v0.11.0 RC1

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+### Purpose
+
+(FILL ME IN) This section describes why this PR is here. Usually it would include a reference to issues.
+
+### Declarations
+
+Check these if you believe they are true
+
+- [ ] The codebase is in a better state after this PR
+- [ ] Has linting/formatting been run? (`make lint`, `make format`, `make check`)
+- [ ] Was it tested locally? (`make test`)
+- [ ] Has the changelog been updated?
+- [ ] Have the docs been updated?
+- [ ] The level of testing this PR includes is appropriate.
+- [ ] No features have been dropped (or note which ones and why).
+
+### Reviewers
+
+(FILL ME IN) Reviewer 1 (If possible, assign the Reviewer for the PR)
+(FILL ME IN, Optional) Any additional notes to reviewers or testers.
+
+### FYIs
+
+(FILL ME IN, Optional) Names of anyone else you wish to be notified of
+
+#### Notes
+
+(FILL ME IN, Optional) Additional context to this PR.

.github/workflows/docker.yml

@@ -14,46 +14,44 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel build
-
-    - name: Build and publish
-      run: |
-        python -m build --wheel .
-
-    - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
-
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v2
-
-    - name: Login to the GitHub Container Registry
-      uses: docker/login-action@v1
-      with:
-        registry: ${{ env.REGISTRY }}
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Extract metadata for Docker
-      id: meta
-      uses: docker/metadata-action@v3
-      with:
-        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-
-    - name: Push the Docker image to the GHCR
-      uses: docker/build-push-action@v3
-      with:
-        context: .
-        push: true
-        platforms: linux/amd64,linux/arm64
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Test-build the Docker image
+        run: make build-docker
+
+      - name: Login to the GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Push the Docker image to the GHCR
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/lint.yml

@@ -2,25 +2,23 @@ name: Lint
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
 
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
+      - name: Set up Python
+        run: uv python install
 
       - name: Lint/Check format with Ruff
-        run: |
-          ruff check . --output-format=github
+        run: make lint-ci
+
+      - name: Check formatting with Ruff
+        run: make format-ci

.github/workflows/publish.yml

@@ -9,19 +9,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-    - 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 }}
-      run: |
-        python -m build --sdist --wheel .
-        twine upload dist/*
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          make build-sdist
+          make build-wheel
+          twine upload dist/*

.github/workflows/tests.yml

@@ -19,28 +19,33 @@ jobs:
       matrix:
         python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, windows-latest, macos-latest]
-        experimental: [false,]
+        experimental: [false]
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v3
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: uv sync --all-extras --dev
-
-    - name: Run unit and system tests
-      run: |
-        uv run pytest -v --cov=mokapot tests/
-
-    - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        fail_ci_if_error: true
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run unit and system tests
+        run: make test
+
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+
+      - name: Set up Docker Buildx
+        if: runner.os == 'Linux'
+        uses: docker/setup-buildx-action@v3
+      - name: Check Build
+        if: runner.os == 'Linux'
+        run: make build

.gitignore

@@ -113,3 +113,6 @@ venv.bak/
 tests/integration_tests/run*
 /temp/
 /.run/
+
+targets.peptides.csv
+targets.psms.csv

.gitlab-ci.yml

@@ -1,14 +1,14 @@
 image: python:3.10.5
 
 variables:
-  PIP_CACHE_DIR: "${CI_PROJECT_DIR}/.cache/pip"
+  PIP_CACHE_DIR: ${CI_PROJECT_DIR}/.cache/pip
 
 stages:
   - publish
   - test
 
 cache:
-  key: "${CI_COMMIT_REF_SLUG}"
+  key: ${CI_COMMIT_REF_SLUG}
   paths:
     - .cache/pip
     - .venv
@@ -35,7 +35,7 @@ publish:
   extends: .with_twine
   stage: publish
   rules:
-    - if: '$CI_COMMIT_TAG != null'
+    - if: $CI_COMMIT_TAG != null
   script:
     - python -m build --sdist --wheel .
     - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.com/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*

.pre-commit-config.yaml

@@ -1,14 +1,23 @@
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  hooks:
-  - id: check-toml
-  - id: check-yaml
-  - id: end-of-file-fixer
-  - id: trailing-whitespace
-  - id: detect-private-key
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.10
-  hooks:
-    - id: ruff
-    - id: ruff-format
+  - 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
+        exclude: ^data/
+      - id: trailing-whitespace
+        exclude: ^data/
+      - id: detect-private-key
+  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+    rev: v2.14.0
+    hooks:
+      - id: pretty-format-toml
+        args: [--autofix, --indent, '2']
+      - id: pretty-format-yaml
+        args: [--autofix, --indent, '2', --offset, '2', '--preserve-quotes']
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.1
+    hooks:
+      - id: ruff
+      - id: ruff-format

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
-

Dockerfile

@@ -1,12 +1,38 @@
-FROM mambaorg/micromamba:latest
-MAINTAINER William E Fondrie <fondriew@gmail.com>
-COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
-COPY --chown=$MAMBA_USER:$MAMBA_USER dist/*.whl /tmp/
+# This dockerfile is pretty much stolen from the uv example
+# https://raw.githubusercontent.com/astral-sh/uv-docker-example/refs/heads/main/Dockerfile
+# Use a Python image with uv pre-installed
+FROM ghcr.io/astral-sh/uv:python3.12-bookworm-slim
 
+# Install the project into `/app`
 WORKDIR /app
 
-RUN micromamba install -y -n base -f /tmp/environment.yml && \
-    micromamba clean --all --yes
+# Enable bytecode compilation
+ENV UV_COMPILE_BYTECODE=1
 
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-RUN WHEEL=$(ls /tmp/*.whl) && pip install ${WHEEL}
+# Copy from the cache instead of linking since it's a mounted volume
+ENV UV_LINK_MODE=copy
+ENV VIRTUAL_ENV=/opt/venv \
+    PATH="/opt/venv/bin:$PATH"
+
+# Install the project's dependencies using the lockfile and settings
+RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
+    uv sync --frozen --no-install-project --no-dev
+
+# Then, add the rest of the project source code and install it
+# Installing separately from its dependencies allows optimal layer caching
+ADD . /app
+# RUN --mount=type=cache,target=/root/.cache/uv \
+#     uv sync --frozen --no-dev
+
+RUN uv venv
+COPY dist/*.whl /tmp/
+RUN --mount=type=cache,target=/root/.cache/uv \
+    WHEEL=$(ls /tmp/*.whl) && uv pip install ${WHEEL}
+
+# Place executables in the environment at the front of the path
+ENV PATH="/app/.venv/bin:$PATH"
+
+# Reset the entrypoint, don't invoke `uv`
+ENTRYPOINT []