limatix 1.2.6__tar.gz

limatix-1.2.6/.github/workflows/push-to-pypi.yml

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+name: Publish Python distribution to PyPI
+# This runs on the public repository after:
+#  1. Tag new version and git push --tags into github main
+#  2. Run this action (Publish Python distribution to PyPI) on public repository
+on: workflow_dispatch
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: perform checkout
+      uses: actions/checkout@v7
+    - name: Get history and tags for SCM versioning to work
+      run: |
+        git fetch --prune --unshallow
+        git fetch --depth=1 origin +refs/tags/*:refs/tags/*	
+    - name: Set up Python
+      uses: actions/setup-python@v7
+      with:
+        python-version: "3.x"
+
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v7
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    #if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/limatix
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v8
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

limatix-1.2.6/.gitignore

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+doc/processtrak_example/.*xlp.bak*
+doc/processtrak_example/*.xlp
+doc/processtrak_example/*.ods
+doc/processtrak_example/creston_jan2016_files/
+build/*
+dist/*
+*egg*
+__pycache__
+*.pyc
+*~
+venv/
+limatix/_version.py

limatix-1.2.6/.hgignore

@@ -0,0 +1,5 @@
+syntax: glob
+
+build/*
+dist/*
+*egg*

limatix-1.2.6/.hgsub

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+limatix/canonicalize_path=limatix/canonicalize_path
+limatix/dc_lxml_treesync=limatix/dc_lxml_treesync

limatix-1.2.6/.hgsubstate

@@ -0,0 +1,2 @@
+e1db23893916ea10615840ccce9574f8d119659e limatix/canonicalize_path
+8f63e99f94c57e9d5c0cd1c92a3c562f1dafae79 limatix/dc_lxml_treesync

limatix-1.2.6/.hgtags

@@ -0,0 +1,20 @@
+05ce5422ef6266698d722abf75c3bba6485b09c9 2.0.0-beta24
+b4aba0c838f526f7dcd46f98dd4f2b83876143fa 2.0.0-beta25
+fbdd51366452373a4d65de1b26993f41d04ff055 2.0.0-beta26
+c255d08871322922d50a630be1a0713ed3826748 2.0.0-beta27
+c255d08871322922d50a630be1a0713ed3826748 2.0.0-beta27
+37e864f5029a5a2afa2eb4e9242a8dd6114ea587 2.0.0-beta27
+795c659855cf3ba0e2077381c020b630a7a031f8 2.0.0-beta28
+280281382f6923b204c88c0f5a45fd6bb459017d 1.0.0
+280281382f6923b204c88c0f5a45fd6bb459017d 1.0.0
+abbd865a9fc0bbf0339fc78a33e742ba98f53d48 1.0.0
+beea46a5a647fc61efde5246525e93615a71992f 1.0.1
+301b07bb203e8012f8f0876c7465cd4ceab6258c 1.0.2
+bb79803b82a1ca4af439259fae09e2f5dab47a66 1.0.3
+8a270d004212e9483278619c80279220f03ed4a7 1.0.4
+5e13088e6400184ef826453b295b13623a566842 1.0.5
+a1f604b49921306dd19cc0fe85727c1d19d89fde 1.0.6
+7c50b1dc25ea7f1cf15fc1665700e20bad5134d0 1.0.7
+895916becffc640003ca2316550cd8406b31900c 1.0.8
+c6133aa8afdb2f5cfff2d2716d476f8d98b54358 1.0.9
+8c4e415248defab76072aabd0e8ec1e563587ee4 1.0.10

limatix-1.2.6/COPYING.txt

@@ -0,0 +1,57 @@
+Limatix is Copyright (c) 2013-2016 Iowa State University and others.
+
+Copyright statement for all files not otherwise marked
+------------------------------------------------------
+
+Copyright (c) 2013-2016, Iowa State University
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of Iowa State University nor the
+      names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL IOWA STATE UNIVERSITY BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+
+
+limatix/widgets/dc_wraplabel.py is modified from wraplabel.py,
+which is Copyright (c) 2005 VMware, Inc.:
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+# Python translation from wrapLabel.{cc|h} by Gian Mario Tagliaretti
+
+

