debian/0000755000000000000000000000000011577700445007200 5ustar debian/changelog0000644000000000000000000004654311577677105011074 0ustar horae (071~svn536-1) unstable; urgency=low * New plugin files in SVN pull * Upgrade to Standards-Version 3.9.2 -- Carlo Segre Mon, 20 Jun 2011 12:04:52 -0500 horae (071~svn533-1) unstable; urgency=low * Prerelease SVN pull * Upgrade to Standards-Version 3.9.0 (no changes) -- Carlo Segre Thu, 29 Jul 2010 02:06:01 -0500 horae (071~svn531-1) unstable; urgency=low * Prerelease SVN pull * Change dependency to libifeffit-perl due to renaming of perl wrapper * Add ${misc:Depends} dependency * Change to source format 3.0 (quilt) * Upgrade to Standards-Version 3.8.4 (no changes) -- Carlo Segre Tue, 11 May 2010 19:01:44 -0500 horae (070-1) unstable; urgency=low * New upstream release * Upgrade to Standards-Version 3.8.2 * Restore Education top level menu item in *.desktop files NOTE: This is not the right solution but conforms to the freedesktop.org standard. KDE and Gnome provide a "Science" top level menu through their own configuration files. XFCE4 currently does not but can be configured to do so. See README.Debian for this information. -- Carlo Segre Sat, 04 Jul 2009 11:16:53 -0500 horae (070~svn512-2) unstable; urgency=low * Remove WWWBrowser.pm from the package (Closes: #519030) * Add dependency on libwwwbrowser-perl. -- Carlo Segre Tue, 10 Mar 2009 21:40:32 -0500 horae (070~svn512-1) unstable; urgency=low * New upstream release * Split horae-doc into separate source and package, add dependency -- Carlo Segre Wed, 04 Mar 2009 23:07:54 -0600 horae (067-1) unstable; urgency=low * New upstream release * Completely changed build system, use quilt for patches * Eliminate horae-examples package and put exmaple tarballs into /usr/share/doc/horae/examples * Rename 'ifeffit_shell.pl' and its manpage to 'ifeffit_shell' * Return to using our own man pages for athena and hephaestus * Update Standards-Version to 3.8.0 (no changes) -- Carlo Segre Mon, 02 Mar 2009 00:34:32 -0600 horae (066-3) unstable; urgency=low * Apply patch to athena_parts/misc.pl for compatibility with perl-tk 804.28. -- Carlo Segre Sat, 23 Feb 2008 23:13:02 -0600 horae (066-2) unstable; urgency=low * Fix Athena to work properly with perl-tk 804.28 (in athena_parts/head.pl) * Update to Standards Version 3.7.3 (no changes) -- Carlo Segre Sat, 23 Feb 2008 14:23:41 -0600 horae (066-1) unstable; urgency=low * New upstream release -- Carlo Segre Sat, 22 Sep 2007 14:56:38 -0500 horae (065-3) unstable; urgency=low * Comply with new menu and desktop policy -- Carlo Segre Sat, 18 Aug 2007 10:42:20 -0500 horae (065-2) unstable; urgency=low * Enlarge default fixed fonts for proper default viewing -- Carlo Segre Tue, 24 Jul 2007 14:00:13 -0500 horae (065-1) unstable; urgency=low * New upstream release -- Carlo Segre Sat, 21 Jul 2007 19:16:07 -0500 horae (064-1) unstable; urgency=low * New upstream release, dropped dependency on libtk-filedialog-perl. -- Carlo Segre Thu, 28 Dec 2006 12:36:48 -0600 horae (063-3) unstable; urgency=high * Fix debian/rules file to account for changes in source tree organization and for case where maintainer forgets to delete unneeded CPAN module sources from upstream tarball. -- Carlo Segre Tue, 26 Dec 2006 11:54:29 -0600 horae (063-2) unstable; urgency=high * Add dependency on libtk-filedialog-perl and don't install the Tk/FileDialog.pm module (Closes: #404006). -- Carlo Segre Sun, 24 Dec 2006 15:51:39 -0600 horae (063-1) unstable; urgency=low * New upstream release -- Carlo Segre Mon, 27 Nov 2006 18:40:35 -0600 horae (062-2) unstable; urgency=low * Added Tag: field to debian/control for Enrico Zini's test. -- Carlo Segre Sat, 9 Sep 2006 01:30:15 -0500 horae (062-1) unstable; urgency=low * First official Debian release (Closes: #373211) * New upstream release * Added dependency on libtext-glob-perl * Flag for Debian build changed to '--platform=debian' -- Carlo Segre Thu, 29 Jun 2006 00:28:04 -0500 horae (061-1) unstable; urgency=low * New upstream release -- Carlo Segre Tue, 28 Mar 2006 10:40:30 -0600 horae (060-2) unstable; urgency=low * Remove menu entry for TkAtoms, which is no longer in horae. -- Carlo Segre Fri, 10 Mar 2006 23:59:05 -0600 horae (060-1) unstable; urgency=low * New upstream release - bug fixes -- Carlo Segre Wed, 8 Feb 2006 16:01:36 -0600 horae (059-1) unstable; urgency=low * New upstream release - bug fixes -- Carlo Segre Tue, 3 Jan 2006 01:51:00 -0600 horae (058-1) unstable; urgency=low * New upstream release -- Carlo Segre Tue, 22 Nov 2005 17:30:13 -0600 horae (057-3) unstable; urgency=low * Corrected Cromer-Liberman calculation close to edge. -- Carlo Segre Tue, 8 Nov 2005 23:31:45 -0600 horae (057-2) unstable; urgency=low * Comment out debugging statement in McMaster.pm -- Carlo Segre Tue, 8 Nov 2005 09:06:52 -0600 horae (057-1) unstable; urgency=low * New upstream release - see following URL for details http://cars9.uchicago.edu/iffwiki/HoraeVersion057 Changes described below in McMaster data incorporated -- Carlo Segre Mon, 7 Nov 2005 14:28:13 -0600 horae (056-3) unstable; urgency=low * Corrected some values in the McMaster data tables: U - a_l(1) Tm - L-beta emission energy Re - atomic number, weight, denssity and conversion factor -- Carlo Segre Fri, 4 Nov 2005 02:34:04 -0600 horae (056-2) unstable; urgency=low * Added dependency on libmath-round-perl. -- Carlo Segre Mon, 17 Oct 2005 13:21:24 -0500 horae (056-1) unstable; urgency=low * New upstream release -- Carlo Segre Fri, 14 Oct 2005 14:08:20 -0500 horae (054-1) unstable; urgency=low * New upstream release - see following for details http://cars9.uchicago.edu/iffwiki/HoraeVersion054 -- Carlo Segre Sun, 4 Sep 2005 11:09:45 -0500 horae (053-2) unstable; urgency=low * restricted FEFF calculations to NLEG=4 to reduce number of paths -- Carlo Segre Fri, 5 Aug 2005 18:39:40 -0500 horae (053-1) unstable; urgency=low * Artemis - version 0.8 released, too many new features to list see: http://leonardo.phys.washington.edu/~ravel/software/doc/Artemis/artemis0.8.pdf * Athena - new features: 1. New plug-in architecture for reading data files 2. Improvements to linear combination fitting 3. Plotting improvements * Hephaestus - new features: 1. Ion chamber utility changes 2. Formula utility changes -- Carlo Segre Sun, 17 Jul 2005 12:02:34 -0500 horae (053-0pre1) unstable; urgency=low * Upstream pre-release * Diana is no more, has become Artemis -- Carlo Segre Sat, 9 Jul 2005 12:14:14 -0500 horae (052-0pre1) unstable; urgency=low * Upstream pre-release -- Carlo Segre Tue, 31 May 2005 16:36:45 -0500 horae (051-1) unstable; urgency=low * New upstream release - bugfixes -- Carlo Segre Thu, 28 Apr 2005 00:23:48 -0500 horae (050-1) unstable; urgency=low * New upstream release - fixed Tk compatibilities -- Carlo Segre Sun, 24 Apr 2005 19:21:57 -0500 horae (049-1) unstable; urgency=low * Athena - new features: 1. Data can now be rebinned using Ifeffit's rebin() function 2. Automatic replotting of data when return is entered after change in textbox 3. Improved information display on main page * Artemis - bugfixes only * Hephaestus - new feature: 1. Added fluorescence line finder * Diana - many new features, see URL below: http://leonardo.phys.washington.edu/~ravel/misc/artemis0.8.pdf -- Carlo Segre Sat, 23 Apr 2005 19:06:15 -0500 horae (048-1) unstable; urgency=low * New upstream release * Mostly bugfixes except for new features in Diana -- Carlo Segre Fri, 14 Jan 2005 01:37:38 -0600 horae (047-2) unstable; urgency=low * Bug fix by Matt Newville for athena (set_properties.pl line 245-254) which allows data files to be read in. -- Carlo Segre Wed, 12 Jan 2005 00:46:26 -0600 horae (047-1) unstable; urgency=low * Artemis - bug fixes only. * Diana - new features: 1. Maintain a history of the fits made with a project such that old fits could be plotted and their log files examined. 2. Develop an interface for examining log files and writing reports from them. 3. Revamp the Feff interpretation page. 4. Revamp the Atoms page. 5. Revert a project to the state from a previous fit. 6. Reduce project file size by removing unused files from the project. 7. Import data directly from Athena project files. 8. Provide in-program documentation. -- Carlo Segre Wed, 5 Jan 2005 20:25:27 -0600 horae (046-1) unstable; urgency=low * Athena - bug fixes and one new feature, which is an indicator at the top of the list of data groups which tells you when your project has been modified and needs to be saved. Clicking on this indicator is the same as choosing "File->Save project". * Artemis - bug fixes only. * Diana - a number of important bug fixes and two major new features: 1. In the Fits menu, there is a menu item for saving a "full data" file. This file records the data, the fit, the residual, the background (if appropriate), and the window as columns in a single file. If chi(R) or chi(q) is saved, the FT parameters appropriate to the chosen fit are used for all the columns. 