From 1ed0b6c3f43462879734a67694cd9cc748ef9f69 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 20 Oct 2023 18:12:33 +0100
Subject: [PATCH 01/10] Update all tests to remove use_datatype flag.

---
 docs/source/pages/documentation.md      | 3 ++-
 tests/tests_integration/test_configs.py | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index bb208b5a..e4cbec50 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -133,7 +133,8 @@ Another example call, which creates a range of subject and session folders, is s
 datashuttle \
 my_first_project \
 
-make-sub-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg histology
+make-sub-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
+```
 
 ```
 ├── sub-001/
diff --git a/tests/tests_integration/test_configs.py b/tests/tests_integration/test_configs.py
index 1ede531c..276e4132 100644
--- a/tests/tests_integration/test_configs.py
+++ b/tests/tests_integration/test_configs.py
@@ -332,6 +332,7 @@ def test_supplied_config_file_changes_wrong_order(self, project, tmp_path):
         any order and just converted to dict?
         """
         bad_order_configs_path = project._datashuttle_path / "new_configs.yaml"
+
         good_order_configs = test_utils.get_test_config_arguments_dict(
             tmp_path, project.project_name
         )

From 05b26fabe0b189196de875621fae5a36519a35bb Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Tue, 24 Oct 2023 12:12:41 +0100
Subject: [PATCH 02/10] Fix documentation.

---
 docs/source/pages/documentation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index e4cbec50..753a939b 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -132,10 +132,10 @@ Another example call, which creates a range of subject and session folders, is s
 ```
 datashuttle \
 my_first_project \
-
 make-sub-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
 ```
 
+
 ```
 ├── sub-001/
 │   ├── ses-010_time-160248/

From 2c8a49c26629cd4fa13113fd540ab476c64e0c23 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 20 Oct 2023 18:12:33 +0100
Subject: [PATCH 03/10] Update all tests to remove use_datatype flag.

---
 docs/source/pages/documentation.md      | 3 +--
 tests/tests_integration/test_configs.py | 4 +++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index 753a939b..5e08aefb 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -132,10 +132,9 @@ Another example call, which creates a range of subject and session folders, is s
 ```
 datashuttle \
 my_first_project \
-make-sub-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
+make-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
 ```
 
-
 ```
 ├── sub-001/
 │   ├── ses-010_time-160248/
diff --git a/tests/tests_integration/test_configs.py b/tests/tests_integration/test_configs.py
index 276e4132..a17a86c5 100644
--- a/tests/tests_integration/test_configs.py
+++ b/tests/tests_integration/test_configs.py
@@ -323,7 +323,9 @@ def test_supplied_config_file_bad_types(self, project, tmp_path):
                     f"Config file was not updated."
                 )
 
-    def test_supplied_config_file_changes_wrong_order(self, project, tmp_path):
+    def test_supplied_config_file_changes_wrong_order(
+        self, project, tmp_path
+    ):
         """
         Test the situation when a config file is passed with variables in
         the wrong order.

From 23ebd4e1fa0d4826c161b69ad20a1b81a20b8cd7 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 20 Oct 2023 20:19:21 +0100
Subject: [PATCH 04/10] Rename histology to anat.

---
 README.md                                     |  8 ++---
 datashuttle/configs/canonical_configs.py      |  2 +-
 datashuttle/configs/canonical_folders.py      |  4 +--
 datashuttle/datashuttle.py                    |  2 +-
 docs/source/pages/documentation.md            | 23 ++++++-------
 tests/test_utils.py                           | 16 +++++-----
 .../file_conflicts_pathtable.py               |  4 +--
 .../test_filesystem_transfer.py               | 22 ++++++-------
 tests/tests_integration/test_logging.py       |  3 +-
 tests/tests_integration/test_make_folders.py  | 32 ++++++++-----------
 .../test_ssh_file_transfer.py                 |  8 ++---
 11 files changed, 60 insertions(+), 64 deletions(-)

diff --git a/README.md b/README.md
index 3b6442e9..c6a336aa 100644
--- a/README.md
+++ b/README.md
@@ -38,14 +38,14 @@ See the SWC-BIDS [specification](https://swc-bids.neuroinformatics.dev/) for mor
         │   └── ses-001/
         │   │   ├── ephys/
         │   │   └── behav/
-        │   └── histology/
+        │   └── anat/
         └── sub-002/
             └── ses-001/
             │   ├── behav/
             │   └── imaging/
             └── ses-002/
             │   └── behav/
-            └── histology/
+            └── anat/
 ```
 
