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4.0.0 (#1452)
 - new Rust-backed core for bamCoverage, bamCompare, computeMatrix, alignmentSieve and multiBamSummary (rayon multithreading, bigtools-based bigWig I/O), replacing the pure-Python implementations for these five tools; the previous Python implementations remain available as bamCoverage_old, bamCompare_old, computeMatrix_old, alignmentSieve_old and multiBamSummary_old during the transition, but will be removed in a future release - gzipped GTF/BED region files are supported in multiBamSummary, computeMatrix and alignmentSieve; gzipped blacklist files are supported in all five Rust-backed tools (multiBamSummary, computeMatrix, alignmentSieve, bamCompare, bamCoverage) - --exactScaling is removed as this is the only scaling option available with the new backend - --ignoreDuplicates has been removed from the bamCoverage and bamCompare tools. Duplicate reads can be removed via the --samFlagExclude option (assuming the provided BAM file has duplicate reads marked) plotPCA re-implemented with a lightweight scipy/numpy SVD backend. Proper handling of --transpose, --log2/--rowCenter and --ntop options. - plotly backend removed entirely; plotCorrelation, plotPCA, plotHeatmap, plotProfile and plotEnrichment now use matplotlib, with a new optional --ggplot theme, and computeGCBias's --plotFileFormat plotly option has also been removed - removed the standalone cm.py colormap module; colormap handling now lives in the plotting tools directly plot labels now show sample names only per default (dropped .filtered.bam/.bed suffixes) - prebuilt wheels now cover Linux manylinux_2_28 and musllinux_1_2 (x86_64 + aarch64) and macOS (Intel + Apple Silicon), built via maturin - CI overhauled: pytest/rust/planemo test workflows split up (test_pytest.yml, test_rust.yml, test_planemo.yml), zizmor hardening for GitHub Actions, dependabot enabled - extensive new pytest/cargo test coverage across the Rust-backed tools and plotCorrelation/plotPCA/plotFingerprint data outputs - --nanAfterEnd doesn't rescale the inner region anymore in reference-point mode - BED output doesn't show wrong blockstart values anymore - blacklist filtering is done at bp level instead of genome chunk level for rewritten tools - alignmentSieve output order matches input order exactly - --missingDataAsZero no longer takes bases exceeding chromosome bounds as 0 values but rather purges the bins large scale values precision slightly altered with new backend (f32 vs f64)
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: github-actions
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directory: /
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schedule:
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interval: weekly
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groups:
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dependencies:
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patterns:
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- "*"

‎.github/workflows/planemo.yml‎

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‎.github/workflows/pypi.yml‎

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‎.github/workflows/test.yml‎

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‎.github/workflows/test_docs.yml‎

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name: tests_docs
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: read
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jobs:
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build-docs:
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name: Build Sphinx documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2
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with:
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environments: default
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- name: build docs
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run: pixi run docs

‎.github/workflows/test_planemo.yml‎

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name: tests_planemo
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: read
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env:
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GALAXY_BRANCH: release_26.0
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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planemo_test:
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name: Planemo test (${{ matrix.tool }})
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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tool:
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- alignmentSieve
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- bamCompare
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- bamCoverage
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- bamPEFragmentSize
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- bigwigCompare
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- bigwigAverage
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- computeGCBias
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- computeMatrix
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- computeMatrixOperations
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- correctGCBias
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- estimateReadFiltering
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- multiBamSummary
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- multiBigwigSummary
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- plotCorrelation
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- plotCoverage
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- plotEnrichment
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- plotFingerprint
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- plotHeatmap
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- plotPCA
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- plotProfiler
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4.0.1
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with:
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miniconda-version: "latest"
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conda-remove-defaults: true
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auto-activate: true
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python-version: "3.12"
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channels: conda-forge,bioconda
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- name: get samtools
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run: |
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conda install -c conda-forge -c bioconda samtools
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- name: pip install
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run: |
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pip install .[actions]
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- name: fix test.bw symlink
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run: |
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unlink galaxy/wrapper/test-data/test.bw
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cp pydeeptools/deeptools/test/test_heatmapper/test.bw galaxy/wrapper/test-data/test.bw
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- name: planemo test
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run: |
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planemo test --no_dependency_resolution \
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--galaxy_branch ${{ env.GALAXY_BRANCH }} \
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--install_galaxy \
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galaxy/wrapper/${{ matrix.tool }}.xml
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- name: upload test report
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if: always()
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uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
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with:
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name: "Tool test output ${{ matrix.tool }}"
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path: tool_test_output*

‎.github/workflows/test_pytest.yml‎

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name: tests_pytest
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: read
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jobs:
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check_versions_matches:
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name: Check deeptools/galaxy/Rust versions stay in sync
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
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with:
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python-version: "3.x"
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- name: Check version sync
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run: python3 scripts/check_version_sync.py
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build-linux:
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name: Test on Linux
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runs-on: ubuntu-latest
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strategy:
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matrix:
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pixi-env: [py312, py313, py314]
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2
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with:
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environments: ${{ matrix.pixi-env }}
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- name: build deeptools
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run: pixi run -e ${{ matrix.pixi-env }} build
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- name: test deeptools
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run: pixi run -e ${{ matrix.pixi-env }} test -v
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- name: build wheel
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run: pixi run -e ${{ matrix.pixi-env }} python -m build
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- name: test wheel
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run: pixi run -e ${{ matrix.pixi-env }} bash -c "pip install dist/*.whl"
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build-osx:
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name: Test on OSX
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runs-on: macOS-latest
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strategy:
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matrix:
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pixi-env: [py312, py313, py314]
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2
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with:
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environments: ${{ matrix.pixi-env }}
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- name: build deeptools
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run: pixi run -e ${{ matrix.pixi-env }} build
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- name: test deeptools
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run: pixi run -e ${{ matrix.pixi-env }} test -v
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- name: build wheel
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run: pixi run -e ${{ matrix.pixi-env }} python -m build
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- name: test wheel
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run: pixi run -e ${{ matrix.pixi-env }} bash -c "pip install dist/*.whl"

‎.github/workflows/test_rust.yml‎

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name: tests_rust
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on:
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push:
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pull_request:
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workflow_dispatch:
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schedule:
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- cron: "0 0 * * 0"
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permissions:
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contents: read
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jobs:
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cargo_test:
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name: run cargo test
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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persist-credentials: false
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- run: rustup update stable && rustup default stable
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- name: cargo build
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run: cargo build --verbose
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- name: cargo test
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run: cargo test --verbose

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