Merge branch 'main' into feat-step4-intg

.github/workflows/python_ci.yml

@@ -6,10 +6,15 @@ jobs:
       fail-fast: false
       matrix:
         version: ['3.9', '3.10', '3.11']
-    runs-on: ubuntu-latest
+        os: [ubuntu-latest,macos-latest]
+    runs-on:  ${{ matrix.os }}
     steps:
-      - name: install mpi
-        run: sudo apt update && sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev 
+      - name: install mpi in ubuntu
+        if: matrix.os == 'ubuntu-latest'
+        run: sudo apt update && sudo apt-get install openmpi-bin
+      - name: install mpi macos
+        if: matrix.os == 'macos-latest'
+        run: brew install open-mpi
       - uses: actions/checkout@v3
       - name: setup python
         uses: actions/setup-python@v4

.github/workflows/test-B01_SL_load_single_file.yml

@@ -24,4 +24,6 @@ jobs:
       - 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
       - name: second step make_spectra
-        run: python src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py SH_20190502_05180312 SH_testSLsinglefile2 True
+        run: python src/icesat2_tracks/analysis_db/B02_make_spectra_gFT.py SH_20190502_05180312 SH_testSLsinglefile2 True
+      - name: third step plot_spectra
+        run: python src/icesat2_tracks/analysis_db/B03_plot_spectra_ov.py SH_20190502_05180312 SH_testSLsinglefile2 True

README.md

@@ -5,7 +5,8 @@
 Prerequisites:
 - A POSIX-compatible system (Linux or macOS)
 - Python 3.9 (run `python --version` to check that your version of python is correct)
-- MPI (e.g. from `brew install open-mpi`)
+- MPI (e.g. from `brew install open-mpi` on macOS)
+- HDF5 (e.g. from `brew install hdf5` on macOS)
 
 > [!IMPORTANT]  
 > Windows is not supported for development work – use [WSL](https://learn.microsoft.com/en-us/windows/wsl/) on Windows hosts
@@ -31,6 +32,20 @@ Installation:
   ```shell
   pip install --upgrade --editable ".[dev]"
   ```
+  > You may need to set the value of the `HDF5_DIR` environment variable to install some of the dependencies, especially when installing on macOS. 
+  > 
+  > For Apple Silicon (M-Series) CPUs:
+  > ```shell
+  > export HDF5_DIR="/opt/homebrew/opt/hdf5"
+  > pip install --upgrade --editable ".[dev]"
+  > ```
+  >
+  > For Intel CPUs:
+  > ```shell
+  > export HDF5_DIR="/usr/local/opt/hdf5"
+  > pip install --upgrade --editable ".[dev]"
+  > ```
+
 - Check the module `icesat2_tracks` is available by loading the module:
   ```shell
   python -c "import icesat2_tracks; print(icesat2_tracks.__version__)"