pymzdata 0.65.5__tar.gz

pymzdata-0.65.5/.cliffignore

@@ -0,0 +1,2 @@
+b0a6b97de1472ee14b19822865ed1a4407cd5cea
+2dc3cf69b0a00fafaf4484898c670a598b2fd52a

pymzdata-0.65.5/.env

@@ -0,0 +1 @@
+RUST_LOG=info

pymzdata-0.65.5/.gitattributes

@@ -0,0 +1,10 @@
+* text=auto
+
+*.rs text
+*.md text
+*.sh text eol=lf
+
+*.mzML binary
+*.mzml binary
+*.gz binary
+*.mgf binary

pymzdata-0.65.5/.github/helpers/vcpkg.json

@@ -0,0 +1,11 @@
+{
+  "$schema": "https://raw.githubusercontent.com/microsoft/vcpkg-tool/main/docs/vcpkg.schema.json",
+  "dependencies": [
+    {
+      "name": "hdf5",
+      "version>=": "1.10.1"
+    }
+  ],
+  "overrides": [{ "name": "hdf5", "version": "1.10.1" }],
+  "builtin-baseline": "e57b2167e66c847f991bd6bce1355b85acd944e8"
+}

pymzdata-0.65.5/.github/workflows/release-pymzdata.yml

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+name: Release pymzdata
+
+# Build the crates/pymzdata wheels + sdist and publish them to PyPI, so downstreams users can
+# `pip install pymzdata` without a Rust toolchain. Mirrors the maturin-action layout used by the
+# ms2rescore-rs, with one crate-specific addition: the `-m crates/pymzdata/Cargo.toml` manifest
+# (pymzdata is a sub-crate). mzdata uses the pure-Rust zlib-rs backend, so no C toolchain is needed.
+on:
+  release:
+    types: [created]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+env:
+  MANIFEST: crates/pymzdata/Cargo.toml
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        target: [
+          x86_64,
+          # aarch64 https://github.com/aws/aws-lc-rs/issues/1022
+        ]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter -m ${{ env.MANIFEST }}
+          sccache: "true"
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.target }}
+          path: dist
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        target: [x64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          architecture: ${{ matrix.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter -m ${{ env.MANIFEST }}
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.target }}
+          path: dist
+
+  macos:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        target: [x86_64, aarch64]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          args: --release --out dist --find-interpreter -m ${{ env.MANIFEST }}
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.target }}
+          path: dist
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist -m ${{ env.MANIFEST }}
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    needs: [linux, windows, macos, sdist]
+    # Trusted Publishing (OIDC): configure a PyPI publisher for this repo + workflow. Swap for
+    # `MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}` if you publish with a token instead.
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

pymzdata-0.65.5/.github/workflows/test-static.yaml

@@ -0,0 +1,31 @@
+on: [push, pull_request]
+
+env:
+  RUST_BACKTRACE: full
+  RUST_LOG: debug
+  CARGO_PROFILE_TEST_BUILD_OVERRIDE_DEBUG: true
+
+name: Test (HDF5 Static Compilation)
+jobs:
+
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+    name: Test Suite
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - name: Run cargo test
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --features hdf5_static,zlib -- --nocapture --show-output

pymzdata-0.65.5/.github/workflows/test.yaml

@@ -0,0 +1,122 @@
+on: [push, pull_request]
+
+env:
+  RUST_BACKTRACE: full
+  RUST_LOG: debug
+  CARGO_PROFILE_TEST_BUILD_OVERRIDE_DEBUG: true
+
+name: Test
+jobs:
+
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    name: Test Suite
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - name: Rust Cache
+        uses: Swatinem/rust-cache@v2
+      - name: Run cargo test
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --features nalgebra,parallelism,async,mzsignal,thermo,numpress,bruker_tdf -- --nocapture --show-output
+
+  test-remote:
+    name: PROXI Test Suite
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - name: Rust Cache
+        uses: Swatinem/rust-cache@v2
+      - name: Run cargo test
+        continue-on-error: true
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --features async,proxi,proxi-async -- --nocapture --show-output
+
+  test-pymzdata:
+    name: pymzdata Python Test Suite
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Build pymzdata wheel
+        uses: PyO3/maturin-action@v1
+        with:
+          args: --release --out dist -m crates/pymzdata/Cargo.toml
+          manylinux: off
+          rust-toolchain: stable
+      - name: Install pymzdata and test dependencies
+        run: |
+          python -m pip install dist/*.whl
+          python -m pip install 'pytest>=7' 'numpy>=1.21' 'pyteomics>=4.6' 'lxml>=4.9' 'psims>=1.3'
+      - name: Run Python tests
+        working-directory: crates/pymzdata
+        run: python -m pytest -v -s
+
+  test-spectra-subset:
+    name: mzdata-spectra
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v4
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+      - name: Rust Cache
+        uses: Swatinem/rust-cache@v2
+
+      - name: Run cargo test
+        continue-on-error: true
+        run: |
+          cd crates/mzdata-spectra && cargo build --features mzsignal,nalgebra,serde
+
+  test-async-subset:
+      name: async_partial
+      runs-on: ubuntu-latest
+      steps:
+        - name: Checkout sources
+          uses: actions/checkout@v4
+
+        - name: Install stable toolchain
+          uses: actions-rs/toolchain@v1
+          with:
+            profile: minimal
+            toolchain: stable
+            override: true
+        - name: Rust Cache
+          uses: Swatinem/rust-cache@v2
+        - name: Run cargo test
+          continue-on-error: true
+          uses: actions-rs/cargo@v1
+          with:
+            command: test
+            args: --features async_partial -- --nocapture --show-output

pymzdata-0.65.5/.gitignore

@@ -0,0 +1,8 @@
+/target
+test/data/*.index.json
+.vscode/*
+Untitled*
+test.mzML
+tmp.mzML
+*.sh
+*.py

pymzdata-0.65.5/.vscode/launch.json

@@ -0,0 +1,30 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "(Windows) Launch",
+            "type": "cppvsdbg",
+            "request": "launch",
+            "program": "${workspaceFolder}/target/debug/mzdata.exe",
+            "args": [],
+            "stopAtEntry": false,
+            "cwd": "${workspaceRoot}",
+            "environment": [],
+            "console": "internalConsole"
+        },
+        {
+            "name": "Run Test Debugger",
+            "type": "cppvsdbg",
+            "request": "launch",
+            "program": "${workspaceRoot}/target/debug/deps/mzdata-d4d3354e8c37294a.exe",
+            "args": [],
+            "stopAtEntry": false,
+            "cwd": "${workspaceRoot}",
+            "environment": [],
+            "console": "internalConsole"
+        }
+    ]
+}

pymzdata-0.65.5/.vscode/tasks.json

@@ -0,0 +1,13 @@
+{
+    "version": "2.0.0",
+    "type": "shell",
+    "label": "cargo test build",
+    "command": "cargo",
+    "args": [
+        "test",
+        "--no-run"
+    ],
+    "problemMatcher": [
+        "$rustc"
+    ]
+}