Merge pull request #37 from prjemian/issue_35

Issue 35
prjemian · Aug 21, 2015 · 26b8d2c · 26b8d2c
2 parents 9bf9c5d + ebdb5d6
commit 26b8d2c
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,75 +1,76 @@
-..
-  This file describes user-visible changes between the versions.
-
-Change History
-##############
-
-Production
-**********
-
-:2015.0214.0: h5toText: handle HDF5 'O' data type (variable length strings)
-:2015.0127.0: spec: ignore bad data lines
-:2015.0125.0: spec: change handling of #L & #X, refactor detection of scanNum and scanCmd
-:2015.0113.0: dropped requirement of *lxml* package
-:2014.1228.1: spec: build mne:name cross-references for counters and positioners
-:2014.1228.0: show version in documentation
-:2014.1028.0: spec: quietly ignore unrecognized scan content *for now*
-:2014.1027.1: spec: major changes in SPEC file support: **custom plugins**
-
-    * **spec** based on plugins for each control line, users can add plugins
-    * declared **prjPySpec** module as legacy, code is frozen at *2014.0623.0* release
-    * added **spec** module to replace **prjPySpec**
-
-:2014.0623.0: updated argparse settings
-:2014.0622.2: added extractSpecScan.py to the suite from the USAXS project
-:2014.0410.0: restore scan.fileName variable to keep interface the same for some legacy clients
-:2014.0404.1: fix sdist utf8 problem, see: http://bugs.python.org/issue11638
-:2014.0404.0: tree_api_parser moved back into NeXpy project
-:2014.0320.6: handle multiple header sections in SPEC data file
-:2014.0320.5: fix the new project URL
-:2014.0320.4: Sphinx cannot build PDF with code-block in a footnote
-:2014.0320.3: note the new home URL in the packaging, too, drop nexpy requirement, default docs theme
-:2014.0320.2: tree_api_parse will go back into nexpy project, remove docs of it here
-:2014.0320.1: allow readthedocs to build Sphinx without extra package requirements
-:2014.0320.0:
-
-    * new home page at http://spec2nexus.readthedocs.org, easier to publish there
-    * move common methods from __init__.py so docs will build at readthedocs.org
-    * new test case fails existing SPEC reader, ignore blank lines
-
-:2014.03.11: documentation
-:2014.03.09: h5toText: option to suppress printing of attributes, put URLs in command-line usage documentation, better test of is_spec_file()
-:2014.03.08: fixed string writer and content display bug in eznx, added h5toText.py, prjPySpec docs improved again
-:2014.03.051: prjPySpec now handles SPEC v6 data file header additions, add new getScanCommands() method
-:2014.03.04: (2014_Mardi_Gras release) removed nexpy project requirement from setup, prjPySpec raises exceptions now
-:2014.03.02: drops nexus tree API (and its dependencies) in favor of native h5py writer
-
-Development: GitHub repository
-******************************
-
-:2014.02.20: version number fits PEP440, LICENSE file included in sdist, more documentation and examples
-:2014-02-19: reference published documentation (re-posted)
-:2014-02-19: add documentation framework
-:2014-02-18: fork to GitHub to make generally available
-
-Development: NeXpy branch
-*************************
-
-:2014-01: briefly, a branch in https://github.com/nexpy/nexpy
-
-  * spec2nexus added during this phase
-  * relies on nexpy.api.nexus for NeXus support
-
-Production: USAXS livedata
-**************************
-
-:2010-2014: production use
-
-  * support livedata WWW page of APS USAXS instrument
-
-    * (http://usaxs.xray.aps.anl.gov/livedata/),
-
-  * https://subversion.xray.aps.anl.gov/trac/small_angle/browser/USAXS/livedata/prjPySpec.py
-  * converted from Tcl
-
-:2000-2010: Tcl code (*readSpecData.tcl*) in production use at APS sectors 32, 33, & 34
+..
+  This file describes user-visible changes between the versions.
+
+Change History
+##############
+
+Production
+**********
+
+:2015.0822.0: extractSpecScan: add option to report scan heading data, such as positioners and Q
+:2015.0214.0: h5toText: handle HDF5 'O' data type (variable length strings)
+:2015.0127.0: spec: ignore bad data lines
+:2015.0125.0: spec: change handling of #L & #X, refactor detection of scanNum and scanCmd
+:2015.0113.0: dropped requirement of *lxml* package
+:2014.1228.1: spec: build mne:name cross-references for counters and positioners
+:2014.1228.0: show version in documentation
+:2014.1028.0: spec: quietly ignore unrecognized scan content *for now*
+:2014.1027.1: spec: major changes in SPEC file support: **custom plugins**
+
+    * **spec** based on plugins for each control line, users can add plugins
+    * declared **prjPySpec** module as legacy, code is frozen at *2014.0623.0* release
+    * added **spec** module to replace **prjPySpec**
+
+:2014.0623.0: updated argparse settings
+:2014.0622.2: added extractSpecScan.py to the suite from the USAXS project
+:2014.0410.0: restore scan.fileName variable to keep interface the same for some legacy clients
+:2014.0404.1: fix sdist utf8 problem, see: http://bugs.python.org/issue11638
+:2014.0404.0: tree_api_parser moved back into NeXpy project
+:2014.0320.6: handle multiple header sections in SPEC data file
+:2014.0320.5: fix the new project URL
+:2014.0320.4: Sphinx cannot build PDF with code-block in a footnote
+:2014.0320.3: note the new home URL in the packaging, too, drop nexpy requirement, default docs theme
+:2014.0320.2: tree_api_parse will go back into nexpy project, remove docs of it here
+:2014.0320.1: allow readthedocs to build Sphinx without extra package requirements
+:2014.0320.0:
+
+    * new home page at http://spec2nexus.readthedocs.org, easier to publish there
+    * move common methods from __init__.py so docs will build at readthedocs.org
+    * new test case fails existing SPEC reader, ignore blank lines
+
+:2014.03.11: documentation
+:2014.03.09: h5toText: option to suppress printing of attributes, put URLs in command-line usage documentation, better test of is_spec_file()
+:2014.03.08: fixed string writer and content display bug in eznx, added h5toText.py, prjPySpec docs improved again
+:2014.03.051: prjPySpec now handles SPEC v6 data file header additions, add new getScanCommands() method
+:2014.03.04: (2014_Mardi_Gras release) removed nexpy project requirement from setup, prjPySpec raises exceptions now
+:2014.03.02: drops nexus tree API (and its dependencies) in favor of native h5py writer
+
+Development: GitHub repository
+******************************
+
+:2014.02.20: version number fits PEP440, LICENSE file included in sdist, more documentation and examples
+:2014-02-19: reference published documentation (re-posted)
+:2014-02-19: add documentation framework
+:2014-02-18: fork to GitHub to make generally available
+
+Development: NeXpy branch
+*************************
+
+:2014-01: briefly, a branch in https://github.com/nexpy/nexpy
+
+  * spec2nexus added during this phase
+  * relies on nexpy.api.nexus for NeXus support
+
+Production: USAXS livedata
+**************************
+
+:2010-2014: production use
+
+  * support livedata WWW page of APS USAXS instrument
+
+    * (http://usaxs.xray.aps.anl.gov/livedata/),
+
+  * https://subversion.xray.aps.anl.gov/trac/small_angle/browser/USAXS/livedata/prjPySpec.py
+  * converted from Tcl
+
+:2000-2010: Tcl code (*readSpecData.tcl*) in production use at APS sectors 32, 33, & 34
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -108,7 +108,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'classic'
 #html_theme = 'sphinxdoc'
 
