to test _check_bin_updates
                 if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
+                    # ensure a sleep so the update doesn't interfere with an existing extraction
                     time.sleep(2)
                     bin_file_name = tissue_data[0] + ".bin"
-                    print(f"Simulating .bin file update on {bin_file_name}")
-                    shutil.copy(
-                        os.path.join(COMBINED_DATA_PATH, bin_file_name),
-                        os.path.join(dest, bin_file_name + ".temp"),
-                    )
-                    print("Renamed bin file to temp")
-                    os.remove(os.path.join(dest, bin_file_name))
-                    print("Removed old bin file")
-                    os.rename(
-                        os.path.join(dest, bin_file_name + ".temp"),
-                        os.path.join(dest, bin_file_name),
-                    )
-                    print("Renamed temp bin file back to orig")
 
-    # # get all .bin files
-    # bin_files = [bfile for bfile in sorted(os.listdir(COMBINED_DATA_PATH)) if ".bin" in bfile]
-
-    # # simulate updating the creation time for some .bin files, this tests _check_bin_updates
-    # for i, bfile in enumerate(bin_files):
-    #     if i % 2 == 0:
-    #         print(f"Simulating a .bin file update for {bfile}")
-    #         shutil.copy(
-    #             os.path.join(COMBINED_DATA_PATH, bfile), os.path.join(dest, bfile + ".temp")
-    #         )
-    #         os.remove(os.path.join(dest, bfile))
-    #         os.rename(os.path.join(dest, bfile + ".temp"), os.path.join(dest, bfile))
+                    # make sure only to update non-blank bin files
+                    if os.path.getsize(os.path.join(dest, bin_file_name)) != 0:
+                        shutil.copy(
+                            os.path.join(COMBINED_DATA_PATH, bin_file_name),
+                            os.path.join(dest, bin_file_name + ".temp"),
+                        )
+                        os.remove(os.path.join(dest, bin_file_name))
+                        os.rename(
+                            os.path.join(dest, bin_file_name + ".temp"),
+                            os.path.join(dest, bin_file_name),
+                        )
 
 
 COMBINED_RUN_JSON_SPOOF = {
@@ -460,13 +453,15 @@ def test_watcher(
 
                     res_scan.get()
 
-            print("Testing log out status")
-            print(log_out)
-            # with open(os.path.join(log_out, "test_run_log.txt")) as f:
-            print(os.listdir("."))
             with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
                 logtxt = f.read()
-                assert add_blank == ("non-zero file size..." in logtxt)
+                print("The log to read is: ")
+                print(logtxt)
+                try:
+                    assert add_blank == ("non-zero file size..." in logtxt)
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
 
             fovs = [
                 bin_file.split(".")[0]
@@ -486,41 +481,70 @@ def test_watcher(
             print("TIFF validator check")
             validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
             if kwargs["extract_prof"]:
-                validators[0](
-                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
-                )
+                try:
+                    validators[0](
+                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
+                    )
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
             else:
-                assert not os.path.exists(
-                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
-                )
+                try:
+                    assert not os.path.exists(
+                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
+                    )
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
 
             # qc check
             print("QC check")
-            validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
+            try:
+                validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
+            except AssertionError as e:
+                _reset_logging_file()
+                raise AssertionError(e)
 
             # mph check
             print("MPH check")
-            validators[2](
-                os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
-                os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
-                fovs,
-                bad_fovs,
-            )
+            try:
+                validators[2](
+                    os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
+                    os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
+                    fovs,
+                    bad_fovs,
+                )
+            except AssertionError as e:
+                _reset_logging_file()
+                raise AssertionError(e)
 
             # stitch images check
             print("Stitch images check")
-            validators[3](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched"))
+            try:
+                validators[3](
+                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched")
+                )
+            except AssertionError as e:
+                _reset_logging_file()
+                raise AssertionError(e)
 
             # pulse heights check
             print("Pulse heights check")
-            validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
+            try:
+                validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
+            except AssertionError as e:
+                _reset_logging_file()
+                raise AssertionError(e)
+
+            # os.remove(os.path.join(Path(__file__).parents[1], "pytest.txt"))
+            # Path(os.path.join(Path(__file__).parents[1], "pytest.txt")).touch()
 
-            with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:
-                infile.write("")
+            _reset_logging_file()
 
     except OSError as ose:
         print("Ran into an error:")
         print(ose)
+        _reset_logging_file()
         # warnings.warn("Temporary file cleanup was incomplete.")
 
 
diff --git a/tests/utils/test_utils.py b/tests/utils/test_utils.py
index f866e31c..ec753fb7 100644
--- a/tests/utils/test_utils.py
+++ b/tests/utils/test_utils.py
@@ -19,7 +19,6 @@
 from toffy.settings import QC_COLUMNS, QC_SUFFIXES
 
 TEST_CHANNELS = [
-    "Calprotectin",
     "Chymase",
     "SMA",
     "Vimentin",

From d7e2eee0080040f15e37007bea79c849001a3763 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 21:37:29 -0800
Subject: [PATCH 43/58] Remove old _slow_copy_tissue... function

---
 tests/fov_watcher_test.py | 66 ---------------------------------------
 1 file changed, 66 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 6e4e07be..da5924a3 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -40,72 +40,6 @@ def _reset_logging_file():
         pass
 
