diff --git a/.travis.yml b/.travis.yml index 14447b0..64ee51c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,7 +18,7 @@ matrix: before_install: - python -m pip install ${PIP_FLAGS} --upgrade pip - - python -m pip install ${PIP_FLAGS} "pytest>=2.8" pytest-cov + - python -m pip install ${PIP_FLAGS} --upgrade "pytest>=2.8,<3.7" pytest-cov - python -m pip install ${PIP_FLAGS} -r requirements.txt install: diff --git a/docs/Makefile b/docs/Makefile index c991f29..639dfe4 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -4,227 +4,17 @@ # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build -PAPER = +SPHINXPROJ = pyomicron +SOURCEDIR = . BUILDDIR = _build -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) - $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don\'t have Sphinx installed, grab it from http://sphinx-doc.org/) -endif +.PHONY: help html -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help +# Put it first so that "make" without argument is like "make help". help: - @echo "Please use \`make ' where is one of" - @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 " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " epub3 to make an epub3" - @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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @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 " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - -.PHONY: clean -clean: - rm -rf $(BUILDDIR)/* - -.PHONY: html -html: apidoc - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -.PHONY: dirhtml -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -.PHONY: singlehtml -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -.PHONY: pickle -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -.PHONY: json -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -.PHONY: htmlhelp -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." - -.PHONY: qthelp -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/PyOmicron.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PyOmicron.qhc" - -.PHONY: applehelp -applehelp: - $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp - @echo - @echo "Build finished. The help book is in $(BUILDDIR)/applehelp." - @echo "N.B. You won't be able to view it unless you put it in" \ - "~/Library/Documentation/Help or install it in your application" \ - "bundle." - -.PHONY: devhelp -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/PyOmicron" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PyOmicron" - @echo "# devhelp" - -.PHONY: epub -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -.PHONY: epub3 -epub3: - $(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3 - @echo - @echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3." - -.PHONY: latex -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)." - -.PHONY: latexpdf -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." - -.PHONY: latexpdfja -latexpdfja: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through platex and dvipdfmx..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -.PHONY: text -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -.PHONY: man -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -.PHONY: texinfo -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)." - -.PHONY: info -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." - -.PHONY: gettext -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." - -.PHONY: changes -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -.PHONY: linkcheck -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." - -.PHONY: doctest -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." - -.PHONY: coverage -coverage: - $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage - @echo "Testing of coverage in the sources finished, look at the " \ - "results in $(BUILDDIR)/coverage/python.txt." - -.PHONY: xml -xml: - $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml - @echo - @echo "Build finished. The XML files are in $(BUILDDIR)/xml." - -.PHONY: pseudoxml -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." - -.PHONY: apidoc -apidoc: - sphinx-apidoc -o api/ ../omicron --no-toc --separate --force - @echo - @echo "APIdoc run is complete." + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +html: + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/conf.py b/docs/conf.py index 1e895f7..b1605fc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -36,7 +36,6 @@ 'sphinx.ext.autosummary', 'numpydoc', 'sphinxcontrib.programoutput', - 'sphinxcontrib.epydoc', ] # Add any paths that contain templates here, relative to this directory. @@ -303,9 +302,3 @@ 'matplotlib': ('http://matplotlib.sourceforge.net/', None), 'gwpy': ('http://gwpy.github.io/docs/latest/', None), } - -# -- Extensions ----------------------------------------------------------- - -epydoc_mapping = { - 'http://software.ligo.org/docs/glue/': [r'glue(\.|$)'], -} diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..9f4fbda --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +sphinx +sphinx_rtd_theme +numpydoc +sphinxcontrib-programoutput diff --git a/omicron/parameters.py b/omicron/parameters.py index 1e88aa4..29aa209 100644 --- a/omicron/parameters.py +++ b/omicron/parameters.py @@ -31,7 +31,7 @@ except ImportError: # python 2.x import ConfigParser as configparser -from gwpy.segments import (Segment, SegmentList) +from ligo.segments import (segmentlist as SegmentList, segment as Segment) from collections import OrderedDict @@ -407,7 +407,7 @@ def distribute_segment(self, start, end, nperjob=1): Returns ------- - jobsegs : :class:`~glue.segments.segmentlist` + jobsegs : :class:`~ligo.segments.segmentlist` a `segmentlist` of [start, stop) times over which to distribute a single segment under condor """ diff --git a/omicron/segments.py b/omicron/segments.py index 49fa9de..c131be3 100644 --- a/omicron/segments.py +++ b/omicron/segments.py @@ -158,7 +158,7 @@ def cache_segments(cache): def segmentlist_from_tree(tree, coalesce=False): - """Read a `~glue.segments.segmentlist` from a 'segments' `ROOT.Tree` + """Read a `~ligo.segments.segmentlist` from a 'segments' `ROOT.Tree` """ segs = SegmentList() for i in range(tree.GetEntries()): diff --git a/setup.py b/setup.py index b9420bc..404ea63 100644 --- a/setup.py +++ b/setup.py @@ -68,16 +68,6 @@ 'pytest_runner', ]) -# extras -extras_require = { - 'doc': [ - 'sphinx', - 'numpydoc', - 'sphinxcontrib-programoutput', - 'sphinxcontrib-epydoc', - ], -} - # -- content ---------------- # Use the find_packages tool to locate all packages and modules @@ -123,7 +113,6 @@ setup_requires=setup_requires, install_requires=install_requires, tests_require=tests_require, - extras_require=extras_require, # content packages=packagenames, scripts=scripts,