Various fixes and improvements for v3.2.0

.github/workflows/publish.yml

@@ -9,29 +9,26 @@ jobs:
   python-package:
     runs-on: ubuntu-latest
     permissions:
-      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv and set the Python version
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: "3.11"
+          enable-cache: true
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade build pytest
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
       - name: Build source and wheel
-        run: |
-          python -m build --sdist --wheel --outdir dist/
+        run: uv build --sdist --wheel --out-dir dist/
 
       - name: Test built package
         run: |
-          pip install --only-binary :all: dist/ms2rescore-*.whl
-          # pytest
-          ms2rescore --help
+          uv run pip install --only-binary :all: dist/ms2rescore-*.whl
+          uv run ms2rescore --help
 
       - name: Upload build artifacts
         uses: actions/upload-artifact@v4
@@ -53,6 +50,7 @@ jobs:
 
       - name: Install package and dependencies
         run: |
+          # Using pip to ensure proper environment discovery by PyInstaller
           python -m pip install --upgrade pip
           pip install --only-binary :all: .[ionmob] pyinstaller
 

.github/workflows/test.yml

@@ -8,38 +8,40 @@ on:
   workflow_dispatch:
 
 jobs:
+  check-python-package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Run Ruff
+        run: uvx ruff check --output-format=github .
+
   test-python-package:
+    needs: check-python-package
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Install uv and set the Python version
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python-version }}
+          enable-cache: true
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-
-      - name: Run Ruff
-        run: ruff check --output-format=github .
+      - name: Install the project
+        run: uv sync --all-extras --dev
 
-      - name: Build and install ms2rescore package
-        run: |
-          pip install --only-binary :all: .[dev]
-
-      - name: Test with pytest
-        run: |
-          pytest
+      - name: Run tests
+        run: uv run pytest
 
       - name: Test installation
-        run: |
-          ms2rescore --help
+        run: uv run ms2rescore --help
 
   test-windows-installer:
     # Only run on push to main (e.g., after PR merge)
@@ -54,6 +56,7 @@ jobs:
 
       - name: Install package and dependencies
         run: |
+          # Using pip to ensure proper environment discovery by PyInstaller
           python -m pip install --upgrade pip
           pip install --only-binary :all: .[ionmob] pyinstaller
 

.pre-commit-config.yaml

@@ -16,19 +16,19 @@ repos:
         args: ["--output-format", "json"]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: trailing-whitespace
       # - id: end-of-file-fixer
 
   # - repo: https://github.com/pycqa/isort
-  #   rev: 5.11.2
+  #   rev: 5.13.2
   #   hooks:
   #     - id: isort
   #       name: isort (python)
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.8.0
     hooks:
       - id: black

Dockerfile

@@ -1,19 +1,43 @@
-FROM python:3.11
-
-# ARG DEBIAN_FRONTEND=noninteractive
+FROM ghcr.io/astral-sh/uv:python3.12-trixie-slim
 
 LABEL name="ms2rescore"
 
-# ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ms2rescore
+# Setup a non-root user
+RUN groupadd --system --gid 999 nonroot \
+    && useradd --system --gid 999 --uid 999 --create-home nonroot
+
+# Install the project into `/ms2rescore`
+WORKDIR /ms2rescore
+
+# Enable bytecode compilation
+ENV UV_COMPILE_BYTECODE=1
+
+# Copy from the cache instead of linking since it's a mounted volume
+ENV UV_LINK_MODE=copy
 
+# Ensure installed tools can be executed out of the box
+ENV UV_TOOL_BIN_DIR=/usr/local/bin
+
+RUN apt-get update && apt-get install -y procps
+
+# Then, add the rest of the project source code and install it
+# Installing separately from its dependencies allows optimal layer caching
 ADD pyproject.toml /ms2rescore/pyproject.toml
 ADD LICENSE /ms2rescore/LICENSE
 ADD README.md /ms2rescore/README.md
 ADD MANIFEST.in /ms2rescore/MANIFEST.in
+ADD uv.lock /ms2rescore/uv.lock
 ADD ms2rescore /ms2rescore/ms2rescore
 
-RUN apt-get update \
-    && apt install -y procps \
-    && pip install /ms2rescore --only-binary :all:
+# Install the project and its dependencies using the lockfile and settings
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --no-dev
+
+# Place executables in the environment at the front of the path
+ENV PATH="/ms2rescore/.venv/bin:$PATH"
+
+# Reset the entrypoint, don't invoke `uv`
+ENTRYPOINT []
 