 
-# def _slow_copy_sample_tissue_data(
-#     dest: str, delta: int = 10, one_blank: bool = False, temp_bin: bool = False
-# ):
-#     """Slowly copies files from ./data/tissue/.
-
-#     Args:
-#         dest (str):
-#             Where to copy tissue files to
-#         delta (int):
-#             Time (in seconds) between each file copy
-#         one_blank (bool):
-#             Add a blank .bin file or not
-#         temp_bin (bool):
-#             Use initial temp bin file paths or not
-#     """
-#     num_bin_files = 0
-#     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
-#         time.sleep(delta)
-#         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
-#             # create blank (0 size) file
-#             open(os.path.join(dest, tissue_file), "w").close()
-#         else:
-#             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
-#             if temp_bin and ".bin" in tissue_file:
-#                 # copy to a temporary file with hash extension, then move to dest folder
-#                 print(f"Copying over a temporary file with hash extension on {tissue_file}")
-#                 new_tissue_path = os.path.join(COMBINED_DATA_PATH, "." + tissue_file + ".aBcDeF")
-#                 shutil.copy(tissue_path, new_tissue_path)
-#                 shutil.copy(new_tissue_path, dest)
-#                 print(f"Removing the old tissue path at .{tissue_file}.aBcDeF")
-#                 os.remove(new_tissue_path)
-
-#                 # simulate a renaming event in dest
-#                 time.sleep(delta)
-#                 print(f"Renaming back to {tissue_file}")
-#                 copied_tissue_path = os.path.join(dest, "." + tissue_file + ".aBcDeF")
-#                 os.rename(copied_tissue_path, os.path.join(dest, tissue_file))
-
-#             else:
-#                 shutil.copy(tissue_path, dest)
-
-#             # simulate a timestamp update if .bin file has been extracted AND not blank
-#             # NOTE: this assumes .json file always copies after the .bin, which does happen on Ionpath
-#             tissue_data = os.path.splitext(tissue_file)
-#             if tissue_data[1] == ".json" and "_processing" not in tissue_data[0]:
-#                 if one_blank:
-#                     one_blank = False
-#                     continue
-#                 elif num_bin_files % 2 == 0:
-#                     bin_file_name = tissue_data[0] + ".bin"
-#                     print(f"Simulating .bin file update on {bin_file_name}")
-#                     shutil.copy(
-#                         os.path.join(COMBINED_DATA_PATH, bin_file_name),
-#                         os.path.join(dest, bin_file_name + ".temp"),
-#                     )
-#                     print("Renamed bin file to temp")
-#                     os.remove(os.path.join(dest, bin_file_name))
-#                     print("Removed old bin file")
-#                     os.rename(
-#                         os.path.join(dest, bin_file_name + ".temp"),
-#                         os.path.join(dest, bin_file_name),
-#                     )
-#                     print("Renamed temp bin file back to orig")
-#                 num_bin_files += 1
-
-
 def _slow_copy_sample_tissue_data(
     dest: str, delta: int = 10, one_blank: bool = False, temp_bin: bool = False
 ):

From 8590206ca163e274e4456bc85db9f75acd5a13e2 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 22:04:55 -0800
Subject: [PATCH 44/58] Linting checks

---
 src/toffy/image_stitching.py | 1 -
 tests/fov_watcher_test.py    | 3 ++-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/toffy/image_stitching.py b/src/toffy/image_stitching.py
index 77b39af1..c41141ff 100644
--- a/src/toffy/image_stitching.py
+++ b/src/toffy/image_stitching.py
@@ -253,7 +253,6 @@ def stitch_images(
             num_cols = math.isqrt(len(folders))
             max_img_size = get_max_img_size(tiff_out_dir, img_sub_folder, run_dir)
 
-            subfolder = "" if img_sub_folder is None else img_sub_folder
             image_data = load_utils.load_imgs_from_tree(
                 tiff_out_dir,
                 img_sub_folder=img_sub_folder,
diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index da5924a3..457f5df7 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -35,8 +35,9 @@
 
 SLOW_COPY_INTERVAL_S = 1
 
+
 def _reset_logging_file():
-    with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w") as infile:
+    with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w"):
         pass
 
 

From 6012a8f3344ff200075dcaa94551ef6f343733fa Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 22:24:17 -0800
Subject: [PATCH 45/58] PYCODESTYLE

---
 tests/fov_watcher_test.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 457f5df7..047dfd40 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -35,7 +35,6 @@
 
 SLOW_COPY_INTERVAL_S = 1
 
-
 def _reset_logging_file():
     with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w"):
         pass

From d1940eb51445e811219747f261681daa00a447cc Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:03:12 -0800
Subject: [PATCH 46/58] Add fixes to temporary work around list_folders and
 list_files in rosetta

---
 src/toffy/rosetta.py  | 4 +++-
 tests/rosetta_test.py | 4 ++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/toffy/rosetta.py b/src/toffy/rosetta.py
index 50728aa6..1f2a2401 100644
--- a/src/toffy/rosetta.py
+++ b/src/toffy/rosetta.py
@@ -288,7 +288,9 @@ def compensate_image_data(
     io_utils.validate_paths([raw_data_dir, comp_data_dir, comp_mat_path])
 
     # get list of all fovs
-    fovs = io_utils.list_folders(raw_data_dir, substrs="fov")
+    # TODO: list_folders does not handle cases such as "fov0" correctly
+    # need to add a fix in to alpineer to deal with this
+    fovs = [f for f in os.listdir(raw_data_dir) if "fov" in f]
 
     # load csv files
     comp_mat = pd.read_csv(comp_mat_path, index_col=0)
diff --git a/tests/rosetta_test.py b/tests/rosetta_test.py
index e518c13a..98043a6d 100644
--- a/tests/rosetta_test.py
+++ b/tests/rosetta_test.py
@@ -360,8 +360,8 @@ def test_compensate_image_data(
 
         for folder in format_folders:
             # check that all files were created
-            output_files = io_utils.list_files(os.path.join(output_dir, fovs[0], folder), ".tif")
-            output_files = [chan.split(".tif")[0] for chan in output_files]
+            output_files = io_utils.list_files(os.path.join(output_dir, fovs[0], folder), ".tiff")
+            output_files = [chan.split(".tiff")[0] for chan in output_files]
 
             if output_masses is None or len(output_masses) == 3:
                 assert set(output_files) == set(panel_info["Target"].values)

From 5b3131b08d0b2b2b9edc78f48baab61b5a44bc11 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:10:44 -0800
Subject: [PATCH 47/58] Strict matching required between underscores:
 "pulse_height" will not match "pulse_heights_..."

---
 tests/normalize_test.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/normalize_test.py b/tests/normalize_test.py
index 89f9a856..cb395cff 100644
--- a/tests/normalize_test.py
+++ b/tests/normalize_test.py
@@ -169,9 +169,9 @@ def test_combine_run_metrics(metrics, warn_overwrite_test):
             name_prof, values_df_prof = metric[0], pd.DataFrame(metric[1])
             values_df_prof.to_csv(os.path.join(temp_dir, name_prof), index=False)
 
-        normalize.combine_run_metrics(temp_dir, "pulse_height")
+        normalize.combine_run_metrics(temp_dir, "pulse_heights")
 
-        combined_data = pd.read_csv(os.path.join(temp_dir, "pulse_height_combined.csv"))
+        combined_data = pd.read_csv(os.path.join(temp_dir, "pulse_heights_combined.csv"))
 
         assert np.array_equal(combined_data.columns, ["pulse_height", "mass", "fov"])
         assert len(combined_data) == len(metrics["deficient"]) * 10
@@ -180,9 +180,9 @@ def test_combine_run_metrics(metrics, warn_overwrite_test):
         # NOTE: only if warn_overwrite turned on
         if warn_overwrite_test:
             with pytest.warns(UserWarning, match="previously generated"):
-                normalize.combine_run_metrics(temp_dir, "pulse_height", warn_overwrite_test)
+                normalize.combine_run_metrics(temp_dir, "pulse_heights", warn_overwrite_test)
         else:
-            normalize.combine_run_metrics(temp_dir, "pulse_height", warn_overwrite_test)
+            normalize.combine_run_metrics(temp_dir, "pulse_heights", warn_overwrite_test)
 
