Galaxy python3 (#659)

* Do planemo tests in a python 3 environment

* Try again

* Not sure if this will work

* Copy over fix from Björn's PR

* Handle python3 loading of python2 files

* Update tests, do Galaxy in both python 2.7 and 3.6

* Right, can't do both

* last test

* Bump to 2.5.6

.planemo.sh

@@ -1,12 +1,11 @@
 #!/bin/bash
-#!/bin/bash
 planemo=./foo/bin/planemo
 owd=`pwd`
 temp_dir=`mktemp -d`
 cd $temp_dir
 conda config --add channels conda-forge
 conda config --add channels bioconda
-conda create -y --name gxtest numpy bx-python pysam
+conda create -y --name gxtest numpy pysam
 source activate gxtest
 git clone --depth 1 https://github.com/galaxyproject/galaxy.git
 cd galaxy
@@ -15,8 +14,8 @@ make client
 cd ..
 # reset what's available in conda
 cd $owd
-conda install --yes -c conda-forge python=2.7 numpy scipy matplotlib==2.1.0 nose flake8 plotly==2.0.12
-conda install --yes -c bioconda -c conda-forge pysam pyBigWig py2bit planemo
+conda install --yes -c conda-forge numpy scipy matplotlib==2.1.0 plotly==2.0.12
+conda install --yes -c bioconda -c conda-forge pysam pyBigWig py2bit
 python setup.py install
 
 #galaxy/wrapper/correctGCBias.xml \

.travis.yml

@@ -1,25 +1,25 @@
 language: c
 env:
   - TRAVIS_PYTHON_VERSION=2.7
-  - TRAVIS_PYTHON_VERSION=3.5
+  - TRAVIS_PYTHON_VERSION=3.6
 os:
   - linux
   - osx
 jobs:
   include:
-    - stage: galaxy
+    - stage: galaxy36
       env:
         - TESTGALAXY="1"
-        - TRAVIS_PYTHON_VERSION=2.7
+        - TRAVIS_PYTHON_VERSION=3.6
 
 # Setup anaconda
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]] ; then pip install virtualenv --user ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]] ; then virtualenv foo; source foo/bin/activate; pip install planemo ; deactivate ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then pip install virtualenv --user ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then virtualenv foo; source foo/bin/activate; pip install planemo ; deactivate ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -o miniconda.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.5" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.6" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o miniconda.sh ; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" && "$TRAVIS_PYTHON_VERSION" == "2.7" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -o miniconda.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" && "$TRAVIS_PYTHON_VERSION" == "3.5" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" && "$TRAVIS_PYTHON_VERSION" == "3.6" ]] ; then curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o miniconda.sh ; fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
@@ -41,9 +41,6 @@ script:
   - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ~/ && nosetests --with-doctest -sv deeptools ; fi
   - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then nosetests --with-doctest -sv deeptoolsintervals ; fi
   - if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ${owd} ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" && ${TESTGALAXY:-"0"} == "1" ]] ; then /home/travis/build/deeptools/deepTools/foo/bin/planemo lint galaxy/wrapper/ ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "2.7" && ${TESTGALAXY:-"0"} == "1" ]] ; then ./.planemo.sh ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then /home/travis/build/deeptools/deepTools/foo/bin/planemo lint galaxy/wrapper/ ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then ./.planemo.sh ; fi
 sudo: false
-
-services:
-  - postgresql

CHANGES.txt

@@ -1,3 +1,7 @@
+2.5.6
+
+ * Fixed a bug where deepTools in python3 can't handle npz file labels created under python 2.
+
 2.5.5
 
  * Updated blacklist handling such that an error is thrown on overlapping regions.

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__ = '2.5.5'
+__version__ = '2.5.6'

deeptools/correlation.py

@@ -12,6 +12,8 @@
 import matplotlib.ticker
 import matplotlib.mlab
 import matplotlib.markers
+from deeptools.utilities import toString
+
 
 old_settings = np.seterr(all='ignore')
 
@@ -83,7 +85,7 @@ def load_matrix(self, matrix_file):
 
             self.matrix = np.ma.compress_rows(np.ma.masked_invalid(self.matrix))
 
-        self.labels = _ma['labels']
+        self.labels = list(map(toString, _ma['labels']))
 
         assert len(self.labels) == self.matrix.shape[1], "ERROR, length of labels is not equal " \
                                                          "to length of matrix samples"

galaxy/wrapper/deepTools_macros.xml

@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.5.5</token>
+    <token name="@WRAPPER_VERSION@">2.5.6</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.5.5">deeptools</requirement>
+            <requirement type="package" version="2.5.6">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />

galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt

@@ -6,11 +6,11 @@ Sample size: 3
 Fragment lengths:
 Min.: 241.0
 1st Qu.: 241.5
-Mean: 244.666666667
+Mean: 244.66666666666666
 Median: 242.0
 3rd Qu.: 246.5
 Max.: 251.0
-Std: 4.49691252108
+Std: 4.496912521077347
 
 Read lengths:
 Min.: 251.0

galaxy/wrapper/test-data/plotEnrichment_output.txt

@@ -1,5 +1,5 @@
 file	featureType	percent
-bowtie2 test1.bam	down	100.00
 bowtie2 test1.bam	up	100.00
 bowtie2 test1.bam	down	100.00
 bowtie2 test1.bam	up	100.00
+bowtie2 test1.bam	down	100.00

galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular

@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	0.0	0.269004498068	0	0	0
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	NA	0.26900449806812143	NA	NA	NA
+bowtie2 test1.bam	0.00493632029863651	0.481650684757865	0.984443061605476	1.1531044350267195e-24	0.9849408836341008	0.5232688298112538	0.0	0.26900449806812143	0	0	0

galaxy/wrapper/test-data/plotPCA_result2.tabular

@@ -1,3 +1,3 @@
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
-1	-0.707106781187	-0.707106781187	6.0
-2	-0.707106781187	0.707106781187	1.23259516441e-32
+1	-0.7071067811865476	-0.7071067811865475	6.000000000000001
+2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32

galaxy/wrapper/test-data/profiler_result2.tabular

@@ -1,3 +1,3 @@
 bin labels		-0.0Kb	0.0Kb
-bins		1	2
+bins		1.0	2.0
 bamCoverage_result4_bw_0	genes	2477942.875	2610260.125