 
@@ -56,12 +56,12 @@ See the SWC-BIDS [specification](https://swc-bids.neuroinformatics.dev/) for mor
         │   ├── ses-001/
         │   │   ├── ephys
         │   │   └── behav
-        │   └── histology
+        │   └── anat
         └── sub-002/
             ├── ses-001/
             │   ├── behav
             │   └── imaging
             ├── ses-002/
             │   └── behav
-            └── histology
+            └── anat
 ```
diff --git a/datashuttle/configs/canonical_configs.py b/datashuttle/configs/canonical_configs.py
index 6bb395a1..212890e8 100644
--- a/datashuttle/configs/canonical_configs.py
+++ b/datashuttle/configs/canonical_configs.py
@@ -46,7 +46,7 @@ def get_datatypes() -> List[str]:
     Canonical list of datatype flags based on
     NeuroBlueprint.
     """
-    return ["ephys", "behav", "funcimg", "histology"]
+    return ["ephys", "behav", "funcimg", "anat"]
 
 
 def get_flags() -> List[str]:
diff --git a/datashuttle/configs/canonical_folders.py b/datashuttle/configs/canonical_folders.py
index 27a505c6..696f75c2 100644
--- a/datashuttle/configs/canonical_folders.py
+++ b/datashuttle/configs/canonical_folders.py
@@ -51,8 +51,8 @@ def get_datatype_folders(cfg: Configs) -> dict:
             name="funcimg",
             level="ses",
         ),
-        "histology": Folder(
-            name="histology",
+        "anat": Folder(
+            name="anat",
             level="sub",
         ),
     }
diff --git a/datashuttle/datashuttle.py b/datashuttle/datashuttle.py
index c7055e79..2bae4a96 100644
--- a/datashuttle/datashuttle.py
+++ b/datashuttle/datashuttle.py
@@ -180,7 +180,7 @@ def make_folders(
                 folders are made.
         datatype :
                 The datatype to make in the sub / ses folders.
-                (e.g. "ephys", "behav", "histology"). If "all"
+                (e.g. "ephys", "behav", "anat"). If "all"
                 is selected, all datatypes permitted in
                 NeuroBlueprint will be created. If "" is passed
                 no datatype will be created.
diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index 5e08aefb..61a32f1f 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -135,30 +135,31 @@ my_first_project \
 make-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
 ```
 
+
 ```
 ├── sub-001/
 │   ├── ses-010_time-160248/
 │   │   ├── behav
 │   │   └── funcimg
-│   └── histology
+│   └── anat
 ├── sub-002/
 │   ├── ses-010_time-160248/
 │   │   ├── behav
 │   │   └── funcimg
-│   └── histology
+│   └── anat
 └── sub-003/
     ├── ses-010_time-160248/
     │   ├── behav
     │   └── funcimg
-    └── histology
+    └── anat
 ```
 
 
 ### Datatype Folders
 
-In [SWC-Blueprint](https://swc-blueprint.neuroinformatics.dev/specification.html), *datatypes* specify where acquired experimental data of currently supported types (`behav`, `ephys`, `funcimg` and `histology`) is stored. See the [*datatypes* section of the SWC-Blueprint for more details](https://swc-blueprint.neuroinformatics.dev/specification.html#datatype).
+In [SWC-Blueprint](https://swc-blueprint.neuroinformatics.dev/specification.html), *datatypes* specify where acquired experimental data of currently supported types (`behav`, `ephys`, `funcimg` and `anat`) is stored. See the [*datatypes* section of the SWC-Blueprint for more details](https://swc-blueprint.neuroinformatics.dev/specification.html#datatype).
 
-At present, `histology` is saved to the `sub-` level, as it is assumed `histology` is conducted *ex vivo* and so session will be possible. Please don't hesitate to get into contact if you have an alternative use case.
+At present, `anat` is saved to the `sub-` level, as it is assumed `anat` is conducted *ex vivo* and so session will be possible. Please don't hesitate to get into contact if you have an alternative use case.
 
 ## Data Transfer
 
@@ -498,7 +499,7 @@ DataShuttle provides a number of keyword arguments to allow separate handling of
 
 `all` : All *session* and non-*session* files and folders within a *subject* level folder (e.g. `sub-001`) will be transferred.
 
-`all_ses` : *Session* <u>folders</u> only (i.e. prefixed with `-ses`) will be transferred. Note that the only exception is the `histology` folder, the transfer of which is determined by the `-dt` flag (below).
+`all_ses` : *Session* <u>folders</u> only (i.e. prefixed with `-ses`) will be transferred. Note that the only exception is the `anat` folder, the transfer of which is determined by the `-dt` flag (below).
 
 `all_non_ses` : All files and folders that are not prefixed with `-sub` will be transferred. Any folders prefixed with `-ses` will not be transferred.
 
@@ -506,7 +507,7 @@ DataShuttle provides a number of keyword arguments to allow separate handling of
 
 `all` : All *datatype* folders at the *subject* or *session* folder level will be transferred, as well as all files and folders within selected *session* folders.
 
-`all_datatype` : All *datatype* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `histology`) residing at either the *subject* or *session* level will be
+`all_datatype` : All *datatype* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `anat`) residing at either the *subject* or *session* level will be
 transferred. Non-*datatype* folders at the *session* level will not be transferred
 
 `all_ses_level_non_datatype` : Non *datatype* folders at the *session* level will not be transferred
@@ -519,7 +520,7 @@ Below, a number of examples are given to exemplify how these arguments effect da
     ├── a_project_related_file.json
     ├── sub-001/
     │   ├── sub-001_extra-file.json
-    │   ├── histology
+    │   ├── anat
     │   └── ses-001/
     │       ├── ses-001_extra-file.json
     │       ├── behav/
@@ -528,7 +529,7 @@ Below, a number of examples are given to exemplify how these arguments effect da
     │           └── ...
     └── sub-002/
         ├── sub-002_extra-file.json
-        ├── histology
+        ├── anat
         └── ses-001/
 			├── behav/
 			│   └── ...
@@ -569,7 +570,7 @@ Would upload:
 
 - Contents residing in the `sub-001` folder only.
 -  The file `sub-001_extra-file.json`
-- All *datatype* folder contents (`histology`, `behav`, `ephys`)
+- All *datatype* folder contents (`anat`, `behav`, `ephys`)
 
 The command:
 
@@ -585,7 +586,7 @@ upload
 Would upload:
 
 - Contents residing in the `sub-001` folder only.
-- All *datatype* folder contents (`histology`, `behav`, `ephys`)
+- All *datatype* folder contents (`anat`, `behav`, `ephys`)
 
