From 4f7c6e2954b1aefe308aafdb8ef8b4130c2d41c7 Mon Sep 17 00:00:00 2001
From: Callum Rollo <c.rollo@outlook.com>
Date: Fri, 10 May 2024 13:46:23 +0200
Subject: [PATCH] env and local proc

---
 environment.yml      |  6 ++++++
 glidertools_plots.py |  7 ++++++-
 gridded_plots.py     |  5 +++++
 pilot_plots.py       |  2 +-
 requirements.txt     | 13 -------------
 5 files changed, 18 insertions(+), 15 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/environment.yml b/environment.yml
index 5417adc..137a966 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,3 +13,9 @@ dependencies:
         - pandas
         - tqdm
         - geopy
+        - pyaml
+        - ioos_qc
+        - polars
+        - scikit-learn
+        - plotly
+        - pyarrow
diff --git a/glidertools_plots.py b/glidertools_plots.py
index 9088781..5016505 100644
--- a/glidertools_plots.py
+++ b/glidertools_plots.py
@@ -18,7 +18,7 @@ def public_plots(nc, plots_dir):
     end = pd.to_datetime(ds.time.max().values)
     ds = ds.sel(time=slice(end - datetime.timedelta(days=60), end))
     # Apply flags from ioos
-    ds = apply_flags(ds, var_max_flags={"oxygen_concentration": 4, "cdom": 3})
+    ds = apply_flags(ds, var_max_flags={"oxygen_concentration": 4, "cdom": 4})
     # Prepare a variable of averaged time per profile. This is used in plotting later
     profile_time = ds.time.values.copy()
     profile_index = ds.profile_index
@@ -73,3 +73,8 @@ def public_plots(nc, plots_dir):
     plt.tight_layout()
     filename = plots_dir / f'SEA{ds.glider_serial}_M{ds.deployment_id}_gt.png'
     plt.savefig(filename, format='png', transparent=True)
+
+
+if __name__ == '__main__':
+    from pathlib import Path
+    public_plots(Path("/data/data_l0_pyglider/nrt/SEA76/M25/timeseries/mission_timeseries.nc"), Path("/home/callum/Downloads"))
\ No newline at end of file
diff --git a/gridded_plots.py b/gridded_plots.py
index ddf810a..705ba18 100644
--- a/gridded_plots.py
+++ b/gridded_plots.py
@@ -362,3 +362,8 @@ def make_map(nc, filename):
     _log.info(f"writing map to {filename_map}")
     fig.savefig(filename_map, format='png', transparent=True)
     return filename_map
+
+
+
+if __name__ == '__main__':
+    create_plots(Path("/data/data_l0_pyglider/nrt/SEA76/M25/gridfiles/mission_grid.nc"), Path("/home/callum/Downloads"), True)
\ No newline at end of file
diff --git a/pilot_plots.py b/pilot_plots.py
index df93fd5..073c02b 100644
--- a/pilot_plots.py
+++ b/pilot_plots.py
@@ -98,4 +98,4 @@ def battery_plots(combined_nav_file, out_dir):
 
 if __name__ == '__main__':
     from pathlib import Path
-    battery_plots(Path('/data/data_l0_pyglider/nrt/SEA76/M25/rawnc/Fibbla-rawgli.parquet'), '.')
+    battery_plots(Path('/data/data_l0_pyglider/nrt/SEA63/M73/rawnc/Fibbla-rawgli.parquet'), '.')
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index ffda1bc..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-numpy
-matplotlib
-xarray
-netcdf4
-cmocean
-gsw
-cartopy
-scipy
-geopy
-tqdm
-polars
-scikit-learn
-pyarrow