From f0baf64d7f3aaeb9761e0ce3e47d63f2ea50fa4a Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 10 Sep 2019 09:32:33 +0200 Subject: [PATCH] Release 3.3.1 (#873) * Develop (#827) * Merged into the wrong branch without noticing :( (#814) * use better conda link (#799) * Estimated filtering fix (#813) * oops * fix testing and set a max number of filtered reads * apparently a bunch of things were getting skipped * fix wrappers * update computeMatrix wrapper * Decrease memory needs (#817) * Use an iterator to not blow memory up * Update a bit more * The GC bias stuff is all deprecated, I'm not fixing that old code * Cache resulting counts rather than just decreasing the bin size (#818) * Cache resulting counts rather than just decreasing the bin size * sanity check * Implement #815 * [skip ci] update change log * Implement #816 (#825) * Implement #816 * expose option * Add a test using pseudocounts and skipZeroOverZero * syntax * Fix tests * Make --skipZeroOverZero a galaxy macro and add to bigwigCompare * [ci skip] a bit of formatting * Fix #822 (#826) * fixes linting issues (#837) * Delete #test.bg# (#859) File is removed upon clean. * release 3.3.1 * try github actions * each action is a file * OK, that's inflexible * OK, the action.yml thing is a mess * syntax * ok, try this * uses * spacing * ok * do anchors work? * boo, so duplicative! * oops * maybe this will work for pypi * ensure dist is empty * nev * rename * bump version number --- .github/workflows/pypi.yml | 37 ++++++++++++ .github/workflows/test.yml | 90 +++++++++++++++++++++++++++++ deeptools/_version.py | 2 +- galaxy/wrapper/deepTools_macros.xml | 4 +- 4 files changed, 130 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/pypi.yml create mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml new file mode 100644 index 000000000..979cc40c7 --- /dev/null +++ b/.github/workflows/pypi.yml @@ -0,0 +1,37 @@ +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/* diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 000000000..64828249b --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,90 @@ +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 }} diff --git a/deeptools/_version.py b/deeptools/_version.py index f201aca3b..35196baaa 100644 --- a/deeptools/_version.py +++ b/deeptools/_version.py @@ -2,4 +2,4 @@ # This file is originally generated from Git information by running 'setup.py # version'. Distribution tarballs contain a pre-generated copy of this file. -__version__ = '3.3.0' +__version__ = '3.3.1' diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml index 51834b53d..40ef25080 100644 --- a/galaxy/wrapper/deepTools_macros.xml +++ b/galaxy/wrapper/deepTools_macros.xml @@ -1,10 +1,10 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 3.3.0.0 + 3.3.1.0 - deeptools + deeptools samtools