Retemplate the repository

.github/workflows/test.yml

@@ -1,41 +1,64 @@
-name: Test
+name: CI
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - 'main'
+      - '*.*'
+    tags:
+      - 'v*'
   pull_request:
-    branches: [ main ]
+  workflow_dispatch:
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.6', '3.7', '3.8']
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install -r requirements/requirements-dev.txt
-        python setup.py install
-    - name: Clone HYDRAD
-      uses: actions/checkout@v2
-      with:
-        repository: rice-solar-physics/HYDRAD
-        path: HYDRAD
-    - name: Test
-      run: |
-        pytest --hydrad-dir=$GITHUB_WORKSPACE/HYDRAD --cov=pydrad --cov-report=xml
-    - name: Report coverage
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: true
-        verbose: true
-        file: ./coverage.xml
+  test:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: "'tox<4' tox-pypi-filter"
+      envs: |
+        - macos: py39
+        - macos: py311
+        - windows: py39
+        - windows: py311
+        - linux: py39
+        - linux: py310
+        - linux: py311
+      coverage: 'codecov'
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  precommit:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: tox-pypi-filter
+      envs: |
+        - linux: pre-commit
+  docs:
+    needs: [test]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: tox-pypi-filter
+      envs: |
+        - linux: build_docs
+          python-version: '3.11'
+  publish:
+    # Build wheels when pushing to any branch except main
+    # publish.yml will only publish if tagged ^v.*
+    if: |
+      (
+        github.event_name != 'pull_request' && (
+          github.ref_name != 'main' ||
+          github.event_name == 'workflow_dispatch'
+        )
+      ) || (
+        github.event_name == 'pull_request' &&
+        contains(github.event.pull_request.labels.*.name, 'Run publish')
+      )
+    needs: [test]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
+    with:
+      test_extras: 'dev'
+      test_command: 'pytest -p no:warnings --doctest-rst --pyargs pydrad'
+      submodules: false
+      python-version: '3.11'
+    secrets:
+      pypi_token: ${{ secrets.PYPI_TOKEN }}

.gitignore

@@ -64,3 +64,6 @@ target/
 
 # pytest
 .pytest_cache
+
+# Project specific
+pydrad/_version.py

.pre-commit-config.yaml

@@ -0,0 +1,71 @@
+repos:
+  # The warnings/errors we check for here are:
+  # E101 - mix of tabs and spaces
+  # W191 - use of tabs
+  # W291 - trailing whitespace
+  # W292 - no newline at end of file
+  # W293 - trailing whitespace
+  # W391 - blank line at end of file
+  # E111 - 4 spaces per indentation level
+  # E112 - 4 spaces per indentation level
+  # E113 - 4 spaces per indentation level
+  # E303 - too many blank lines (3)
+  # E304 - blank lines found after function decorator
+  # E305 - expected 2 blank lines after class or function definition
+  # E306 - expected 1 blank line before a nested definition
+  # E502 - the backslash is redundant between brackets
+  # E722 - do not use bare except
+  # E901 - SyntaxError or IndentationError
+  # E902 - IOError
+  # F822: undefined name in __all__
+  # F823: local variable name referenced before assignment
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: [flake8-use-pathlib]
+        args: ['--count', '--select', 'E101,W191,W291,W292,W293,W391,E111,E112,E113,E303,E304,E306,E502,E722,E901,E902,F822,F823,PL100,PL102,PL103,PL104,PL105,PL110,PL112,PL113,PL18,PL120,PL122,PL123']
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-ast
+      - id: check-case-conflict
+      - id: trailing-whitespace
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro)$"
+      - id: check-yaml
+      - id: debug-statements
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.bib|tca.*)$"
+      - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.txt|.bib|tca.*)$"
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+    - id: pyupgrade
+      args: [--keep-runtime-typing, --py38-plus]
+      files: ^fiasco/
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.2
+    hooks:
+      - id: codespell
+        args: ['--config setup.cfg']
+
+  - repo: https://github.com/MarcoGorelli/absolufy-imports
+    rev: v0.3.1
+    hooks:
+    - id: absolufy-imports
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    - id: isort
+      name: isort
+      entry: isort
+      require_serial: true
+      language: python
+      types:
+      - python

.readthedocs.yml

@@ -5,17 +5,21 @@
 # Required
 version: 2
 
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: []
-
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
-    - requirements: requirements/requirements-dev.txt
-    - method: setuptools
-      path: .
+  - method: pip
+    path: .
+    extra_requirements:
+      - docs
+      - all