 3) The final example shows the effect of transferring `all_non_sub` files only. The command:
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index b5fdcb2a..818fa4dc 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -321,7 +321,7 @@ def check_datatype_sub_ses_uploaded_correctly(
         sub_names = glob_basenames(join(base_path_to_check, "*"))
         assert sub_names == sorted(subs_to_upload)
 
-        # Check ses are all uploaded + histology if transferred
+        # Check ses are all uploaded + anat if transferred
         if ses_to_upload:
             for sub in subs_to_upload:
                 ses_names = glob_basenames(
@@ -331,9 +331,9 @@ def check_datatype_sub_ses_uploaded_correctly(
                         "*",
                     )
                 )
-                if datatype_to_transfer == ["histology"]:
-                    assert ses_names == ["histology"]
-                    return  # handle the case in which histology
+                if datatype_to_transfer == ["anat"]:
+                    assert ses_names == ["anat"]
+                    return  # handle the case in which anat
                     # only is transferred,
                     # and there are no sessions to transfer.
 
@@ -359,12 +359,12 @@ def check_and_strip_within_sub_data_folders(ses_names, datatype_to_transfer):
     up when sessions are searched for with wildcard. Remove
     so that sessions can be explicitly tested next.
     """
-    if "histology" in datatype_to_transfer:
-        assert "histology" in ses_names
+    if "anat" in datatype_to_transfer:
+        assert "anat" in ses_names
 
-        ses_names.remove("histology")
+        ses_names.remove("anat")
         copy_ = copy.deepcopy(datatype_to_transfer)
-        copy_.remove("histology")
+        copy_.remove("anat")
         return copy_
     return datatype_to_transfer
 
diff --git a/tests/tests_integration/file_conflicts_pathtable.py b/tests/tests_integration/file_conflicts_pathtable.py
index 3227e8b4..224a0c11 100644
--- a/tests/tests_integration/file_conflicts_pathtable.py
+++ b/tests/tests_integration/file_conflicts_pathtable.py
@@ -18,7 +18,7 @@ def get_pathtable(base_folder):
             [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "non_data" / "non_data.mp4",                  False,      False,       True,                       "sub-001",                  "ses-003_date-20231901",    None],
             [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "nondatatype_level_file.csv",                False,      False,       True,                       "sub-001",                  "ses-003_date-20231901",    None],
             [base_folder, Path("rawdata") / "sub-001" / "random-ses_level_file.mp4",                                            False,      True,        False,                      "sub-001",                  None,                       None],
-            [base_folder, Path("rawdata") / "sub-001" / "histology" / "sub-001_histology.file",                                 False,      False,       False,                      "sub-001",                  None,                       "histology"],
+            [base_folder, Path("rawdata") / "sub-001" / "anat" / "sub-001_anat.file",                                 False,      False,       False,                      "sub-001",                  None,                       "anat"],
             [base_folder, Path("rawdata") / "sub-002_random-value" / "sub-002_random-value.file",                               False,      True,        False,                      "sub-002_random-value",     None,                       None],
             [base_folder, Path("rawdata") / "sub-002_random-value" / "ses-001" / "non_datatype_level_folder" / "file.csv",        False,      False,       True,                       "sub-002_random-value",     "ses-001",                  None],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-001" / "funcimg" / ".myfile.xlsx",                   False,      False,       False,                      "sub-003_date-20231901",    "ses-001",                  "funcimg"],
@@ -26,7 +26,7 @@ def get_pathtable(base_folder):
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-003_date-20231901" / "funcimg" / "funcimg.nii",      False,      False,       False,                      "sub-003_date-20231901",    "ses-003_date-20231901",    "funcimg"],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "seslevel_non-prefix_folder" / "nonlevel.mat",               False,      True,        False,                      "sub-003_date-20231901",    "seslevel_non-prefix_folder",  None],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "sub-ses-level_file.txt",                                 False,      True,        False,                      "sub-003_date-20231901",    None,                       None],
-            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "histology" / ".histology.file",                          False,      False,       False,                      "sub-003_date-20231901",    None,                       "histology"],
+            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "anat" / ".anat.file",                          False,      False,       False,                      "sub-003_date-20231901",    None,                       "anat"],
             [base_folder, Path("rawdata") / "project_level_file.txt",                                                           True,       False,       False,                      None,                       None,                       None],
             [base_folder, Path("rawdata") / "sublevel_non_sub-prefix_folder" / "ses_non_folder.file",                                 True,       False,       False,                      None,                       None,                       None],
             ]
diff --git a/tests/tests_integration/test_filesystem_transfer.py b/tests/tests_integration/test_filesystem_transfer.py
index 98f80c35..221c16c6 100644
--- a/tests/tests_integration/test_filesystem_transfer.py
+++ b/tests/tests_integration/test_filesystem_transfer.py
@@ -137,12 +137,12 @@ def test_transfer_all_top_level_folders(self, project, upload_or_download):
             ["behav"],
             ["ephys"],
             ["funcimg"],
-            ["histology"],
+            ["anat"],
             ["behav", "ephys"],
-            ["ephys", "histology"],
-            ["behav", "ephys", "histology"],
-            ["funcimg", "histology", "behav"],
-            ["behav", "ephys", "funcimg", "histology"],
+            ["ephys", "anat"],
+            ["behav", "ephys", "anat"],
+            ["funcimg", "anat", "behav"],
+            ["behav", "ephys", "funcimg", "anat"],
         ],
     )
     @pytest.mark.parametrize("upload_or_download", ["upload", "download"])
@@ -179,10 +179,10 @@ def test_transfer_empty_folder_specific_dataal_data(
     @pytest.mark.parametrize(
         "datatype_to_transfer",
         [
-            ["histology"],
+            ["anat"],
             ["behav", "ephys"],
-            ["funcimg", "histology", "behav"],
-            ["behav", "ephys", "funcimg", "histology"],
+            ["funcimg", "anat", "behav"],
+            ["behav", "ephys", "funcimg", "anat"],
         ],
     )
     @pytest.mark.parametrize("upload_or_download", ["upload" "download"])
@@ -223,7 +223,7 @@ def test_transfer_empty_folder_specific_subs(
     @pytest.mark.parametrize("sub_idx_to_upload", [[0], [1, 2], [0, 1, 2]])
     @pytest.mark.parametrize(
         "datatype_to_transfer",
-        [["ephys"], ["funcimg", "histology", "behav"]],
+        [["ephys"], ["funcimg", "anat", "behav"]],
     )
     @pytest.mark.parametrize("upload_or_download", ["upload", "download"])
     def test_transfer_empty_folder_specific_ses(
@@ -429,10 +429,10 @@ def test_rclone_overwrite_modified_file(
         the version in source is newer than target.
         """
         path_to_test_file = (
-            Path("rawdata") / "sub-001" / "histology" / "test_file.txt"
+            Path("rawdata") / "sub-001" / "anat" / "test_file.txt"
         )
 
