Revert "Feat/remove ignore errors in mypy settings (#78)" (#80)

This reverts commit 3c799d0.

Author: DiogoRibeiro7

.flake8

@@ -1,26 +1,67 @@
 # .github/workflows/bump-version.yml
-name: Tag Version on Merge to Main
-
+name: Bump Version on Merge to Main
+ 
 on:
   push:
     branches:
       - main
 
 jobs:
-  tag-version:
+  bump-version:
     runs-on: ubuntu-latest
     permissions:
       contents: write
+      id-token: write
 
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0
+          fetch-depth: 0  # Fetch all history for all branches and tags
 
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - name: Tag repository from pyproject
-        run: python scripts/check_version_match.py --fix
+      - run: pip install python-semantic-release
+
+      - name: Configure Git
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Run Semantic Release
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: semantic-release version
 
+      - name: Push changes
+        run: |
+          git push --follow-tags
+      - name: "Install Poetry"
+        run: pip install poetry
+      - name: "Determine version bump type"
+        run: |
+            git fetch --tags
+            # This defaults to a patch type, unless a feature commit was pushed, then set type to minor
+            LAST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
+            LAST_COMMIT=$(git log -1 --format='%H')
+            echo "Last git tag: $LAST_TAG"
+            echo "Last git commit: $LAST_COMMIT"
+            echo "Commits:"
+            git log --no-merges --pretty=oneline $LAST_TAG...$LAST_COMMIT
+            git log --no-merges --pretty=format:"%s" $LAST_TAG...$LAST_COMMIT | grep -q ^feat: && BUMP_TYPE="minor" || BUMP_TYPE="patch"
+            echo "Version bump type: $BUMP_TYPE"
+            echo "BUMP_TYPE=$BUMP_TYPE" >> $GITHUB_ENV
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: "Version bump"
+        run: |
+            poetry version $BUMP_TYPE
+      - name: "Push new version"
+        run: |
+            git add pyproject.toml
+            git commit -m "Update version to $(poetry version -s)"
+            git pull --ff-only origin main
+            git push origin main --follow-tags
+        env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/bump-version.yml

@@ -0,0 +1,38 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Run tests
+        run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term
+
+        
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}  # optional if public repo

.github/workflows/ci.yml

@@ -50,4 +50,3 @@ dist/
 # Temporary
 *.log
 *.tmp
-.hypothesis/

.github/workflows/docs.yml

@@ -4,22 +4,10 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
-  jobs:
-    post_create_environment:
-      - pip install poetry
-    post_install:
-      - poetry config virtualenvs.create false
-      - poetry install --with docs
 
 python:
   install:
-    - method: pip
-      path: .
+    - requirements: docs/requirements.txt
 
 sphinx:
   configuration: docs/source/conf.py
-  fail_on_warning: false
-
-formats:
-  - pdf
-  - epub

.github/workflows/publish.yml

@@ -1,40 +1,5 @@
 # CHANGELOG
 
-## v1.0.9 (2025-08-02)
-
-### Features
-- export datasets to RDS files
-- test workflow runs on a Python version matrix
-- scikit-learn compatible data generator
-- compatibility helpers for lifelines and scikit-survival
-
-### Documentation
-- updated usage examples and tutorials
-- document optional scikit-survival dependency throughout the docs
-
-### Continuous Integration
-- auto-tag releases using the version check script
-
-### Misc
-- README quick example uses `covariate_range`
-
-## v1.0.8 (2025-07-30)
-
-### Documentation
-- ensure absolute path resolution in `conf.py`
-- drop unsupported theme option
-- define bibliography anchors and headings
-- fix tutorial links to non-existing docs
-- add additional references to the bibliography
-
-### Testing
-- add CLI integration test
-- expand piecewise generator test coverage
-
-### Misc
-- remove fix_recommendations.md
-
-
 
 ## v1.0.0 (2025-06-06)