Merge pull request #78 from compomics/project

Project and CI changes

.github/workflows/test.yml

@@ -5,39 +5,42 @@ on:
     branches:
       - main
   pull_request:
+  workflow_dispatch:
 
 jobs:
-  test-with-codecov:
+  linting-and-coverage:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.8"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flit flake8
+          pip install ruff
 
-      - 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: Check with Ruff
+        run: ruff check --output-format=github .
 
-      - name: Install with Flit
-        run: flit install --deps all
+      - name: Install package and its dependencies
+        run: pip install --editable .[dev]
 
       - name: Test with pytest and codecov
         run: |
-          pytest --cov=psm_utils tests
+          pytest --cov=psm_utils  --cov-report=xml tests/
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
 
   test-platforms:
     runs-on: ubuntu-latest
@@ -48,24 +51,17 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install package and its dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flit flake8
-
-      - 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 .[dev]
 
-      - name: Install with Flit
-        run: flit install --deps all
+      - name: Test imports
+        run: python -c "import psm_utils"
 
       - name: Test with pytest
         run: |

.vscode/settings.json

@@ -2,9 +2,11 @@
   "esbonio.sphinx.confDir": "${workspaceFolder}/docs/source",
   "[python]": {
     "editor.formatOnSave": true,
+    "editor.formatOnType": true,
     "editor.codeActionsOnSave": {
       "source.organizeImports": "explicit"
     },
+    "editor.defaultFormatter": "charliermarsh.ruff",
     "editor.rulers": [99]
   },
   "python.testing.pytestArgs": ["tests"],

docs/source/conf.py

@@ -52,7 +52,7 @@
 
 
 def setup(app):
-    config = {
+    config = {  # noqa: F841
         # "auto_toc_tree_section": "Contents",
         "enable_eval_rst": True,
     }

online/Home.py

@@ -1,6 +1,5 @@
 """psm_utils Streamlit-based web server."""
 
-import streamlit as st
 from _base import StreamlitPage
 
 

online/pages/2_PSM_file_conversion.py

@@ -75,7 +75,7 @@ def _convert(self):
 
                 # Open converted file in memory for download button
                 with open("output_filename", "rb") as file:
-                    is_downloaded = st.download_button(
+                    _ = st.download_button(
                         "Download",
                         data=file,
                         file_name=output_filename,

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-dev = ["black", "isort>5", "pytest", "pytest-cov"]
+dev = ["ruff", "isort>5", "pytest", "pytest-cov"]
 docs = [
     "sphinx",
     "numpydoc>=1,<2",
@@ -56,11 +56,15 @@ CompOmics = "https://www.compomics.com"
 psm_utils = "psm_utils.__main__:main"
 
 [build-system]
-requires = ["flit_core >=3.2,<4"]
-build-backend = "flit_core.buildapi"
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
 
-[tool.flit.module]
-name = "psm_utils"
+[tool.setuptools.packages.find]
+include = ["psm_utils*"]
+
+
+[tool.setuptools.dynamic]
+version = { attr = "psm_utils.__version__" }
 
 [tool.isort]
 profile = "black"

tests/test_io/test__base_classes.py

@@ -1,14 +1,8 @@
 """Tests for psm_utils.io._base_classes."""
 
-import pytest
-
-from psm_utils.io._base_classes import ReaderBase
-from psm_utils.io.exceptions import (
-    InvalidModificationDefinitionError,
-    InvalidModificationError,
-    UnresolvableModificationError,
-)
+from psm_utils.io._base_classes import ReaderBase  # noqa: F401
 
 
 class TestBaseReader:
+    # TODO
     pass

tests/test_io/test_maxquant.py

@@ -1,7 +1,6 @@
 import pytest
 
 import psm_utils.io.maxquant as maxquant
-from psm_utils import peptidoform, psm, psm_list
 
 TEST_COL = [
     "Raw file",

tests/test_io/test_mzid.py

@@ -1,7 +1,6 @@
 import xml.etree.ElementTree as ET
 
 import psm_utils.io.mzid as mzid
-from psm_utils import peptidoform, psm, psm_list
 
 PEAKS_TEST_FILE = "./tests/test_data/test_peaks.mzid"
 MSGF_TEST_FILE = "./tests/test_data/test_msgf.mzid"

tests/test_io/test_tsv.py

@@ -1,6 +1,6 @@
 """Tests for psm_utils.io.tsv."""
 
-from psm_utils.io.tsv import TSVReader, TSVWriter
+from psm_utils.io.tsv import TSVReader, TSVWriter  # noqa: F401
 
 test_cases = [
     (

tests/test_psm_list.py

@@ -12,7 +12,7 @@
 
 class TestPSMList:
     def test___init__(self):
-        psm_list = PSMList(psm_list=sample_psm_list)
+        _ = PSMList(psm_list=sample_psm_list)
 
     def test___iter__(self):
         for psm in PSMList(psm_list=sample_psm_list):