Merge pull request #84 from duncanmmacleod/glue-docs

Updated documentation and its dependencies
gwpy · Jan 18, 2019 · 3f11875 · 3f11875
2 parents 1c3f4ad + d0c030b
commit 3f11875
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diff --git 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
@@ -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 <target>' where <target> 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
@@ -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
@@ -0,0 +1,4 @@
+sphinx
+sphinx_rtd_theme
+numpydoc
+sphinxcontrib-programoutput
diff --git 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
@@ -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
@@ -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,