Merge pull request #1243 from deeptools/develop

Develop
deeptools · Aug 29, 2023 · 83f1929 · 83f1929
2 parents be3b947 + 292b492
commit 83f1929
Show file tree

Hide file tree

Showing 75 changed files with 818 additions and 1,009 deletions.
diff --git a/.github/test_and_build.yml b/.github/test_and_build.yml
@@ -0,0 +1,20 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python >= 3.7
+  - numpy
+  - scipy
+  - flake8
+  - pysam
+  - deeptoolsintervals
+  - pytest
+  - samtools
+  - py2bit
+  - pyBigWig
+  - twine
+  - pip
+  - tomli  # remove dependency when lowest supported version is py 3.11
+  - pip:
+    - build
+    - planemo
diff --git a/.github/workflows/planemo.yml b/.github/workflows/planemo.yml
@@ -1,7 +1,17 @@
 name: Planemo
 on: [push, pull_request]
+
 env:
-  GALAXY_BRANCH: release_22.05
+  GALAXY_BRANCH: release_23.1
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+# setup micromamba doesn't work as galaxy setup by planemo requires conda.
+# installing conda over into micromamba built env screws up the PATH
+# setup-miniconda + changing over to libmamba to solve is the easiest workaround
+
 jobs:
   planemo_test:
     name: Planemo test
@@ -10,12 +20,24 @@ jobs:
       matrix:
         chunk: [1, 2, 3]
     steps:
-    - uses: actions/checkout@v1
-    - uses: "dpryan79/github-actions/@master"
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: "latest"
+        auto-activate-base: true
+    - name: setup env
+      run: |
+        conda env list
+        conda install -n base conda-libmamba-solver
+        conda config --set solver libmamba
+        conda env create -f .github/test_and_build.yml -n test_and_build
+    - name: pip install
+      run: |
+        conda activate test_and_build
+        pip install .
     - name: planemo
       run: |
-        source activate foo
-        conda update -c conda-forge -c bioconda samtools
+        conda activate test_and_build
         ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
     - uses: actions/upload-artifact@v3
       with:
@@ -27,7 +49,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.7', '3.11']
     steps:
     - uses: actions/download-artifact@v3
       with:

