New upstream version 0.2.3

.coveragerc

+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    if self.debug:
+    if settings.DEBUG
+    raise AssertionError
+    raise NotImplementedError
+    if 0:
+    if __name__ == .__main__.:
+
+[run]
+omit =
+	versioneer.py
+	src/punx/_version.py
+	src/punx/github_handler.py
+	tests/github_handler_test.py

.gitattributes

+src/punx/_version.py export-subst

.gitignore

+*.py[cod]
+
+# local creds for authenticated access
+src/punx/__github_creds__.txt
+
+# local NXDL source cache (to be packaged with sdist)
+#src/punx/cache/*
+
+# eclipse/PyDev
+.pydevproject
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Installer logs
+pip-log.txt
+
+# Python logging package output
+log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+htmlcov
+tests/__pycache__
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+/.settings
+/.idea
+/src/punx/data/local

.landscape.yml

+doc-warnings: true
+test-warnings: false
+strictness: medium
+max-line-length: 120
+autodetect: true
+requirements:
+  - pyRestTable
+  - PyGitHub>=1.32
+  - PyQt
+  - numpy
+  - h5py
+  - lxml
+  - requests
+  - coverage
+  - docopt
+  - coveralls
+ignore-paths:
+  - docs
+  - src/punx/cache
+  - src/punx/data
+  - src/punx/ignore_now
+  - versioneer.py
+  - src/punx/_version.py
+  - install_NXDL_file_sets.py
+  - _installer.py
+ignore-patterns:
+  - ^example/doc_.*\.py$
+  - (^|/)docs(/|$)
+python-targets:
+  - 2
+  - 3
+pylint:
+  disable:
+    - unused-argument
+    - arguments-differ
+    - protected-access
+    - cyclic-import

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>punx</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.python.pydev.pythonNature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+	</natures>
+</projectDescription>

.pydevproject.example

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?eclipse-pydev version="1.0"?><pydev_project>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Python 3.6 and PyQt5</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 3.6</pydev_property>
+<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
+<path>/${PROJECT_DIR_NAME}/src</path>
+</pydev_pathproperty>
+</pydev_project>

.readthedocs.yml

+conda:
+   file: environment.yml

.travis.yml

+# :file: .travis.yml
+#
+# :url:  https://travis-ci.org/prjemian/punx
+#
+# for advice, see:
+#  https://docs.travis-ci.com/user/customizing-the-build#The-Build-Lifecycle
+
+language: python
+python:
+  - "2.7"
+  - "3.5"
+  - "3.6"
+
+before_script:
+  - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH=$HOME/miniconda/bin:$PATH
+  - export PY_ENV=travis-$TRAVIS_PYTHON_VERSION
+  - conda create -y -n $PY_ENV python=$TRAVIS_PYTHON_VERSION pyqt numpy h5py lxml requests coverage docopt
+  - source activate $PY_ENV
+  - which pip
+  - which python
+  - which conda
+  - python --version
+  - pip install pyRestTable
+  - pip install "PyGitHub>=1.32"
+  - pip install coveralls
+  - which coveralls
+  - conda list
+
+# command to run tests
+script:
+  - # python ./src/punx/main.py -h
+  - # python ./src/punx/main.py update --force
+  - which coverage
+  - coverage run tests/
+
+after_success:
+  - coverage report
+  - which coveralls
+  - coveralls
+  - source deactivate
+  - conda env remove -y -n $PY_ENV
+  
\ No newline at end of file

