Develop

.github/workflows/test.yml

@@ -6,56 +6,33 @@ jobs:
     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:$PATH
-        source activate foo
-        python -m pip install . --no-deps --ignore-installed -vvv
+    - uses: "dpryan79/github-actions/@master"
     - name: PEP8
       run: |
-        export PATH=$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
+    - name: make an artifact
+      run: |
+        source activate foo
+        rm -f dist/*
+        python setup.py sdist
+    - uses: actions/upload-artifact@master
+      with:
+        name: "Dist files"
+        path: "dist"
   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:$PATH
-        source activate foo
-        python -m pip install . --no-deps --ignore-installed -vvv
+    - uses: "dpryan79/github-actions/@master"
     - name: Test deepTools
       run: |
-        export PATH=$HOME/miniconda/bin:$PATH
+
         source activate foo
         nosetests --with-doctest -sv deeptools
   planemo:
@@ -67,24 +44,8 @@ jobs:
         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:$PATH
-        source activate foo
-        python -m pip install . --no-deps --ignore-installed -vvv
+    - uses: "dpryan79/github-actions/@master"
     - name: planemo
       run: |
-        export PATH=$HOME/miniconda/bin:$PATH
         source activate foo
         ./.planemo.sh ${{ matrix.chunk }}

.planemo.sh

@@ -27,5 +27,6 @@ else
     galaxy/wrapper/plotProfiler.xml"
 fi
 
+planemo lint ${wrappers}
 planemo test --no_dependency_resolution --galaxy_branch release_18.05 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
 test ${PIPESTATUS[0]} -eq 0

CHANGES.txt

@@ -1,3 +1,13 @@
+3.3.2
+
+ * Fixed --yAxisLabel in plotProfile (issue #889)
+ * Fixed a small X-axis tick offset issue. This caused the location of tick marks in profile plots to be shifted to the left by 0.5 to 1 bin. This was generally not notable, only really appearing when very few bins (e.g., 4) were used. The issue was mostly that the end tick would appear after the end of the plot, since its coordinate was the end of the bin. (issue #888)
+ * multiBamSummary and multiBigwigSummary no longer exclude small bins at the end of genomic chunks. multiBamSummary now has a `--genomicChunkSize` option in case users need to control the size of the genome used for multiprocessing for consistency. (issue #887)
+ * Added 4 new colormaps, which were copied from the seaborn project (issue #879). These are: rocket, mako, vlag, and icefire.
+ * Fixed an issue in the Galaxy wrapper of plotCorrelation where the X and Y.
+ * Fixed an issue with the `--Offset` option, where a single negative value wouldn't include only a single position, but rather that base through the end of the read. (stems from issue #902)
+ * Clustered output from plotHeatmap and plotProfile now allow computing the silhouette score of each row. This is printed in the returned BED file as the last column.
+
 3.3.1
 
  * Fixed `--plotNumbers` not working in `plotCorrelation`. This was issue #838.