         # check that files with different lengths raises error
         name, bad_vals = metrics["deficient"][0][0], pd.DataFrame(metrics["deficient"][0][1])
@@ -190,14 +190,14 @@ def test_combine_run_metrics(metrics, warn_overwrite_test):
         bad_vals.to_csv(os.path.join(temp_dir, name), index=False)
 
         with pytest.raises(ValueError, match="files are the same length"):
-            normalize.combine_run_metrics(temp_dir, "pulse_height")
+            normalize.combine_run_metrics(temp_dir, "pulse_heights")
 
         # empty directory raises error
         empty_dir = os.path.join(temp_dir, "empty")
         os.makedirs(empty_dir)
 
         with pytest.raises(ValueError, match="No files"):
-            normalize.combine_run_metrics(empty_dir, "pulse_height")
+            normalize.combine_run_metrics(empty_dir, "pulse_heights")
 
 
 @parametrize_with_cases("dir_names, mph_dfs, count_dfs", test_cases.TuningCurveFiles)

From f66a6ffe60be417a78deff3689b18a3c1c2d343b Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:18:21 -0800
Subject: [PATCH 48/58] Fix list_folders in normalize_image.py to correctly
 list all FOVs, add TODO for fixing verify_same_elements edge case

---
 src/toffy/normalize.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/toffy/normalize.py b/src/toffy/normalize.py
index 956352f8..212472fa 100644
--- a/src/toffy/normalize.py
+++ b/src/toffy/normalize.py
@@ -831,7 +831,9 @@ def normalize_image_data(
     # create normalization function for mapping MPH to counts
     norm_json = read_json_file(norm_func_path)
 
-    img_fovs = io_utils.list_folders(img_dir, "fov")
+    # TODO: list_folders does not handle cases such as "fov0" correctly
+    # need to add a fix in to alpineer to deal with this
+    img_fovs = [f for f in os.listdir(img_dir) if "fov" in f]
 
     norm_weights, norm_name = norm_json["weights"], norm_json["name"]
     norm_func = create_prediction_function(norm_name, norm_weights)
@@ -852,6 +854,9 @@ def normalize_image_data(
 
     # make sure FOVs used to construct tuning curve are same ones being normalized
     pulse_fovs = np.unique(pulse_height_df["fov"])
+
+    # TODO: verify_same_elements needs to throw a ValueError in the special case
+    # where one list is empty but the other isn't
     misc_utils.verify_same_elements(image_data_fovs=img_fovs, pulse_height_csv_files=pulse_fovs)
 
     # loop over each fov

From 5c871257e5ab64c085431404acd4461a386459d4 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:41:43 -0800
Subject: [PATCH 49/58] Fix list_folders in merge_partial_runs

---
 src/toffy/reorg.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/toffy/reorg.py b/src/toffy/reorg.py
index 61c2e8ba..bdba40a2 100644
--- a/src/toffy/reorg.py
+++ b/src/toffy/reorg.py
@@ -20,7 +20,9 @@ def merge_partial_runs(cohort_dir, run_string):
         os.makedirs(output_folder)
 
     # get list of matching subfolders
-    partial_folders = io_utils.list_folders(cohort_dir, substrs=run_string)
+    # TODO: list_folders does not handle cases such as "run_dup2" correctly
+    # need to add a fix in to alpineer to deal with this
+    partial_folders = [f for f in os.listdir(cohort_dir) if run_string in f]
     partial_folders = [partial for partial in partial_folders if partial != run_string]
 
     if len(partial_folders) == 0:

From 542b5cca639df9b1483d3b47be162385e1fd7361 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:44:03 -0800
Subject: [PATCH 50/58] Formatting

---
 tests/fov_watcher_test.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 047dfd40..457f5df7 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -35,6 +35,7 @@
 
 SLOW_COPY_INTERVAL_S = 1
 
+
 def _reset_logging_file():
     with open(os.path.join(Path(__file__).parents[1], "pytest.txt"), "w"):
         pass

From 51cb85befe61194785245f98e58ca29e0be56d49 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:48:52 -0800
Subject: [PATCH 51/58] Remove print statements

---
 tests/fov_watcher_test.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 457f5df7..0b7498c3 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -59,12 +59,10 @@ def _slow_copy_sample_tissue_data(
     for tissue_file in sorted(os.listdir(COMBINED_DATA_PATH)):
         time.sleep(delta)
         if one_blank and ".bin" in tissue_file and tissue_file[0] != ".":
-            print(f"Creating a blank .bin file at {os.path.join(dest, tissue_file)}")
             # create blank (0 size) file
             open(os.path.join(dest, tissue_file), "w").close()
             one_blank = False
         else:
-            print(f"Copying over file {tissue_file}")
             tissue_path = os.path.join(COMBINED_DATA_PATH, tissue_file)
             if temp_bin and ".bin" in tissue_file:
                 # copy to a temporary file with hash extension, then move to dest folder
@@ -390,8 +388,6 @@ def test_watcher(
 
             with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
                 logtxt = f.read()
-                print("The log to read is: ")
-                print(logtxt)
                 try:
                     assert add_blank == ("non-zero file size..." in logtxt)
                 except AssertionError as e:

From 87c2b1ba9a72ca3e7d8d6688faf668ccba3024d3 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:49:36 -0800
Subject: [PATCH 52/58] Remove debug comment

---
 .github/workflows/test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index aedf2ac7..534c9d21 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -52,9 +52,6 @@ jobs:
         run: |
           poetry install --no-interaction
 
-      # - name: Debug
-      #   uses: lhotari/action-upterm@v1
-
       - name: Run Tests
         run: |
           poetry install --with test --no-interaction --no-root

From 9222a0f040b5ed7c17d111b482121952616eaed9 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:50:31 -0800
Subject: [PATCH 53/58] Reset fov_watcher.py back to original

---
 src/toffy/fov_watcher.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index 19004839..f16456f8 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -221,7 +221,6 @@ def __init__(
             filemode="a",
             format="%(name)s - %(levelname)s - %(message)s",
         )
-        logging.info(f"Starting run on {run_folder}\n")
 
         # create run structure
         self.run_structure = RunStructure(run_folder, fov_timeout=fov_timeout)
@@ -508,6 +507,7 @@ def file_timer(self, fov_timeout, watcher_timeout):
             if time_elapsed > watcher_timeout:
                 fov_num = self.last_fov_num_processed
                 fov_name = list(self.run_structure.fov_progress.keys())[fov_num]
+                print(f"Timed out waiting for {fov_name} files to be generated.")
                 logging.info(
                     f'{datetime.now().strftime("%d/%m/%Y %H:%M:%S")} -- Timed out'
                     f"waiting for {fov_name} files to be generated.\n"

