Merge branch 'main' into update-docker-file

.gitattributes

@@ -0,0 +1 @@
+*.tar.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/publish_pypi.yml

@@ -0,0 +1,36 @@
+name: Publish Icesat2 to PyPI
+
+on:    
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+        # IMPORTANT: this permission is mandatory for trusted publishing
+        id-token: write
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: |
+        python -m build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages_dir: dist
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/test_icesat2_tracks_pipeline.yml

@@ -0,0 +1,40 @@
+name: Smoke Tests
+on:
+  pull_request: {}
+  push:
+    branches: [ main ]
+jobs:
+  python_run_scripts:
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ['3.11']
+    runs-on: ubuntu-22.04
+    steps:
+      - name: install mpi
+        run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev 
+      - uses: actions/checkout@v3
+      - name: setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.version }} # install the python version needed
+          cache: "pip"
+      - name: install icesat2-tracks using pip
+        run: pip install .
+      - name: List dependencies
+        run: pip list
+      - name: first step B01_SL_load_single_file
+        run: icesat2waves load-file --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: second step make_spectra
+        run: icesat2waves make-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: third step plot_spectra
+        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: icesat2waves make-b04-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: sixth step B04_define_angle
+        run: icesat2waves define-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: seventh step B06_correct_separate
+        run: icesat2waves correct-separate --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./work
+

.github/workflows/test-B01_SL_load_single_file.yml → .github/workflows/test_test_suite.yml

@@ -14,18 +14,17 @@ jobs:
       - name: install mpi
         run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev 
       - uses: actions/checkout@v3
+        with:
+          lfs: true
       - name: setup python
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.version }} # install the python version needed
           cache: "pip"
       - name: install icesat2-tracks using pip
         run: pip install .
-      - name: List dependencies
-        run: pip list
-      - name: test icesat2waves app
-        run: icesat2waves --help
-      - name: test command for step 1
-        run: load_single_file --help
-      - name: first step B01_SL_load_single_file
-        run: python src/icesat2_tracks/analysis_db/B01_SL_load_single_file.py --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./work
+      - name: install pytest
+        run: pip install pytest pytest-xdist pytest-sugar pytest-durations
+      - name: Run tests
+        run: pytest --capture=sys --verbose --showlocals --tb=long --numprocesses=auto tests/test_steps.py
+

.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