Merge pull request #19 from larrybradley/packaging

Move package metadata to pyproject.toml

.github/workflows/ci_tests.yml

@@ -2,11 +2,15 @@ name: CI Tests
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - main
+    tags:
+      - '*'
   pull_request:
   schedule:
-    # run every Monday at 6am UTC
-    - cron: '0 6 * * 1'
+    # run every Monday at 5am UTC
+    - cron: '0 5 * * 1'
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -15,54 +19,98 @@ concurrency:
 env:
   TOXARGS: '-v'
 
+permissions:
+  contents: read
+
 jobs:
-  ci-tests:
-    name: ${{ matrix.os }}, ${{ matrix.tox_env }}
+  tests:
+    name: ${{ matrix.prefix }} ${{ matrix.os }}, ${{ matrix.tox_env }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.allow_failure }}
     strategy:
       matrix:
         include:
-          - os: ubuntu-latest
-            python: '3.8'
-            tox_env: 'py38-test-alldeps'
           - os: ubuntu-latest
             python: '3.9'
             tox_env: 'py39-test-alldeps'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
             python: '3.10'
             tox_env: 'py310-test-alldeps'
+            allow_failure: false
+            prefix: ''
+
+          - os: ubuntu-latest
+            python: '3.11'
+            tox_env: 'py311-test-alldeps-cov'
+            toxposargs: --remote-data=any
+            allow_failure: false
+            prefix: ''
+
           - os: macos-latest
-            python: '3.10'
-            tox_env: 'py310-test-alldeps'
+            python: '3.11'
+            tox_env: 'py311-test-alldeps'
+            allow_failure: false
+            prefix: ''
+
           - os: windows-latest
-            python: '3.10'
-            tox_env: 'py310-test-alldeps'
+            python: '3.11'
+            tox_env: 'py311-test-alldeps'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test'
+            python: '3.11'
+            tox_env: 'py311-test'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.10'
+            python: '3.11'
+            tox_env: 'linkcheck'
+            allow_failure: false
+            prefix: ''
+
+          - os: ubuntu-latest
+            python: '3.11'
             tox_env: 'codestyle'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'linkcheck'
+            python: '3.11'
+            tox_env: 'pep517'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.10'
+            python: '3.11'
             tox_env: 'bandit'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.8'
-            tox_env: 'py38-test-alldeps-astropylts-numpy118'
+            python: '3.9'
+            tox_env: 'py39-test-oldestdeps'
+            allow_failure: false
+            prefix: ''
+
           - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-alldeps-devdeps'
+            python: '3.11'
+            tox_env: 'py311-test-devdeps'
+            toxposargs: --remote-data=any
+            allow_failure: true
+            prefix: '(Allowed failure)'
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
     - name: Install base dependencies
@@ -78,8 +126,8 @@ jobs:
     - name: Run tests
       run: tox -e ${{ matrix.tox_env }} -- ${{ matrix.toxposargs }}
     - name: Upload coverage to codecov
-      if: "contains(matrix.tox_env, '-cov')"
+      if: ${{ contains(matrix.tox_env, '-cov') }}
       uses: codecov/codecov-action@v3
       with:
-        file: ./coverage.xml
+        files: ./coverage.xml
         verbose: true

.github/workflows/publish.yml

@@ -0,0 +1,46 @@
+name: Wheel building
+
+on:
+  schedule:
+    # run every Monday at 5am UTC
+    - cron: '0 5 * * 1'
+  pull_request:
+    # We also want this workflow triggered if the 'Build all wheels'
+    # label is added or present when PR is updated
+    types:
+      - synchronize
+      - labeled
+  push:
+    branches:
+      - '*'
+    tags:
+      - '*'
+      - '!*dev*'
+      - '!*pre*'
+      - '!*post*'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build_and_publish:
+    # This job builds the wheels and publishes them to PyPI for all
+    # tags, except those ending in ".dev". For PRs with the "Build all
+    # wheels" label, wheels are built, but are not uploaded to PyPI.
+
+    permissions:
+      contents: none
+
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
+
+    if: (github.repository == 'larrybradley/lacosmic' && (github.event_name == 'push' ||  github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' || contains(github.event.pull_request.labels.*.name, 'Build all wheels')))
+    with:
+      # We upload to PyPI for all tag pushes, except tags ending in .dev
+      upload_to_pypi: ${{ startsWith(github.ref, 'refs/tags/') && !endsWith(github.ref, '.dev') && (github.event_name == 'push' || github.event_name == 'workflow_dispatch') }}
+
+      test_extras: test
+      test_command: pytest -p no:warnings --pyargs lacosmic
+
+    secrets:
+      pypi_token: ${{ secrets.pypi_token }}