From 085e900b25458f28d939cc9d5d80cb9d4e641eaa Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:51:03 -0800
Subject: [PATCH 54/58] More resetting

---
 src/toffy/fov_watcher.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/toffy/fov_watcher.py b/src/toffy/fov_watcher.py
index f16456f8..85f6104b 100644
--- a/src/toffy/fov_watcher.py
+++ b/src/toffy/fov_watcher.py
@@ -123,6 +123,7 @@ def check_run_condition(self, path: str) -> Tuple[bool, str]:
 
                     time.sleep(self.timeout / 10)
                     wait_time += self.timeout / 10
+
                 self.fov_progress[fov_name][extension] = True
 
             if all(self.fov_progress[fov_name].values()):

From f2f97ea8e8ba5b34bb7a4b0f160877fe1af73464 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:52:10 -0800
Subject: [PATCH 55/58] Remove unnecessary try-except block in
 fov_watcher_test.py

---
 tests/fov_watcher_test.py | 313 ++++++++++++++++++--------------------
 1 file changed, 150 insertions(+), 163 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 0b7498c3..09400890 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -268,108 +268,88 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
-    print(existing_data)
-    print(add_blank)
-    print(temp_bin)
-    try:
-        with tempfile.TemporaryDirectory() as tmpdir:
-            tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)
-            qc_out_dir = os.path.join(tmpdir, "cb_1", RUN_DIR_NAME)
-            mph_out_dir = os.path.join(tmpdir, "cb_2", RUN_DIR_NAME)
-            plot_dir = os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME)
-            pulse_out_dir = os.path.join(tmpdir, "cb_3", RUN_DIR_NAME)
-
-            # add directories to kwargs
-            kwargs["tiff_out_dir"] = tiff_out_dir
-            kwargs["qc_out_dir"] = qc_out_dir
-            kwargs["mph_out_dir"] = mph_out_dir
-            kwargs["pulse_out_dir"] = pulse_out_dir
-            kwargs["plot_dir"] = plot_dir
-
-            # ensure warn_overwrite set to False if intermediate callbacks set, otherwise True
-            kwargs["warn_overwrite"] = True if int_cbs else False
-
-            run_data = os.path.join(tmpdir, "test_run")
-            log_out = os.path.join(tmpdir, "log_output")
-            os.makedirs(run_data)
-            fov_callback, run_callback, intermediate_callback = build_callbacks(
-                run_cbs, int_cbs, fov_cbs, **kwargs
-            )
-            write_json_file(
-                json_path=os.path.join(run_data, "test_run.json"),
-                json_object=COMBINED_RUN_JSON_SPOOF,
-                encoding="utf-8",
-            )
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)
+        qc_out_dir = os.path.join(tmpdir, "cb_1", RUN_DIR_NAME)
+        mph_out_dir = os.path.join(tmpdir, "cb_2", RUN_DIR_NAME)
+        plot_dir = os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME)
+        pulse_out_dir = os.path.join(tmpdir, "cb_3", RUN_DIR_NAME)
 
-            # if existing_data set to True, test case where a FOV has already been extracted
-            if existing_data[0]:
-                os.makedirs(os.path.join(tiff_out_dir, "fov-2-scan-1"))
-                channels_write = TEST_CHANNELS if existing_data[1] == "Full" else [TEST_CHANNELS[1]]
-                for channel in channels_write:
-                    random_img = np.random.rand(32, 32)
-                    imsave(
-                        os.path.join(tiff_out_dir, "fov-2-scan-1", f"{channel}.tiff"), random_img
-                    )
+        # add directories to kwargs
+        kwargs["tiff_out_dir"] = tiff_out_dir
+        kwargs["qc_out_dir"] = qc_out_dir
+        kwargs["mph_out_dir"] = mph_out_dir
+        kwargs["pulse_out_dir"] = pulse_out_dir
+        kwargs["plot_dir"] = plot_dir
 
-                os.makedirs(qc_out_dir)
-                for qcs, qcc in zip(QC_SUFFIXES, QC_COLUMNS):
-                    df_qc = pd.DataFrame(
-                        np.random.rand(len(TEST_CHANNELS), 3), columns=["fov", "channel", qcc]
-                    )
-                    df_qc["fov"] = "fov-2-scan-1"
-                    df_qc["channel"] = TEST_CHANNELS
-                    df_qc.to_csv(os.path.join(qc_out_dir, f"fov-2-scan-1_{qcs}.csv"), index=False)
+        # ensure warn_overwrite set to False if intermediate callbacks set, otherwise True
+        kwargs["warn_overwrite"] = True if int_cbs else False
 
-                os.makedirs(mph_out_dir)
-                df_mph = pd.DataFrame(
-                    np.random.rand(1, 4), columns=["fov", "MPH", "total_count", "time"]
-                )
-                df_mph["fov"] = "fov-2-scan-1"
-                df_mph.to_csv(os.path.join(mph_out_dir, "fov-2-scan-1-mph_pulse.csv"), index=False)
-
-                os.makedirs(pulse_out_dir)
-                df_ph = pd.DataFrame(np.random.rand(10, 3), columns=["mass", "fov", "pulse_height"])
-                df_ph["fov"] = "fov-2-scan-1"
-                df_ph.to_csv(
-                    os.path.join(pulse_out_dir, "fov-2-scan-1_pulse_heights.csv"), index=False
+        run_data = os.path.join(tmpdir, "test_run")
+        log_out = os.path.join(tmpdir, "log_output")
+        os.makedirs(run_data)
+        fov_callback, run_callback, intermediate_callback = build_callbacks(
+            run_cbs, int_cbs, fov_cbs, **kwargs
+        )
+        write_json_file(
+            json_path=os.path.join(run_data, "test_run.json"),
+            json_object=COMBINED_RUN_JSON_SPOOF,
+            encoding="utf-8",
+        )
+
+        # if existing_data set to True, test case where a FOV has already been extracted
+        if existing_data[0]:
+            os.makedirs(os.path.join(tiff_out_dir, "fov-2-scan-1"))
+            channels_write = TEST_CHANNELS if existing_data[1] == "Full" else [TEST_CHANNELS[1]]
+            for channel in channels_write:
+                random_img = np.random.rand(32, 32)
+                imsave(
+                    os.path.join(tiff_out_dir, "fov-2-scan-1", f"{channel}.tiff"), random_img
                 )
 
