cm.py removal

deeptools · Jan 31, 2025 · a9ea6bc · a9ea6bc
2 parents 61d1f30 + 121de42
commit a9ea6bc
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diff --git a/.github/workflows/maturin_builds.yml b/.github/workflows/maturin_builds.yml
@@ -0,0 +1,172 @@
+name: maturin builds
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  # linux:
+  #   runs-on: ${{ matrix.platform.runner }}
+  #   strategy:
+  #     matrix:
+  #       platform:
+  #         - runner: ubuntu-latest
+  #           target: x86_64
+  #           manylinux: 2_28
+  #         - runner: ubuntu-latest
+  #           target: x86
+  #           manylinux: 2_28
+  #         #- runner: ubuntu-latest
+  #         #  target: aarch64
+  #         #- runner: ubuntu-latest
+  #         #  target: armv7
+  #         #- runner: ubuntu-latest
+  #         #  target: s390x
+  #         #- runner: ubuntu-latest
+  #         #  target: ppc64le
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: 3.x
+  #     - name: Build wheels
+  #       uses: PyO3/maturin-action@v1
+  #       with:
+  #         target: ${{ matrix.platform.target }}
+  #         manylinux: ${{ matrix.platform.manylinux }}
+  #         args: --release --out dist --find-interpreter
+  #         sccache: 'true'
+  #     - name: Upload wheels
+  #       uses: actions/upload-artifact@v4
+  #       with:
+  #         name: wheels-linux-${{ matrix.platform.target }}
+  #         path: dist
+
+  # musllinux:
+  #   runs-on: ${{ matrix.platform.runner }}
+  #   strategy:
+  #     matrix:
+  #       platform:
+  #         - runner: ubuntu-latest
+  #           target: x86_64
+  #         - runner: ubuntu-latest
+  #           target: x86
+  #         - runner: ubuntu-latest
+  #           target: aarch64
+  #         - runner: ubuntu-latest
+  #           target: armv7
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: 3.x
+  #     - name: Build wheels
+  #       uses: PyO3/maturin-action@v1
+  #       with:
+  #         target: ${{ matrix.platform.target }}
+  #         args: --release --out dist --find-interpreter
+  #         sccache: 'true'
+  #         manylinux: musllinux_1_2
+  #     - name: Upload wheels
+  #       uses: actions/upload-artifact@v4
+  #       with:
+  #         name: wheels-musllinux-${{ matrix.platform.target }}
+  #         path: dist
+
+  # windows:
+  #   runs-on: ${{ matrix.platform.runner }}
+  #   strategy:
+  #     matrix:
+  #       platform:
+  #         - runner: windows-latest
+  #           target: x64
+  #         - runner: windows-latest
+  #           target: x86
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: 3.x
+  #         architecture: ${{ matrix.platform.target }}
+  #     - name: Build wheels
+  #       uses: PyO3/maturin-action@v1
+  #       with:
+  #         target: ${{ matrix.platform.target }}
+  #         args: --release --out dist --find-interpreter
+  #         sccache: 'true'
+  #     - name: Upload wheels
+  #       uses: actions/upload-artifact@v4
+  #       with:
+  #         name: wheels-windows-${{ matrix.platform.target }}
+  #         path: dist
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-latest
+            target: x86_64
+          - runner: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.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
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  # release:
+  #   name: Release
+  #   runs-on: ubuntu-latest
+  #   if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
+  #   needs: [linux, musllinux, windows, macos, sdist]
+  #   permissions:
+  #     # Use to sign the release artifacts
+  #     id-token: write
+  #     # Used to upload release artifacts
+  #     contents: write
+  #     # Used to generate artifact attestation
+  #     attestations: write
+  #   steps:
+  #     - uses: actions/download-artifact@v4
+  #     - name: Generate artifact attestation
+  #       uses: actions/attest-build-provenance@v1
+  #       with:
+  #         subject-path: 'wheels-*/*'
+  #     - name: Publish to PyPI
+  #       if: "startsWith(github.ref, 'refs/tags/')"
+  #       uses: PyO3/maturin-action@v1
+  #       env:
+  #         MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+  #       with:
+  #         command: upload
+  #         args: --non-interactive --skip-existing wheels-*/*
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -4,6 +4,9 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
+    rust: "1.82"
+  apt_packages:
+    - clang
 
 sphinx:
   configuration: docs/conf.py

diff --git a/Cargo.toml b/Cargo.toml
@@ -9,14 +9,13 @@ name = "hp"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = { version = "0.22.5", features = ["extension-module"] }
-rust-htslib = "0.47.0"
+pyo3 = { version = "0.23.4", features = ["extension-module"] }
+rust-htslib = "0.49.0"
 rayon = "1.10.0"
-itertools = "0.12.1"
+itertools = "0.14.0"
 bigtools = "0.5.3"
 tokio = "*"
 flate2 = "*"
 tempfile = "*"
 ndarray = "0.16.1"
-npyz = "*"
-zip = "*"
+ndarray-npy = "*"
diff --git a/deeptools4.0.0_changes.md b/deeptools4.0.0_changes.md
@@ -33,6 +33,9 @@
 