-        project.make_folders("sub-001", datatype="histology")
+        project.make_folders("sub-001", datatype="anat")
 
         local_test_file_path = project.cfg["local_path"] / path_to_test_file
         central_test_file_path = (
diff --git a/tests/tests_integration/test_logging.py b/tests/tests_integration/test_logging.py
index 88167bbb..46d57ece 100644
--- a/tests/tests_integration/test_logging.py
+++ b/tests/tests_integration/test_logging.py
@@ -271,7 +271,8 @@ def test_logs_upload_and_download(
 
         assert "Using config file from" in log
         assert "Local file system at" in log
-        assert """ "--include" "sub-11/histology/**" """ in log
+
+        assert """ "--include" "sub-11/anat/**" """ in log
         assert """/central/test_project/rawdata""" in log
         assert "Waiting for checks to finish" in log
 
diff --git a/tests/tests_integration/test_make_folders.py b/tests/tests_integration/test_make_folders.py
index 3011c048..85276a5a 100644
--- a/tests/tests_integration/test_make_folders.py
+++ b/tests/tests_integration/test_make_folders.py
@@ -133,17 +133,13 @@ def test_explicitly_session_list(self, project):
                 test_utils.check_and_cd_folder(
                     join(base_folder, sub, ses, "funcimg")
                 )
-                test_utils.check_and_cd_folder(
-                    join(base_folder, sub, "histology")
-                )
+                test_utils.check_and_cd_folder(join(base_folder, sub, "anat"))
 
     @pytest.mark.parametrize("behav", [True, False])
     @pytest.mark.parametrize("ephys", [True, False])
     @pytest.mark.parametrize("funcimg", [True, False])
-    @pytest.mark.parametrize("histology", [True, False])
-    def test_every_datatype_passed(
-        self, project, behav, ephys, funcimg, histology
-    ):
+    @pytest.mark.parametrize("anat", [True, False])
+    def test_every_datatype_passed(self, project, behav, ephys, funcimg, anat):
         """
         Check every combination of data type used and ensure only the
         correct ones are made.
@@ -157,8 +153,8 @@ def test_every_datatype_passed(
             datatypes_to_make.append("ephys")
         if funcimg:
             datatypes_to_make.append("funcimg")
-        if histology:
-            datatypes_to_make.append("histology")
+        if anat:
+            datatypes_to_make.append("anat")
 
         # Make folder tree
         subs = ["sub-001", "sub-002"]
@@ -176,7 +172,7 @@ def test_every_datatype_passed(
                 "behav": behav,
                 "ephys": ephys,
                 "funcimg": funcimg,
-                "histology": histology,
+                "anat": anat,
             },
         )
 
@@ -188,7 +184,7 @@ def test_custom_folder_names(self, project):
         # Change folder names to custom names
         project.cfg.datatype_folders["ephys"].name = "change_ephys"
         project.cfg.datatype_folders["behav"].name = "change_behav"
-        project.cfg.datatype_folders["histology"].name = "change_histology"
+        project.cfg.datatype_folders["anat"].name = "change_anat"
         project.cfg.datatype_folders["funcimg"].name = "change_funcimg"
 
         # Make the folders
@@ -214,17 +210,15 @@ def test_custom_folder_names(self, project):
             join(base_folder, sub, ses, "change_funcimg")
         )
 
-        test_utils.check_and_cd_folder(
-            join(base_folder, sub, "change_histology")
-        )
+        test_utils.check_and_cd_folder(join(base_folder, sub, "change_anat"))
 
     @pytest.mark.parametrize(
         "files_to_test",
         [
             ["all"],
             ["ephys", "behav"],
-            ["ephys", "behav", "histology"],
-            ["ephys", "behav", "histology", "funcimg"],
+            ["ephys", "behav", "anat"],
+            ["ephys", "behav", "anat", "funcimg"],
             ["funcimg", "ephys"],
             ["funcimg"],
         ],
@@ -248,9 +242,9 @@ def test_datatypes_subsection(self, project, files_to_test):
             join(base_folder, sub, "*"),
             exclude=ses,
         )
-        if "histology" in files_to_test:
-            assert "histology" in sub_file_names
-            files_to_test.remove("histology")
+        if "anat" in files_to_test:
+            assert "anat" in sub_file_names
+            files_to_test.remove("anat")
 