limatix-1.2.6/INSTALL.txt

@@ -0,0 +1,60 @@
+
+Prerequisites:
+  python (version 3.8 or later)
+  python-lxml (often distributed with operating system or Python distribution)
+  numpy (often distributed with operating system or Python distribution)
+  pytz (Python timezone library; sometimes listed as 'python-tz')
+  gtk3 and python bindings (on python3;  required to use datacollect2 GUI components)
+  setuptools (often distributed with operating system or Python distribution)
+  setuptools_scm
+  platformdirs
+  pint (optional, for advanced units support)
+
+
+Recommended:
+  python-pillow (required for Ricoh camera support and for representing parameters that are images)
+  limatix-qautils (not used directly, but documents checklist
+         	   format/structure and can render checklists as PDF)
+  ipython (with PySide/PySide2/PyQt4/PyQt5 QT bindings) for interactive debugging of processtrak scripts
+  ipykernel for ipython interactive debugging
+  matplotlib (with QT4 and/or QT5 support) for use with ipython for interactive
+             debugging of processtrak scripts
+
+Limatix should work on all major platforms with the above packages.
+In most cases you will want to use a package manager or a Python
+distribution such as Canopy or Anaconda to provide the packages. 
+Detailed installation instructions for Windows are included below. 
+
+Limatix is built with Python setuptools:
+
+
+To install into Python site-packages (as root)
+  pip install --no-deps --no-build-isolation .
+
+
+Windows installation instructions
+---------------------------------
+For processtrak, pip install as above.
+
+Prerequisites:
+  pywin32
+
+For datacollect2, TBD
+
+
+Running datacollect2 on Windows under Python3
+---------------------------------------------
+datacollect2 under Python3 requires Gtk3 and PyGObject, which have
+traditionally been hard to obtain for Windows. You may have luck
+installing PyGObject through MSYS2(https://www.msys2.org/) or with
+Anaconda via conda-forge.  This has not been rigorously tested.
+
+
+
+Getting Started
+---------------
+See doc/LIMATIX.xhtml for quickstart documentation and
+examples. 
+
+
+see README.txt for basic information on LIMATIX

