fix: updated from cruft template

.cookiecutter.json

@@ -3,7 +3,6 @@
         "*.github"
     ],
     "_template": "https://github.com/MartinBernstorff/swift-python-cookiecutter",
-    "add_makefile": "y",
     "author": "Kenneth Enevoldsen",
     "copyright_year": "2023",
     "email": "[email protected]",

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/MartinBernstorff/swift-python-cookiecutter",
-  "commit": "691543da74e08c82a24f26eae89536b1c5581673",
+  "commit": "7fdb02999e8596c525377c208ca902645d134f97",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -12,7 +12,6 @@
       "github_user": "centre-for-humanities-computing",
       "version": "2.4.2",
       "copyright_year": "2023",
-      "add_makefile": "y",
       "license": "MIT",
       "_copy_without_render": [
         "*.github"

.github/workflows/documentation.yml

@@ -16,6 +16,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+          token: ${{ secrets.PAT }}
 
       - name: Install dependencies
         shell: bash
@@ -32,5 +33,5 @@ jobs:
         if: ${{ github.event_name == 'push' }}
         uses: ad-m/[email protected]
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_token: ${{ secrets.PAT }}
           branch: gh-pages

.github/workflows/pre-commit.yml

@@ -64,7 +64,7 @@ jobs:
             🏎️ Get results locally by running `pre-commit run --all-files`
             🕵️ Examine the results in the `Run pre-commit` section of this workflow `pre-commit` 
 
-            We also strongly recommend setting up the `ruff` and `black` extensions to auto-format on save in your chosen editor.
+            We also recommend setting up the `ruff` and `black` extensions to auto-format on save in your chosen editor.
 
       - name: Commit formatting
         if: ${{ steps.pre_commit.outputs.pre_commit_failed == 1 && github.event_name == 'pull_request' }}

.github/workflows/release.yml

@@ -8,12 +8,21 @@ name: Release
 on:
   push:
     branches: [main]
+  workflow_run:
+    workflows: ["tests"]
+    types:
+      - completed
+
 jobs:
   release:
     runs-on: ubuntu-latest
     concurrency: release
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing using PyPI 
+      # a guide on how to set it up is available here: https://blog.pypi.org/posts/2023-04-20-introducing-trusted-publishers/
+
 
-    if: ${{ github.ref == 'refs/heads/main' }}
+    if: ${{ github.ref == 'refs/heads/main' && github.event.workflow_run.conclusion == 'success'}}
     steps:
       # Checkout action is required for token to persist
       - uses: actions/checkout@v3
@@ -22,14 +31,20 @@ jobs:
           token: ${{ secrets.PAT }}
 
       - name: Python Semantic Release
-        uses: relekang/[email protected]
+        uses: python-semantic-release/[email protected]
+        id: release
+        with:
+          github_token: ${{ secrets.PAT }}
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        if: steps.release.outputs.released == 'true'
+        # This action supports PyPI's trusted publishing implementation, which allows authentication to PyPI without a manually 
+        # configured API token or username/password combination. To perform trusted publishing with this action, your project's 
+        # publisher must already be configured on PyPI.
+
+      - name: Publish package distributions to GitHub Releases
+        uses: python-semantic-release/upload-to-gh-release@main
+        if: steps.release.outputs.released == 'true'
         with:
           github_token: ${{ secrets.PAT }}
-          # Remember to copy the [tool.semantic_release] section from pyproject.toml
-          # as well
-          # To enable pypi,
-          # 1) Set upload_to_pypi to true in  pyproject.toml and
-          # 2) Set the pypi_token in the repo
-          # 3) Uncomment the two lines below
-          repository_username: __token__
-          repository_password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/static_type_checks.yml

@@ -0,0 +1,97 @@
+# We do not include static_type_checks as a pre-commit hook because pre-commit hooks
+# are installed in their own virtual environment, so static_type_checks cannot
+# use stubs from imports
+name: static_type_checks
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+jobs:
+  static_type_checks:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    concurrency:
+      group: "${{ github.workflow }} @ ${{ github.ref }}"
+      cancel-in-progress: true
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.9"]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Cache tox
+        uses: actions/[email protected]
+        id: cache_tox
+        with:
+          path: |
+            .tox
+          key: ${{ runner.os }}-${{ matrix.python-version }}-static-type-checks
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        id: setup_python
+        with:
+          python-version: ${{ matrix.python-version}}
+
+      - name: Install dependencies
+        shell: bash
+        run: |
+          pip install invoke tox
+
+      - name: Run static type checker
+        id: pyright
+        continue-on-error: true
+        run: |
+          if inv static-type-checks; then
+            echo "pyright check passed"
+            echo "pyright_failed=0" >> $GITHUB_OUTPUT
+          else
+            echo "pyright check failed"
+            echo "pyright_failed=1" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Find Comment
+        uses: peter-evans/find-comment@v2
+        id: find_comment
+        if: ${{github.event_name == 'pull_request'}}
+        continue-on-error: true
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: "github-actions[bot]"
+          body-includes: ✨ Looks like pyright failed ✨
+
+      - uses: mshick/add-pr-comment@v2
+        if: ${{ steps.pyright.outputs.pyright_failed == 1 && github.event_name == 'pull_request'}}
+        id: add_comment
+        with:
+          message: |
+            ✨ Looks like pyright failed ✨
+          
+            If you want to fix this, we recommend doing it locally by either:
+            
+              a) Enabling pyright in VSCode and going through the errors in the problems tab 
+            
+            `VSCode settings > Python > Analysis: Type checking mode > "basic"`
+            
+              b) Debugging via the command line
+            
+                1. Installing pyright, which is included in the dev dependencies: `pip install -e ".[dev]"`
+                2. Diagnosing the errors by running `pyright .`
+
+      - uses: mshick/add-pr-comment@v2
+        if: ${{ steps.pyright.outputs.pyright_failed == 0 && steps.find_comment.outputs.comment-id != '' && github.event_name == 'pull_request'}}
+        with:
+          message-id: ${{ steps.find_comment.outputs.comment-id }}
+          message: |
+            🌟 pyright succeeds! 🌟
+
+      - name: Show pyright output
+        id: fail_run
+        if: ${{steps.pyright.outputs.pyright_failed == 1}}
+        run: |
+          inv static-type-checks # Rerunning pyright isn't optimal computationally, but typically takes no more than a couple of seconds, and this ensures that the errors are in the failing step

