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
deeptools · Sep 10, 2019 · f0baf64 · f0baf64
1 parent 2560d13
commit f0baf64
Show file tree

Hide file tree

Showing 4 changed files with 130 additions and 3 deletions.
diff --git a/.github/workflows/pypi.yml 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
@@ -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
@@ -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
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.3.0.0</token>
+    <token name="@WRAPPER_VERSION@">3.3.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.3.0">deeptools</requirement>
+            <requirement type="package" version="3.3.1">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />