Merge branch 'main' of https://github.com/Adibvafa/CodonTransformer

.github/workflows/ci.yml

@@ -0,0 +1,39 @@
+# .github/workflows/ci.yml
+
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install coverage
+
+    - name: Run tests with coverage
+      run: |
+        make test_with_coverage
+        coverage report
+        coverage xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: true

.gitignore

@@ -158,3 +158,20 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Coverage reports
+coverage.xml
+
+# Jupyter Notebook checkpoints
+.ipynb_checkpoints/
+
+# Temporary files
+*.tmp
+*.temp
+
+# PyTorch Lightning checkpoints
+lightning_logs/
+
+# PyTorch model weights
+*.pth
+*.pt

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+# Don't run pre-commit on files under third-party/
+exclude: "^\
+  (third-party/.*)\
+  "
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-added-large-files # prevents giant files from being committed.
+      - id: check-case-conflict # checks for files that would conflict in case-insensitive filesystems.
+      - id: check-merge-conflict # checks for files that contain merge conflict strings.
+      - id: check-yaml # checks yaml files for parseable syntax.
+      - id: detect-private-key # detects the presence of private keys.
+      - id: end-of-file-fixer # ensures that a file is either empty, or ends with one newline.
+      - id: fix-byte-order-marker # removes utf-8 byte order marker.
+      - id: mixed-line-ending # replaces or checks mixed line ending.
+      - id: requirements-txt-fixer # sorts entries in requirements.txt.
+      - id: trailing-whitespace # trims trailing whitespace.
+
+  - repo: https://github.com/sirosen/check-jsonschema
+    rev: 0.23.2
+    hooks:
+      - id: check-github-actions
+      - id: check-github-workflows
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.13
+    hooks:
+      - id: ruff
+      - id: ruff-format