-ENTRYPOINT [""]
+# Use the non-root user to run our application
+USER nonroot

docs/source/api/ms2rescore.feature_generators.rst

@@ -35,6 +35,14 @@ ms2rescore.feature_generators.deeplc
 
 
 
+ms2rescore.feature_generators.im2deep
+####################################
+
+.. automodule:: ms2rescore.feature_generators.im2deep
+   :members:
+
+
+
 ms2rescore.feature_generators.ionmob
 ####################################
 

docs/source/config_schema.md

@@ -67,9 +67,22 @@
     - **One of**
       - *string*
       - *null*
-  - **`write_flashlfq`** *(boolean)*: Write results to a FlashLFQ-compatible file. Default: `false`.
-  - **`write_report`** *(boolean)*: Write an HTML report with various QC metrics and charts. Default: `false`.
-  - **`profile`** *(boolean)*: Write a txt report using cProfile for profiling. Default: `false`.
+  - **`write_flashlfq`**: Write results to a FlashLFQ-compatible file. Default: `false`.
+    - **One of**
+      - *boolean*
+      - *null*
+  - **`write_report`**: Write an HTML report with various QC metrics and charts. Default: `true`.
+    - **One of**
+      - *boolean*
+      - *null*
+  - **`disable_update_check`**: Disable the automatic update check. Default: `false`.
+    - **One of**
+      - *boolean*
+      - *null*
+  - **`profile`**: Write a txt report using cProfile for profiling. Default: `false`.
+    - **One of**
+      - *boolean*
+      - *null*
 ## Definitions
 
 - <a id="definitions/feature_generator"></a>**`feature_generator`** *(object)*: Feature generator configuration. Can contain additional properties.

ms2rescore/__init__.py

@@ -1,6 +1,9 @@
 """Modular and user-friendly platform for AI-assisted rescoring of peptide identifications ."""
 
-__version__ = "3.2.0.dev2"
+# __version__ is provided by the small helper module _version which prefers
+# installed distribution metadata and falls back to reading pyproject.toml.
+# The single source of truth for the version is pyproject.toml.
+
 __all__ = [
     "parse_configurations",
     "rescore",
@@ -16,5 +19,8 @@
     module="psims.mzmlb",
 )
 
+from ms2rescore._version import get_version  # noqa: E402
 from ms2rescore.config_parser import parse_configurations  # noqa: E402
 from ms2rescore.core import rescore  # noqa: E402
+
+__version__ = get_version()

ms2rescore/__main__.py

@@ -14,6 +14,7 @@
 from rich.text import Text
 
 from ms2rescore import __version__, package_data
+from ms2rescore._version import check_for_update
 from ms2rescore.config_parser import parse_configurations
 from ms2rescore.core import rescore
 from ms2rescore.exceptions import MS2RescoreConfigurationError
@@ -148,18 +149,24 @@ def _argument_parser() -> argparse.ArgumentParser:
     )
     parser.add_argument(
         "--write-report",
-        # metavar="BOOL",
         action="store_true",
+        default=None,
         dest="write_report",
-        help="boolean to enable profiling with cProfile",
+        help="boolean whether to write an HTML report (default: True)",
+    )
+    parser.add_argument(
+        "--disable-update-check",
+        action="store_true",
+        default=None,
+        dest="disable_update_check",
+        help="Disable automatic check for software updates (default: False)",
     )
     parser.add_argument(
         "--profile",
-        # metavar="BOOL",
         action="store_true",
-        # type=bool,
-        # dest="profile",
-        help="boolean to enable profiling with cProfile",
+        default=None,
+        dest="profile",
+        help="Enable profiling with cProfile",
     )
 
     return parser
@@ -228,6 +235,16 @@ def main(tims=False):
         config["ms2rescore"]["log_level"], config["ms2rescore"]["output_path"] + ".log.txt"
     )
 
+    # Check for updates
+    if config["ms2rescore"]["disable_update_check"] is False:
+        update_info = check_for_update()
+        if update_info["update_available"]:
+            LOGGER.info(
+                f"New version of MS²Rescore available: {update_info['latest_version']} "
+                f"(you are using {update_info['current_version']})"
+            )
+            LOGGER.info(f"Download the latest version at: {update_info['html_url']}")
+
     # Run MS²Rescore
     try:
         if cli_args.profile: