Core features

.coveragerc

@@ -1,6 +1,6 @@
 [run]
-source = src
-omit = ./tests/*
-concurrency = multiprocessing
-parallel = true
-sigterm = true
+branch = True
+source = error_align
+
+[report]
+omit = src/error_align/baselines/*

.github/CODEOWNERS

@@ -1,5 +1 @@
-* @corticph/machine-learning-r-d
-
-# No owners of dependencies to allow @github-actions[bot] to approve and auto-merge dependabot PRs.
-pyproject.toml
-poetry.lock
+* @borgholt

.github/pull_request_template.md

@@ -5,18 +5,6 @@ Do not leave this blank.
 This PR [adds/removes/fixes/replaces] the [feature/bug/etc] because [reason] by doing [x].
 -->
 
-## Related Issue(s)
-
-<!--
-We like to follow [Linear's guidance on linking issues to pull requests](https://linear.app/docs/github?tabs=206cad22125a#link-using-pull-requests).
-For example, writing "Closes RD-1234" would connect the current pull request to issue RD-1234,
-and when we merge the pull request, Linear will automatically close the issue.
--->
-
-Related to RD-XXXX
-<!-- OR -->
-Closes RD-XXXX
-
 <!--
 Before submitting a Pull Request, please ensure you've done the following:
 - 👷‍♀️ Create small PRs. In most cases, this will be possible.

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Ruff
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Run Ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: latest
+          args: "check"
+          src: "."

.github/workflows/tests_and_coverage.yml

@@ -0,0 +1,40 @@
+name: Tests and Coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11, 3.12]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install test dependencies with Poetry
+        run: |
+          python -m pip install --upgrade pip
+          pip install poetry
+          poetry install --with test
+
+      - name: Run tests with coverage
+        run: poetry run pytest
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.gitignore

@@ -146,3 +146,9 @@ tests/reports
 
 # MacOS
 .DS_Store
+
+# Data files generated for evaluation
+evaluation/transcribed_data/
+evaluation/primock57/
+evaluation/results/
+evaluation/visualize/

.pre-commit-config.yaml

@@ -14,11 +14,10 @@ repos:
     -   id: end-of-file-fixer  # Ensure files end with a newline.
     -   id: trailing-whitespace  # Check for trailing whitespace.
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.13
+    rev: v0.13.2
     hooks:
-    - id: ruff  # Check for Python file linting issues and fix them.
-      args: ["check", "--select", "I", "--fix"]
-    - id: ruff-format  # Format Python files.
+      - id: ruff-format
+      - id: ruff-check
 -   repo: https://github.com/asottile/yesqa
     rev: v1.5.0
     hooks:
@@ -29,8 +28,3 @@ repos:
     -   id: poetry-check  # Validate the pyproject.toml file.
     -   id: poetry-lock  # Lock dependencies on changes to the pyproject.toml.
     -   id: poetry-install  # Install dependencies from the lock file on checkout and merge.
-- repo: https://github.com/corticph/ml-pre-commit-hooks
-  rev: v0.2.0
-  hooks:
-  - id: update-readme-title
-  - id: update-readme-settings

Makefile

@@ -15,21 +15,6 @@ install:  ## Install the package for development along with pre-commit hooks.
 	poetry install --with dev --with test
 	poetry run pre-commit install
 
-.PHONY: test
-test:  ## Run the tests with pytest and generate coverage reports.
-	poetry run pytest -vvs tests --typeguard-packages=src --junitxml=test-results.xml --cov --cov-report=xml \
-		--cov-report=html --cov-report=term
-
-.PHONY: pre-commit
-pre-commit:  ## Run the pre-commit hooks.
-	poetry run pre-commit run --all-files --verbose
-
-.PHONY: pre-commit-pipeline
-pre-commit-pipeline:  ## Run the pre-commit hooks for the pipeline.
-	for hook in ${PRE_COMMIT_HOOKS_IN_PIPELINE}; do \
-		poetry run pre-commit run $$hook --all-files --verbose; \
-	done
-
 .PHONY: clean
 clean:  ## Clean up the project directory removing __pycache__, .coverage, test results, etc.
 	find . -type d -name "__pycache__" | xargs rm -rf {};