  - unmapped reads to unfiltered_out
 
+## multiBamSummary
+ - npz output has labels encoded as u8s, no longer strings.
+
 # Todo
 
 - AlignmentSieve: Shift, Bed, Optimization.

diff --git a/docs/index.rst b/docs/index.rst
@@ -21,6 +21,17 @@ currently available.
 If the file names in the figure mean nothing to you,
 please make sure to check our :doc:`content/help_glossary`.
 
+deepTools 4.0.0
+---------------
+As of deepTools 4.0.0, quite big changes have been made to the computation backend (which is now written in `rust <https://www.rust-lang.org/>`_).
+The main idea behind this change is to make some tools faster and more robust. 
+Useability of the tools are not affected. But note that the output (read precision) might be slightly different than before.
+
+ - :doc:`content/tools/bamCoverage`
+ - :doc:`content/tools/bamCompare`
+ - :doc:`content/tools/computeMatrix`
+ - :doc:`content/tools/multiBamSummary`
+
 
 Contents:
 ---------

diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
@@ -184,7 +184,6 @@
             <param name="bamFile1" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="showAdvancedOpt" value="no"/>
-            <param name="outFileFormat" value="bigwig"/>
             <param name="outFileFormat" value="bedgraph"/>
             <param name="binSize" value="5"/>
             <param name="type" value="ratio"/>
@@ -195,11 +194,91 @@
             <param name="bamFile2" value="bowtie2 test1.bam" ftype="bam"/>
             <param name="showAdvancedOpt" value="yes"/>
             <param name="outFileFormat" value="bigwig"/>
-            <param name="outFileFormat" value="bigwig"/>
             <param name="binSize" value="10"/>
             <param name="type" value="ratio"/>
             <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
         </test>
+        <!-- Test with BAM and CRAM file as input-->
+        <test expect_num_outputs="1">
+            <param name="bamFile1" value="testA.bam" ftype="bam"/>
+            <param name="bamFile2" value="testA.cram" ftype="cram"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="binSize" value="10"/>
+            <param name="type" value="ratio"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="3R\t0\t200\t1"/>
+                    <has_text_matching expression="chr_cigar\t0\t200\t1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test with BAM and CRAM files and substract option-->
+        <test expect_num_outputs="1">
+            <param name="bamFile1" value="testA.bam" ftype="bam"/>
+            <param name="bamFile2" value="testA.cram" ftype="cram"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="binSize" value="10"/>
+            <param name="type" value="substract"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="3R\t0\t200\t0"/>
+                    <has_text_matching expression="chr_cigar\t0\t200\t0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test with BAM files with pseudocounts-->
+        <test expect_num_outputs="1">
+            <param name="bamFile1" value="testA.bam" ftype="bam"/>
+            <param name="bamFile2" value="testB.bam" ftype="bam"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="binSize" value="10"/>
+            <param name="type" value="ratio"/>
+            <param name="pseudocount" value="1 1"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="3R\t0\t50\t1"/>
+                    <has_text_matching expression="3R\t50\t100\t0.571429"/>
+                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
+                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test with BAM files with skipZeroOverZero -->
+        <test expect_num_outputs="1">
+            <param name="bamFile1" value="testA.bam" ftype="bam"/>
+            <param name="bamFile2" value="testB.bam" ftype="bam"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="binSize" value="10"/>
+            <param name="type" value="ratio"/>
+            <param name="skipZeroOverZero" value="--skipZeroOverZero"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="3R\t50\t100\t0.571429"/>
+                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
+                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test with BAM files with skipNAs -->
+        <test expect_num_outputs="1">
+            <param name="bamFile1" value="testA.bam" ftype="bam"/>
+            <param name="bamFile2" value="testB.bam" ftype="bam"/>
+            <param name="showAdvancedOpt" value="yes"/>
+            <param name="outFileFormat" value="bedgraph"/>
+            <param name="binSize" value="10"/>
+            <param name="type" value="ratio"/>
+            <param name="skipNAs" value="true"/>
+            <output name="outFileName" ftype="bedgraph">
+                <assert_contents>
+                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
+                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -244,4 +323,4 @@ Like BAM files, bigWig files are compressed, binary files. If you would like to
 ]]>
     </help>
     <expand macro="citations"/>
-</tool>
+</tool>