 # Theme options are theme-specific and customize the look and feel of a theme

diff --git a/docs/source/extractSpecScan.rst b/docs/source/extractSpecScan.rst
@@ -19,7 +19,7 @@ the usage message::
 
    [linux,511]$ extractSpecScan
    usage: extractSpecScan [-h] [-v] [--nolabels] -s SCAN [SCAN ...] -c COLUMN
-                          [COLUMN ...] [--quiet | --verbose]
+                          [COLUMN ...] [-G] [-P] [-Q] [-V] [--quiet | --verbose]
                           spec_file
    extractSpecScan: error: too few arguments
 
@@ -31,7 +31,7 @@ the version number::
 the help message::
 
    usage: extractSpecScan [-h] [-v] [--nolabels] -s SCAN [SCAN ...] -c COLUMN
-                          [COLUMN ...] [--quiet | --verbose]
+                          [COLUMN ...] [-G] [-P] [-Q] [-V] [--quiet | --verbose]
                           spec_file
    
    Save columns from SPEC data file scan(s) to TSV files
@@ -53,6 +53,10 @@ the help message::
      --quiet               suppress all program output (except errors),
                            do not use with --verbose option
      --verbose             print more program output, do not use with --quiet option
+     -G                    report scan Geometry (#G) header information
+     -P                    report scan Positioner (#P) header information
+     -Q                    report scan Q (#Q) header information
+     -V                    report scan (UNICAT-style #H & #V) header information
 