-            # `_slow_copy_sample_tissue_data` mimics the instrument computer uploading data to the
-            # client access computer.  `start_watcher` is made async here since these processes
-            # wouldn't block each other in normal use
-            with Pool(processes=4) as pool:
-                pool.apply_async(
-                    _slow_copy_sample_tissue_data,
-                    (run_data, SLOW_COPY_INTERVAL_S, add_blank, temp_bin),
+            os.makedirs(qc_out_dir)
+            for qcs, qcc in zip(QC_SUFFIXES, QC_COLUMNS):
+                df_qc = pd.DataFrame(
+                    np.random.rand(len(TEST_CHANNELS), 3), columns=["fov", "channel", qcc]
                 )
-                time.sleep(watcher_start_lag)
+                df_qc["fov"] = "fov-2-scan-1"
+                df_qc["channel"] = TEST_CHANNELS
+                df_qc.to_csv(os.path.join(qc_out_dir, f"fov-2-scan-1_{qcs}.csv"), index=False)
 
-                watcher_warnings = []
-                if not add_blank:
-                    watcher_warnings.append(
-                        r"Re-extracting incompletely extracted FOV fov-1-scan-1"
-                    )
-                if existing_data[0] and existing_data[1] == "Full":
-                    watcher_warnings.append(r"already extracted for FOV fov-2-scan-1")
-
-                if len(watcher_warnings) > 0:
-                    with pytest.warns(UserWarning, match="|".join(watcher_warnings)):
-                        res_scan = pool.apply_async(
-                            start_watcher,
-                            (
-                                run_data,
-                                log_out,
-                                fov_callback,
-                                run_callback,
-                                intermediate_callback,
-                                2700,
-                                1,
-                                SLOW_COPY_INTERVAL_S,
-                            ),
-                        )
+            os.makedirs(mph_out_dir)
+            df_mph = pd.DataFrame(
+                np.random.rand(1, 4), columns=["fov", "MPH", "total_count", "time"]
+            )
+            df_mph["fov"] = "fov-2-scan-1"
+            df_mph.to_csv(os.path.join(mph_out_dir, "fov-2-scan-1-mph_pulse.csv"), index=False)
+
+            os.makedirs(pulse_out_dir)
+            df_ph = pd.DataFrame(np.random.rand(10, 3), columns=["mass", "fov", "pulse_height"])
+            df_ph["fov"] = "fov-2-scan-1"
+            df_ph.to_csv(
+                os.path.join(pulse_out_dir, "fov-2-scan-1_pulse_heights.csv"), index=False
+            )
+
+        # `_slow_copy_sample_tissue_data` mimics the instrument computer uploading data to the
+        # client access computer.  `start_watcher` is made async here since these processes
+        # wouldn't block each other in normal use
+        with Pool(processes=4) as pool:
+            pool.apply_async(
+                _slow_copy_sample_tissue_data,
+                (run_data, SLOW_COPY_INTERVAL_S, add_blank, temp_bin),
+            )
+            time.sleep(watcher_start_lag)
+
+            watcher_warnings = []
+            if not add_blank:
+                watcher_warnings.append(
+                    r"Re-extracting incompletely extracted FOV fov-1-scan-1"
+                )
+            if existing_data[0] and existing_data[1] == "Full":
+                watcher_warnings.append(r"already extracted for FOV fov-2-scan-1")
 
-                        res_scan.get()
-                else:
+            if len(watcher_warnings) > 0:
+                with pytest.warns(UserWarning, match="|".join(watcher_warnings)):
                     res_scan = pool.apply_async(
                         start_watcher,
                         (
@@ -385,98 +365,105 @@ def test_watcher(
                     )
 
                     res_scan.get()
-
-            with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
-                logtxt = f.read()
-                try:
-                    assert add_blank == ("non-zero file size..." in logtxt)
-                except AssertionError as e:
-                    _reset_logging_file()
-                    raise AssertionError(e)
-
-            fovs = [
-                bin_file.split(".")[0]
-                for bin_file in sorted(io_utils.list_files(COMBINED_DATA_PATH, substrs=[".bin"]))
-            ]
-
-            # callbacks are not performed on moly points, remove fov-3-scan-1
-            bad_fovs = [fovs[-2]]
-            fovs = fovs[:-2] + [fovs[-1]]
-
-            # callbacks are not performed for skipped fovs, remove blank fov (fov-1-scan-1)
-            if add_blank:
-                bad_fovs.append(fovs[0])
-                fovs = fovs[1:]
-
-            # extract tiffs check
-            print("TIFF validator check")
-            validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
-            if kwargs["extract_prof"]:
-                try:
-                    validators[0](
-                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
-                    )
-                except AssertionError as e:
-                    _reset_logging_file()
-                    raise AssertionError(e)
             else:
-                try:
-                    assert not os.path.exists(
-                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
-                    )
-                except AssertionError as e:
-                    _reset_logging_file()
-                    raise AssertionError(e)
+                res_scan = pool.apply_async(
+                    start_watcher,
+                    (
+                        run_data,
+                        log_out,
+                        fov_callback,
+                        run_callback,
+                        intermediate_callback,
+                        2700,
+                        1,
+                        SLOW_COPY_INTERVAL_S,
+                    ),
+                )
+
+                res_scan.get()
 
-            # qc check
-            print("QC check")
+        with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
+            logtxt = f.read()
             try:
-                validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
+                assert add_blank == ("non-zero file size..." in logtxt)
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
 
-            # mph check
-            print("MPH check")
+        fovs = [
+            bin_file.split(".")[0]
+            for bin_file in sorted(io_utils.list_files(COMBINED_DATA_PATH, substrs=[".bin"]))
+        ]
+
+        # callbacks are not performed on moly points, remove fov-3-scan-1
+        bad_fovs = [fovs[-2]]
+        fovs = fovs[:-2] + [fovs[-1]]
+
+        # callbacks are not performed for skipped fovs, remove blank fov (fov-1-scan-1)
+        if add_blank:
+            bad_fovs.append(fovs[0])
+            fovs = fovs[1:]
+
+        # extract tiffs check
+        print("TIFF validator check")
+        validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
+        if kwargs["extract_prof"]:
             try:
-                validators[2](
-                    os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
-                    os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
-                    fovs,
-                    bad_fovs,
+                validators[0](
+                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
                 )
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
-
-            # stitch images check
-            print("Stitch images check")
+        else:
             try:
-                validators[3](
-                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched")
+                assert not os.path.exists(
+                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
                 )
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
 
-            # pulse heights check
-            print("Pulse heights check")
-            try:
-                validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
-            except AssertionError as e:
-                _reset_logging_file()
-                raise AssertionError(e)
+        # qc check
+        print("QC check")
+        try:
+            validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
+        except AssertionError as e:
+            _reset_logging_file()
+            raise AssertionError(e)
+
+        # mph check
+        print("MPH check")
+        try:
+            validators[2](
+                os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
+                os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
+                fovs,
+                bad_fovs,
+            )
+        except AssertionError as e:
+            _reset_logging_file()
+            raise AssertionError(e)
 
-            # os.remove(os.path.join(Path(__file__).parents[1], "pytest.txt"))
-            # Path(os.path.join(Path(__file__).parents[1], "pytest.txt")).touch()
+        # stitch images check
+        print("Stitch images check")
+        try:
+            validators[3](
+                os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched")
+            )
+        except AssertionError as e:
+            _reset_logging_file()
+            raise AssertionError(e)
 
+        # pulse heights check
+        print("Pulse heights check")
+        try:
+            validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
+        except AssertionError as e:
             _reset_logging_file()
+            raise AssertionError(e)
 
-    except OSError as ose:
-        print("Ran into an error:")
-        print(ose)
         _reset_logging_file()
-        # warnings.warn("Temporary file cleanup was incomplete.")
 
 
 def test_watcher_missing_fovs():

From d15c69fa4cdcc3bf47f5877915772ea8a0ad748f Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Wed, 20 Nov 2024 23:54:36 -0800
Subject: [PATCH 56/58] Never mind, add old try-except back in (but don't print
 watcher lag)

---
 tests/fov_watcher_test.py | 308 +++++++++++++++++++-------------------
 1 file changed, 156 insertions(+), 152 deletions(-)

diff --git a/tests/fov_watcher_test.py b/tests/fov_watcher_test.py
index 09400890..674ea96a 100644
--- a/tests/fov_watcher_test.py
+++ b/tests/fov_watcher_test.py
@@ -268,88 +268,105 @@ def test_watcher(
     add_blank,
     temp_bin,
 ):
-    with tempfile.TemporaryDirectory() as tmpdir:
-        tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)
-        qc_out_dir = os.path.join(tmpdir, "cb_1", RUN_DIR_NAME)
-        mph_out_dir = os.path.join(tmpdir, "cb_2", RUN_DIR_NAME)
-        plot_dir = os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME)
-        pulse_out_dir = os.path.join(tmpdir, "cb_3", RUN_DIR_NAME)
-
-        # add directories to kwargs
-        kwargs["tiff_out_dir"] = tiff_out_dir
-        kwargs["qc_out_dir"] = qc_out_dir
-        kwargs["mph_out_dir"] = mph_out_dir
-        kwargs["pulse_out_dir"] = pulse_out_dir
-        kwargs["plot_dir"] = plot_dir
+    try:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            tiff_out_dir = os.path.join(tmpdir, "cb_0", RUN_DIR_NAME)
+            qc_out_dir = os.path.join(tmpdir, "cb_1", RUN_DIR_NAME)
+            mph_out_dir = os.path.join(tmpdir, "cb_2", RUN_DIR_NAME)
+            plot_dir = os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME)
+            pulse_out_dir = os.path.join(tmpdir, "cb_3", RUN_DIR_NAME)
+
+            # add directories to kwargs
+            kwargs["tiff_out_dir"] = tiff_out_dir
+            kwargs["qc_out_dir"] = qc_out_dir
+            kwargs["mph_out_dir"] = mph_out_dir
+            kwargs["pulse_out_dir"] = pulse_out_dir
+            kwargs["plot_dir"] = plot_dir
+
+            # ensure warn_overwrite set to False if intermediate callbacks set, otherwise True
+            kwargs["warn_overwrite"] = True if int_cbs else False
+
+            run_data = os.path.join(tmpdir, "test_run")
+            log_out = os.path.join(tmpdir, "log_output")
+            os.makedirs(run_data)
+            fov_callback, run_callback, intermediate_callback = build_callbacks(
+                run_cbs, int_cbs, fov_cbs, **kwargs
+            )
+            write_json_file(
+                json_path=os.path.join(run_data, "test_run.json"),
+                json_object=COMBINED_RUN_JSON_SPOOF,
+                encoding="utf-8",
+            )
 
-        # ensure warn_overwrite set to False if intermediate callbacks set, otherwise True
-        kwargs["warn_overwrite"] = True if int_cbs else False
+            # if existing_data set to True, test case where a FOV has already been extracted
+            if existing_data[0]:
+                os.makedirs(os.path.join(tiff_out_dir, "fov-2-scan-1"))
+                channels_write = TEST_CHANNELS if existing_data[1] == "Full" else [TEST_CHANNELS[1]]
+                for channel in channels_write:
+                    random_img = np.random.rand(32, 32)
+                    imsave(
+                        os.path.join(tiff_out_dir, "fov-2-scan-1", f"{channel}.tiff"), random_img
+                    )
 
-        run_data = os.path.join(tmpdir, "test_run")
-        log_out = os.path.join(tmpdir, "log_output")
-        os.makedirs(run_data)
-        fov_callback, run_callback, intermediate_callback = build_callbacks(
-            run_cbs, int_cbs, fov_cbs, **kwargs
-        )
-        write_json_file(
-            json_path=os.path.join(run_data, "test_run.json"),
-            json_object=COMBINED_RUN_JSON_SPOOF,
-            encoding="utf-8",
-        )
+                os.makedirs(qc_out_dir)
+                for qcs, qcc in zip(QC_SUFFIXES, QC_COLUMNS):
+                    df_qc = pd.DataFrame(
+                        np.random.rand(len(TEST_CHANNELS), 3), columns=["fov", "channel", qcc]
+                    )
+                    df_qc["fov"] = "fov-2-scan-1"
+                    df_qc["channel"] = TEST_CHANNELS
+                    df_qc.to_csv(os.path.join(qc_out_dir, f"fov-2-scan-1_{qcs}.csv"), index=False)
 