limatix-1.2.6/Makefile

@@ -0,0 +1,159 @@
+
+include defs.mk
+
+
+DIST_FILES=.
+
+
+#PUBEXCLUDE=--exclude .hg --exclude limatix/canonicalize_path/.hg  --exclude limatix/dc_lxml_treesync/.hg
+
+
+PYSUBDIRS=widgets steps
+CHXSUBDIRS=checklists
+
+
+SUBDIRS=xslt #matlab
+
+
+
+
+PROGS=dc_checklist dc_glade datacollect2 dc_paramdb2 dc_ricohphoto processtrak dc_checkprovenance dc_xlg2dpd dc_chx2chf dc_getpath
+
+
+all:
+	@for i in $(SUBDIRS) ; do if [ -d $$i ] && [ -f $$i/Makefile ] ; then $(MAKE) $(MFLAGS) -C $$i ; fi done
+
+
+
+
+#$(TOPYCHECK:.py=.pycheck)
+#ifeq ($(PYCHECKER), /none)
+#	@echo "WARNING: pychecker not found (install from pychecker.sourceforge.net)"
+#endif
+
+
+#%.pycheck: %.py
+#	$(PYCHECKER) --only $<
+#	touch $@
+
+clean:
+	@for i in $(SUBDIRS) ; do if [ -d $$i ] && [ -f $$i/Makefile ] ; then $(MAKE) $(MFLAGS) -C $$i clean; fi done
+	rm -f *.bak *~ core.* *.o *.pyc a.out octave-core *.pycheck limatix/widgets/*~ limatix/steps/*~ limatix/widgets/core.* limatix/steps/core.* limatix/widgets/*.pyc limatix/steps/*.pyc checklists/*~ plans/*~ limatix/widgets/glade-3/*~ limatix/widgets/glade-3/glade_catalogs/*~ limatix/widgets/glade-3/glade_catalogs/*.pyc limatix/widgets/glade-3/glade_modules/*~ limatix/widgets/glade-3/glade_modules/*.pyc limatix/*~ limatix/core.* limatix/*.o limatix/*.pyc limatix/a.out limatix/octave-core limatix/*.pycheck conf/*~ conf/core.* conf/*.bak conf/*.pyc doc/*.bak doc/*.pyc doc/*~ doc/processtrak_example/*~ doc/processtrak_example/*.pyc doc/processtrak_example/creston_jan2016/*.png  doc/processtrak_example/creston_jan2016/*.kml doc/processtrak_example/*.xlp doc/processtrak_example/creston_jan2016_out.ods  doc/processtrak_example/.creston*.bak*  limatix/bin/*~ limatix/bin/*.bak limatix/bin/*.pyc limatix/pt_steps/*.pyc limatix/pt_steps/*~
+	rm -rf lib/__pycache__ steps/__pycache__ widgets/__pycache__ doc/processtrak_example/__pycache__
+	rm -rf build/
+	rm -rf dist/
+	rm -rf limatix.egg-info
+
+distclean: clean
+	@for i in $(SUBDIRS) ; do if [ -d $$i ] && [ -f $$i/Makefile ] ; then $(MAKE) $(MFLAGS) -C $$i distclean ; fi done
+
+realclean: distclean
+
+
+depend:
+	@for i in $(SUBDIRS) ; do if [ -d $$i ] && [ -f $$i/Makefile ] ; then $(MAKE) $(MFLAGS) -C $$i depend ; fi done
+
+install:
+	( for i in $(PROGS) ; do rm -f $(PREFIX)/bin/$$i ; done )
+ifneq ($(PYTHON2.6), /none)
+	$(PYTHON2.6) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(PYTHON2.7), /none)
+	$(PYTHON2.7) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(PYTHON3.4), /none)
+	$(PYTHON3.4) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(PYTHON3.6), /none)
+	$(PYTHON3.6) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(PYTHON3.7), /none)
+	$(PYTHON3.7) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(PYTHON3.8), /none)
+	$(PYTHON3.8) ./setup.py install --prefix=$(PREFIX) 
+endif
+ifneq ($(DEFAULTPY), /none)
+	$(DEFAULTPY) ./setup.py install --prefix=$(PREFIX) 
+	$(DEFAULTPY) ./setup.py install_data # --prefix=$(PREFIX) 
+endif
+
+
+	#	$(INSTALL) -d $(DCINSTDIR)
+	#rm -f $(PREFIX)/limatix
+	#ln -s $(DCINSTDIR) $(PREFIX)/limatix
+	#$(INSTALL) -d $(DCINSTDIR)/lib
+	#$(INSTALL) -d $(DCINSTDIR)/conf
+	#$(INSTALL) -d $(DCINSTDIR)/doc
+	#$(INSTALL) -d $(DCINSTDIR)/bin
+	#@for i in $(PYSUBDIRS) ; do if [ -d $$i ] ; then $(INSTALL) -d $(DCINSTDIR)/$$i/ ; echo $$i/*.py $$i/*.glade ; $(INSTALL) $$i/*.py $$i/*.glade $(DCINSTDIR)/$$i/; fi done