         # Check at the session level
         ses_file_names = test_utils.glob_basenames(
diff --git a/tests/tests_integration/test_ssh_file_transfer.py b/tests/tests_integration/test_ssh_file_transfer.py
index 73070bd3..f249d827 100644
--- a/tests/tests_integration/test_ssh_file_transfer.py
+++ b/tests/tests_integration/test_ssh_file_transfer.py
@@ -151,9 +151,9 @@ def central_from_local(self, path_):
             ["all_datatype"],
             ["behav"],
             ["ephys"],
-            ["histology"],
+            ["anat"],
             ["funcimg"],
-            ["histology", "behav", "all_ses_level_non_datatype"],
+            ["anat", "behav", "all_ses_level_non_datatype"],
         ],
     )
     @pytest.mark.parametrize("upload_or_download", ["upload", "download"])
@@ -296,9 +296,9 @@ def make_pathtable_search_filter(self, sub_names, ses_names, datatype):
             if sub == "all_non_sub":
                 extra_arguments += ["is_non_sub == True"]
             else:
-                if "histology" in datatype:
+                if "anat" in datatype:
                     sub_ses_dtype_arguments += [
-                        f"(parent_sub == '{sub}' & (parent_datatype == 'histology' | parent_datatype == 'histology'))"
+                        f"(parent_sub == '{sub}' & (parent_datatype == 'anat' | parent_datatype == 'anat'))"
                     ]
 
                 for ses in ses_names:

From b90dbda72348b0aead7c5d7d30955db9a97420d9 Mon Sep 17 00:00:00 2001
From: JoeZiminski <Joseph.j.ziminski@gmail.com>
Date: Fri, 20 Oct 2023 20:32:10 +0100
Subject: [PATCH 05/10] Change position of anat.

---
 datashuttle/configs/canonical_folders.py |  2 +-
 tests/test_utils.py                      | 31 ++----------------------
 2 files changed, 3 insertions(+), 30 deletions(-)

diff --git a/datashuttle/configs/canonical_folders.py b/datashuttle/configs/canonical_folders.py
index 696f75c2..83e78625 100644
--- a/datashuttle/configs/canonical_folders.py
+++ b/datashuttle/configs/canonical_folders.py
@@ -53,7 +53,7 @@ def get_datatype_folders(cfg: Configs) -> dict:
         ),
         "anat": Folder(
             name="anat",
-            level="sub",
+            level="ses",
         ),
     }
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 818fa4dc..49f3ea96 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -331,42 +331,15 @@ def check_datatype_sub_ses_uploaded_correctly(
                         "*",
                     )
                 )
-                if datatype_to_transfer == ["anat"]:
-                    assert ses_names == ["anat"]
-                    return  # handle the case in which anat
-                    # only is transferred,
-                    # and there are no sessions to transfer.
-
-                copy_datatype_to_transfer = (
-                    check_and_strip_within_sub_data_folders(
-                        ses_names, datatype_to_transfer
-                    )
-                )
                 assert ses_names == sorted(ses_to_upload)
 
                 # check datatype folders in session folder
-                if copy_datatype_to_transfer:
+                if datatype_to_transfer:
                     for ses in ses_names:
                         data_names = glob_basenames(
                             join(base_path_to_check, sub, ses, "*")
                         )
-                        assert data_names == sorted(copy_datatype_to_transfer)
-
-
-def check_and_strip_within_sub_data_folders(ses_names, datatype_to_transfer):
-    """
-    Check if datatype folders at the sub level are picked
-    up when sessions are searched for with wildcard. Remove
-    so that sessions can be explicitly tested next.
-    """
-    if "anat" in datatype_to_transfer:
-        assert "anat" in ses_names
-
-        ses_names.remove("anat")
-        copy_ = copy.deepcopy(datatype_to_transfer)
-        copy_.remove("anat")
-        return copy_
-    return datatype_to_transfer
+                        assert data_names == sorted(datatype_to_transfer)
 
 
 def make_and_check_local_project_folders(

From 19687753e2c6d466917b00e71d1f090b32f1cb89 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Sat, 21 Oct 2023 13:21:12 +0100
Subject: [PATCH 06/10] Fix tests.

---
 .../file_conflicts_pathtable.py                 | 14 +++++++-------
 .../test_filesystem_transfer.py                 |  4 ++--
 tests/tests_integration/test_logging.py         |  6 +++---
 tests/tests_integration/test_make_folders.py    | 17 ++++++++++-------
 .../tests_integration/test_ssh_file_transfer.py |  5 -----
 5 files changed, 22 insertions(+), 24 deletions(-)

