Commit d17b1d0d authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 3.3.1

parent 98135869

.azure-pipelines/test-template.yml

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steps:

- bash: conda create -n foo -q --yes -c conda-forge -c bioconda numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython

- bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals

  displayName: Installing dependencies

- bash: |

    source activate foo

    python setup.py install

    python -m pip install . --no-deps --ignore-installed -vvv

  displayName: Installing deeptools

- bash: |

    source activate foo

.github/workflows/pypi.yml

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name: pypi

on: [push]

jobs:

  pypi:

    name: upload to pypi

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v1

    - name: Setup conda

      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')

      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

      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        conda create -n foo -q --yes -c conda-forge -c bioconda python=3.7 twine

    - name: sdist

      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        rm -f dist/*

        python setup.py sdist

    - name: upload

      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')

      env:

        TWINE_USERNAME: "__token__"

        TWINE_PASSWORD: ${{ secrets.pypi_password }}

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        twine upload dist/*

.github/workflows/test.yml

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name: Test

on: [push]

jobs:

  build-linux:

    name: Test on Linux

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v1

    - name: Setup conda

      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 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals

    - name: install deeptools

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        python -m pip install . --no-deps --ignore-installed -vvv

    - name: PEP8

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        flake8 . --exclude=.venv,.build,build --ignore=E501,F403,E402,F999,F405,E722,W504,W605

    - name: Test deepTools

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        nosetests --with-doctest -sv deeptools

  build-osx:

    name: Test on OSX

    runs-on: macOS-latest

    steps:

    - uses: actions/checkout@v1

    - name: Setup conda

      run: |

        curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-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 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals

    - name: install deeptools

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        python -m pip install . --no-deps --ignore-installed -vvv

    - name: Test deepTools

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        nosetests --with-doctest -sv deeptools

  planemo:

    name: First planemo chunk

    runs-on: ubuntu-latest

    needs: build-linux

    strategy:

      matrix:

        chunk: [1, 2, 3]

    steps:

    - uses: actions/checkout@v1

    - name: Setup conda

      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 numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals planemo samtools

    - name: install deeptools

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        python -m pip install . --no-deps --ignore-installed -vvv

    - name: planemo

      run: |

        export PATH=$HOME/miniconda/bin:$PATH

        source activate foo

        ./.planemo.sh ${{ matrix.chunk }}

CHANGES.txt

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3.3.1



 * Fixed `--plotNumbers` not working in `plotCorrelation`. This was issue #838.

 * Fixed compatibility with matplotlib 3 and restrict to at least that version.

 * The Y-axis labels should once again appear in both plotHeatmap and plotProfile (issue #844). This was related to the previous point.

 * Testing is no longer performed with python 2.7, which will reach end of life in a couple months.

 * Various documentation updates (issues #868, #867 and #851).

 * Increased support for BED files with track header lines (issue #866).



3.3.0



 * `plotCoverage` now has a `--BED` option, to restrict plots and output to apply to a specific set of regions given by a BED or GTF file or files (issue #829).

azure-pipelines.yml

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@@ -8,8 +8,6 @@ jobs: 
    vmImage: 'ubuntu-16.04'

  strategy:

    matrix:

      Python27:

        python.version: '2.7'

      Python37:

        python.version: '3.7'

    maxParallel: 4
@@ -24,8 +22,6 @@ jobs: 
    vmImage: 'macOS-10.13'

  strategy:

    matrix:

      Python27:

        python.version: '2.7'

      Python37:

        python.version: '3.7'

    maxParallel: 1
@@ -54,7 +50,7 @@ jobs: 
  steps:

  - bash: echo "##vso[task.prependpath]$CONDA/bin"

    displayName: Add conda to PATH

  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda numpy scipy matplotlib==2.1.2 nose flake8 plotly==2.0.12 pysam pyBigWig py2bit deeptoolsintervals cython planemo setuptools

  - bash: conda create -n foo -q --yes -c conda-forge -c bioconda python=$(python.version) numpy scipy matplotlib==3.1.1 nose flake8 plotly pysam pyBigWig py2bit deeptoolsintervals planemo samtools

    displayName: Installing dependencies

  - bash: |

      source activate foo