+	#@for i in $(CHXSUBDIRS) ; do if [ -d $$i ] ; then $(INSTALL) -d $(DCINSTDIR)/$$i/ ; echo $$i/*.chx ; $(INSTALL) $$i/*.chx $(DCINSTDIR)/$$i/ ; $(INSTALL) $$i/*.png $(DCINSTDIR)/$$i/ ; fi done	
+	#$(INSTALL) -d $(DCINSTDIR)/glade-3
+	#$(INSTALL) glade-3/*.txt $(DCINSTDIR)/glade-3/
+	#$(INSTALL) -d $(DCINSTDIR)/glade-3/glade_catalogs
+	#$(INSTALL) glade-3/glade_catalogs/* $(DCINSTDIR)/glade-3/glade_catalogs/
+	#$(INSTALL) -d $(DCINSTDIR)/glade-3/glade_modules
+	#$(INSTALL) glade-3/glade_modules/* $(DCINSTDIR)/glade-3/glade_modules/
+	#$(INSTALL) README.txt $(DCINSTDIR)/
+	#$(INSTALL) lib/*.glade $(DCINSTDIR)/lib
+	#$(INSTALL) lib/*.py $(DCINSTDIR)/lib
+	#$(INSTALL) conf/*.glade $(DCINSTDIR)/conf
+	#$(INSTALL) conf/*.dcc $(DCINSTDIR)/conf
+	#$(INSTALL) doc/* $(DCINSTDIR)/doc
+	#( for i in $(PROGS) ; do $(INSTALL) bin/$$i $(DCINSTDIR)/bin/ ; done )
+	#( for i in $(PROGS) ; do rm -f $(PREFIX)/bin/$$i ; ln -s $(DCINSTDIR)/bin/$$i $(PREFIX)/bin/$$i ; done )
+
+
+
+checklib:
+	@for i in lib/*.py ; do $(PYCHECKER) --only --limit=30 $$i ; done 
+
+checksteps:
+	( export PYTHONPATH=lib/:widgets/:$$PYTHONPATH ; for i in steps/*.py ; do $(PYCHECKER) --only --limit=30 $$i ; done  )
+
+
+checkwidgets:
+	( export PYTHONPATH=lib/:$$PYTHONPATH ;for i in widgets/*.py ; do $(PYCHECKER) --only --limit=30 $$i ; done )
+
+commit: realclean
+	git add -A # hg addremove
+	git commit -a  # hg commit
+
+
+dist:
+	#	mv VERSION VERSIONtmp
+	#sed 's/-[^-]*$$//' <VERSIONtmp >VERSION    # remove trailing -devel
+	#date "+%B %d, %Y" >VERSIONDATE
+	#rm -f VERSIONtmp
+	#
+	#$(MAKE) $(MFLAGS) commit
+	#$(MAKE) $(MFLAGS) all
+	#$(MAKE) $(MFLAGS) realclean
+	#git checkout master
+	#git merge --no-ff develop
+	#git tag -f `cat VERSION` -a -m `cat VERSION`
+	#
+	#tar -cvzf /tmp/realclean-limatix-`cat VERSION`.tar.gz $(DIST_FILES)
+	#
+	#tar $(PUBEXCLUDE) -cvzf /tmp/realclean-limatix-pub-`cat VERSION`.tar.gz $(DIST_FILES)
+	#
+	#@for archive in  limatix-`cat VERSION`  ; do mkdir /tmp/$$archive ; tar -C /tmp/$$archive  -x -f /tmp/realclean-$$archive.tar.gz ; make -C /tmp/$$archive all ; make -C /tmp/$$archive distclean ; tar -C /tmp -c -v -z -f /home/sdh4/research/software/archives/$$archive.tar.gz $$archive ; ( cd /tmp; zip -r /home/sdh4/research/software/archives/$$archive.zip $$archive ) ;  done
+	#git checkout develop
+	#git merge --no-ff master
+	#
+	#mv VERSION VERSIONtmp
+	#awk -F . '{ print $$1 "." $$2 "." $$3+1 "-devel"}' <VERSIONtmp >VERSION  # increment version number and add trailing-devel
+	#rm -f VERSIONtmp
+	#rm -f VERSIONDATE
+	#git commit -a
+	#@echo "If everything worked, you should do a git push --all ; git push --tags"
+	#@echo "Then on github define a new release... Include mention of downloading the built archives. Upload the saved archive as a "binary"
+	#
+	mkdir /tmp/limatix_rel$$PPID
+	git clone . /tmp/limatix_rel$$PPID/limatix-$(VERSION)
+	git clone limatix/canonicalize_path /tmp/limatix_rel$$PPID/limatix-$(VERSION)/limatix/canonicalize_path
+	git clone limatix/dc_lxml_treesync /tmp/limatix_rel$$PPID/limatix-$(VERSION)/limatix/dc_lxml_treesync
+	(cd /tmp/limatix_rel$$PPID; zip  -r limatix-$(VERSION).zip limatix-$(VERSION)/ --exclude "limatix-$(VERSION)/.git/*" --exclude "limatix-$(VERSION)/limatix/canonicalize_path/.git/*" --exclude "limatix-$(VERSION)/limatix/dc_lxml_treesync/.git/*")
+	@echo 'created archive for limatix' $(VERSION)
+	@echo 'described as' `git describe --tags`
+	@echo 'Wrote archive as'  /tmp/limatix_rel$$PPID/limatix-$(VERSION).zip

