Merge pull request #201 from compomics/v4.0.0

v4.0.0
compomics · Jul 17, 2024 · 9202563 · 9202563
2 parents f9c3f71 + 92df74d
commit 9202563
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diff --git a/.gitattributes b/.gitattributes
@@ -1 +1 @@
-ms2pip/models/**/*.c filter=lfs diff=lfs merge=lfs -text
+ms2pip/_models_c/**/*.c filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/build_and_publish.yml b/.github/workflows/build_and_publish.yml
@@ -9,61 +9,54 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
-          lfs: 'true'
+          lfs: "true"
+
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: "3.11"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools oldest-supported-numpy cython flake8
-      - name: Check for syntax errors
-        run: |
-          flake8 ./ms2pip ./fasta2speclib --count --select=E9,F63,F7,F82 --show-source --statistics
+          pip install build
+
       - name: Build sdist
-        run: python setup.py sdist
-      - uses: actions/upload-artifact@v2
+        run: python -m build --sdist --outdir dist
+
+      - uses: actions/upload-artifact@v4
         with:
-          name: dist
-          path: dist/*.tar.gz
+          name: dist-source
+          path: dist
 
   build-wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14] # macos-13 for intel, macos-14 for apple silicon
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
-          lfs: 'true'
-      - uses: actions/setup-python@v2
-        name: Install Python
+          lfs: "true"
+
+      - uses: actions/setup-python@v5
+        name: Set up Python
         with:
-          python-version: '3.10'
-      - name: Check for syntax errors
-        run: |
-          python -m pip install flake8
-          flake8 ./ms2pip ./fasta2speclib --count --select=E9,F63,F7,F82 --show-source --statistics
+          python-version: "3.11"
+
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.3.1
+        run: python -m pip install cibuildwheel>=2
+
       - name: Build wheels
         run: python -m cibuildwheel --output-dir dist
-        env:
-          # No XGBoost wheels for 32bit Windows
-          CIBW_BUILD: "cp3*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64"
-          CIBW_SKIP: "cp36-* cp39-macosx_x86_64"  # EOL & build issue #216
-          CIBW_BEFORE_ALL_MACOS: "brew install libomp"
-          CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
-          CIBW_TEST_REQUIRES: "pytest"
-          CIBW_TEST_COMMAND: "pytest {project}/tests"
-      - uses: actions/upload-artifact@v2
+
+      - uses: actions/upload-artifact@v4
         with:
-          name: dist
-          path: dist/ms2pip-*.whl
+          name: dist-${{ matrix.os }}
+          path: dist
 