-        # if existing_data set to True, test case where a FOV has already been extracted
-        if existing_data[0]:
-            os.makedirs(os.path.join(tiff_out_dir, "fov-2-scan-1"))
-            channels_write = TEST_CHANNELS if existing_data[1] == "Full" else [TEST_CHANNELS[1]]
-            for channel in channels_write:
-                random_img = np.random.rand(32, 32)
-                imsave(
-                    os.path.join(tiff_out_dir, "fov-2-scan-1", f"{channel}.tiff"), random_img
+                os.makedirs(mph_out_dir)
+                df_mph = pd.DataFrame(
+                    np.random.rand(1, 4), columns=["fov", "MPH", "total_count", "time"]
                 )
-
-            os.makedirs(qc_out_dir)
-            for qcs, qcc in zip(QC_SUFFIXES, QC_COLUMNS):
-                df_qc = pd.DataFrame(
-                    np.random.rand(len(TEST_CHANNELS), 3), columns=["fov", "channel", qcc]
+                df_mph["fov"] = "fov-2-scan-1"
+                df_mph.to_csv(os.path.join(mph_out_dir, "fov-2-scan-1-mph_pulse.csv"), index=False)
+
+                os.makedirs(pulse_out_dir)
+                df_ph = pd.DataFrame(np.random.rand(10, 3), columns=["mass", "fov", "pulse_height"])
+                df_ph["fov"] = "fov-2-scan-1"
+                df_ph.to_csv(
+                    os.path.join(pulse_out_dir, "fov-2-scan-1_pulse_heights.csv"), index=False
                 )
-                df_qc["fov"] = "fov-2-scan-1"
-                df_qc["channel"] = TEST_CHANNELS
-                df_qc.to_csv(os.path.join(qc_out_dir, f"fov-2-scan-1_{qcs}.csv"), index=False)
-
-            os.makedirs(mph_out_dir)
-            df_mph = pd.DataFrame(
-                np.random.rand(1, 4), columns=["fov", "MPH", "total_count", "time"]
-            )
-            df_mph["fov"] = "fov-2-scan-1"
-            df_mph.to_csv(os.path.join(mph_out_dir, "fov-2-scan-1-mph_pulse.csv"), index=False)
-
-            os.makedirs(pulse_out_dir)
-            df_ph = pd.DataFrame(np.random.rand(10, 3), columns=["mass", "fov", "pulse_height"])
-            df_ph["fov"] = "fov-2-scan-1"
-            df_ph.to_csv(
-                os.path.join(pulse_out_dir, "fov-2-scan-1_pulse_heights.csv"), index=False
-            )
 
-        # `_slow_copy_sample_tissue_data` mimics the instrument computer uploading data to the
-        # client access computer.  `start_watcher` is made async here since these processes
-        # wouldn't block each other in normal use
-        with Pool(processes=4) as pool:
-            pool.apply_async(
-                _slow_copy_sample_tissue_data,
-                (run_data, SLOW_COPY_INTERVAL_S, add_blank, temp_bin),
-            )
-            time.sleep(watcher_start_lag)
-
-            watcher_warnings = []
-            if not add_blank:
-                watcher_warnings.append(
-                    r"Re-extracting incompletely extracted FOV fov-1-scan-1"
+            # `_slow_copy_sample_tissue_data` mimics the instrument computer uploading data to the
+            # client access computer.  `start_watcher` is made async here since these processes
+            # wouldn't block each other in normal use
+            with Pool(processes=4) as pool:
+                pool.apply_async(
+                    _slow_copy_sample_tissue_data,
+                    (run_data, SLOW_COPY_INTERVAL_S, add_blank, temp_bin),
                 )
-            if existing_data[0] and existing_data[1] == "Full":
-                watcher_warnings.append(r"already extracted for FOV fov-2-scan-1")
+                time.sleep(watcher_start_lag)
 
-            if len(watcher_warnings) > 0:
-                with pytest.warns(UserWarning, match="|".join(watcher_warnings)):
+                watcher_warnings = []
+                if not add_blank:
+                    watcher_warnings.append(
+                        r"Re-extracting incompletely extracted FOV fov-1-scan-1"
+                    )
+                if existing_data[0] and existing_data[1] == "Full":
+                    watcher_warnings.append(r"already extracted for FOV fov-2-scan-1")
+
+                if len(watcher_warnings) > 0:
+                    with pytest.warns(UserWarning, match="|".join(watcher_warnings)):
+                        res_scan = pool.apply_async(
+                            start_watcher,
+                            (
+                                run_data,
+                                log_out,
+                                fov_callback,
+                                run_callback,
+                                intermediate_callback,
+                                2700,
+                                1,
+                                SLOW_COPY_INTERVAL_S,
+                            ),
+                        )
+
+                        res_scan.get()
+                else:
                     res_scan = pool.apply_async(
                         start_watcher,
                         (
@@ -365,105 +382,92 @@ def test_watcher(
                     )
 
                     res_scan.get()
-            else:
-                res_scan = pool.apply_async(
-                    start_watcher,
-                    (
-                        run_data,
-                        log_out,
-                        fov_callback,
-                        run_callback,
-                        intermediate_callback,
-                        2700,
-                        1,
-                        SLOW_COPY_INTERVAL_S,
-                    ),
-                )
 
-                res_scan.get()
+            with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
+                logtxt = f.read()
+                try:
+                    assert add_blank == ("non-zero file size..." in logtxt)
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
+
+            fovs = [
+                bin_file.split(".")[0]
+                for bin_file in sorted(io_utils.list_files(COMBINED_DATA_PATH, substrs=[".bin"]))
+            ]
+
+            # callbacks are not performed on moly points, remove fov-3-scan-1
+            bad_fovs = [fovs[-2]]
+            fovs = fovs[:-2] + [fovs[-1]]
+
+            # callbacks are not performed for skipped fovs, remove blank fov (fov-1-scan-1)
+            if add_blank:
+                bad_fovs.append(fovs[0])
+                fovs = fovs[1:]
+
+            # extract tiffs check
+            print("TIFF validator check")
+            validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
+            if kwargs["extract_prof"]:
+                try:
+                    validators[0](
+                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
+                    )
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
+            else:
+                try:
+                    assert not os.path.exists(
+                        os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
+                    )
+                except AssertionError as e:
+                    _reset_logging_file()
+                    raise AssertionError(e)
 
-        with open(os.path.join(Path(__file__).parents[1], "pytest.txt")) as f:
-            logtxt = f.read()
+            # qc check
+            print("QC check")
             try:
-                assert add_blank == ("non-zero file size..." in logtxt)
+                validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
 
-        fovs = [
-            bin_file.split(".")[0]
-            for bin_file in sorted(io_utils.list_files(COMBINED_DATA_PATH, substrs=[".bin"]))
-        ]
-
-        # callbacks are not performed on moly points, remove fov-3-scan-1
-        bad_fovs = [fovs[-2]]
-        fovs = fovs[:-2] + [fovs[-1]]
-
-        # callbacks are not performed for skipped fovs, remove blank fov (fov-1-scan-1)
-        if add_blank:
-            bad_fovs.append(fovs[0])
-            fovs = fovs[1:]
-
-        # extract tiffs check
-        print("TIFF validator check")
-        validators[0](os.path.join(tmpdir, "cb_0", RUN_DIR_NAME), fovs, bad_fovs)
-        if kwargs["extract_prof"]:
+            # mph check
+            print("MPH check")
             try:
-                validators[0](
-                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME + "_proficient"), fovs, bad_fovs
+                validators[2](
+                    os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
+                    os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
+                    fovs,
+                    bad_fovs,
                 )
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
-        else:
+
+            # stitch images check
+            print("Stitch images check")
             try:
-                assert not os.path.exists(
-                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME) + "_proficient"
+                validators[3](
+                    os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched")
                 )
             except AssertionError as e:
                 _reset_logging_file()
                 raise AssertionError(e)
 
