Clean up unused vars and fix makefile for windows (#377)

* Clean up unused vars and fix makefile for windows

* Update release notes

Author: rly

docs/format/Makefile

@@ -7,15 +7,13 @@ SPHINXBUILD    = sphinx-build
 SPHINXAPIDOC   = sphinx-apidoc
 PAPER          =
 BUILDDIR       = _build
-SRCDIR         = ../src
 RSTDIR         = source
-PKGNAME        = pynwb
-CONFDIR       = $(PWD)/source
+CONFDIR        = $(PWD)/$(RSTDIR)
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(RSTDIR)
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
@@ -25,7 +23,7 @@ help:
 	@echo "To update documentation sources from the format specification please use \`make apidoc'"
 	@echo ""
 	@echo "To build the documenation please use \`make <target>' where <target> is one of"
-	@echo "  fulldoc    to rebuild the apidoc, html, and latexpdf all at once"
+	@echo "  fulldoc    to rebuild the apidoc, html, and latexpdf documents all at once"
 	@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"
@@ -45,20 +43,20 @@ help:
 	@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)"
-	@echo "  apidoc     to to build RST from source code"
+	@echo "  apidoc     to build RST from source code"
 	@echo "  clean      to clean all documents built by Sphinx in _build"
 	@echo "  allclean   to clean all autogenerated documents both from Sphinx and apidoc"
 
 allclean:
-	-rm -rf $(BUILDDIR)/* $(RSTDIR)/$(PKGNAME)* $(RSTDIR)/modules.rst
+	$(MAKE) clean
 	-rm $(RSTDIR)/_format_auto_docs/*.png
 	-rm $(RSTDIR)/_format_auto_docs/*.pdf
 	-rm $(RSTDIR)/_format_auto_docs/*.rst
 	-rm $(RSTDIR)/_format_auto_docs/*.inc
 	-rm $(RSTDIR)/_format_auto_docs/git_hash.txt
 
 clean:
-	-rm -rf $(BUILDDIR)/* $(RSTDIR)/$(PKGNAME)* $(RSTDIR)/modules.rst
+	-rm -rf $(BUILDDIR)/*
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@@ -182,4 +180,4 @@ fulldoc:
 	@echo "Rebuilding apidoc, html, latexpdf"
 	$(MAKE) apidoc
 	$(MAKE) html
-	$(MAKE) latexpdf
+	$(MAKE) latexpdf

docs/format/make.bat

@@ -6,7 +6,8 @@ if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
 set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set RSTDIR=source
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% %RSTDIR%
 set I18NSPHINXOPTS=%SPHINXOPTS% .
 if NOT "%PAPER%" == "" (
 	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
@@ -18,6 +19,7 @@ if "%1" == "" goto help
 if "%1" == "help" (
 	:help
 	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  fulldoc    to rebuild the apidoc, html, and latex documents all at once
 	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
@@ -35,6 +37,19 @@ if "%1" == "help" (
 	echo.  changes    to make an overview over 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
+	echo.  apidoc     to build RST from source code
+	echo.  clean      to clean all documents built by Sphinx in _build
+	echo.  allclean   to clean all autogenerated documents both from Sphinx and apidoc
+	goto end
+)
+
+if "%1" == "allclean" (
+  make clean
+	del /q %RSTDIR%\_format_auto_docs\*.png
+	del /q %RSTDIR%\_format_auto_docs\*.pdf
+	del /q %RSTDIR%\_format_auto_docs\*.rst
+	del /q %RSTDIR%\_format_auto_docs\*.inc
+	del /q %RSTDIR%\_format_auto_docs\git_hash.txt
 	goto end
 )
 
@@ -187,4 +202,23 @@ results in %BUILDDIR%/doctest/output.txt.
 	goto end
 )
 
+if "%1" == "apidoc" (
+  set PYTHONPATH=%cd%/source;%PYTHONPATH%
+	nwb_generate_format_docs
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Generate rst source files from NWB spec.
+	goto end
+)
+
+if "%1" == "fulldoc" (
+  make allclean
+	echo.
+	echo.Rebuilding apidoc, html, latexpdf
+	make apidoc
+	make html
+	make latex
+	goto end
+)
+
 :end

docs/format/source/format_release_notes.rst

@@ -33,6 +33,8 @@ Release Notes
 
 - Add "doc" key to ImagingRetinotopy.axis_2_power_map for schema language compliance
 
+- Fix makefiles for generating documentation on Windows.
+
 - Add optional "reference" column in "electrodes" table
 
 - Change dims of ImageSeries from (frame, y, x) to (frame, x, y) and (frame, z, y, x) to (frame, x, y, z) to be consistent with the dimension ordering in PlaneSegmentation.

