Merge branch 'develop'

.bumpversion.cfg

@@ -0,0 +1,10 @@
+[bumpversion]
+current_version = 0.2.0
+commit = False
+tag = False
+
+[bumpversion:file:setup.py]
+
+[bumpversion:file:conda/meta.yaml]
+search = version: {current_version}
+replace = version: {new_version}

.coveragerc

@@ -1,5 +1,2 @@
 [run]
 source = imfusion
-
-[report]
-omit = src/imfusion/_version.py

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.gitignore

@@ -1,11 +1,65 @@
-im_fusion.egg-info
-__pycache__
-*.pyc
-.DS_Store
-.cache
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+# build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-htmlcov
-.idea
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# User-defined
+.DS_Store
 .vscode
-docs/_build
-RELEASE-VERSION
+_pybiomart_cache.sqlite
+.ipynb_checkpoints

.travis.yml

@@ -23,9 +23,9 @@ install:
   # 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=0.8.4 toolz scipy seaborn pyfaidx intervaltree pathlib2
-    r rpy2 tophat bowtie subread mock pytest pytest-datafiles
-    pytest-mock pytest-helpers-namespace"
+    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'"
 
   # Activate environment and install im-fusion.
   - source activate test

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Julian de Ruiter <julianderuiter@gmail.com>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

@@ -0,0 +1,106 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/jrderuiter/imfusion/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+IM-Fusion could always use more documentation, whether as part of the
+official IM-Fusion docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/jrderuiter/imfusion/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `imfusion` for local development.
+
+1. Fork the `imfusion` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/imfusion.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv imfusion
+    $ cd imfusion/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 imfusion tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+   https://travis-ci.org/jrderuiter/imfusion/pull_requests
+   and make sure that the tests pass for all supported Python versions.

HISTORY.rst

@@ -0,0 +1,17 @@
+=======
+History
+=======
+
+0.2.0 (2017-03-09)
+------------------
+
+* Added support for the STAR aligner.
+* 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)
+------------------
+
+* First release on GitHub.

MANIFEST.in

@@ -1,3 +1,13 @@
-include readme.md
-include versioneer.py
-include src/imfusion/_version.py
+
+include AUTHORS.rst
+
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

Makefile

@@ -0,0 +1,94 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+try:
+	from urllib import pathname2url
+except:
+	from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+BROWSER := python -c "$$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
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -f .coverage
+	rm -fr htmlcov/
+
+lint: ## check style with flake8
+	flake8 src tests
+
+test: ## run tests quickly with the default Python
+	py.test
+
+coverage: ## check code coverage quickly with the default Python
+	py.test --cov=geneviz --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
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: clean ## package and upload a release
+	python setup.py sdist upload
+	python setup.py bdist_wheel upload
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	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
+
+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