Merge remote-tracking branch 'origin/main' into specsscan-crop

.github/workflows/linting.yml

@@ -0,0 +1,46 @@
+name: linting
+
+# Triggers the workflow on push for all branches
+on:
+  push:
+    branches:
+      - '*'
+    paths-ignore:
+      pyproject.toml
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+
+# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
+      - name: checkout test data
+        run: |
+          eval `ssh-agent -s`
+          ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
+          git submodule sync --recursive
+          git submodule update --init --recursive
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # Linting steps, excute all linters even if one fails
+      - name: ruff
+        run:
+          poetry run ruff specsanalyzer specsscan tests
+      - name: ruff formating
+        if: ${{ always() }}
+        run:
+          poetry run ruff format --check specsanalyzer specsscan tests
+      - name: mypy
+        if: ${{ always() }}
+        run:
+          poetry run mypy specsanalyzer specsscan tests

.github/workflows/testing_coverage.yml

@@ -0,0 +1,47 @@
+name: pytest and coverage report
+
+# Triggers the workflow on push for all branches and PR only for main
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
+      - name: checkout test data
+        run: |
+          eval `ssh-agent -s`
+          ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
+          git submodule sync --recursive
+          git submodule update --init --recursive
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # Run pytest with coverage report, saving to xml
+      - name: Run tests on python 3.8
+        run: |
+          poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/
+
+      # Take report and upload to coveralls
+#      - name: Coveralls
+#        uses: coverallsapp/github-action@v2
+#        with:
+#          github-token: ${{ secrets.GITHUB_TOKEN }}
+#          file: ./cobertura.xml

.github/workflows/testing_multiversion.yml

@@ -0,0 +1,41 @@
+name: unit tests [Python 3.8|3.9|3.10|3.11]
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+    paths-ignore:
+      pyproject.toml
+
+jobs:
+  pytest:
+    # Using matrix strategy
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - name: Check out the repository
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
+      - name: checkout test data
+        run: |
+          eval `ssh-agent -s`
+          ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
+          git submodule sync --recursive
+          git submodule update --init --recursive
+
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: ${{matrix.python-version}}
+          poetry-version: 1.2.2
+
+      # Use cached python and dependencies, install poetry
+      - name: Run tests on python ${{matrix.python-version}}
+        run: |
+          poetry run pytest --full-trace --show-capture=no -sv -n auto tests/

.github/workflows/update_dependencies.yml

@@ -0,0 +1,74 @@
+name: Update depencies in poetry lockfile
+
+on:
+  schedule:
+    - cron:  '0 1 * * 1'
+  workflow_dispatch:
+  push:
+    branches: main
+    paths:
+      - .github/workflows/update_dependencies.yml
+
+jobs:
+  update_dependencies:
+    runs-on: ubuntu-latest
+    steps:
+      # Check out repo and set up Python
+      - uses: actions/checkout@v3
+        with:
+          lfs: true
+
+# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions
+      - name: checkout test data
+        run: |
+          eval `ssh-agent -s`
+          ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
+          git submodule sync --recursive
+          git submodule update --init --recursive
+
+
+# see https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md
+      - uses: tibdex/github-app-token@v1
+        id: generate-token
+        with:
+          app_id: ${{ secrets.APP_ID }}
+          private_key: ${{ secrets.APP_PRIVATE_KEY }}
+
+      # Use cached python and dependencies, install poetry
+      - name: "Setup Python, Poetry and Dependencies"
+        uses: packetcoders/action-setup-cache-python-poetry@main
+        with:
+          python-version: 3.8
+          poetry-version: 1.2.2
+
+      # update poetry lockfile
+      - name: "Update poetry lock file"
+        id: update
+        run: |
+          poetry self update
+          exec 5>&1
+          UPDATE_OUTPUT=$(poetry update|tee >(cat - >&5))
+          echo "UPDATE_OUTPUT<<EOF" >> $GITHUB_OUTPUT
+          echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      - name: Obtain git status
+        id: status
+        run: |
+          exec 5>&1
+          STATUS=$(git status|tee >(cat - >&5))
+          echo "STATUS<<EOF" >> $GITHUB_OUTPUT
+          echo "$STATUS" >> $GITHUB_OUTPUT
+          echo "EOF" >> $GITHUB_OUTPUT
+
+      # create pull request if necessary
+      - name: "Create Pull Request"
+        uses: peter-evans/create-pull-request@v5
+        if: ${{ contains(steps.status.outputs.STATUS, 'poetry.lock')}}
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          commit-message: Update dependencies
+          title: "Update dependencies"
+          body: |
+            Dependency updates using Poetry:
+            ${{ steps.update.outputs.UPDATE_OUTPUT }}

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tests/data"]
+	path = tests/data
+	url = [email protected]:OpenCOMPES/specsanalyzer-testdata.git

.pre-commit-config.yaml

@@ -11,15 +11,18 @@ repos:
     -   id: check-ast
     -   id: check-docstring-first
 
--   repo: https://github.com/psf/black
-    rev: 22.3.0
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.7
     hooks:
-    -   id: black
-        args: [--line-length=100]
--   repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+      # Run the formatter.
+      - id: ruff-format
+      # Run the linter.
+      - id: ruff
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.1
     hooks:
-    -   id: flake8
+      - id: mypy
 -   repo: https://github.com/asottile/reorder_python_imports
     rev: v3.8.2
     hooks:

MANIFEST.in

@@ -1 +1,2 @@
 include specsanalyzer/config/*
+include specsscan/config/*