limatix-1.2.6/PKG-INFO

@@ -0,0 +1,89 @@
+Metadata-Version: 2.4
+Name: limatix
+Version: 1.2.6
+Summary: Automated data collection
+Author: Stephen D. Holland
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Requires-Python: >=3.8
+Description-Content-Type: text/plain
+License-File: COPYING.txt
+Dynamic: author
+Dynamic: license-file
+Dynamic: summary
+
+About LIMATIX
+------------------
+
+LIMATIX is a collection of tools for performing and recording
+scientific experiments, based on the twin ideas of checklists and
+experiment logs.  It does not address the problem of data acquisition
+per se -- it assumes you have another software package handling
+that. Instead, it addresses the parallel problems of keeping track of
+procedures, recording which procedures were performed (checklists),
+and keeping a log (like a laboratory notebook) of the progress of an
+experiment. It also includes a tool (processtrak) to assist in
+organizing and executing processing tasks.
+
+
+
+Programs
+--------
+datacollect2 -- Main program for performing checklist-based experiment logging
+dc_checklist -- Main program for standalone checklists and plans
+dc_chx2chf -- create a filled checklist file from an unfilled .chx file
+dc_getpath -- get the path to the datacollect2 installation
+dc_glade   -- run the glade 3.6.7 user interface builder to create custom
+              GUI interfaces
+dc_gui     -- Run a custom GUI interface created with dc_glade
+dc_paramdb2 -- Run a parameter database server with a simple tabular GUI
+processtrak -- command line tool for controlling postprocessing steps
+pt_checkprovenance -- Tool to check provenance status of processed experiment
+                      logs
+dc_ricohphoto -- Tool to use Ricoh WiFi camera to capture pictures of
+                 and experiment
+dc_xlg2dpd -- tool to extract a datacollect parameter dump (.dpd file) from
+              an experiment log (OBSOLETE)
+thermal2limatix -- Tool to convert obsolete XML namespaces to the new
+                   limatix namespaces
+limatix-git -- Tool for automating committing raw data and scripts into main branch and processed output also into processed branches.
+
+Primary libraries in the limatix package
+----------------------------------------
+dc_value     -- value classes that support units and serialize to XML
+xmldoc       -- representation of an XML document such as an experiment log,
+                with routines to add and extract data.
+provenance   -- Provenance tracking within XML documents
+paramdb2     -- Database of parameters to be written to experiment log
+
+
+Documentation
+-------------
+Installation instructions are in INSTALL.txt
+Primary LIMATIX documentation is in doc/LIMATIX.xhtml.
+Some additional documentation on processtrak is in the presentation
+that can be accessed as doc/processtrak.odp or doc/processtrak.pdf
+
+
+
+Acknowledgments
+---------------
+Thanks to the LIMATIX proposal team for their input and support:
+  Hui Hu, Iowa State University
+  Amy Kaleita, Iowa State University 
+  Brian Mennecke, Iowa State University  1960-2016 RIP
+  Hridesh Rajan, Iowa State University
+  Michael Thompson, Cornell University
+
+Thanks also to Dave Forsyth and Carl Magnuson of TRI-Austin
+for their input and support. 
+
+Thanks to Joseph Hynek for providing the RF survey data used in the
+ProcessTrak example. 
+
+This material includes work based on work supported by the Air Force
+Research Laboratory under Contract #FA8650-10-D-5210, Task Order #023
+and performed at Iowa State University; Case number 88ABW-2016-4385
+
+This material includes work based on work supported by the NASA Early
+Stage Innovation (ESI) program under grant #NNX15AD75G

