Fix continuous integration (#68)

* Update GitHub Actions

* Reformat with Ruff

* Replace black by Ruff

* Remove unused import

* Fix documentation badge

* Update Python version in various configs

.github/workflows/lint.yml

@@ -2,13 +2,9 @@ name: Lint
 
 on:
   push:
-    branches:
-      - main
-      - dev
+    branches: [ main, dev ]
   pull_request:
-    branches:
-      - main
-      - dev
+    branches: [ main, dev ]
 
 jobs:
   lint:
@@ -20,13 +16,15 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: Lint with black
-        uses: psf/black@stable
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Lint with Ruff
+        run: |
+          ruff check . --output-format=github
 
-      - name: Check for debugging print statements
+      - name: Check formatting with Ruff
         run: |
-          if grep -rq "print(" spectrum_utils; then
-              echo "Found the following print statements:"
-              grep -r "print(" spectrum_utils
-              exit 1
-          fi
+          ruff format --check .

.github/workflows/publish.yml

@@ -1,11 +1,8 @@
-# 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:
-    types: [created]
+    types: [ created ]
 
 jobs:
   deploy:

.github/workflows/tests.yml

@@ -1,17 +1,10 @@
-# 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: Run tests
 
 on:
   push:
-    branches:
-      - main
-      - dev
+    branches: [ main, dev ]
   pull_request:
-    branches:
-      - main
-      - dev
+    branches: [ main, dev ]
   schedule:
   - cron: "0 0 1 1/1 *" # Run monthly.
 
@@ -20,8 +13,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [ ubuntu-latest, windows-latest, macos-latest ]
+        python-version: [ "3.10", "3.11", "3.12" ]
 
     steps:
     - uses: actions/checkout@v4
@@ -32,21 +25,15 @@ jobs:
 
     - 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
+        pip install uv
+        uv pip install pytest pytest-cov wheel --system
+        uv pip install -e . --system
     - name: Run unit and system tests
       run: |
-        pytest --cov=spectrum_utils tests/
+        pytest --cov=spectrum_utils --verbose tests/
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
+        verbose: true

.pre-commit-config.yaml

@@ -1,6 +1,12 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.8.0 # 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/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.4.1
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

.readthedocs.yml

@@ -1,7 +1,7 @@
 version: 2
 
 python:
-   version: 3.8
+   version: 3.10
    install:
       - method: pip
         path: .

README.md

@@ -3,7 +3,7 @@
 [![conda](https://img.shields.io/conda/vn/bioconda/spectrum_utils?color=green)](http://bioconda.github.io/recipes/spectrum_utils/README.html)
 [![PyPI](https://img.shields.io/pypi/v/spectrum_utils?color=green)](https://pypi.org/project/spectrum_utils/)
 [![Build status](https://github.com/bittremieux/spectrum_utils/workflows/tests/badge.svg)](https://github.com/bittremieux/spectrum_utils/actions?query=workflow:tests)
-[![docs](https://readthedocs.org/projects/spectrum_utils/badge/?version=latest)](https://spectrum_utils.readthedocs.io/en/latest/?badge=latest)
+[![docs](https://readthedocs.org/projects/spectrum-utils/badge/?version=latest)](https://spectrum-utils.readthedocs.io/en/latest/?badge=latest)
 
 spectrum_utils is a Python package for efficient mass spectrometry data processing and visualization.
 
@@ -18,7 +18,7 @@ spectrum_utils contains the following features:
 
 ## Installation
 
-spectrum_utils requires Python version 3.8+ and can be installed with pip or conda.
+spectrum_utils requires Python version 3.10+ and can be installed with pip or conda.
 
 Using pip:
 

docs/src/conf.py

@@ -16,7 +16,6 @@
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "..")))
 