 
 Example

diff --git a/src/spec2nexus/__init__.py b/src/spec2nexus/__init__.py
@@ -1,52 +1,52 @@
-# -*- coding: iso-8859-1 -*-
-
-'''command-line tool to convert SPEC data files to NeXus HDF5'''
-
-#-----------------------------------------------------------------------------
-# :author:    Pete R. Jemian
-# :email:     prjemian@gmail.com
-# :copyright: (c) 2014-2015, Pete R. Jemian
-#
-# Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
-#
-# The full license is in the file LICENSE.txt, distributed with this software.
-#-----------------------------------------------------------------------------
-
-__version__   = '2015.0214.0'
-__release__   = __version__
-__author__    = 'Pete R. Jemian'
-__email__     = 'prjemian@gmail.com'
-__copyright__ = '2014-2015, Pete R. Jemian'
-
-__package_name__ = 'spec2nexus'
-__license_url__  = 'http://creativecommons.org/licenses/by/4.0/deed.en_US'
-__license__      = 'Creative Commons Attribution 4.0 International Public License (see LICENSE file)'
-__description__  = 'Converts SPEC data files and scans into NeXus HDF5 files'
-__author_name__  = __author__
-__author_email__ = __email__
-__url__          = u'http://spec2nexus.readthedocs.org'
-__download_url__ = u'https://github.com/prjemian/spec2nexus/tarball/' + __version__
-__keywords__     = ['SPEC', 'diffraction', 'data acquisition', 'NeXus', 'HDF5']
-
-__install_requires__ = ('h5py','numpy', )
-__classifiers__ = [
-     'Development Status :: 5 - Production/Stable',
-     'Environment :: Console',
-     'Intended Audience :: Science/Research',
-     'License :: Freely Distributable',
-     'License :: Public Domain',
-     'Programming Language :: Python',
-     'Programming Language :: Python :: 2',
-     'Programming Language :: Python :: 2.7',
-     'Topic :: Scientific/Engineering',
-     'Topic :: Scientific/Engineering :: Astronomy',
-     'Topic :: Scientific/Engineering :: Bio-Informatics',
-     'Topic :: Scientific/Engineering :: Chemistry',
-     'Topic :: Scientific/Engineering :: Information Analysis',
-     'Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator',
-     'Topic :: Scientific/Engineering :: Mathematics',
-     'Topic :: Scientific/Engineering :: Physics',
-     'Topic :: Scientific/Engineering :: Visualization',
-     'Topic :: Software Development',
-     'Topic :: Utilities',
-   ]
+# -*- coding: iso-8859-1 -*-
+
+'''command-line tool to convert SPEC data files to NeXus HDF5'''
+
+#-----------------------------------------------------------------------------
+# :author:    Pete R. Jemian
+# :email:     prjemian@gmail.com
+# :copyright: (c) 2014-2015, Pete R. Jemian
+#
+# Distributed under the terms of the Creative Commons Attribution 4.0 International Public License.
+#
+# The full license is in the file LICENSE.txt, distributed with this software.
+#-----------------------------------------------------------------------------
+
+__version__   = '2015.0822.0'
+__release__   = __version__
+__author__    = 'Pete R. Jemian'
+__email__     = 'prjemian@gmail.com'
+__copyright__ = '2014-2015, Pete R. Jemian'
+
+__package_name__ = 'spec2nexus'
+__license_url__  = 'http://creativecommons.org/licenses/by/4.0/deed.en_US'
+__license__      = 'Creative Commons Attribution 4.0 International Public License (see LICENSE file)'
+__description__  = 'Converts SPEC data files and scans into NeXus HDF5 files'
+__author_name__  = __author__
+__author_email__ = __email__
+__url__          = u'http://spec2nexus.readthedocs.org'
+__download_url__ = u'https://github.com/prjemian/spec2nexus/tarball/' + __version__
+__keywords__     = ['SPEC', 'diffraction', 'data acquisition', 'NeXus', 'HDF5']
+
+__install_requires__ = ('h5py','numpy', )
+__classifiers__ = [
+     'Development Status :: 5 - Production/Stable',
+     'Environment :: Console',
+     'Intended Audience :: Science/Research',
+     'License :: Freely Distributable',
+     'License :: Public Domain',
+     'Programming Language :: Python',
+     'Programming Language :: Python :: 2',
+     'Programming Language :: Python :: 2.7',
+     'Topic :: Scientific/Engineering',
+     'Topic :: Scientific/Engineering :: Astronomy',
+     'Topic :: Scientific/Engineering :: Bio-Informatics',
+     'Topic :: Scientific/Engineering :: Chemistry',
+     'Topic :: Scientific/Engineering :: Information Analysis',
+     'Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator',
+     'Topic :: Scientific/Engineering :: Mathematics',
+     'Topic :: Scientific/Engineering :: Physics',
+     'Topic :: Scientific/Engineering :: Visualization',
+     'Topic :: Software Development',
+     'Topic :: Utilities',
+   ]