limatix-1.2.6/README.txt

@@ -0,0 +1,75 @@
+About LIMATIX
+------------------
+
+LIMATIX is a collection of tools for performing and recording
+scientific experiments, based on the twin ideas of checklists and
+experiment logs.  It does not address the problem of data acquisition
+per se -- it assumes you have another software package handling
+that. Instead, it addresses the parallel problems of keeping track of
+procedures, recording which procedures were performed (checklists),
+and keeping a log (like a laboratory notebook) of the progress of an
+experiment. It also includes a tool (processtrak) to assist in
+organizing and executing processing tasks.
+
+
+
+Programs
+--------
+datacollect2 -- Main program for performing checklist-based experiment logging
+dc_checklist -- Main program for standalone checklists and plans
+dc_chx2chf -- create a filled checklist file from an unfilled .chx file
+dc_getpath -- get the path to the datacollect2 installation
+dc_glade   -- run the glade 3.6.7 user interface builder to create custom
+              GUI interfaces
+dc_gui     -- Run a custom GUI interface created with dc_glade
+dc_paramdb2 -- Run a parameter database server with a simple tabular GUI
+processtrak -- command line tool for controlling postprocessing steps
+pt_checkprovenance -- Tool to check provenance status of processed experiment
+                      logs
+dc_ricohphoto -- Tool to use Ricoh WiFi camera to capture pictures of
+                 and experiment
+dc_xlg2dpd -- tool to extract a datacollect parameter dump (.dpd file) from
+              an experiment log (OBSOLETE)
+thermal2limatix -- Tool to convert obsolete XML namespaces to the new
+                   limatix namespaces
+limatix-git -- Tool for automating committing raw data and scripts into main branch and processed output also into processed branches.
+
+Primary libraries in the limatix package
+----------------------------------------
+dc_value     -- value classes that support units and serialize to XML
+xmldoc       -- representation of an XML document such as an experiment log,
+                with routines to add and extract data.
+provenance   -- Provenance tracking within XML documents
+paramdb2     -- Database of parameters to be written to experiment log
+
+
+Documentation
+-------------
+Installation instructions are in INSTALL.txt
+Primary LIMATIX documentation is in doc/LIMATIX.xhtml.
+Some additional documentation on processtrak is in the presentation
+that can be accessed as doc/processtrak.odp or doc/processtrak.pdf
+
+
+
+Acknowledgments
+---------------
+Thanks to the LIMATIX proposal team for their input and support:
+  Hui Hu, Iowa State University
+  Amy Kaleita, Iowa State University 
+  Brian Mennecke, Iowa State University  1960-2016 RIP
+  Hridesh Rajan, Iowa State University
+  Michael Thompson, Cornell University
+
+Thanks also to Dave Forsyth and Carl Magnuson of TRI-Austin
+for their input and support. 
+
+Thanks to Joseph Hynek for providing the RF survey data used in the
+ProcessTrak example. 
+
+This material includes work based on work supported by the Air Force
+Research Laboratory under Contract #FA8650-10-D-5210, Task Order #023
+and performed at Iowa State University; Case number 88ABW-2016-4385
+
+This material includes work based on work supported by the NASA Early
+Stage Innovation (ESI) program under grant #NNX15AD75G

