ci: General repo update, move to pyproject.toml

.cruft.json

@@ -0,0 +1,21 @@
+{
+  "template": "https://github.com/tlambert03/pyrepo-cookiecutter",
+  "commit": "a9545077bbb7a5c6d62addbe8a3484f844e7d5b2",
+  "context": {
+    "cookiecutter": {
+      "full_name": "Talley Lambert",
+      "email": "talley.lambert@gmail.com",
+      "github_username": "tlambert03",
+      "project_name": "nd2",
+      "project_slug": "nd2",
+      "project_short_description": "Yet another nd2 (Nikon NIS Elements) file reader",
+      "pypi_username": "talley",
+      "version_control": "setuptools-scm",
+      "_copy_without_render": [
+        ".github/workflows/*"
+      ],
+      "_template": "https://github.com/tlambert03/pyrepo-cookiecutter"
+    }
+  },
+  "directory": null
+}

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+profile = black
+exclude = docs,.eggs,examples
+max-line-length = 88
+docstring-convention = numpy
+docstring_style = numpy
+ignore = D100, D213, D401, D413, D107, W503

.github/TEST_FAIL_TEMPLATE.md

@@ -0,0 +1,12 @@
+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ payload.repository.full_name }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

.github/workflows/test.yml → .github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: Test
+name: CI
 
 on:
   push:
@@ -12,6 +12,14 @@ on:
   workflow_dispatch:
 
 jobs:
+  check-manifest:
+    name: Check Manifest
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - run: pip install check-manifest && check-manifest
+
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
     runs-on: ${{ matrix.platform }}
@@ -22,14 +30,14 @@ jobs:
         platform: [macos-latest, windows-latest, "ubuntu-latest"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         id: cache
         with:
           path: tests/data
@@ -43,7 +51,7 @@ jobs:
 
       - name: Build
         # -e seems necessary for coverage to work
-        run: pip install -e .[testing]
+        run: pip install -e .[test]
         env:
           CYTHON_TRACE: "1"
 

.github/workflows/cron.yml

@@ -0,0 +1,62 @@
+name: --pre Test
+# An "early warning" cron job that will install dependencies
+# with `pip install --pre` periodically to test for breakage
+# (and open an issue if a test fails)
+
+on:
+  schedule:
+    - cron: '0 */12 * * *'  # every 12 hours
+  workflow_dispatch:
+
+jobs:
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10']
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v3
+        id: cache
+        with:
+          path: tests/data
+          key: ${{ hashFiles('scripts/download_samples.py') }}
+
+      - name: Download Samples
+        if: steps.cache.outputs.cache-hit != 'true'
+        run: |
+          pip install requests
+          python scripts/download_samples.py
+
+      - name: Build
+        run: pip install --pre -e .[test]
+        env:
+          CYTHON_TRACE: "1"
+
+      - name: Test
+        run: pytest -v --cov=nd2 --cov-report=xml --cov-report=term
+
+      # If something goes wrong, we can open an issue in the repo
+      - name: Report Failures
+        if: ${{ failure() }}
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: '[test-bot] pip install --pre is failing'
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true

.github/workflows/deploy.yml

@@ -18,9 +18,9 @@ jobs:
         os: [ubuntu-20.04, windows-2019, macos-10.15]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v3
         name: Install Python
         with:
           python-version: "3.9"
@@ -30,7 +30,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install build
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
         id: cache
         with:
           path: tests/data
@@ -43,9 +43,9 @@ jobs:
           python scripts/download_samples.py
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.2.0a1
+        uses: pypa/cibuildwheel@2.6.0
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
 
@@ -56,7 +56,7 @@ jobs:
           check-manifest
           python -m build --sdist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: matrix.os == 'ubuntu-20.04'
         with:
           path: dist/*.tar.gz
@@ -66,12 +66,12 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.4.2
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.TWINE_API_KEY }}

.github_changelog_generator

@@ -0,0 +1,5 @@
+user=tlambert03
+project=nd2
+issues=false
+exclude-labels=duplicate,question,invalid,wontfix,hide
+add-sections={"tests":{"prefix":"**Tests & CI:**","labels":["tests"]}}

.pre-commit-config.yaml

@@ -1,41 +1,62 @@
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style: [pre-commit.ci] auto fixes [...]"
+  autoupdate_commit_msg: "ci: [pre-commit.ci] autoupdate"
+
+default_install_hook_types: [pre-commit, commit-msg]
+
 exclude: src/sdk
+
 repos:
+
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v1.3.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.2.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
       - id: trailing-whitespace
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v1.20.1
-    hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-typing-imports==1.7.0]
+
   - repo: https://github.com/myint/autoflake
     rev: v1.4
     hooks:
       - id: autoflake
         args: ["--in-place", "--remove-all-unused-imports"]
+
   - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:
       - id: isort
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
+
   - repo: https://github.com/asottile/pyupgrade
     rev: v2.32.1
     hooks:
       - id: pyupgrade
         args: [--py37-plus, --keep-runtime-typing]
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        args: [--min-python-version=3.7.0]
+        additional_dependencies:
+          - flake8-typing-imports
+          - flake8-bugbear
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.950
+    rev: v0.960
     hooks:
       - id: mypy
-        additional_dependencies: [numpy]
+        files: "^src/"
         exclude: scripts
+        additional_dependencies: [numpy]