MANIFEST.in

@@ -1,3 +1,5 @@
 include README.md
 include LICENSE
-include pydrad/configure/templates/*
+include pyproject.toml
+include pydrad/configure/templates/*
+include pydrad/configure/data/*

conftest.py

@@ -1,23 +1,30 @@
 """
 Test rendering of templates for configuration and header files
 """
-import pytest
 import astropy.units as u
+import pytest
 
 import pydrad.configure
+from pydrad.configure.util import get_clean_hydrad
 
 
 def pytest_addoption(parser):
     parser.addoption('--hydrad-dir', action='store', default=None)
 
 
-@pytest.fixture
-def hydrad_clean(request):
-    return request.config.getoption('--hydrad-dir')
+@pytest.fixture(scope='session')
+def hydrad_clean(tmpdir_factory, request):
+    # Returns a local path to a copy of the HYDRAD code
+    # If a path is not passed as a command line argument to pytest,
+    # a new copy is cloned from GitHub
+    hydrad_dir = request.config.getoption('--hydrad-dir')
+    if hydrad_dir is None:
+        hydrad_dir = tmpdir_factory.mktemp('hydrad_tmp_clean')
+        get_clean_hydrad(hydrad_dir, base_path=None, from_github=True, overwrite=True)
+    return hydrad_dir
 
 
-@pytest.fixture
-def configuration_dict():
+def get_configuration_dict():
     return {
         'general': {
             'footpoint_height': 5.e+08*u.cm,
@@ -105,20 +112,22 @@ def configuration_dict():
     }
 
 
-@pytest.fixture
-def configuration(configuration_dict):
-    return pydrad.configure.Configure(configuration_dict, freeze_date=True)
+@pytest.fixture(scope='function')
+def configuration():
+    return pydrad.configure.Configure(get_configuration_dict(), freeze_date=True)
 
 
-@pytest.fixture
-def hydrad(tmp_path, configuration, hydrad_clean):
-    if hydrad_clean is None:
-        pytest.skip('Path to HYDRAD code not specified. Skipping those tests that require HYDRAD.')
-    else:
-        hydrad_tmp = tmp_path / 'hydrad_tmp'
-        configuration.setup_simulation(hydrad_tmp, hydrad_clean)
-        pydrad.configure.util.run_shell_command(
-            ['./HYDRAD.exe'],
-            hydrad_tmp,
-        )
-        return hydrad_tmp
+@pytest.fixture(scope='session')
+def hydrad(tmpdir_factory, hydrad_clean):
+    # NOTE: purposefully reconstructing the configuration here, rather than using the fixture
+    # above in order to keep configuration at the function scope level
+    configuration = pydrad.configure.Configure(get_configuration_dict(), freeze_date=True)
+    # Run a HYDRAD simulation for the given configuration and return the path to the directory
+    # containing the results.
+    hydrad_tmp = tmpdir_factory.mktemp('hydrad_tmp')
+    configuration.setup_simulation(hydrad_tmp, hydrad_clean, overwrite=True)
+    pydrad.configure.util.run_shell_command(
+        ['./HYDRAD.exe'],
+        hydrad_tmp,
+    )
+    return hydrad_tmp

docs/conf.py

@@ -69,14 +69,14 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
-import sphinx_rtd_theme
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_theme = 'sphinx_book_theme'
+
+# -- Sphinx Book Theme Options -----------------------------------------------------
+html_theme_options = {
+    "repository_url": 'https://github.com/rice-solar-physics/pydrad',
+    "use_repository_button": True,
+    "use_issues_button": True,
+}
 
 # -- Sphinx-gallery ----------------------------------------------------------
 extensions += [

pydrad/__init__.py

@@ -5,6 +5,8 @@
 import logging
 from astropy.logger import AstropyLogger
 
+from .version import version as __version__
+
 
 def _init_log():
     """
@@ -25,3 +27,5 @@ def _init_log():
 
 log = logging.getLogger()
 log = _init_log()
+
+__all__ = ['__version__', 'log']

pydrad/configure/tests/__init__.py

@@ -0,0 +1,10 @@
+import os
+
+
+def assert_ignore_blanks(string_1, string_2):
+    """
+    Compare two multiline strings, ignoring lines that are blank
+    """
+    string_1_stripped = os.linesep.join([l for l in string_1.splitlines() if l])
+    string_2_stripped = os.linesep.join([l for l in string_2.splitlines() if l])
+    assert string_1_stripped == string_2_stripped

pydrad/configure/tests/test_configure.py

@@ -15,4 +15,5 @@
      pathlib.Path('Initial_Conditions') / 'profiles' / 'initial.amr.phy',
      pathlib.Path('Initial_Conditions') / 'profiles' / 'initial.amr.sol'])
 def test_generated_files_exist(hydrad, filename):
-    assert (hydrad / filename).is_file()
+    generated_file = pathlib.Path(hydrad / filename)
+    assert generated_file.is_file()