diff --git a/tests/tests_integration/file_conflicts_pathtable.py b/tests/tests_integration/file_conflicts_pathtable.py
index 224a0c11..56b63dd8 100644
--- a/tests/tests_integration/file_conflicts_pathtable.py
+++ b/tests/tests_integration/file_conflicts_pathtable.py
@@ -16,19 +16,19 @@ def get_pathtable(base_folder):
             [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "behav" / "behav.csv",                        False,      False,       False,                      "sub-001",                  "ses-003_date-20231901",    "behav"],
             [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "ephys" / "ephys.bin",                        False,      False,       False,                      "sub-001",                  "ses-003_date-20231901",    "ephys"],
             [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "non_data" / "non_data.mp4",                  False,      False,       True,                       "sub-001",                  "ses-003_date-20231901",    None],
-            [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "nondatatype_level_file.csv",                False,      False,       True,                       "sub-001",                  "ses-003_date-20231901",    None],
+            [base_folder, Path("rawdata") / "sub-001" / "ses-003_date-20231901" / "nondatatype_level_file.csv",                 False,      False,       True,                       "sub-001",                  "ses-003_date-20231901",    None],
             [base_folder, Path("rawdata") / "sub-001" / "random-ses_level_file.mp4",                                            False,      True,        False,                      "sub-001",                  None,                       None],
-            [base_folder, Path("rawdata") / "sub-001" / "anat" / "sub-001_anat.file",                                 False,      False,       False,                      "sub-001",                  None,                       "anat"],
+            [base_folder, Path("rawdata") / "sub-001" / "ses-004" / "anat" / "sub-001_anat.file",                               False,      False,       False,                      "sub-001",                  "ses-004",                 "anat"],
             [base_folder, Path("rawdata") / "sub-002_random-value" / "sub-002_random-value.file",                               False,      True,        False,                      "sub-002_random-value",     None,                       None],
-            [base_folder, Path("rawdata") / "sub-002_random-value" / "ses-001" / "non_datatype_level_folder" / "file.csv",        False,      False,       True,                       "sub-002_random-value",     "ses-001",                  None],
+            [base_folder, Path("rawdata") / "sub-002_random-value" / "ses-001" / "non_datatype_level_folder" / "file.csv",      False,      False,       True,                       "sub-002_random-value",     "ses-001",                  None],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-001" / "funcimg" / ".myfile.xlsx",                   False,      False,       False,                      "sub-003_date-20231901",    "ses-001",                  "funcimg"],
-            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-003_date-20231901" / "nondatatype_level_file.csv",  False,      False,       True,                       "sub-003_date-20231901",    "ses-003_date-20231901",    None],
+            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-003_date-20231901" / "nondatatype_level_file.csv",   False,      False,       True,                       "sub-003_date-20231901",    "ses-003_date-20231901",    None],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-003_date-20231901" / "funcimg" / "funcimg.nii",      False,      False,       False,                      "sub-003_date-20231901",    "ses-003_date-20231901",    "funcimg"],
-            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "seslevel_non-prefix_folder" / "nonlevel.mat",               False,      True,        False,                      "sub-003_date-20231901",    "seslevel_non-prefix_folder",  None],
+            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "seslevel_non-prefix_folder" / "nonlevel.mat",            False,      True,        False,                      "sub-003_date-20231901",    "seslevel_non-prefix_folder",  None],
             [base_folder, Path("rawdata") / "sub-003_date-20231901" / "sub-ses-level_file.txt",                                 False,      True,        False,                      "sub-003_date-20231901",    None,                       None],
-            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "anat" / ".anat.file",                          False,      False,       False,                      "sub-003_date-20231901",    None,                       "anat"],
+            [base_folder, Path("rawdata") / "sub-003_date-20231901" / "ses-004" / "anat" / ".anat.file",                        False,      False,       False,                      "sub-003_date-20231901",    "ses-004",                "anat"],
             [base_folder, Path("rawdata") / "project_level_file.txt",                                                           True,       False,       False,                      None,                       None,                       None],
-            [base_folder, Path("rawdata") / "sublevel_non_sub-prefix_folder" / "ses_non_folder.file",                                 True,       False,       False,                      None,                       None,                       None],
+            [base_folder, Path("rawdata") / "sublevel_non_sub-prefix_folder" / "ses_non_folder.file",                           True,       False,       False,                      None,                       None,                       None],
             ]
 
 
diff --git a/tests/tests_integration/test_filesystem_transfer.py b/tests/tests_integration/test_filesystem_transfer.py
index 221c16c6..14ec77da 100644
--- a/tests/tests_integration/test_filesystem_transfer.py
+++ b/tests/tests_integration/test_filesystem_transfer.py
@@ -429,10 +429,10 @@ def test_rclone_overwrite_modified_file(
         the version in source is newer than target.
         """
         path_to_test_file = (
-            Path("rawdata") / "sub-001" / "anat" / "test_file.txt"
+            Path("rawdata") / "sub-001" / "ses-001" / "anat" / "test_file.txt"
         )
 
-        project.make_folders("sub-001", datatype="anat")
+        project.make_folders("sub-001", "ses-001", datatype="anat")
 
         local_test_file_path = project.cfg["local_path"] / path_to_test_file
         central_test_file_path = (
diff --git a/tests/tests_integration/test_logging.py b/tests/tests_integration/test_logging.py
index 46d57ece..42951f2f 100644
--- a/tests/tests_integration/test_logging.py
+++ b/tests/tests_integration/test_logging.py
@@ -271,9 +271,9 @@ def test_logs_upload_and_download(
 
         assert "Using config file from" in log
         assert "Local file system at" in log
-
-        assert """ "--include" "sub-11/anat/**" """ in log
-        assert """/central/test_project/rawdata""" in log
+        assert "--include" in log
+        assert "sub-11/ses-123/anat/**" in log
+        assert "/central/test_project/rawdata" in log
         assert "Waiting for checks to finish" in log
 
