Merge branch 'main' into clean-files-modules

.gitattributes

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

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every month
+      interval: "monthly"

.github/workflows/publish_pypi.yml

@@ -0,0 +1,35 @@
+name: Publish icesat2waves 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

.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_test_suite.yml

@@ -0,0 +1,30 @@
+name: Test Steps
+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
+        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: 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
+

README.md

@@ -12,6 +12,10 @@ Prerequisites:
 > Windows is not supported for development work – use [WSL](https://learn.microsoft.com/en-us/windows/wsl/) on Windows hosts
 
 Installation:
+> [!NOTE]
+> For testing purposes this repository uses Git Large File Storage (LFS) to handle large data files. If you want to clone the repository with the LFS files, make sure you have Git LFS installed on your system. You can download it from [here](https://git-lfs.github.com/). After installing, you can clone the repository as usual with `git clone`. Git LFS files will be downloaded automatically. If you've already cloned the repository, you can download the LFS files with `git lfs pull`.
+
+
 - Clone the repository:
   - Navigate to https://github.com/brown-ccv/icesat2-tracks
   - Click the "<> Code" button and select a method to clone the repository, then follow the prompts
@@ -87,7 +91,7 @@ conda env create --name "2021-icesat2-tracks" --file environment.yml
 ```
 ... but this has more steps and is thus more likely to fail. Since the installation step takes a long period of time, it is recommended to use the separate commands instead.)
 
-## Conda Configuration
+## Conda Configuration (Deprecated)
 
 Conda draws its configuration from multiple places, and will behave differently when the configuration is different, even when using the same `environment.yml` file.
 
@@ -201,3 +205,74 @@ unset CONDA_ENVS_PATH
 envs_dirs:
   - /users/username/anaconda/envs
 ```
+
+## Command line interface
+
+The `icesat2waves` package comes with a command-line interface (CLI) that facilitates interaction with the package directly from your terminal. This can be particularly useful for scripting and automation. You can access the help documentation for the CLI by running the following command:
+
+```shell
+icesat2waves --help
+```
+
+As suggested in the help, to run a specific command run `icesat2waves [OPTIONS] COMMAND [ARGS]...`.  To view help on running a command, run `icesat2waves COMMAND --help`. For example, to get help about the `load-file` command, you may issue `icesat2waves load-file --help` to get the following output:
+
+```shell
+(.venv) $ icesat2waves load-file --help
+Usage: icesat2waves load-file [OPTIONS]
+
+  Open an ICEsat2 tbeam_stats.pyrack, apply filters and corrections, and
+  output smoothed photon heights on a regular grid in an .nc file.
+
+Options:
+  --track-name TEXT         [required]
+  --batch-key TEXT          [required]
+  --id-flag / --no-id-flag  [default: id-flag]
+  --output-dir TEXT         [required]
+  --verbose / --no-verbose  [default: no-verbose]
+  --help                    Show this message and exit.
+
+```
+
+## Sample workflow
+Below is a sample workflow that leverages the included CLI.
+1. **Load single file**
+```shell
+icesat2waves load-file --track-name 20190502052058_05180312_005_01 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+
+2. **Make spectra from downloaded data**
+```shell
+icesat2waves make-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+3. **Plot spectra**
+```shell
+icesat2waves plot-spectra --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+
+4. **Build IOWAGA priors**
+```shell
+icesat2waves make-iowaga-threads-prior --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+
+5. **Build angles**
+
+```shell
+icesat2waves make-b04-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+
+
+6. **Define and plot angles**
+```shell
+icesat2waves define-angle --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```
+
+
+7. **Make corrections and separations**
+```shell
+icesat2waves correct-separate --track-name SH_20190502_05180312 --batch-key SH_testSLsinglefile2 --output-dir ./output
+```