CHANGES.rst

+..
+  This file describes user-visible changes between the versions.
+
+Change History
+##############
+
+Production
+**********
+
+--none--
+
+Development
+***********
+
+:0.2.0: 2018-07-02 -- first tag after major refactor (#72, #105)
+:0.1.9: 2017-07-09 -- last tag before major refactor (#72), no changes here since 2017-03-31
+:0.1.8: 2017-03-12 -- package .json file in the cache file sets
+:0.1.7: 2017-03-11 -- NeXus def 3.2 bundled into repo now
+:0.1.4: 2016-12-09 -- validation reports sorted by HDF5 address
+:0.1.3: 2016-12-07 -- Py2 & Py3: passes all unit tests
+:0.1.2: 2016-11-21 -- unit tests added for reports
+:0.0.9: 2016-06-29 -- retry failed https requests to GitHub and cleanup a QString
+:0.0.8: 2016-06-29 -- refactor update procedure 
+:0.0.7: 2016-06-27 -- add "report" arguments to "demo" subcommand
+:0.0.6: 2016-06-22 -- resolved some UnicodeDecodeError exceptions
+:0.0.5: 2016-06-20 -- added subcommand shortcuts and logging
+:0.0.4: 2016-06-17 -- work-in-progress to test installation with remote user
+:0.0.3: 2016-06-11 -- basic UI established, **demo** command added
+:0.0.2: 2016-06-11 -- basic UI established
+:0.0.1: 2016-06-10 -- basic functions
+:started: 2016-05-20 -- initial project creation

MANIFEST.in

@@ -5,10 +5,5 @@ include src/punx/cache/*/__github_info__.json
 include src/punx/cache/*/*.xsd
 include src/punx/cache/*/*/*.xml
 include src/punx/cache/*/*/*.xsl
-include src/qa_qc/*.txt
 include src/punx/_version.py
 include versioneer.py 
-
-# Do NOT package the file "__use_source_cache__" with the sdist created from setup.py.
-# do NOT include __use_source_cache__
-# Its presence is a boolean to update user or source cache.

PKG-INFO

-Metadata-Version: 1.1
-Name: punx
-Version: 0.1.9
-Summary: Python Utilities for NeXus
-Home-page: http://punx.readthedocs.io
-Author: Pete R. Jemian
-Author-email: prjemian@gmail.com
-License: Creative Commons Attribution 4.0 International Public License (see LICENSE file)
-Description: ####
-        punx
-        ####
-        
-        Python Utilities for NeXus HDF5 files: validation, structure, hierarchy
-        
-        * Validation of NeXus NXDL files
-        * Validation of NeXus HDF5 data files
-        * Display of NeXus HDF5 data file structure
-        * Display of NeXus base class hierarchy (stretch goal, graphical output)
-        
-        NOTE: project is under initial construction
-        
-        :author:    Pete R. Jemian
-        :email:     prjemian@gmail.com
-        :copyright: 2017, Pete R. Jemian
-        :license:   Creative Commons Attribution 4.0 International Public License (see *LICENSE.txt*)
-        :URL:       http://punx.readthedocs.io
-        :git:       https://github.com/prjemian/punx
-        :PyPI:      https://pypi.python.org/pypi/punx/ 
-        :TODO list: https://github.com/prjemian/punx/issues
-        
-        :build badges:
-        
-           ..  see http://shields.io/ for more badge ideas
-        
-           .. image:: https://travis-ci.org/prjemian/punx.svg?branch=master
-              :target: https://travis-ci.org/prjemian/punx
-           .. image:: https://coveralls.io/repos/github/prjemian/punx/badge.svg?branch=master
-              :target: https://coveralls.io/github/prjemian/punx?branch=master
-        
-        :release badges:
-              
-           .. image:: https://img.shields.io/github/tag/prjemian/punx.svg
-              :target: https://github.com/prjemian/punx/tags
-           .. image:: https://img.shields.io/github/release/prjemian/punx.svg
-              :target: https://github.com/prjemian/punx/releases
-           .. image:: https://img.shields.io/pypi/v/punx.svg
-              :target: https://pypi.python.org/pypi/punx/
-        
-        :social badges:
-              
-           .. image:: http://depsy.org/api/package/pypi/punx/badge.svg
-              :target: http://depsy.org/package/python/punx
-           .. image:: https://badges.gitter.im/punx-nexus/Lobby.svg
-              :target: https://gitter.im/punx-nexus/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
-        
-Keywords: NeXus,HDF5
-Platform: any
-Classifier: Development Status :: 3 - Alpha
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: Freely Distributable
-Classifier: License :: Public Domain
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
-Classifier: Programming Language :: Python :: 2.7
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.4
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Classifier: Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator
-Classifier: Topic :: Scientific/Engineering :: Mathematics
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: Topic :: Scientific/Engineering :: Visualization
-Classifier: Topic :: Software Development
-Classifier: Topic :: Utilities

