Merge branch 'main' into chore-cleanup-app.py

brown-ccv · Mar 4, 2024 · 54033d7 · 54033d7
2 parents 7d8e0dc + 7169d79
commit 54033d7
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diff --git a/.github/workflows/test_icesat2_tracks_pipeline.yml b/.github/workflows/test_icesat2_tracks_pipeline.yml
@@ -23,28 +23,18 @@ jobs:
         run: pip install .
       - name: List dependencies
         run: pip list
-      - name: test icesat2waves app
-        run: |
-            icesat2waves --help
-            icesat2waves load-file --help
-            icesat2waves make-spectra --help
-            icesat2waves plot-spectra --help
-            icesat2waves make-iowaga-threads-prior --help
-            icesat2waves make-b04-angle --help # prelim name
-            icesat2waves define-angle --help
-            icesat2waves correct-separate --help # prelim name
-
       - name: first step B01_SL_load_single_file
-        run: load-file --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves load-file --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: second step make_spectra
-        run: make-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves make-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: third step plot_spectra
-        run: plot-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
-      - name: fourth step IOWAGA threads 
-        run:  make-iowaga-threads-prior --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves plot-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: fouth step IOWAGA threads 
+        run: icesat2waves make-iowaga-threads-prior --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: fifth step B04_angle
-        run: make-b04-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves make-b04-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: sixth step B04_define_angle
-        run: define-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves define-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: seventh step B06_correct_separate
-        run: correct-separate --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work --verbose
+        run: icesat2waves correct-separate --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+
diff --git a/src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py b/src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py
@@ -32,17 +32,8 @@
     makeapp,
 )
 
-color_schemes.colormaps2(21)
-matplotlib.use("Agg")  # prevent plot windows from opening
 
-dtime = 4  # in hours
-
-# IOWAGA constants
-data_url = "https://tds3.ifremer.fr/thredds/IOWAGA-WW3-FORECAST/IOWAGA-WW3-FORECAST_GLOBMULTI_GLOB-30M.xml"
-dataset_key = "IOWAGA-WW3-FORECAST_GLOBMULTI_GLOB-30M_FIELD_NC_MARC_WW3-GLOB-30M"
-
-
-def get_iowaga(data_url=data_url, dataset_key=dataset_key):
+def get_iowaga(data_url, dataset_key):
     ## load WW3 data
     # ECMWF hindcast
     # data_url = 'https://tds3.ifremer.fr/thredds/IOWAGA-WW3-HINDCAST/IOWAGA-GLOBAL_ECMWF-WW3-HINDCAST_FULL_TIME_SERIE.xml'
@@ -191,14 +182,20 @@ def run_A02c_IOWAGA_thredds_prior(
     track_name: str = typer.Option(..., callback=validate_track_name_steps_gt_1),
     batch_key: str = typer.Option(..., callback=validate_batch_key),
     ID_flag: bool = True,
-    data_url: str = typer.Option(data_url),
-    dataset_key: str = typer.Option(dataset_key),
     output_dir: str = typer.Option(..., callback=validate_output_dir),
     verbose: bool = False,
 ):
     """
     TODO: add docstring
     """
+    color_schemes.colormaps2(21)
+    matplotlib.use("Agg")  # prevent plot windows from opening
+
+    dtime = 4  # in hours
+
+    # IOWAGA constants
+    data_url = "https://tds3.ifremer.fr/thredds/IOWAGA-WW3-FORECAST/IOWAGA-WW3-FORECAST_GLOBMULTI_GLOB-30M.xml"
+    dataset_key = "IOWAGA-WW3-FORECAST_GLOBMULTI_GLOB-30M_FIELD_NC_MARC_WW3-GLOB-30M"
 
     track_name, batch_key, _ = io.init_from_input(
         [
@@ -646,7 +643,9 @@ def plot_prior(Prior, axx):
         echo("done")
 
 
-make_iowaga_threads_prior_app = makeapp(run_A02c_IOWAGA_thredds_prior, name="threads-prior")
+make_iowaga_threads_prior_app = makeapp(
+    run_A02c_IOWAGA_thredds_prior, name="threads-prior"
+)
 
 if __name__ == "__main__":
     make_iowaga_threads_prior_app()
diff --git a/src/icesat2_tracks/app.py b/src/icesat2_tracks/app.py
@@ -24,7 +24,9 @@
 
 from icesat2_tracks.analysis_db.B05_define_angle import define_angle as _define_angle
 
-from icesat2_tracks.analysis_db.B06_correct_separate_var import run_B06_correct_separate_var as _run_correct_separate_var
+from icesat2_tracks.analysis_db.B06_correct_separate_var import (
+    run_B06_correct_separate_var as _run_correct_separate_var,
+)
 
 
 from icesat2_tracks.clitools import (
@@ -48,7 +50,13 @@ def run_job(
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    analysis_func(track_name, batch_key, ID_flag, output_dir, verbose)
+    analysis_func(
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
 
 
 @app.command(help=_loadfile.__doc__)
@@ -59,7 +67,14 @@ def load_file(
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_loadfile, track_name, batch_key, ID_flag, output_dir, verbose)
+    run_job(
+        analysis_func=_loadfile,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
 
 
 @app.command(help=_makespectra.__doc__)
@@ -70,7 +85,14 @@ def make_spectra(
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_makespectra, track_name, batch_key, ID_flag, output_dir, verbose)
+    run_job(
+        analysis_func=_makespectra,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
 
 
 @app.command(help=_plotspectra.__doc__)
@@ -81,7 +103,14 @@ def plot_spectra(
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_plotspectra, track_name, batch_key, ID_flag, output_dir, verbose)
+    run_job(
+        analysis_func=_plotspectra,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
 
 
 @app.command(help=_threddsprior.__doc__)
@@ -92,7 +121,14 @@ def make_iowaga_threads_prior(  # TODO: revise naming @mochell
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_threddsprior, track_name, batch_key, ID_flag, output_dir, verbose)
+    run_job(
+        analysis_func=_threddsprior,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
 
 
 @app.command(help=_run_B04_angle.__doc__)
@@ -103,7 +139,15 @@ def make_b04_angle(  # TODO: revise naming @mochell
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_run_B04_angle, track_name, batch_key, ID_flag, output_dir, verbose)
+    run_job(
+        analysis_func=_run_B04_angle,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
+
 
 @app.command(help=_define_angle.__doc__)
 def define_angle(
@@ -113,8 +157,15 @@ def define_angle(
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_define_angle, track_name, batch_key, ID_flag, output_dir, verbose)
-
+    run_job(
+        analysis_func=_define_angle,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
+
 
 @app.command(help=_run_correct_separate_var.__doc__)
 def correct_separate(  # TODO: rename with a verb or something
@@ -124,7 +175,15 @@ def correct_separate(  # TODO: rename with a verb or something
     output_dir: str = validate_output_dir_opt,
     verbose: bool = False,
 ):
-    run_job(_run_correct_separate_var, track_name, batch_key, ID_flag, output_dir)
+    run_job(
+        analysis_func=_run_correct_separate_var,
+        track_name=track_name,
+        batch_key=batch_key,
+        ID_flag=ID_flag,
+        output_dir=output_dir,
+        verbose=verbose,
+    )
+
 
 if __name__ == "__main__":
     app()