     @pytest.mark.parametrize("upload_or_download", ["upload", "download"])
diff --git a/tests/tests_integration/test_make_folders.py b/tests/tests_integration/test_make_folders.py
index 85276a5a..dde4a6e4 100644
--- a/tests/tests_integration/test_make_folders.py
+++ b/tests/tests_integration/test_make_folders.py
@@ -133,7 +133,9 @@ def test_explicitly_session_list(self, project):
                 test_utils.check_and_cd_folder(
                     join(base_folder, sub, ses, "funcimg")
                 )
-                test_utils.check_and_cd_folder(join(base_folder, sub, "anat"))
+                test_utils.check_and_cd_folder(
+                    join(base_folder, sub, ses, "anat")
+                )
 
     @pytest.mark.parametrize("behav", [True, False])
     @pytest.mark.parametrize("ephys", [True, False])
@@ -210,7 +212,9 @@ def test_custom_folder_names(self, project):
             join(base_folder, sub, ses, "change_funcimg")
         )
 
-        test_utils.check_and_cd_folder(join(base_folder, sub, "change_anat"))
+        test_utils.check_and_cd_folder(
+            join(base_folder, sub, ses, "change_anat")
+        )
 
     @pytest.mark.parametrize(
         "files_to_test",
@@ -238,13 +242,10 @@ def test_datatypes_subsection(self, project, files_to_test):
         base_folder = test_utils.get_top_level_folder_path(project)
 
         # Check at the subject level
-        sub_file_names = test_utils.glob_basenames(
+        test_utils.glob_basenames(
             join(base_folder, sub, "*"),
             exclude=ses,
         )
-        if "anat" in files_to_test:
-            assert "anat" in sub_file_names
-            files_to_test.remove("anat")
 
         # Check at the session level
         ses_file_names = test_utils.glob_basenames(
@@ -253,7 +254,9 @@ def test_datatypes_subsection(self, project, files_to_test):
         )
 
         if files_to_test == ["all"]:
-            assert ses_file_names == sorted(["ephys", "behav", "funcimg"])
+            assert ses_file_names == sorted(
+                ["ephys", "behav", "funcimg", "anat"]
+            )
         else:
             assert ses_file_names == sorted(files_to_test)
 
diff --git a/tests/tests_integration/test_ssh_file_transfer.py b/tests/tests_integration/test_ssh_file_transfer.py
index f249d827..989dbfbf 100644
--- a/tests/tests_integration/test_ssh_file_transfer.py
+++ b/tests/tests_integration/test_ssh_file_transfer.py
@@ -296,11 +296,6 @@ def make_pathtable_search_filter(self, sub_names, ses_names, datatype):
             if sub == "all_non_sub":
                 extra_arguments += ["is_non_sub == True"]
             else:
-                if "anat" in datatype:
-                    sub_ses_dtype_arguments += [
-                        f"(parent_sub == '{sub}' & (parent_datatype == 'anat' | parent_datatype == 'anat'))"
-                    ]
-
                 for ses in ses_names:
                     if ses == "all_non_ses":
                         extra_arguments += [

From bf3ce11a089e8ded07973babdf5f417dfa9cfcfe Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Mon, 23 Oct 2023 11:29:26 +0100
Subject: [PATCH 07/10] Fix documentation.

---
 docs/source/pages/documentation.md | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index 61a32f1f..41bf1bb8 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -93,7 +93,6 @@ ssh \
 --overwrite_old_files
 ```
 
-
 Now setup is complete! _Configuration_ settings can be edited at any time with the `update-config` command. Alternatively, custom *configuration* files can be supplied using the `supply-config` command (this simplifies setting up projects across multiple *local* machines).
 
 Next, we can start setting up the project by automatically creating standardised project folder trees.
@@ -154,13 +153,10 @@ make-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
     └── anat
 ```
 
-
 ### Datatype Folders
 
 In [SWC-Blueprint](https://swc-blueprint.neuroinformatics.dev/specification.html), *datatypes* specify where acquired experimental data of currently supported types (`behav`, `ephys`, `funcimg` and `anat`) is stored. See the [*datatypes* section of the SWC-Blueprint for more details](https://swc-blueprint.neuroinformatics.dev/specification.html#datatype).
 
-At present, `anat` is saved to the `sub-` level, as it is assumed `anat` is conducted *ex vivo* and so session will be possible. Please don't hesitate to get into contact if you have an alternative use case.
-
 ## Data Transfer
 
 Once a local machine is setup, created folders can be filled with acquired experimental data. Once data collection is complete, it is often required to transfer this data to a central storage machine. This is especially important if data of different types (e.g. *behaviour*, *electrophysiology*) is acquired across multiple local machines.
@@ -499,7 +495,7 @@ DataShuttle provides a number of keyword arguments to allow separate handling of
 
 `all` : All *session* and non-*session* files and folders within a *subject* level folder (e.g. `sub-001`) will be transferred.
 
-`all_ses` : *Session* <u>folders</u> only (i.e. prefixed with `-ses`) will be transferred. Note that the only exception is the `anat` folder, the transfer of which is determined by the `-dt` flag (below).
+`all_ses` : *Session* <u>folders</u> only (i.e. prefixed with `-ses`) will be transferred.
 
 `all_non_ses` : All files and folders that are not prefixed with `-sub` will be transferred. Any folders prefixed with `-ses` will not be transferred.
 
@@ -507,7 +503,7 @@ DataShuttle provides a number of keyword arguments to allow separate handling of
 
 `all` : All *datatype* folders at the *subject* or *session* folder level will be transferred, as well as all files and folders within selected *session* folders.
 
