Merge pull request #88 from brown-ccv/87-cli-step-1-b01_sl_load_singl…

…e_filepy

CLI Tools, CLI for Steps 1-7

.github/workflows/test-B01_SL_load_single_file.yml

@@ -1,4 +1,4 @@
-name: Test B01_SL_load_single_file
+name: Test Steps
 on:
   pull_request: {}
   push:
@@ -23,18 +23,28 @@ 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: python src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py 20190502052058_05180312_005_01 SH_testSLsinglefile2 True
+        run: load-file --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: second step make_spectra
-        run: python src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py SH_20190502_05180312 SH_testSLsinglefile2 True
+        run: make-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
       - name: third step plot_spectra
-        run: python src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py SH_20190502_05180312 SH_testSLsinglefile2 True
-      - name: fourth step IOWAGA thredds
-        run: python src/icesat2_tracks/analysis_db/A02c_IOWAGA_thredds_prior.py SH_20190502_05180312 SH_testSLsinglefile2 True
-      - name: Fifth step B04_angle
-        run: python src/icesat2_tracks/analysis_db/B04_angle.py SH_20190502_05180312 SH_testSLsinglefile2 True
-      - name: Sixth step B05_define_angle
-        run: python src/icesat2_tracks/analysis_db/B05_define_angle.py SH_20190502_05180312 SH_testSLsinglefile2 True
-      - name: Seventh step B06_correct_separate_var
-        run: python src/icesat2_tracks/analysis_db/B06_correct_separate_var.py SH_20190502_05180312 SH_testSLsinglefile2 True
-
+        run: plot-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: fouth step IOWAGA threads 
+        run:  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
+      - name: sixth step B04_define_angle
+        run: 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

.gitignore

@@ -38,13 +38,14 @@ analysis_db/support_files/
 *.egg-info/
 .installed.cfg
 *.egg
-
+logs/
 *__pycache__/
 *__pycache__/*
 
 # Environments
 .env
 .venv
+.venv39/
 env/
 venv/
 ENV/
@@ -57,4 +58,4 @@ dist/
 
 #visual code
 .vscode/
-*.h5
+*.h5

pyproject.toml

@@ -120,7 +120,9 @@ dependencies = [ # Optional
   "emcee >=3.1.4, <4.0.0",
   "netCDF4 >=1.6.5, <2.0.0",
   "siphon >=0.9, <1.0.0",
-  "h5py >=3.5.0, < 4.0.0"
+  "h5py >=3.5.0, < 4.0.0",
+  "termcolor >=2.4.0, < 3.0.0",
+  "typer >=0.9.0, < 1.0.0",
 ]
 
 # List additional groups of dependencies   here (e.g. development
@@ -132,8 +134,16 @@ dependencies = [ # Optional
 # Similar to `dependencies` above, these must be valid existing
 # projects.
 [project.optional-dependencies] # Optional
-dev = ["check-manifest","black","icesat2-tracks[test]"]
-test = ["coverage"]
+dev = [
+  "check-manifest",
+  "black",
+  "icesat2-tracks[test]"
+]
+test = [
+  "coverage",
+  "pytest >=7.4.4, <8.0.0",
+  "pytest-xdist >=3.5.0, <4.0.0"
+]
 
 # List URLs that are relevant to your project
 #
@@ -155,6 +165,15 @@ test = ["coverage"]
 [project.scripts]  # Optional
 #TODO: ADD ANY SCRIPTS WE WANT TO HAVE
 download = "icesat2_tracks.icesat2_tools_scripts.nsidc_icesat2_associated2:main"
+load-file = "icesat2_tracks.analysis_db.B01_SL_load_single_file:load_file_app"
+make-spectra = "icesat2_tracks.analysis_db.B02_make_spectra_gFT:make_spectra_app"
+plot-spectra = "icesat2_tracks.analysis_db.B03_plot_spectra_ov:plot_spectra"
+make-iowaga-threads-prior = "icesat2_tracks.analysis_db.A02c_IOWAGA_thredds_prior:make_iowaga_threads_prior_app"
+make-b04-angle = "icesat2_tracks.analysis_db.B04_angle:make_b04_angle_app"
+define-angle = "icesat2_tracks.analysis_db.B05_define_angle:define_angle_app"
+correct-separate = "icesat2_tracks.analysis_db.B06_correct_separate_var:correct_separate_app"
+icesat2waves = "icesat2_tracks.app:app"
+
 
 # This is configuration specific to the `setuptools` build backend.
 # If you are using a different build backend, you will need to change this.

src/icesat2_tracks/ICEsat2_SI_tools/iotools.py

@@ -39,7 +39,7 @@ def init_from_input(arguments):
         batch_key = arguments[2]
         # $(hemisphere) $(coords) $(config)
 
-        print("read vars from file: " + str(arguments[1]))
+        # print("read vars from file: " + str(arguments[1]))
 
         if len(arguments) >= 4:
             if arguments[3] == "True":
@@ -49,13 +49,16 @@ def init_from_input(arguments):
             else:
                 test_flag = arguments[3]
 
-            print("test_flag found, test_flag= " + str(test_flag))
+            # print("test_flag found, test_flag= " + str(test_flag))
         else:
             test_flag = False
-    print(track_name)
 
-    print("----- batch =" + batch_key)
-    print("----- test_flag: " + str(test_flag))
+    # TODO: print statements to be handled with logger
+    # # print(track_name)
+
+    # print("----- batch =" + batch_key)
+    # print("----- test_flag: " + str(test_flag))
+
     return track_name, batch_key, test_flag