docs/general/Makefile

@@ -7,14 +7,12 @@ SPHINXBUILD    = sphinx-build
 SPHINXAPIDOC   = sphinx-apidoc
 PAPER          =
 BUILDDIR       = _build
-SRCDIR         = ../src
 RSTDIR         = source
-PKGNAME        = nwbstorage
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(RSTDIR)
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
@@ -44,6 +42,7 @@ help:
 	@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)"
+	@echo "  clean      to clean all documents built by Sphinx in _build"
 
 clean:
 	-rm -rf $(BUILDDIR)/*

docs/general/make.bat

@@ -6,7 +6,8 @@ if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
 set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set RSTDIR=source
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% %RSTDIR%
 set I18NSPHINXOPTS=%SPHINXOPTS% .
 if NOT "%PAPER%" == "" (
 	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
@@ -18,6 +19,7 @@ if "%1" == "" goto help
 if "%1" == "help" (
 	:help
 	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  fulldoc    to rebuild the html and latex documents all at once
 	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
@@ -35,6 +37,7 @@ if "%1" == "help" (
 	echo.  changes    to make an overview over 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
+	echo.  clean      to clean all documents built by Sphinx in _build
 	goto end
 )
 
@@ -187,4 +190,13 @@ results in %BUILDDIR%/doctest/output.txt.
 	goto end
 )
 
+if "%1" == "fulldoc" (
+  make clean
+	echo.
+	echo.Rebuilding html, latex
+	make html
+	make latex
+	goto end
+)
+
 :end

docs/language/Makefile

@@ -7,14 +7,12 @@ SPHINXBUILD    = sphinx-build
 SPHINXAPIDOC   = sphinx-apidoc
 PAPER          =
 BUILDDIR       = _build
-SRCDIR         = ../src
 RSTDIR         = source
-PKGNAME        = pynwb
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(RSTDIR)
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
@@ -44,9 +42,10 @@ help:
 	@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)"
+	@echo "  clean      to clean all documents built by Sphinx in _build"
 
 clean:
-	-rm -rf $(BUILDDIR)/* $(RSTDIR)/$(PKGNAME)* $(RSTDIR)/modules.rst
+	-rm -rf $(BUILDDIR)/*
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

docs/language/make.bat

@@ -6,7 +6,8 @@ if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
 set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set RSTDIR=source
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% %RSTDIR%
 set I18NSPHINXOPTS=%SPHINXOPTS% .
 if NOT "%PAPER%" == "" (
 	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
@@ -18,6 +19,7 @@ if "%1" == "" goto help
 if "%1" == "help" (
 	:help
 	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  fulldoc    to rebuild the html and latex documents all at once
 	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
@@ -35,6 +37,7 @@ if "%1" == "help" (
 	echo.  changes    to make an overview over 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
+	echo.  clean      to clean all documents built by Sphinx in _build
 	goto end
 )
 
@@ -187,4 +190,13 @@ results in %BUILDDIR%/doctest/output.txt.
 	goto end
 )
 
+if "%1" == "fulldoc" (
+  make clean
+	echo.
+	echo.Rebuilding html, latex
+	make html
+	make latex
+	goto end
+)
+
 :end

docs/storage/Makefile

@@ -7,14 +7,12 @@ SPHINXBUILD    = sphinx-build
 SPHINXAPIDOC   = sphinx-apidoc
 PAPER          =
 BUILDDIR       = _build
-SRCDIR         = ../src
 RSTDIR         = source
-PKGNAME        = nwbstorage
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
 PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(RSTDIR)
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
@@ -44,6 +42,7 @@ help:
 	@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)"
+	@echo "  clean      to clean all documents built by Sphinx in _build"
 
 clean:
 	-rm -rf $(BUILDDIR)/*

docs/storage/make.bat

@@ -6,7 +6,8 @@ if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
 set BUILDDIR=_build
-set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set RSTDIR=source
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% %RSTDIR%
 set I18NSPHINXOPTS=%SPHINXOPTS% .
 if NOT "%PAPER%" == "" (
 	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
@@ -18,6 +19,7 @@ if "%1" == "" goto help
 if "%1" == "help" (
 	:help
 	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  fulldoc    to rebuild the html and latex documents all at once
 	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
@@ -35,6 +37,7 @@ if "%1" == "help" (
 	echo.  changes    to make an overview over 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
+	echo.  clean      to clean all documents built by Sphinx in _build
 	goto end
 )
 
@@ -187,4 +190,13 @@ results in %BUILDDIR%/doctest/output.txt.
 	goto end
 )
 
+if "%1" == "fulldoc" (
+  make clean
+	echo.
+	echo.Rebuilding html, latex
+	make html
+	make latex
+	goto end
+)
+
 :end