Initial commit

.gitignore

@@ -0,0 +1,15 @@
+__pycache__
+build
+dist
+.settings
+*.egg-info
+*.pyc
+*.swp
+*ont_fast5_api.egg-info
+fast5_api.rst
+fast5_api.*.rst
+.#*
+#*
+*#
+*~
+.nfs*

MANIFEST.in

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+# This file tells sdist which addional files to include in the distribution it builds.
+# That distribution is used as the base for building the .deb with stdeb, and certain files
+# (such as header files and .md files) are not included by default.
+# See https://docs.python.org/2/distutils/sourcedist.html#manifest-template
+
+include README.md
+include LICENSE.md
+prune test
+prune build
+prune docs

Makefile

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+ifndef PYTHON
+PYTHON=$(shell which python3)
+endif
+LATEST_TAG := $(shell git tag --list release_* | sort -V | tail -n 1 | sed "s/release[-_]\([\.0-9]*\)/\1/g")
+VERSION_CODE=${shell lsb_release -cs}
+
+all:
+	@echo "make clean - remove build dirs and pyc files"
+	@echo "make doc - build Sphinx docs. Requires the ability to find dependency libraries (e.g. dragonet / chimaera)"
+	@echo "make test - run tests"
+	@echo "make get_latest_tag - look up the latest release and check out that version"
+	@echo "make builddeb - generate a deb package"
+	@echo "make develop - set up repo for local use"
+	@echo "make develop_uninstall - remove easy_install hook for the repo"
+
+clean:
+	$(PYTHON) setup.py clean
+	rm -rf deb_dist ont_fast5_api.egg-info dist ont_fast5_api-*.tar.gz
+	find . -name '*.pyc' -delete
+
+doc:
+	cd docs && $(MAKE) api && $(MAKE) html VERSION=$(LATEST_TAG)
+
+test:
+	$(PYTHON) -m unittest discover
+
+get_latest_tag:
+	git checkout release_$(LATEST_TAG)
+
+builddeb: clean
+	$(PYTHON) setup.py --command-packages=stdeb.command sdist_dsc --debian-version 1~$(VERSION_CODE) bdist_deb
+
+develop:
+	$(PYTHON) setup.py develop --user || $(PYTHON) setup.py develop
+
+develop_uninstall:
+	$(PYTHON) setup.py develop --user --uninstall || $(PYTHON) setup.py develop --uninstall
+
+.PHONY : all clean doc test get_latest_tag builddeb develop develop_uninstall

README.md

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+ont_fast5_api Python Project
+====================================
+Oxford Nanopore Technologies fast5 API software.
+-------------------------------------
+
+This project provides classes and utility functions for working with read fast5
+files. It provides an abstraction layer between the underlying h5py library and
+the various concepts central to read fast5 files, such as "reads", "analyses",
+"analysis summaries", and "analysis datasets". Ideally all interaction with a
+read fast5 file should be possible via this API, without having to directly
+invoke the h5py library.

docs/Makefile

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+VERSION       ?= unknown 
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) -D version=$(VERSION) -D release=$(VERSION) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  api        to autogenerate API documentation"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	$(eval NON_INDEX_FILES := $(filter-out source/index.rst, $(wildcard source/*.rst)))
+	-rm -rf $(BUILDDIR)
+	mkdir $(BUILDDIR)
+ifneq ($(NON_INDEX_FILES),)
+	rm $(NON_INDEX_FILES)
+endif
+
+api:
+	$(eval NON_INDEX_FILES := $(filter-out source/index.rst, $(wildcard source/*.rst)))
+ifneq ($(NON_INDEX_FILES),)
+	rm $(NON_INDEX_FILES)
+endif
+	sphinx-apidoc --no-toc -o source/ ..
+	rm source/test.rst
+	rm source/setup.rst
+	@echo
+	@echo "API gubbins generated in source directory for version $(VERSION)."
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/fast5_api.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/fast5_api.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/ont_fast5_api"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/ont_fast5_api"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."