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
@@ -1,35 +1,33 @@
 name: pypi
+
 on:
   create:
     tags:
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   pypi:
     name: upload to pypi
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - name: Setup conda
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@main
+      with:
+        environment-file: .github/test_and_build.yml
+        cache-downloads: true
+        environment-name: test_and_build
+    - name: build
       run: |
-        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh
-        bash miniconda.sh -b -p $HOME/miniconda
-        export PATH="$HOME/miniconda/bin:$PATH"
-        hash -r
-        conda config --set always_yes yes --set changeps1 no
-    - name: create env
-      run: |
-        export PATH=$HOME/miniconda/bin:$PATH
-        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine
-    - name: sdist
-      run: |
-        export PATH=$HOME/miniconda/bin:$PATH
-        source activate foo
+        micromamba activate test_and_build
         rm -f dist/*
-        python setup.py sdist
+        python -m build
     - name: upload
       env:
         TWINE_USERNAME: "__token__"
         TWINE_PASSWORD: ${{ secrets.pypi_password }}
       run: |
-        export PATH=$HOME/miniconda/bin:$PATH
-        source activate foo
+        micromamba activate test_and_build
         twine upload dist/*
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,16 +1,21 @@
 name: Test
 on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   check_versions_matches:
     name: Check deeptools version matches galaxy tools
     runs-on: ubuntu-latest
     if: github.base_ref == 'master'
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
     - name: Check path
-      run: find /home/runner/work/deepTools/deepTools -name "_version.py"
+      run: find /home/runner/work/deepTools/deepTools -name "pyproject.toml"
     - name: Get Version of Deeptools
-      run: echo "deeptools_version=$(grep "__version__" /home/runner/work/deepTools/deepTools/deeptools/_version.py | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
+      run: echo "deeptools_version=$(grep "version" /home/runner/work/deepTools/deepTools/pyproject.toml | awk '{print substr($NF, 2, length($NF) - 2)}')" >> $GITHUB_ENV
     - name: Get Version of Galaxy tools
       run: echo "galaxy_deeptools_version=$(grep "token.*TOOL_VERSION" /home/runner/work/deepTools/deepTools/galaxy/wrapper/deepTools_macros.xml | awk -F '>|<' '{print $3}')" >> $GITHUB_ENV
     - name: Versions
@@ -35,32 +40,73 @@ jobs:
     name: Test on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: "dpryan79/github-actions/@master"
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@main
+      with:
+        environment-file: .github/test_and_build.yml
+        cache-downloads: true
+        environment-name: test_and_build
+    - name: pip install
+      run: |
+        micromamba activate test_and_build
+        pip install .
     - name: PEP8
       run: |
-        source activate foo
+        micromamba activate test_and_build
         flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605
     - name: Test deepTools
       run: |
-        source activate foo
-        nosetests --with-doctest -sv deeptools
+        micromamba activate test_and_build
+        pytest -v
     - name: make an artifact
       run: |
-        source activate foo
+        micromamba activate test_and_build
         rm -f dist/*
-        python setup.py sdist
+        python -m build
     - uses: actions/upload-artifact@master
       with:
         name: "Dist files"
         path: "dist"
+  test-wheels:
+    name: test wheel
+    runs-on: ubuntu-latest
+    needs: build-linux
+    strategy:
+      matrix:
+        python-version: ['3.7','3.8','3.9','3.10', '3.11']
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/download-artifact@v3
+        with:
+          name: "Dist files"
+          path: ~/dist/
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: install wheel
+        run: |
+          pip install ~/dist/*whl
+          deeptools -h
+      - name: pytest
+        run: |
+          pip install pytest
+          pytest -v
   build-osx:
     name: Test on OSX
     runs-on: macOS-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: "dpryan79/github-actions/@master"
+    - uses: actions/checkout@v3
+    - uses: mamba-org/setup-micromamba@main
+      with:
+        environment-file: .github/test_and_build.yml
+        cache-downloads: true
+        environment-name: test_and_build
+    - name: pip install
+      run: |
+        micromamba activate test_and_build
+        pip install .
     - name: Test deepTools
       run: |
-        source activate foo
-        nosetests --with-doctest -sv deeptools
+        micromamba activate test_and_build
+        pytest -v
diff --git a/.planemo.sh b/.planemo.sh
@@ -28,6 +28,7 @@ else
     galaxy/wrapper/plotProfiler.xml"
 fi
 
+planemo --version
 planemo lint ${wrappers}
 planemo test --no_dependency_resolution --galaxy_branch $2 --install_galaxy ${wrappers} 2>&1
 mkdir upload

diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,3 +1,13 @@
+3.5.3
+* requirement cap for matplotlib lifted (changes in plotting can occur)
+* nose has been deprecated in favor of pytests
+* pytests run with python 3.7 - 3.11
+* toml file for installation, requirements, versioning and executables
+* planemo tests updated to galaxy 23.1
+* custom github action runner deprecated
+* deprecation of np types for builtin types
+* stricter label checks and validator in galaxy
+
 3.5.2
 * new subcommand: Bigwig average #1169
 * dendogram of plotCorrelation now matches each cell correctly

diff --git a/bin/alignmentSieve b/bin/alignmentSieve
diff --git a/bin/bamCompare b/bin/bamCompare
diff --git a/bin/bamCoverage b/bin/bamCoverage
diff --git a/bin/bamPEFragmentSize b/bin/bamPEFragmentSize
diff --git a/bin/bigwigAverage b/bin/bigwigAverage
diff --git a/bin/bigwigCompare b/bin/bigwigCompare
diff --git a/bin/computeGCBias b/bin/computeGCBias
diff --git a/bin/computeMatrix b/bin/computeMatrix
diff --git a/bin/computeMatrixOperations b/bin/computeMatrixOperations
diff --git a/bin/correctGCBias b/bin/correctGCBias