README.rst

@@ -13,7 +13,7 @@ NOTE: project is under initial construction
 
 :author:    Pete R. Jemian
 :email:     prjemian@gmail.com
-:copyright: 2017, Pete R. Jemian
+:copyright: 2017-2018, Pete R. Jemian
 :license:   Creative Commons Attribution 4.0 International Public License (see *LICENSE.txt*)
 :URL:       http://punx.readthedocs.io
 :git:       https://github.com/prjemian/punx
@@ -26,8 +26,13 @@ NOTE: project is under initial construction
 
    .. image:: https://travis-ci.org/prjemian/punx.svg?branch=master
       :target: https://travis-ci.org/prjemian/punx
+      :alt: Unit Testing
    .. image:: https://coveralls.io/repos/github/prjemian/punx/badge.svg?branch=master
       :target: https://coveralls.io/github/prjemian/punx?branch=master
+      :alt: Code Coverage
+   .. image:: https://landscape.io/github/prjemian/punx/master/landscape.svg?style=plastic
+      :target: https://landscape.io/github/prjemian/punx/master
+      :alt: Code Health
 
 :release badges:
       
@@ -42,5 +47,7 @@ NOTE: project is under initial construction
       
    .. image:: http://depsy.org/api/package/pypi/punx/badge.svg
       :target: http://depsy.org/package/python/punx
+      :alt: Depsy (impact)
    .. image:: https://badges.gitter.im/punx-nexus/Lobby.svg
       :target: https://gitter.im/punx-nexus/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
+      :alt: gitter (chat)

_starter_.py

+#!/usr/bin/env python
+
+import sys, os
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), 'src')))
+
+# developer use
+# if len(sys.argv) == 1:
+#     sys.argv.append("demo")
+#     sys.argv.append("conf")
+#     sys.argv.append("valid")
+#     sys.argv.append("src/punx/data/33837rear_1D_1.75_16.5_NXcanSAS_v3.h5")
+#     # sys.argv.append("C:/Users/Pete/Downloads/1998spheres.h5")
+#     # sys.argv.append("src/punx/cache/v3.3/applications/NXcanSAS.nxdl.xml")
+#     sys.argv.append("tree")
+#     sys.argv.append("src/punx/data/gov_5.h5")
+#     # sys.argv.append("src/punx/data/compression.h5")
+#     # sys.argv.append("src/punx/data/writer_1_3.hdf5")
+#     # sys.argv.append("src/punx/data/prj_test.nexus.hdf5")
+
+
+from punx import main
+print(main.__file__)
+main.main()

check_data.sh

+#!/bin/bash
+
+# file: check_data.sh
+# test that punx program can process all the files in the data directory
+
+DATA_DIR=src/punx/data
+
+for f in `ls -1 ${DATA_DIR}`; do
+   echo src/punx/data/$f
+   ./_starter_.py tree ${DATA_DIR}/$f
+   ./_starter_.py validate ${DATA_DIR}/$f
+done

docs/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+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
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(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 doctest gettext
+
+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 "  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 "  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)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	touch $(BUILDDIR)/html/.nojekyll
+	@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/punx.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/punx.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/punx"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/punx"
+	@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."
+
+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:
+	$(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."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/make.bat

+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
+set I18NSPHINXOPTS=%SPHINXOPTS% source
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "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.  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.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over 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
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	echo '' >  %BUILDDIR%/html/.nojekyll
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\punx.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\punx.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end

docs/source/changes.rst

+..
+	CHANGES
+	=======
+	
+	title provided in CHANGES.rst file
+
+.. include:: ../../CHANGES.rst

