Merge branch 'main' into single_test

.devcontainer/devcontainer.json

@@ -11,7 +11,7 @@
 		"python.languageServer": "Pylance",
 		"python.linting.enabled": true,
 		"python.linting.pylintEnabled": true,
-		"python.formatting.blackPath": "/home/vscode/.local/bin/black",
+		"python.formatting.blackPath": "/usr/local/bin/black",
 		"python.formatting.provider": "black",
 		"python.formatting.blackArgs": [
 			"--line-length",
@@ -22,31 +22,35 @@
 		"python.linting.lintOnSave": true,
 		"python.linting.flake8Enabled": true,
 		"editor.formatOnSave": true,
-		"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
-		"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
-		"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
-		"python.linting.pycodestylePath": "/home/vscode/.local/bin/pycodestyle",
-		"python.linting.pydocstylePath": "/home/vscode/.local/bin/pydocstyle",
+		"python.linting.banditPath": "/usr/local/bin/bandit",
+		"python.linting.flake8Path": "/usr/local/bin/flake8",
+		"python.linting.mypyPath": "/usr/local/bin/mypy",
+		"python.linting.pycodestylePath": "/usr/local/bin/pycodestyle",
+		"python.linting.pydocstylePath": "/usr/local/bin/pydocstyle",
 		"python.linting.pylintPath": "/usr/bin/pylint",
+		"terminal.integrated.defaultProfile.linux": "bash (login)",
 		"terminal.integrated.profiles.linux": {
 			"bash (login)": {
-				"path": "/bin/bash",
-				"args": [
-					""
-				]
+				"path": "bash"
 			}
 		}
 	},
 	// Add the IDs of extensions you want installed when the container is created.
 	"extensions": [
 		"ms-python.python",
 		"ms-python.vscode-pylance",
-		"marklarah.pre-commit-vscode"
-	]
+		"marklarah.pre-commit-vscode",
+		"ms-toolsai.jupyter",
+		"ms-toolsai.jupyter-renderers",
+		"ms-toolsai.jupyter-keymap",
+		"jithurjacob.nbpreviewer"
+	],
+	// Mount to a volume if you'd like to persist data to your disk
+	// "mounts": ["source=<add your /path/on/host here>, target=/workspaces/hermes_core, type=bind"],
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
 	// Use 'postCreateCommand' to run commands after the container is created.
 	//"postCreateCommand": "bash -i -c 'pip3 install --user .[all]'",
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
-	// "remoteUser": "vscode"
+	"remoteUser": "vscode"
 }

.github/workflows/codestyle.yml

@@ -8,6 +8,9 @@ on:
   pull_request:
     branches:
       - main
+  workflow_dispatch: # For on demand runs
+  schedule:
+    - cron: 0 0 * * * # Scheduled run every day at midnight
 jobs:
   build:
 
@@ -16,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,8 +29,11 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[dev]
+        pip install pip setuptools wheel --upgrade
+        # Install spacepy without build isolation to avoid issues with numpy
+        pip install numpy
+        pip install spacepy --no-build-isolation
+        python -m pip install -e '.[style]'
     - name: Lint with Black
       run: |
         black --check --diff hermes_eea

.github/workflows/docs.yml

@@ -8,6 +8,9 @@ on:
   pull_request:
     branches:
       - main
+  workflow_dispatch: # For on demand runs
+  schedule:
+    - cron: 0 0 * * * # Scheduled run every day at midnight
 jobs:
   build:
 
@@ -16,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,8 +29,11 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[docs]
+        pip install pip setuptools wheel --upgrade
+        # Install spacepy without build isolation to avoid issues with numpy
+        pip install numpy
+        pip install spacepy --no-build-isolation
+        python -m pip install -e '.[docs]'
     - name: Build docs
       working-directory: ./docs
       run: make html

.github/workflows/testing.yml

@@ -8,6 +8,9 @@ on:
   pull_request:
     branches:
       - main
+  workflow_dispatch: # For on demand runs
+  schedule:
+    - cron: 0 0 * * * # Scheduled run every day at midnight
 jobs:
   build:
 
@@ -16,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v2
@@ -26,12 +29,19 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install -e .[test]
+        pip install pip setuptools wheel --upgrade
+        # Install spacepy without build isolation to avoid issues with numpy
+        pip install numpy
+        pip install spacepy --no-build-isolation
+        pip install -e .[test]
+      if: ${{ !(matrix.platform == 'windows-latest' && matrix.python-version == '3.11') }}
     - name: Run tests
       run: pytest --pyargs hermes_eea --cov hermes_eea
       env:
         PLATFORM: ${{ matrix.platform }}
+      # Skip Windows Python 3.11 tests until SpacePy is updated
+      if: ${{ !(matrix.platform == 'windows-latest' && matrix.python-version == '3.11') }}
     - name: Upload coverage reports to Codecov with GitHub Action
       uses: codecov/codecov-action@v3
-
+      # Skip Windows Python 3.11 tests until SpacePy is updated
+      if: ${{ !(matrix.platform == 'windows-latest' && matrix.python-version == '3.11') }}

.gitignore

@@ -147,7 +147,7 @@ docs/_build
 docs/generated
 docs/api
 docs/whatsnew/latest_changelog.txt
-hermes_eea/version.py
+hermes_eea/_version.py
 htmlcov/
 
 

docs/Makefile

@@ -16,7 +16,7 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)
-	rm -rf api
+	rm -rf ./generated
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/conf.py

@@ -41,6 +41,9 @@
     "sphinx_automodapi.smart_resolver",
 ]
 
+# Set automodapi to generate files inside the generated directory
+automodapi_toctreedirnm = "generated/api"
+
 # Set automodapi to generate files inside the generated directory
 # automodapi_toctreedirnm = "_build/html/api"
 numpydoc_show_class_members = False

hermes_eea/tests/test_calibration.py

@@ -8,6 +8,7 @@
 import sys
 
 
+
 @pytest.fixture(scope="session") # this is a pytest fixture
 def small_level0_file(tmp_path_factory):
     fn = Path(os.path.join(_data_directory, "hermes_EEA_l0_2023042-000000_v0.bin"))