.github/workflows/tests.yml

@@ -30,23 +30,34 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+
+      - name: Cache tox
+        uses: actions/[email protected]
+        id: cache_tox
+        with:
+          path: |
+            .tox
+          key: ${{ runner.os }}-${{ matrix.python-version }}-tests
+
       - name: Set up Python
         uses: actions/setup-python@v4
-        id: setup_python
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip' # caching pip dependencies
 
       - name: Install dependencies
         shell: bash
         run: |
-          pip install .[tests]
+          pip install invoke tox
 
       - name: Run and write pytest
         shell: bash
         run: |
-          python -m pytest --durations=0 -x --junitxml=pytest.xml --cov-report=term-missing --cov=src/ tests/
-
+          source .venv/bin/activate
+          pytest --durations=0 -n 2 -x --junitxml=pytest.xml --cov-report=term-missing --cov=src/ tests/
+          # Specifying two sets of "--pytest-args" is required for invoke to parse it as a list
+          inv test --pytest-args="--durations=0" --pytest-args="--junitxml=pytest.xml --cov-report=term-missing --cov=src/"
+         
       - name: Test report on failures
         uses: EnricoMi/publish-unit-test-result-action@v2
         id: test_report_with_annotations
@@ -62,6 +73,6 @@ jobs:
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9' &&  github.actor != 'dependabot[bot]' && github.event_name == 'pull_request' && (success() || failure()) }}
         with:
           create-new-comment: false
-          report-only-changed-files: true
+          report-only-changed-files: false
           pytest-coverage-path: pytest-coverage.txt
           junitxml-path: ./pytest.xml

pyproject.toml

@@ -25,6 +25,8 @@ classifiers = [
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
 ]
 
 keywords = ["nlp", "danish", "spacy-universe"]
@@ -46,13 +48,7 @@ repository = "https://github.com/centre-for-humanities-computing/DaCy"
 file = "LICENSE"
 name = "Apache License 2.0"
 [project.optional-dependencies]
-dev = [
-  "cruft",
-  "mypy",
-  "pre-commit>=2.20.0",
-  "ruff>=0.0.262",
-  "black[jupyter]>=23.3.0",
-]
+dev = ["cruft", "pre-commit>=2.20.0", "ruff>=0.0.262", "black[jupyter]>=23.3.0"]
 tests = [
   "pytest>=7.1.2",
   "pytest-cov>=3.0.0",
@@ -109,10 +105,9 @@ where = ["src"]
 [tool.coverage.run]
 omit = ["**/tests/*", "**/about.py", "**/dev/*"]
 
-[tool.mypy]
-ignore_missing_imports = true
-no_implicit_optional = true
-warn_unreachable = true
+[tool.pyright]
+exclude = [".*venv*", ".tox"]
+pythonPlatform = "Darwin"
 
 [tool.ruff]
 # Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
@@ -164,7 +159,6 @@ exclude = [
   ".eggs",
   ".git",
   ".hg",
-  ".mypy_cache",
   ".nox",
   ".pants.d",
   ".pytype",
@@ -206,10 +200,38 @@ max-complexity = 10
 
 [tool.semantic_release]
 branch = "main"
-version_variable = ["pyproject.toml:version"]
-upload_to_pypi = true
-upload_to_release = true
+version_toml = ["pyproject.toml:project.version"]
 build_command = "python -m pip install build; python -m build"
 
 [tool.setuptools]
 include-package-data = true
+
+
+[tool.tox]
+legacy_tox_ini = """
+[tox]
+envlist = py{39,310}
+
+[testenv]
+description: run unit tests
+extras = tests
+use_develop = true
+commands =
+  pytest -n auto {posargs:test}
+
+[testenv:type]
+description: run type checks
+extras = tests, dev
+basepython = py39 # Setting these explicitly avoid recreating env if your shell is set to a different version
+use_develop = true
+commands =
+  pyright src/
+
+[testenv:docs]
+description: build docs
+extras = docs
+basepython = py39 # Setting these explicitly avoid recreating env if your shell is set to a different version
+use_develop = true
+commands =
+  sphinx-build -b html docs docs/_build/html
+"""