limatix-1.2.6/TODO

@@ -0,0 +1,27 @@
+Bugs:
+
+- Second experiment photograph
+    Uploading a second photo results in the following error message:
+
+    Traceback (most recent call last):
+	  File "./../lib/xmldoc.py", line 3445, in requestvalcallback
+	    self.synchronize(dest,requestedvalue=newvalue)
+	  File "./../lib/xmldoc.py", line 3335, in synchronize
+	    raise ValueError("Error merging information for parameter %s from file %s: %s" % (self.controlparam.xmlname, str(filename),str(e)))
+	ValueError: Error merging information for parameter expphotos from file /tmp/tylertest/XLG/2016-01-06.xlg: Cannot merge values: Orig=2016-01-06_expphoto-001.jpg; descendents 2016-01-06_expphoto-001.jpg
+	2016-01-06_expphoto-002.jpg and 2016-01-06_expphoto-001.jpg
+
+- Multiple parameters in the same checklist (Slow Behavior)
+
+- Double check the measchecklist parameter
+
++ dc:process hostname bug
+    "Fixed" on 1/6 TL - This wasn't a bug as much as a confusion.  The code that validates hostname
+      only does so when <prx:hostname> is not None, but the output at the propmt says the value is
+      None rather than "" because of the split command in the format string, leading to confusion.
+      Clarified in the error message that the correct way to eliminate hostname requirement is to 
+      completely remove or comment out the <prx:hostname> tag.
+
+Features:
+
+- COMSOL from Python

