Merge pull request #98 from kundajelab/circleci-project-setup

Adding Circleci continuous integration

.circleci/config.yml

@@ -0,0 +1,73 @@
+version: 2.1
+
+jobs:
+  build-and-test:
+    docker: # run the steps with Docker
+      - image: circleci/python:3.8
+    steps:
+      - checkout
+      #Install miniconda and create the testing environment
+      - run: wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+      - run: bash miniconda.sh -b -p $HOME/miniconda
+      #writing to $BASH_ENV is apparently the way to preserve an environment variable between "run" steps
+      - run: echo 'export PATH="$HOME/miniconda/bin:$PATH"' >> $BASH_ENV
+      - run: echo $PATH
+      - run: ls $HOME/miniconda/bin
+      - run: hash -r
+      - run: conda config --set always_yes yes --set changeps1 no
+      - run: conda update -q conda
+      - run: conda info -a
+      - run: conda create -q -n test-environment python=3.8 pytest nose
+      #MEME installation
+      - run: sudo apt-get install -y ghostscript-x
+      - run: mkdir -p ~/.config/matplotlib/
+      - run: "echo backend : Agg >  ~/.config/matplotlib/matplotlibrc"
+      - run: cat ~/.config/matplotlib/matplotlibrc
+      - run: which gs
+      - run: echo 'export PERL5LIB="$HOME/perl5/lib/perl5:$PERL5LIB"' >> $BASH_ENV
+      - run: curl -L http://cpanmin.us | perl - File::Which
+      - run: curl -L http://cpanmin.us | perl - HTML::PullParser
+      - run: curl -L http://cpanmin.us | perl - HTML::Template
+      - run: curl -L http://cpanmin.us | perl - HTML::TreeBuilder
+      - run: curl -L http://cpanmin.us | perl - JSON
+      - run: curl -L http://cpanmin.us | perl - XML::Simple
+      - run: curl -L http://cpanmin.us | perl - XML::Parser::Expat
+      - run: wget http://meme-suite.org/meme-software/5.1.1/meme-5.1.1.tar.gz
+      - run: tar zxf meme-5.1.1.tar.gz
+      - run:
+          command: | #this seems necessary for multi-line commands
+            cd meme-5.1.1
+            perl scripts/dependencies.pl
+      - run:
+          command: | #this seems necessary for multi-line commands
+            cd meme-5.1.1
+            ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/  --enable-serial --enable-build-libxml2 --enable-build-libxslt
+      - run:
+          command: | #this seems necessary for multi-line commands
+            cd meme-5.1.1
+            make
+      #skip the MEME tests since some of them are buggy and stall the build
+      # (see: https://groups.google.com/forum/#!topic/meme-suite/D3XR7Ws1gec)
+      - run:
+          command: | #this seems necessary for multi-line commands
+            cd meme-5.1.1
+            make install
+      - run: echo 'export PATH="$HOME/meme/bin:$PATH"' >> $BASH_ENV
+      - run: echo $PATH
+      #Install modisco (and associated dependencies) - note that tensorflow is not automatically installed, so we install separately
+      - run:
+          command: | #this seems necessary for multi-line commands
+            source activate test-environment
+            pip install -e .[tensorflow]
+      - run: pwd
+      - run: ls
+      #Actually run the tests
+      - run:
+          command: |
+            source activate test-environment
+            pytest 
+
+workflows:
+  main:
+    jobs:
+      - build-and-test

README.md

@@ -1,6 +1,6 @@
 ## TF-MoDISco
 
-[![Build Status](https://api.travis-ci.org/kundajelab/tfmodisco.svg?branch=master)](https://travis-ci.org/kundajelab/tfmodisco) [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/kundajelab/tfmodisco/blob/master/LICENSE) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4728132.svg)](https://doi.org/10.5281/zenodo.4728132)
+[![CircleCI](https://circleci.com/gh/kundajelab/tfmodisco.svg?style=shield)](https://app.circleci.com/pipelines/github/kundajelab/tfmodisco) [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/kundajelab/tfmodisco/blob/master/LICENSE) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4728132.svg)](https://doi.org/10.5281/zenodo.4728132)
 
 **NOTE: we are still refining the multi-task version of TF-MoDISco. If you encounter difficulties running TF-MoDISco with multiple tasks, our recommendation is to run it on one task at a time.**
 

setup.py

@@ -6,7 +6,7 @@
           description='TF MOtif Discovery from Importance SCOres',
           long_description="""Algorithm for discovering consolidated patterns from base-pair-level importance scores""",
           url='https://github.com/kundajelab/tfmodisco',
-          version='0.5.16.0',
+          version='0.5.16.1',
           packages=find_packages(),
           package_data={
                 '': ['cluster/phenograph/louvain/*convert*', 'cluster/phenograph/louvain/*community*', 'cluster/phenograph/louvain/*hierarchy*']