-        # qc check
-        print("QC check")
-        try:
-            validators[1](os.path.join(tmpdir, "cb_1", RUN_DIR_NAME), fovs, bad_fovs)
-        except AssertionError as e:
-            _reset_logging_file()
-            raise AssertionError(e)
-
-        # mph check
-        print("MPH check")
-        try:
-            validators[2](
-                os.path.join(tmpdir, "cb_2", RUN_DIR_NAME),
-                os.path.join(tmpdir, "cb_2_plots", RUN_DIR_NAME),
-                fovs,
-                bad_fovs,
-            )
-        except AssertionError as e:
-            _reset_logging_file()
-            raise AssertionError(e)
-
-        # stitch images check
-        print("Stitch images check")
-        try:
-            validators[3](
-                os.path.join(tmpdir, "cb_0", RUN_DIR_NAME, f"{RUN_DIR_NAME}_stitched")
-            )
-        except AssertionError as e:
-            _reset_logging_file()
-            raise AssertionError(e)
+            # pulse heights check
+            print("Pulse heights check")
+            try:
+                validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
+            except AssertionError as e:
+                _reset_logging_file()
+                raise AssertionError(e)
 
-        # pulse heights check
-        print("Pulse heights check")
-        try:
-            validators[4](os.path.join(tmpdir, "cb_3", RUN_DIR_NAME), fovs, bad_fovs)
-        except AssertionError as e:
             _reset_logging_file()
-            raise AssertionError(e)
 
-        _reset_logging_file()
+    except OSError:
+        warnings.warn("Temporary file cleanup was incomplete.")
 
 
 def test_watcher_missing_fovs():

From 4ef4bb7ab4cbc62e549e2d2f111d13b87964bc0e Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Thu, 21 Nov 2024 00:56:26 -0800
Subject: [PATCH 57/58] Fix copy_image_files with bad list_folders calls
 removed

---
 src/toffy/rosetta.py  | 6 ++++--
 tests/rosetta_test.py | 8 +++++---
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/toffy/rosetta.py b/src/toffy/rosetta.py
index 1f2a2401..04b109a0 100644
--- a/src/toffy/rosetta.py
+++ b/src/toffy/rosetta.py
@@ -706,6 +706,8 @@ def create_rosetta_matrices(
         mult_matrix.to_csv(os.path.join(save_dir, comp_name))
 
 
+# TODO: anything with [f for f in os.listdir(...) ...] needs to be changed
+# after list_folders with substrs specified is fixed
 def copy_image_files(
     cohort_name, run_names, rosetta_testing_dir, extracted_imgs_dir, fovs_per_run=5
 ):
@@ -728,7 +730,7 @@ def copy_image_files(
     for run in run_names:
         if not os.path.exists(os.path.join(extracted_imgs_dir, run)):
             raise ValueError(f"{run} is not a valid run name found in {extracted_imgs_dir}")
-        fovs_in_run = io_utils.list_folders(os.path.join(extracted_imgs_dir, run), substrs="fov")
+        fovs_in_run = [f for f in os.listdir(os.path.join(extracted_imgs_dir, run)) if "fov" in f]
         # check number of fovs in each run
         if len(fovs_in_run) < fovs_per_run:
             small_runs.append(run)
@@ -758,7 +760,7 @@ def copy_image_files(
     for i, run in enumerate(ns.natsorted(run_names_process)):
         run_path = os.path.join(extracted_imgs_dir, run)
 
-        fovs_in_run = io_utils.list_folders(run_path, substrs="fov")
+        fovs_in_run = [f for f in os.listdir(run_path) if "fov" in f]
         fovs_in_run = ns.natsorted(fovs_in_run)
         rosetta_fovs = random.sample(fovs_in_run, k=fovs_per_run)
 
diff --git a/tests/rosetta_test.py b/tests/rosetta_test.py
index 98043a6d..b2332422 100644
--- a/tests/rosetta_test.py
+++ b/tests/rosetta_test.py
@@ -694,6 +694,8 @@ def mock_img_size(run_dir, fov_list=None):
     return sizes[run]
 
 
+# TODO: anything with [f for f in os.listdir(...) ...] needs to be changed
+# after list_folders with substrs specified is fixed
 def test_copy_image_files(mocker):
     mocker.patch("toffy.image_stitching.get_max_img_size", mock_img_size)
 
@@ -733,7 +735,7 @@ def test_copy_image_files(mocker):
             extracted_fov_dir = os.path.join(temp_dir2, "cohort_name", "extracted_images")
             assert len(io_utils.list_folders(extracted_fov_dir)) == 12
             for i in range(1, 4):
-                assert len(list(io_utils.list_folders(extracted_fov_dir, f"run_{i}"))) == 4
+                assert len([f for f in os.listdir(extracted_fov_dir) if f"run_{i}" in f]) == 4
             assert len(list(io_utils.list_folders(extracted_fov_dir, "stitched_images"))) == 0
 
             # check that files in fov folders are copied
@@ -750,8 +752,8 @@ def test_copy_image_files(mocker):
             # check that correct total and per run fovs are copied, assert run 3 didn't get copied
             assert len(io_utils.list_folders(extracted_fov_dir)) == 10
             for i in range(1, 3):
-                assert len(io_utils.list_folders(extracted_fov_dir, f"run_{i}")) == 5
-            assert len(io_utils.list_folders(extracted_fov_dir, "run_3")) == 0
+                assert len([f for f in os.listdir(extracted_fov_dir) if f"run_{i}" in f]) == 5
+            assert len([f for f in os.listdir(extracted_fov_dir) if f"run_3" in f]) == 0
 
             # check that files in fov folders are copied
             for folder in io_utils.list_folders(extracted_fov_dir):

From 948baa545e0044d3aa902a2e10e65c10b30e3fc9 Mon Sep 17 00:00:00 2001
From: Alex Kong <alkong@ucdavis.edu>
Date: Thu, 21 Nov 2024 00:57:53 -0800
Subject: [PATCH 58/58] ruff linting

---
 tests/rosetta_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/rosetta_test.py b/tests/rosetta_test.py
index b2332422..b190d49a 100644
--- a/tests/rosetta_test.py
+++ b/tests/rosetta_test.py
@@ -753,7 +753,7 @@ def test_copy_image_files(mocker):
             assert len(io_utils.list_folders(extracted_fov_dir)) == 10
             for i in range(1, 3):
                 assert len([f for f in os.listdir(extracted_fov_dir) if f"run_{i}" in f]) == 5
-            assert len([f for f in os.listdir(extracted_fov_dir) if f"run_3" in f]) == 0
+            assert len([f for f in os.listdir(extracted_fov_dir) if "run_3" in f]) == 0
 
             # check that files in fov folders are copied
             for folder in io_utils.list_folders(extracted_fov_dir):