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# punx documentation build configuration file, created by
+# sphinx-quickstart on Tue Feb 18 21:05:31 2014.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# 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.abspath('.'))
+sys.path.insert(0, os.path.abspath(os.path.join('..', '..', 'src')))
+import punx
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.inheritance_diagram',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = punx.__package_name__
+copyright = punx.__copyright__
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+versioneer_version = punx.__version__.split('+')
+version = versioneer_version[0]
+# The full version, including alpha/beta/rc tags.
+#release = punx.__release__
+#release = version
+if len(versioneer_version) == 2:
+    release = versioneer_version[1]
+else:
+    release = ''
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'classic'
+#html_theme = 'sphinxdoc'
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'punxdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  ('index', 
+   punx.__package_name__+'.tex', 
+   punx.__package_name__+u' Documentation',
+   punx.__author__, 
+   'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True

docs/source/configuration.rst

+.. _config:
+.. index:: configuration
+
+User interface: subcommand: **configuration**
+#############################################
+
+The *configuration* subcommand shows the internal configuration
+of the ``punx`` program.  It shows a table with the available 
+*NXDL file sets*.
+
+::
+
+   console> punx configuration
+   Locally-available versions of NeXus definitions (NXDL files)                 
+   ============= ======= ====== =================== ======= ==========================================
+   NXDL file set type    cache  date & time         commit  path                 
+   ============= ======= ====== =================== ======= ==========================================
+   a4fd52d       commit  source 2016-11-19 01:07:45 a4fd52d C:\source_path\punx\cache\a4fd52d
+   v2018.5       release source 2018-05-15 16:34:19 a3045fd C:\source_path\punx\src\punx\cache\v2018.5
+   v3.3          release source 2017-07-12 17:41:13 9285af9 C:\source_path\punx\src\punx\cache\v3.3   
+   9eab          commit  user   2016-10-19 17:58:51 9eab281 C:\user_path\AppData\Roaming\punx\9eab
+   master        branch  user   2018-05-16 02:07:48 2dc081e C:\user_path\AppData\Roaming\punx\master
+   ============= ======= ====== =================== ======= ==========================================
+   
+   default NXDL file set:  master
+
+
+An NXDL file set is the complete set of NXDL (XML) files that 
+provide a version of the NeXus standard, including the XML Schema
+files that provide all the default and basic structures of the NXDL
+files.
+
+Above, the user cache has a version of the GitHub *master* branch (
+the master branch contains the latest
+revisions by the developers on that date).
+
+.. index:: NXDL file set
+
+An NXDL file set is *referenced* by one of the GitHub identifiers:
+
+=========   ==========  ==========================================
+identifier  example     description
+=========   ==========  ==========================================
+commit      9eab        SHA-1 hash tag [#]_ that identifies a specific commit to the repository
+branch      master      name of a branch [#]_ in the repository
+tag         Schema-3.4  name of a tag [#]_ in the repository
+release     v2018.5     name of a repository release [#]_
+=========   ==========  ==========================================
+
+.. [#] commit (hash): A commit is a snapshot of the GitHub repository.
+   A SHA-1 hash code is the unique identifier of a commit.
+   It is a 40-character sequence of hexadecimals.
+   It may be shortened to just the first characters which identify
+   it uniquely in the repository.  Three or four characters *may* be 
+   unique (1:16^3 or 1:16^4) while
+   seven characters are almost certain (1:16^7) to be a unique reference.
+   
+   For example. the commit `9eab` may also be identified
+   as `9eab281`, or by its full SHA-1 has
+   `9eab2816e19440f8601fdf81ee972e330319c28f`
+   (https://github.com/nexusformat/definitions/commit/9eab281).  
+   All point to the same commit on 2016-10-19 17:58:51.
+.. [#] branch: https://help.github.com/articles/about-branches/
+.. [#] tag: a user-provided text name for a commit
+.. [#] release: https://help.github.com/articles/about-releases/
+
+
+.. index:: 
+   !ref
+   NXDL file set, ref
+
+When a *ref* (a reference to a specific NXDL file set identifier) 
+is not provided, the default NXDL file set will be chosen as the one 
+with the most recent date & time.  That date & time is provided by
+GitHub as the time the changes were to committed to the repository.
+
+.. index:: 
+   source cache
+   user cache
+   cache, source
+   cache, user
+
+NXDL file sets may be found in the *source cache* (as distributed 
+with the program) or in the *user cache* as maintained by the ``punx`` 
+:ref:`update` subcommand.  The full path to the file set is provided.