Fix the publish action

.github/workflows/docs.yml

@@ -3,26 +3,26 @@ name: Push docs
 on:
   push:
     branches:
-      - main
-      - documentation
+    - main
+    - documentation
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: 3.x
 
-      - name: Install font
-        run: |
-          cd /usr/share/fonts
-          wget https://github.com/JulietaUla/Montserrat/archive/refs/tags/v7.222.tar.gz
-          tar -xvzf v7.222.tar.gz
-          sudo chmod -R --reference=/usr/share/fonts/truetype Montserrat-7.222
-          sudo fc-cache -fv
-          fc-match Montserrat
+    - name: Install font
+      run: |
+        cd /usr/share/fonts
+        wget https://github.com/JulietaUla/Montserrat/archive/refs/tags/v7.222.tar.gz
+        tar -xvzf v7.222.tar.gz
+        sudo chmod -R --reference=/usr/share/fonts/truetype Montserrat-7.222
+        sudo fc-cache -fv
+        fc-match Montserrat
 
-      - run: pip install ".[docs]"
-      - run: mkdocs gh-deploy --force
+    - run: pip install ".[docs]"
+    - run: mkdocs gh-deploy --force

.github/workflows/publish.yml

@@ -1,7 +1,4 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: PyPI
+name: Publish to PyPI
 
 on:
   release:
@@ -10,21 +7,24 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
-
+    environment: pypi
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
+    - name: Checkout project
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine build
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        python-version-file: pyproject.toml
+
+    - name: Build
       run: |
-        python -m build --sdist --wheel .
-        twine upload dist/*
+        uv build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -1,45 +1,55 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: tests
+name: Lint and Test
 
 on:
   push:
-    branches: [ master ]
+    branches: [main]
   pull_request:
-    branches: [ master ]
-  schedule:
-  - cron: "0 0 1 1/1 *" # Run monthly
+    branches: [main]
 
 jobs:
-  build:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: pyproject.toml
+
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: --all-files
+
+    - name: Check Linting
+      uses: astral-sh/ruff-action@v3
+
+    - name: Check Formatting
+      uses: astral-sh/ruff-action@v3
+      with:
+        args: format --check --diff
+
+
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.10
+    - name: Checkout project
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+
+    - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version-file: pyproject.toml
 
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov wheel
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Run unit and system tests
       run: |
-        pytest --cov=ppx tests/
-    - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
-      with:
-        fail_ci_if_error: true
+        uv run pytest tests/

.pre-commit-config.yaml

@@ -1,6 +1,28 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 25.1.0 # Replace by any tag/version: https://github.com/psf/black/tags
-    hooks:
-      - id: black
-        language_version: python3 # Should be a command that runs python3.6+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: detect-private-key
+  - id: pretty-format-json
+    args: [--autofix]
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.15.0
+  hooks:
+  - id: pretty-format-toml
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.12.7
+  hooks:
+    # Run the linter.
+  - id: ruff
+    types_or: [python, pyi, jupyter]
+    args: [--fix, --show-fixes]
+    # Run the formatter.
+  - id: ruff-format
+    types_or: [python, pyi, jupyter]

AGENTS.md

@@ -0,0 +1,41 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+- Python package lives in `gopher/`; `gopher/gopher.py` is the CLI entry point wired to `gopher` console script.
+- Shared utilities and domain logic sit in modules like `annotations.py`, `enrichment.py`, `graph_search.py`, and `normalize.py`.
+- Tests are split by scope: unit tests in `tests/unit_tests/`, integration/system checks in `tests/system_tests/`, and fixtures/data in `tests/data/`.
+- Documentation sources are in `docs/`; MkDocs configuration is at `mkdocs.yml`.
+
+## Build, Test, and Development Commands
+- Install for development (creates editable install with extras):
+  `uv sync --dev` or `pip install -e .[dev]`
+- Run the test suite:
+  `uv run pytest` or `pytest`
+- Lint and format with Ruff (configured in `pyproject.toml`):
+  `uv run ruff check .` and `uv run ruff format .`
+- Pre-commit hooks (lint/format/metadata checks):
+  `pre-commit run --all-files`
+- Build docs locally:
+  `uv run mkdocs serve`
+
+## Coding Style & Naming Conventions
+- Ruff enforces PEP8-style rules; line length is 79. Target Python 3.10+.
+- Prefer type hints and docstrings for public functions; docstring checks are relaxed for tests and `__init__.py`.
+- Use snake_case for functions/variables, CapWords for classes, and UPPER_SNAKE_CASE for constants.
+- Keep modules focused; place CLI-only code in `gopher/gopher.py` and reusable logic elsewhere.
+
+## Testing Guidelines
+- Write fast, deterministic tests; mock network/filesystem when practical.
+- Place new unit tests beside related code in `tests/unit_tests/`; heavier end-to-end flows go in `tests/system_tests/`.
+- Name tests descriptively (`test_handles_missing_annotations`), and prefer given/when/then structure in assertions.
+- Aim to cover new branches and edge cases before opening a PR; run `pytest -q` to keep output compact.
+
+## Commit & Pull Request Guidelines
+- Commit messages in this repo are short, imperative phrases (e.g., `Update pre-commit hooks`, `Migrate to uv and ruff`). Match that style.
+- Keep commits focused; include only related changes plus updated tests.
+- PRs should state the problem, the solution, and validation (tests, screenshots for visual changes). Link related issues and note breaking changes explicitly.
+- Ensure lint, tests, and (if touched) docs build succeed before requesting review.
+
+## Security & Configuration Notes
+- Avoid committing secrets or private keys; pre-commit includes a detector, but double-check before pushing.
+- Network calls (e.g., ontology downloads) should remain in well-scoped helper functions in `gopher/` so they can be mocked in tests.

CHANGELOG.md

@@ -1,6 +1,14 @@
-# Changelog for gopher-enrich
+# Changelog for gopher
+
+## [v0.3.0] - 2025-12-09
+### Changed
+- Modernized codebase for uv.
+
+### Fixed
+- Linting errors.
+- Publish action.
 
 ## [v0.2.0] - 2025-05-08
 - Update github actions
 - Update mkdocs.yml
-- Add `read_diann` function 
+- Add `read_diann` function

CODE_OF_CONDUCT.md

@@ -120,4 +120,3 @@ version 2.0, available at
 
 [homepage]: https://www.contributor-covenant.org
 [v2.0]: https://www.contributor-covenant.org/version/2/0/code_of_conduct.html
-

CONTRIBUTING.md

@@ -19,7 +19,7 @@ There are three exceptions to this:
 
 2. The Vignettes are created from Jupyter notebooks.
 
-3. The Code of Conduct, Release Notes, and this Contributing document are 
+3. The Code of Conduct, Release Notes, and this Contributing document are
    markdown files that live in the root of the gopher-enrich repository.
 
 ### Editing most documents
@@ -39,7 +39,7 @@ way.
 
 ## Contributing to the code
 
-We welcome contributions to the source code of gopher-enrich---particularly 
+We welcome contributions to the source code of gopher-enrich---particularly
 ones that address discussed [issues](https://github.com/TalusBio/gopher/issues).
 
 Contributions to gopher-enrich follow a standard GitHub contribution workflow:

README.md

@@ -19,5 +19,5 @@ pip install gopher-enrich
 ```python
 import gopher                                   # import the package
 
-gopher.test_enrichment(proteins=protein_quant)  # run the enrichment 
-```
+gopher.test_enrichment(proteins=protein_quant)  # run the enrichment
+```

docs/api.md

@@ -12,4 +12,4 @@
 ::: gopher.normalize_values
 ::: gopher.get_rankings
 ::: gopher.in_term
-::: gopher.roc
+::: gopher.roc

docs/examples.md

@@ -26,7 +26,7 @@ Gopher returns a dataframe with the following columns:
 - GO Aspect: String with the gene ontology aspect. Either C (cellular component), F (molecular function), and B (biological process).
 - Columns containing p-values from the GO enrichment.
 
-Example output: 
+Example output:
 
 GO ID | GO Name | GO Aspect | Sample 1 | Sample 2 | Sample 3
 ---------- | ----------- | ---------- | ---------- | ---------- | ----------
@@ -107,4 +107,4 @@ normalized_proteins = gopher.normalize_values(quant_proteins, "human_fasta.fasta
 
 # Peform the GO enrichment analysis:
 results = gopher.test_enrichment(proteins=normalized_proteins)
-```
+```

docs/index.md

@@ -12,4 +12,4 @@ Gopher be pip installed using:
 
 ```python
 pip install gopher-enrich
-```
+```