   publish-to-pypi:
     needs: [build-sdist, build-wheels]
@@ -74,10 +67,6 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/download-artifact@v2
-        with:
-          name: dist
-          path: dist
+      - uses: actions/download-artifact@v4
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -5,42 +5,42 @@ on:
     branches:
       - releases
   pull_request:
+  workflow_dispatch:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
-      with:
-        lfs: 'true'
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install wheel flake8 pytest oldest-supported-numpy cython
-    - 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: Build and install ms2pip
-      run: |
-        python setup.py bdist_wheel
-        pip install dist/ms2pip*.whl
-    - name: Test with pytest
-      run: |
-        pytest
-    - uses: actions/upload-artifact@v2
-      with:
-        name: wheels
-        path: dist/ms2pip*.whl
+      - uses: actions/checkout@v4
+        with:
+          lfs: "true"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      - name: Check with Ruff
+        run: ruff check --output-format=github ./ms2pip
+
+      - name: Build and install ms2pip
+        run: |
+          pip install .[dev]
+
+      - name: Test with pytest
+        run: |
+          pytest
+
+      - name: Test installation
+        run: |
+          ms2pip --help
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,34 @@
+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.8"
+  jobs:
+    post_checkout:
+      # Download and uncompress the binary
+      # https://git-lfs.github.com/
+      - wget https://github.com/git-lfs/git-lfs/releases/download/v3.1.4/git-lfs-linux-amd64-v3.1.4.tar.gz
+      - tar xvfz git-lfs-linux-amd64-v3.1.4.tar.gz
+      # Modify LFS config paths to point where git-lfs binary was downloaded
+      - git config filter.lfs.process "`pwd`/git-lfs filter-process"
+      - git config filter.lfs.smudge  "`pwd`/git-lfs smudge -- %f"
+      - git config filter.lfs.clean "`pwd`/git-lfs clean -- %f"
+      # Make LFS available in current repository
+      - ./git-lfs install
+      # Download content from remote
+      - ./git-lfs fetch
+      # Make local files to have the real content on them
+      - ./git-lfs checkout
+    post_install:
+      - rm -r ms2pip
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+sphinx:
+  builder: dirhtml
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,40 +1,53 @@
 cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 authors:
-- family-names: "Gabriels"
-  given-names: "Ralf"
-  orcid: "https://orcid.org/0000-0002-1679-1711"
-- family-names: "Velghe"
-  given-names: "Kevin"
-  orcid: "https://orcid.org/0000-0002-9968-6043"
-- family-names: "Martens"
-  given-names: "Lennart"
-  orcid: "https://orcid.org/0000-0003-4277-658X"
-- family-names: "Degroeve"
-  given-names: "Sven"
-  orcid: "https://orcid.org/0000-0001-8349-3370"
-title: "MS²PIP"
-url: "https://github.com/compomics/ms2pip_c"
-license: "Apache-2.0"
-preferred-citation:
-  type: article
-  authors:
   - family-names: "Gabriels"
     given-names: "Ralf"
     orcid: "https://orcid.org/0000-0002-1679-1711"
+  - family-names: "Velghe"
+    given-names: "Kevin"
+    orcid: "https://orcid.org/0000-0002-9968-6043"
   - family-names: "Martens"
     given-names: "Lennart"
     orcid: "https://orcid.org/0000-0003-4277-658X"
   - family-names: "Degroeve"
     given-names: "Sven"
     orcid: "https://orcid.org/0000-0001-8349-3370"
-  doi: "10.1093/nar/gkz299"
+title: "MS²PIP"
+url: "https://github.com/compomics/ms2pip"
+license: "Apache-2.0"
+preferred-citation:
+  type: article
+  doi: "10.1093/nar/gkad335"
   journal: "Nucleic Acids Research"
-  month: 9
-  start: W295
-  end: W299
-  title: "Updated MS²PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques"
-  issue: 1
-  volume: 47
-  year: 2019
+  title: "Updated MS²PIP web server supports cutting-edge proteomics applications"
+  year: 2023
   abstract: "MS²PIP is a data-driven tool that accurately predicts peak intensities for a given peptide's fragmentation mass spectrum. Since the release of the MS²PIP web server in 2015, we have brought significant updates to both the tool and the web server. In addition to the original models for CID and HCD fragmentation, we have added specialized models for the TripleTOF 5600+ mass spectrometer, for TMT-labeled peptides, for iTRAQ-labeled peptides, and for iTRAQ-labeled phosphopeptides. Because the fragmentation pattern is heavily altered in each of these cases, these additional models greatly improve the prediction accuracy for their corresponding data types. We have also substantially reduced the computational resources required to run MS²PIP, and have completely rebuilt the web server, which now allows predictions of up to 100 000 peptide sequences in a single request. The MS²PIP web server is freely available at https://iomics.ugent.be/ms2pip/."
+  authors:
+    - family-names: "Declercq"
+      given-names: "Arthur"
+      orcid: "https://orcid.org/0000-0002-9376-1399"
+    - family-names: "Bouwmeester"
+      given-names: "Robbin"
+      orcid: "https://orcid.org/0000-0001-6807-7029"
+    - family-names: "Cristina"
+      given-names: "Chiva"
+      orcid: "https://orcid.org/0000-0001-8150-6203"
+    - family-names: "Sabidó"
+      given-names: "Eduard"
+      orcid: "https://orcid.org/0000-0001-6506-7714"
+    - family-names: "Hirschler"
+      given-names: "Aurélie"
+      orcid: "https://orcid.org/0000-0001-5066-6263"
+    - family-names: "Carapito"
+      given-names: "Christine"
+      orcid: "https://orcid.org/0000-0002-0079-319X"
+    - family-names: "Martens"
+      given-names: "Lennart"
+      orcid: "https://orcid.org/0000-0003-4277-658X"
+    - family-names: "Degroeve"
+      given-names: "Sven"
+      orcid: "https://orcid.org/0000-0001-8349-3370"
+    - family-names: "Gabriels"
+      given-names: "Ralf"
+      orcid: "https://orcid.org/0000-0002-1679-1711"
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,3 @@
-include ms2pip/cython_modules/*.c
-include ms2pip/models/*/*.c
-include ms2pip/models/*.h
+include ms2pip/_cython_modules/*.c
+include ms2pip/_models_c/*/*.c
+include ms2pip/_models_c/*.h