Switch to pyscaffold 2.5.11

.coveragerc

@@ -1,7 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = */sigma0/*
+source = sigma0
 # omit = bad_file.py
 
 [report]
@@ -20,4 +20,4 @@ exclude_lines =
 
     # Don't complain if non-runnable code isn't run:
     if 0:
-    if __name__ == .__main__.:
+    if __name__ == .__main__.:

README.rst

@@ -50,5 +50,5 @@ If you want to contribute please follow these steps:
 Note
 ====
 
-This project has been set up using PyScaffold 3.0.3. For details and usage
-information on PyScaffold see http://pyscaffold.org/.
+This project has been set up using PyScaffold 2.5.11. For details and usage
+information on PyScaffold see http://pyscaffold.readthedocs.org/.

docs/Makefile

@@ -6,10 +6,6 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
-AUTODOCDIR    = api
-AUTODOCBUILD  = sphinx-apidoc
-PROJECT       = sigma0
-MODULEDIR     = ../src/sigma0
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
@@ -23,7 +19,7 @@ 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 clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext doc-requirements
+.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"
@@ -51,143 +47,131 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
+	rm -rf $(BUILDDIR)/*
 
-$(AUTODOCDIR): $(MODULEDIR)
-	mkdir -p $@
-	$(AUTODOCBUILD) -f -o $@ $^
-
-doc-requirements: $(AUTODOCDIR)
-
-html: doc-requirements
+html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-dirhtml: doc-requirements
+dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
-singlehtml: doc-requirements
+singlehtml:
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
-pickle: doc-requirements
+pickle:
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
-json: doc-requirements
+json:
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
-htmlhelp: doc-requirements
+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: doc-requirements
+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 $(BUILDDIR)/qthelp/$(PROJECT).qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/sigma0.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(PROJECT).qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sigma0.qhc"
 
-devhelp: doc-requirements
+devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $HOME/.local/share/devhelp/$(PROJECT)"
-	@echo "# ln -s $(BUILDDIR)/devhelp $HOME/.local/share/devhelp/$(PROJEC)"
+	@echo "# mkdir -p $HOME/.local/share/devhelp/sigma0"
+	@echo "# ln -s $(BUILDDIR)/devhelp $HOME/.local/share/devhelp/sigma0"
 	@echo "# devhelp"
 
-epub: doc-requirements
+epub:
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
-patch-latex:
-	find _build/latex -iname "*.tex" | xargs -- \
-		sed -i'' 's~includegraphics{~includegraphics\[keepaspectratio,max size={\\textwidth}{\\textheight}\]{~g'
-
-latex: doc-requirements
+latex:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	$(MAKE) patch-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: doc-requirements
+latexpdf:
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
-	$(MAKE) patch-latex
 	@echo "Running LaTeX files through pdflatex..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
-latexpdfja: doc-requirements
+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."
 
-text: doc-requirements
+text:
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
-man: doc-requirements
+man:
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
-texinfo: doc-requirements
+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: doc-requirements
+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: doc-requirements
+gettext:
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
-changes: doc-requirements
+changes:
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
-linkcheck: doc-requirements
+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: doc-requirements
+doctest:
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
-xml: doc-requirements
+xml:
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
-pseudoxml: doc-requirements
+pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/changes.rst

@@ -0,0 +1,2 @@
+.. _changes:
+.. include:: ../CHANGES.rst

docs/conf.py

@@ -8,53 +8,33 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import os
 import sys
-import inspect
-import shutil
-
-__location__ = os.path.join(os.getcwd(), os.path.dirname(
-    inspect.getfile(inspect.currentframe())))
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.join(__location__, '../src'))
+# sys.path.insert(0, os.path.abspath('.'))
 
-# -- Run sphinx-apidoc ------------------------------------------------------
+# -- Hack for ReadTheDocs ------------------------------------------------------
 # This hack is necessary since RTD does not issue `sphinx-apidoc` before running
 # `sphinx-build -b html . _build/html`. See Issue:
 # https://github.com/rtfd/readthedocs.org/issues/1139
 # DON'T FORGET: Check the box "Install your project inside a virtualenv using
 # setup.py install" in the RTD Advanced Settings.
-# Additionally it helps us to avoid running apidoc manually
-
-try:  # for Sphinx >= 1.7
-    from sphinx.ext import apidoc
-except ImportError:
+import os
+on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
+if on_rtd:
+    import inspect
     from sphinx import apidoc
 
-output_dir = os.path.join(__location__, "api")
-module_dir = os.path.join(__location__, "../src/sigma0")
-try:
-    shutil.rmtree(output_dir)
-except FileNotFoundError:
-    pass
-
-try:
-    import sphinx
-    from distutils.version import LooseVersion
+    __location__ = os.path.join(os.getcwd(), os.path.dirname(
+        inspect.getfile(inspect.currentframe())))
 
+    output_dir = os.path.join(__location__, "../docs/api")
+    module_dir = os.path.join(__location__, "../sigma0")
     cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
     cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
-
-    args = cmd_line.split(" ")
-    if LooseVersion(sphinx.__version__) >= LooseVersion('1.7'):
-        args = args[1:]
-
-    apidoc.main(args)
-except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
+    apidoc.main(cmd_line.split(" "))
 
 # -- General configuration -----------------------------------------------------
 
@@ -259,11 +239,11 @@
 # -- External mapping ------------------------------------------------------------
 python_version = '.'.join(map(str, sys.version_info[0:2]))
 intersphinx_mapping = {
-    'sphinx': ('http://www.sphinx-doc.org/en/stable', None),
-    'python': ('https://docs.python.org/' + python_version, None),
-    'matplotlib': ('https://matplotlib.org', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
+    'sphinx': ('http://sphinx.pocoo.org', None),
+    'python': ('http://docs.python.org/' + python_version, None),
+    'matplotlib': ('http://matplotlib.sourceforge.net', None),
+    'numpy': ('http://docs.scipy.org/doc/numpy', None),
     'sklearn': ('http://scikit-learn.org/stable', None),
     'pandas': ('http://pandas.pydata.org/pandas-docs/stable', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
 }

docs/index.rst

@@ -46,7 +46,7 @@ Contents
 
    License <license>
    Authors <authors>
-   Changelog <changelog>
+   Changelog <changes>
    Module Reference <api/modules>