-`all_datatype` : All *datatype* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `anat`) residing at either the *subject* or *session* level will be
+`all_datatype` : All *datatype* folders (i.e. folders with the pre-determined name: `behav`, `ephys`, `funcimg`, `anat`) residing at the *session* level will be
 transferred. Non-*datatype* folders at the *session* level will not be transferred
 
 `all_ses_level_non_datatype` : Non *datatype* folders at the *session* level will not be transferred

From 76fb054c31d293e35a69eba49979f670a8486821 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Tue, 24 Oct 2023 12:25:34 +0100
Subject: [PATCH 08/10] Fix documentation.

---
 README.md                          | 26 +++++++++++++-------------
 docs/source/pages/documentation.md |  8 ++++----
 tests/test_utils.py                |  2 +-
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index c6a336aa..20ecc463 100644
--- a/README.md
+++ b/README.md
@@ -36,32 +36,32 @@ See the SWC-BIDS [specification](https://swc-bids.neuroinformatics.dev/) for mor
     └── raw_data/
         ├── sub-001/
         │   └── ses-001/
-        │   │   ├── ephys/
-        │   │   └── behav/
-        │   └── anat/
+        │       ├── ephys/
+        │       └── behav/
+        │       └── anat/
         └── sub-002/
             └── ses-001/
             │   ├── behav/
             │   └── imaging/
             └── ses-002/
-            │   └── behav/
-            └── anat/
+                └── behav/
+                └── anat/
 ```
 
 
 ```+
 └── project_name/
-    └── rawdata/
+    └── rawdata/[test_utils.py](tests%2Ftest_utils.py)
         ├── sub-001  /
-        │   ├── ses-001/
-        │   │   ├── ephys
-        │   │   └── behav
-        │   └── anat
+        │   └── ses-001/
+        │       ├── ephys
+        │       └── behav
+        │       └── anat
         └── sub-002/
             ├── ses-001/
             │   ├── behav
             │   └── imaging
-            ├── ses-002/
-            │   └── behav
-            └── anat
+            └── ses-002/
+                └── behav
+                └── anat
 ```
diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index 41bf1bb8..01dd4671 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -147,10 +147,10 @@ make-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
 │   │   └── funcimg
 │   └── anat
 └── sub-003/
-    ├── ses-010_time-160248/
-    │   ├── behav
-    │   └── funcimg
-    └── anat
+    └── ses-010_time-160248/
+        ├── behav
+        ├── funcimg
+        └── anat
 ```
 
 ### Datatype Folders
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 49f3ea96..143b71d8 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -321,7 +321,7 @@ def check_datatype_sub_ses_uploaded_correctly(
         sub_names = glob_basenames(join(base_path_to_check, "*"))
         assert sub_names == sorted(subs_to_upload)
 
-        # Check ses are all uploaded + anat if transferred
+        # Check ses are all uploaded
         if ses_to_upload:
             for sub in subs_to_upload:
                 ses_names = glob_basenames(

From 829ec80e6754381929f86552c5d8948379e04f15 Mon Sep 17 00:00:00 2001
From: JoeZiminski <joseph.j.ziminski@gmail.com>
Date: Tue, 24 Oct 2023 12:50:29 +0100
Subject: [PATCH 09/10] Fix linting after rebase.

---
 tests/tests_integration/test_configs.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/tests_integration/test_configs.py b/tests/tests_integration/test_configs.py
index a17a86c5..276e4132 100644
--- a/tests/tests_integration/test_configs.py
+++ b/tests/tests_integration/test_configs.py
@@ -323,9 +323,7 @@ def test_supplied_config_file_bad_types(self, project, tmp_path):
                     f"Config file was not updated."
                 )
 
-    def test_supplied_config_file_changes_wrong_order(
-        self, project, tmp_path
-    ):
+    def test_supplied_config_file_changes_wrong_order(self, project, tmp_path):
         """
         Test the situation when a config file is passed with variables in
         the wrong order.

From 4ef00f2a615a28b444646b394e1879373c103395 Mon Sep 17 00:00:00 2001
From: Joe Ziminski <55797454+JoeZiminski@users.noreply.github.com>
Date: Tue, 24 Oct 2023 14:44:30 +0100
Subject: [PATCH 10/10] Fix documentation again.

---
 docs/source/pages/documentation.md | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/docs/source/pages/documentation.md b/docs/source/pages/documentation.md
index 01dd4671..d65f3b59 100644
--- a/docs/source/pages/documentation.md
+++ b/docs/source/pages/documentation.md
@@ -137,15 +137,15 @@ make-folders -sub 001@TO@003 -ses 010_@TIME@ -dt behav funcimg anat
 
 ```
 ├── sub-001/
-│   ├── ses-010_time-160248/
-│   │   ├── behav
-│   │   └── funcimg
-│   └── anat
+│   └── ses-010_time-160248/
+│       ├── behav
+│       └── funcimg
+│       └── anat
 ├── sub-002/
-│   ├── ses-010_time-160248/
-│   │   ├── behav
-│   │   └── funcimg
-│   └── anat
+│   └── ses-010_time-160248/
+│       └── behav
+│       └── funcimg
+│       └── anat
 └── sub-003/
     └── ses-010_time-160248/
         ├── behav
@@ -516,7 +516,6 @@ Below, a number of examples are given to exemplify how these arguments effect da
     ├── a_project_related_file.json
     ├── sub-001/
     │   ├── sub-001_extra-file.json
-    │   ├── anat
     │   └── ses-001/
     │       ├── ses-001_extra-file.json
     │       ├── behav/
@@ -525,7 +524,6 @@ Below, a number of examples are given to exemplify how these arguments effect da
     │           └── ...
     └── sub-002/
         ├── sub-002_extra-file.json
-        ├── anat
         └── ses-001/
 			├── behav/
 			│   └── ...