.gitignore

@@ -14,7 +14,7 @@ __pycache__
 */cython_version.py
 MANIFEST
 htmlcov
-.coverage
+.coverage*
 .ipynb_checkpoints
 .pytest_cache
 
@@ -41,6 +41,7 @@ pip-wheel-metadata
 # Other
 .cache
 .tox
+.tmp
 .*.sw[op]
 *~
 

.pre-commit-config.yaml

@@ -0,0 +1,86 @@
+ci:
+  autofix_prs: false
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+        # Prevent giant files from being committed.
+      - id: check-ast
+        # Simply check whether files parse as valid python.
+      - id: check-case-conflict
+        # Check for files with names that would conflict on a case-insensitive
+        # filesystem like MacOS HFS+ or Windows FAT.
+      - id: check-json
+        # Attempts to load all json files to verify syntax.
+      - id: check-merge-conflict
+        # Check for files that contain merge conflict strings.
+      - id: check-symlinks
+        # Checks for symlinks which do not point to anything.
+      - id: check-toml
+        # Attempts to load all TOML files to verify syntax.
+      - id: check-xml
+        # Attempts to load all xml files to verify syntax.
+      - id: check-yaml
+        # Attempts to load all yaml files to verify syntax.
+      - id: debug-statements
+        # Check for debugger imports and py37+ breakpoint() calls in python
+        # source.
+      - id: detect-private-key
+        # Checks for the existence of private keys.
+      - id: end-of-file-fixer
+        # Makes sure files end in a newline and only a newline.
+        exclude: ".*(svg.*|extern.*|_templates.*)$"
+      - id: trailing-whitespace
+        # Trims trailing whitespace.
+        exclude: ".*(data.*|extern.*)$"
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-mock-methods
+        # Prevent common mistakes of assert mck.not_called(), assert
+        # mck.called_once_with(...) and mck.assert_called.
+      - id: rst-directive-colons
+        # Detect mistake of rst directive not ending with double colon.
+      - id: rst-inline-touching-normal
+        # Detect mistake of inline code touching normal text in rst.
+      - id: text-unicode-replacement-char
+        # Forbid files which have a UTF-8 Unicode replacement character.
+      - id: python-check-blanket-noqa
+        # Enforce that all noqa annotations always occur with specific codes.
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.11.0
+    hooks:
+      - id: pyupgrade
+        args: ["--py39-plus"]
+        exclude: ".*(extern.*)$"
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        additional_dependencies: [toml]
+      - id: isort
+        name: isort (cython)
+        types: [cython]
+        additional_dependencies: [toml]
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        args: ["--ignore", "E501,W503"]
+
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.5.0
+    hooks:
+      - id: yesqa
+
+  # - repo: https://github.com/MarcoGorelli/absolufy-imports
+  #   rev: v0.3.1
+  #   hooks:
+  #   - id: absolufy-imports

.readthedocs.yml → .readthedocs.yaml

@@ -5,7 +5,12 @@ build:
   apt_packages:
     - graphviz
   tools:
-    python: "3.10"
+    python: "3.11"
+  jobs:
+    post_checkout:
+      - git fetch --shallow-since=2022-04-01 || true
+    pre_install:
+      - git update-index --assume-unchanged docs/conf.py
 
 sphinx:
   builder: html

CHANGES.rst

@@ -1,7 +1,19 @@
 1.1.0 (unreleased)
 ------------------
 
-- No changes yet
+General
+^^^^^^^
+
+- The minimum required Python version is 3.9. [#19]
+
+- The minimum required Numpy version is 1.22. [#19]
+
+- The minimum required Scipy version is 1.7.2. [#19]
+
+- The minimum required Astropy version is 5.0. [#19]
+
+- The project metadata is now stored in ``pyproject.toml`` (PEP 621).
+  [#19]
 
 
 1.0.0 (2022-04-19)

codecov.yml

@@ -0,0 +1,10 @@
+comment: off
+codecov:
+  branch: main
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        # this allows a small drop from the previous base commit coverage
+        threshold: 0.05%

docs/Makefile

@@ -129,5 +129,5 @@ linkcheck:
 	      "or in $(BUILDDIR)/linkcheck/output.txt."
 
 doctest:
-	@echo "Run 'python setup.py test' in the root directory to run doctests " \
+	@echo "Run 'pytest' in the root directory to run doctests " \
 	@echo "in the documentation."