limatix-1.2.6/VERSION

@@ -0,0 +1 @@
+1.1.4-devel

limatix-1.2.6/defs.mk

@@ -0,0 +1,36 @@
+
+# Installation prefix
+PREFIX=/usr/local
+PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
+
+VERSION=$(shell if [ -f VERSION ] ; then cat VERSION ; elif [ -f ../VERSION ] ; then cat ../VERSION ; elif [ -f ../../VERSION ] ; then cat ../../VERSION ; elif [ -f ../../../VERSION ] ; then cat ../../../VERSION ; fi )
+
+DCINSTDIR=$(PREFIX)/datacollect2-$(VERSION)
+
+INSTALL=/usr/bin/install
+
+PYCHECKER_PATH=$(shell if [ -x /bin/pychecker ] ; then echo "/bin/pychecker" ; elif [ -x /usr/bin/pychecker ] ; then echo "/usr/bin/pychecker" ; elif [ -x /usr/local/bin/pychecker ] ; then echo "/usr/local/bin/pychecker" ; elif [ -x /opt/bin/pychecker ] ; then echo "/opt/bin/pychecker" ; else echo "/none" ; fi )
+
+
+ifneq ($(PYCHECKER_PATH), /none)
+# only use pychecker 0.8.17 or later
+PYCHECKER=$(shell if [[ `$(PYCHECKER_PATH) -V | awk -F . '{print $$1}'` > 0 ||  `$(PYCHECKER_PATH) -V | awk -F . '{print $$2}'` > 8 || `$(PYCHECKER_PATH) -V | awk -F . '{print $$3}'` > 16 ]] ; then echo $(PYCHECKER_PATH) ; else echo "/none" ; fi )
+else
+PYCHECKER=/none
+endif
+
+
+PYTHON2.7=$(shell if [ -x /bin/python2.7 ] ; then echo "/bin/python2.7" ; elif [ -x /usr/bin/python2.7 ] ; then echo "/usr/bin/python2.7" ; elif [ -x /usr/local/bin/python2.7 ] ; then echo "/usr/local/bin/python2.7" ; elif [ -x /opt/bin/python2.7 ] ; then echo "/opt/bin/python2.7" ; else echo "/none" ; fi )
+
+PYTHON2.6=$(shell if [ -x /bin/python2.6 ] ; then echo "/bin/python2.6" ; elif [ -x /usr/bin/python2.6 ] ; then echo "/usr/bin/python2.6" ; elif [ -x /usr/local/bin/python2.6 ] ; then echo "/usr/local/bin/python2.6" ; elif [ -x /opt/bin/python2.6 ] ; then echo "/opt/bin/python2.6" ; else echo "/none" ; fi )
+
+PYTHON3.4=$(shell if [ -x /bin/python3.4 ] ; then echo "/bin/python3.4" ; elif [ -x /usr/bin/python3.4 ] ; then echo "/usr/bin/python3.4" ; elif [ -x /usr/local/bin/python3.4 ] ; then echo "/usr/local/bin/python3.4" ; elif [ -x /opt/bin/python3.4 ] ; then echo "/opt/bin/python3.4" ; else echo "/none" ; fi )
+
+PYTHON3.6=$(shell if [ -x /bin/python3.6 ] ; then echo "/bin/python3.6" ; elif [ -x /usr/bin/python3.6 ] ; then echo "/usr/bin/python3.6" ; elif [ -x /usr/local/bin/python3.6 ] ; then echo "/usr/local/bin/python3.6" ; elif [ -x /opt/bin/python3.6 ] ; then echo "/opt/bin/python3.6" ; elif [ -x /bin/python36 ] ; then echo "/bin/python36" ; elif [ -x /usr/bin/python36 ] ; then echo "/usr/bin/python36" ; elif [ -x /usr/local/bin/python36 ] ; then echo "/usr/local/bin/python36" ; elif [ -x /opt/bin/python36 ] ; then echo "/opt/bin/python36" ; elif [ -x /opt/rh/rh-python36/root/bin/python3.6 ] ; then echo "/opt/rh/rh-python36/root/bin/python3.6" ;else echo "/none" ; fi )
+
+PYTHON3.7=$(shell if [ -x /bin/python3.7 ] ; then echo "/bin/python3.7" ; elif [ -x /usr/bin/python3.7 ] ; then echo "/usr/bin/python3.7" ; elif [ -x /usr/local/bin/python3.7 ] ; then echo "/usr/local/bin/python3.7" ; elif [ -x /opt/bin/python3.7 ] ; then echo "/opt/bin/python3.7" ; elif [ -x /bin/python37 ] ; then echo "/bin/python37" ; elif [ -x /usr/bin/python37 ] ; then echo "/usr/bin/python37" ; elif [ -x /usr/local/bin/python37 ] ; then echo "/usr/local/bin/python37" ; elif [ -x /opt/bin/python37 ] ; then echo "/opt/bin/python37" ; elif [ -x /opt/rh/rh-python37/root/bin/python3.7 ] ; then echo "/opt/rh/rh-python37/root/bin/python3.7" ;else echo "/none" ; fi )
+
+PYTHON3.8=$(shell if [ -x /bin/python3.8 ] ; then echo "/bin/python3.8" ; elif [ -x /usr/bin/python3.8 ] ; then echo "/usr/bin/python3.8" ; elif [ -x /usr/local/bin/python3.8 ] ; then echo "/usr/local/bin/python3.8" ; elif [ -x /opt/bin/python3.8 ] ; then echo "/opt/bin/python3.8" ; elif [ -x /bin/python38 ] ; then echo "/bin/python38" ; elif [ -x /usr/bin/python38 ] ; then echo "/usr/bin/python38" ; elif [ -x /usr/local/bin/python38 ] ; then echo "/usr/local/bin/python38" ; elif [ -x /opt/bin/python38 ] ; then echo "/opt/bin/python38" ; elif [ -x /opt/rh/rh-python38/root/bin/python3.8 ] ; then echo "/opt/rh/rh-python38/root/bin/python3.8" ;else echo "/none" ; fi )
+
+DEFAULTPY=$(shell if [ -x /bin/python ] ; then echo "/bin/python" ; elif [ -x /usr/bin/python ] ; then echo "/usr/bin/python" ; elif [ -x /usr/local/bin/python ] ; then echo "/usr/local/bin/python" ; elif [ -x /opt/bin/python ] ; then echo "/opt/bin/python" ; else echo "/none" ; fi )
+