Core features (#2)

Includes: All source code for initial version of error-align. All source code for reproducing results from paper. Basic CI workflow. Basic documentation.

Author: borgholt

.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/assets/logo.svg

@@ -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/dependabot.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/pull_request_template.md

@@ -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

.github/workflows/dependabot_automation.yml

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