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"))