-import pyteomics.usi
 import spectrum_utils
 
 

docs/src/index.md

@@ -3,7 +3,7 @@
 [![conda](https://img.shields.io/conda/vn/bioconda/spectrum_utils?color=green)](http://bioconda.github.io/recipes/spectrum_utils/README.html)
 [![PyPI](https://img.shields.io/pypi/v/spectrum_utils?color=green)](https://pypi.org/project/spectrum_utils/)
 [![Build status](https://github.com/bittremieux/spectrum_utils/workflows/tests/badge.svg)](https://github.com/bittremieux/spectrum_utils/actions?query=workflow:tests)
-[![docs](https://readthedocs.org/projects/spectrum_utils/badge/?version=latest)](https://spectrum_utils.readthedocs.io/en/latest/?badge=latest)
+[![docs](https://readthedocs.org/projects/spectrum_utils/badge/?version=latest)](https://spectrum-utils.readthedocs.io/en/latest/?badge=latest)
 
 ## About spectrum_utils
 

environment.yml

@@ -13,4 +13,4 @@ dependencies:
   - pandas
   - platformdirs
   - pyteomics>=4.5
-  - python>=3.8
+  - python>=3.10

pyproject.toml

@@ -1,28 +1,10 @@
 [build-system]
-requires = ['setuptools>=45', 'wheel', 'setuptools_scm[toml]>=6.0']
-build-backend = 'setuptools.build_meta'
+requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 
-[tool.black]
+[tool.ruff]
 line-length = 79
-target-version = ['py312']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
-)
-'''
+target-version = "py310"
+include = ["*.py"]

setup.cfg

@@ -22,7 +22,7 @@ classifiers =
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.8
+python_requires = >=3.10
 install_requires =
     fastobo
     lark>=1.0
@@ -34,9 +34,9 @@ install_requires =
 
 [options.extras_require]
 dev =
-    black
     pytest
     pytest-cov
+    ruff
 docs =
     myst-parser
     numpydoc>=1.1.0

spectrum_utils/proforma.py

@@ -689,7 +689,9 @@ def parse(proforma: str) -> List[Proteoform]:
 
 
 @functools.lru_cache
-def _import_cv(cv_id: str, cache: Optional[str]) -> Union[
+def _import_cv(
+    cv_id: str, cache: Optional[str]
+) -> Union[
     Tuple[Dict[str, Tuple[float, str]], Dict[str, Tuple[float, str]]],
     Dict[str, float],
 ]:
@@ -869,8 +871,9 @@ def _parse_obo(
                     ):
                         term_mass = float(
                             term_xref[
-                                term_xref.index('"')
-                                + 1 : term_xref.rindex('"')
+                                term_xref.index('"') + 1 : term_xref.rindex(
+                                    '"'
+                                )
                             ]
                         )
                 elif (

spectrum_utils/spectrum.py

@@ -129,7 +129,7 @@ def remove_precursor_peak(
         fragment_tol_mass: float,
         fragment_tol_mode: str,
         isotope: int = 0,
-    ) -> "MsmsSpectrumJit":
+    ) -> MsmsSpectrumJit:
         # TODO: This assumes [M+H]x charged ions.
         adduct_mass = 1.007825
         neutral_mass = (
@@ -504,19 +504,19 @@ def remove_precursor_peak(
         """
         Remove fragment peak(s) close to the precursor m/z.
 
-        Note: This peak manipulation will reset any ProForma annotations that
-        were applied previously.
+        Note: This peak manipulation will reset any ProForma annotations
+        that were applied previously.
 
         Parameters
         ----------
         fragment_tol_mass : float
-            Fragment mass tolerance around the precursor mass to remove the
-            precursor peak.
+            Fragment mass tolerance around the precursor mass to remove
+            the precursor peak.
         fragment_tol_mode : {'Da', 'ppm'}
             Fragment mass tolerance unit. Either 'Da' or 'ppm'.
         isotope : int
-            The number of precursor isotopic peaks to be checked (the default
-            is 0 to check only the mono-isotopic peaks).
+            The number of precursor isotopic peaks to be checked (the
+            default is 0 to check only the mono-isotopic peaks).
 
         Returns
         -------