Merge branch 'develop'

.bumpversion.cfg

@@ -1,10 +1,13 @@
 [bumpversion]
-current_version = 0.2.0
-commit = False
-tag = False
+current_version = 0.3.0
 
 [bumpversion:file:setup.py]
 
 [bumpversion:file:conda/meta.yaml]
 search = version: {current_version}
 replace = version: {new_version}
+
+[bumpversion:file:src/imfusion/__init__.py]
+search = __version__ = '{current_version}'
+replace = __version__ = '{new_version}'
+

.gitignore

@@ -63,3 +63,5 @@ target/
 .vscode
 _pybiomart_cache.sqlite
 .ipynb_checkpoints
+
+matplotlibrc

.travis.yml

@@ -3,12 +3,13 @@ language: python
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
   - '2.7'
+  - '3.4'
   - '3.5'
 
 install:
   - sudo apt-get update
 
-  # Install Anaconda.
+  # Install Miniconda.
   - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
     -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
@@ -20,27 +21,23 @@ install:
   # Useful for debugging any issues with conda.
   - conda info -a
 
-  # Create conda environment and install dependencies.
-  - "conda create -q -n test -c jrderuiter -c bioconda -c r
-    python=$TRAVIS_PYTHON_VERSION intervaltree future pandas
-    numexpr pysam>=0.9.1 toolz scipy seaborn pyfaidx intervaltree pathlib2
-    r rpy2 samtools bowtie subread mock pytest pytest-datafiles
-    pytest-mock pytest-helpers-namespace 'htslib<1.4'"
+  # Create conda environment and install matplotlib dependency
+  # (as this can't be installed outside of conda on OSX).
+  - "conda create -q -n test -c bioconda -c r -c defaults -c conda-forge
+    python=$TRAVIS_PYTHON_VERSION matplotlib"
 
-  # Activate environment and install im-fusion.
+  # Activate environment and install IM-Fusion.
   - source activate test
-  - pip install .
-
-  # Install coverage dependencies.
-  - pip install pytest-cov python-coveralls
+  - pip install .[dev]
 
 before_script:
   # Use xvfb during testing for matplotlib.
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
   - sleep 3 # give xvfb some time to start
 
-script: py.test --cov imfusion --cov-report term-missing
+script:
+    py.test --cov imfusion --cov-report term-missing
 
 after_success:
     - coveralls

HISTORY.rst

@@ -2,15 +2,29 @@
 History
 =======
 
+0.3.0 (2017-05-04)
+------------------
+
+* Refactored external tools into the ``imfusion.external`` module.
+* Use docker/tox for testing against multiple Python versions locally.
+* Added additional checks for inputs and improved error messages.
+* Added support for DataFrame insertion inputs to DE testing functions.
+* Added building of exon gtf as part of imfusion-build.
+* Added identification of endogenous fusions using STAR-Fusion as part
+  of imfusion-insertions (using STAR). Also adds script for building
+  (murine) STAR-Fusion references.
+* Made matplotlib/seaborn lazy imports that are only required when actually
+  using the plotting functions. This makes IM-Fusion easier to use on
+  headless servers/HPCs.
+
 0.2.0 (2017-03-09)
 ------------------
 
 * Added support for the STAR aligner.
-* Added detection of novel transcripts using Stringtie.
+* Added detection of novel transcripts using StringTie.
 * Changed reference building to generate a self-contained reference.
 * Refactored differential expression tests + added gene-level test.
 
-
 0.1.0 (2016-03-26)
 ------------------
 

Makefile

@@ -26,7 +26,8 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
-clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+## remove all build, test, coverage and Python artifacts
+clean: clean-build clean-pyc clean-test
 
 clean-build: ## remove build artifacts
 	rm -fr build/
@@ -45,26 +46,36 @@ clean-test: ## remove test and coverage artifacts
 	rm -f .coverage
 	rm -fr htmlcov/
 
-lint: ## check style with flake8
-	flake8 src tests
+lint: ## check style with pylint
+	pylint src/imfusion
 
-test: ## run tests quickly with the default Python
-	py.test
+test: clean-pyc ## run tests quickly with the default Python
+	py.test tests
 
 coverage: ## check code coverage quickly with the default Python
-	py.test --cov=geneviz --cov-report=html
+	py.test tests --cov=imfusion --cov-report=html
 	$(BROWSER) htmlcov/index.html
 
-docs: ## generate Sphinx HTML documentation, including API docs
-	rm -f docs/geneviz.rst
-	rm -f docs/modules.rst
-	sphinx-apidoc -o docs/ geneviz
-	$(MAKE) -C docs clean
-	$(MAKE) -C docs html
-	$(BROWSER) docs/_build/html/index.html
+tox: clean-pyc ## run tests in multiple pythons using tox
+	rm -rf .tox
+	cp tests/matplotlibrc ./
+	docker run -v `pwd`:/app -t -i jrderuiter/tox-base
+	rm -rf matplotlibrc .tox
 
-servedocs: docs ## compile the docs watching for changes
-	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+docs: ## generate and serve Sphinx documentation
+	sphinx-autobuild docs docs/_build
+
+gh-pages:
+	git checkout gh-pages
+	find ./* -not -path '*/\.*' -prune -exec rm -r "{}" \;
+	git checkout develop docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	git reset HEAD
+	(cd docs && make html)
+	mv -fv docs/_build/html/* ./
+	rm -rf docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
+	touch .nojekyll
+	git add -A
+	git commit -m "Generated gh-pages for `git log develop -1 --pretty=short --abbrev-commit`" && git push origin gh-pages ; git checkout develop
 
 release: clean ## package and upload a release
 	python setup.py sdist upload
@@ -75,20 +86,11 @@ dist: clean ## builds source and wheel package
 	python setup.py bdist_wheel
 	ls -l dist
 
-conda-build: clean-pyc ## build a conda release
-	conda build ./conda -c r -c bioconda -c jrderuiter
+conda: clean-pyc ## build a conda release
+	conda build --python 3.5 -c bioconda -c r -c jrderuiter conda
+
+conda-docker: clean-pyc
+	docker run -v `pwd`:/imfusion -t -i condaforge/linux-anvil /bin/sh -c 'cd /imfusion && ./scripts/conda_build_docker.sh'
 
 install: clean ## install the package to the active Python's site-packages
 	python setup.py install
-
-gh-pages:
-	git checkout gh-pages
-	rm -rf ./*
-	git checkout develop docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
-	git reset HEAD
-	(cd docs && make html)
-	mv -fv docs/_build/html/* ./
-	rm -rf docs Makefile src AUTHORS.rst CONTRIBUTING.rst HISTORY.rst README.rst
-	touch .nojekyll
-	git add -A
-	git commit -m "Generated gh-pages for `git log develop -1 --pretty=short --abbrev-commit`" && git push origin gh-pages ; git checkout develop

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: imfusion
-  version: 0.2.0
+  version: 0.3.0
 
 build:
   number: 0
@@ -23,11 +23,12 @@ requirements:
     - seaborn
     - pyfaidx >=0.4.8.1
     - intervaltree
-    - pathlib2 # [py27]
-    - typing # [py27]
-    - r
-    - rpy2 >=2.7.4
+    - pathlib2
+    - typing # [py27 or py34]
     - htslib <1.4
+    - htseq >=0.7.2
+    - matplotlib
+    - seaborn
 
   run:
     # Python dependencies.
@@ -42,17 +43,18 @@ requirements:
     - seaborn
     - pyfaidx >=0.4.8.1
     - intervaltree
-    - pathlib2 # [py27]
-    - typing # [py27]
-    - r
-    - rpy2 >=2.7.4
+    - pathlib2
+    - typing # [py27 or py34]
     - htslib <1.4
+    - htseq >=0.7.2
+    - matplotlib
+    - seaborn
 
     # External dependencies.
     - star
     - subread
     - stringtie
-    - tophat2 # [py27]
+    - tophat >=2.1.0 # [py27]
     - bowtie # [py27]
 
 test:

docker/tox/Dockerfile

@@ -0,0 +1,5 @@
+FROM themattrix/tox-base
+
+MAINTAINER Julian de Ruiter <[email protected]>
+
+RUN set -x && apt-get update && apt-get -y install liblzma-dev