2. You can now revert your project to a previous fitting model by selecting that fit from the Data and Paths List and selecting the restore option from the Fits menu. Fit model restoration can also be done with the right-click menu on the list on the log viewer page. I'll be eager to hear how well this works for others. -- Carlo Segre Fri, 5 Nov 2004 21:29:39 -0600 horae (045-1) unstable; urgency=low * Athena - small change to avoid a bug in reading files with energies which are not in increasing order -- Carlo Segre Fri, 8 Oct 2004 18:52:38 -0500 horae (044-1) unstable; urgency=low * Diana - new release of development version 1. A revamped feff interpretation page with new functionality 2. A revamped atoms page with new functionality 3. Major improvements to the fit history system 4. Direct import of data from Athena project files 5. New type of parameter on the GDS page -- an "after" parameter is like a def in that it takes a math expression, but it is not part of the fit and is evaluated only after the fit finishes and then is recorded in the log file 6. Lots of bug fixes and minor feature enhancements. -- Carlo Segre Wed, 6 Oct 2004 18:21:57 -0500 horae (042-1) unstable; urgency=low * Diana - new release of development version 1. Revamped Feff interpretation page. a. Four combinations of font and color serve for various states of paths b. Plot paths + data from right-click menu c. Extended selection + right-click menu entries for operating on the set of selected paths 2. Added extended selection to the GDS list. Right-click menu now used to change type or discard selected parameters 3. Edit menu option to compact a project, which means to delete all unused files from a Feff calculation, thus making the project file smaller 4. Many bug fixes to the Fit history system -- Carlo Segre Tue, 7 Sep 2004 17:37:50 -0500 horae (041-2) unstable; urgency=low * Install Bruce Ravel's icons in the menu. -- Carlo Segre Thu, 2 Sep 2004 17:00:21 -0500 horae (041-1) unstable; urgency=low * Artemis: 1. Now reading CIF files 2. Updated to Archive::Zip 1.12 3. Better error checking on the Atoms page 4. Added an rmax_out configuration variable 5. Fixed bugs: a. importing multiple data sets with the same name into a project b. Plotting after fitting multiple data sets in q-space c. A problem writing fit column files * Diana: Development branch of Artemis 1. Moved Path_dev.pm to PathDev.pm and changed all instances of Ifeffit::Path to Ifeffit::PathDev in the diana branch 2. Fixed a problem saving fits, backgrounds, and residuals when a fit was not anchored in the Data and Paths List. 3. Fixed the triggering of the new version messages in artemis and diana and made them independent * Athena: 1. Using native menubar 2. Handle very long file and project names better 3. Added an rmax_out configuration variable 4. Nifty special effect as the mouse passes over items in the group list 5. Improved convolution dialog 6. do autoplot when changing the x-axis in the column selection dialog 7. do ln(abs()) of transmission data to deal with the odd situation of a scalar going negative 8. labels not group names in text reports 9. bugs: a. default energy column for feff's xmu.dat file b. renaming groups might have made them unclickable c. Alt-j and Alt-k in an empty project * Hephaestus: 1. New look to the button box 2. Added the edge finder 3. fixed a bug in how pressure was used in the ion utility 4. added energy and density units to the formula utility 5. formula utility now computes the mass needed for one absorption length even if the density of the sample is not provided. 6. for some inscrutable reason, I had commented out the report of the mass needed for an absorption length if the absorption length was quite long 7. added a reset button to the ion chamber utility 8. changed the button color scheme 9. made formula results area an ROtext and disabled the mouse-3 menu -- Carlo Segre Wed, 1 Sep 2004 01:02:36 -0500 horae (038-2) unstable; urgency=low * Artemis - bug fixes plus the following: 1. An autosave file is written at certain times so that you can recover work in the event of a crash. 2. Artemis now uses a native menubar. This means that the menus can be driven entirely from the keyboard using (on PC keyboards) the Alt key. 3. There are a couple of small changes in functionality on the GDS page. Now, if you click on a different variable while editing a variable, the first variable will be defined before the new one is displayed. 4. The General->workspace variable is no longer used. I apologize to those who used this feature, but it was the source of too many problems. 5. The writing of trap files has been disabled in this version, but the same information still gets written to the console and should * Athena - bug fixes * Haphaestus - new page with chart of electronic transitions. -- Carlo Segre Wed, 28 Jul 2004 00:19:08 -0500 horae (038-1rc2) unstable; urgency=low * New upstream release candidate -- Carlo Segre Wed, 14 Jul 2004 22:59:46 -0500 horae (038-1rc1) unstable; urgency=low * New upstream release candidate -- Carlo Segre Sat, 10 Jul 2004 12:10:13 -0500 horae (037-1) unstable; urgency=low * New upstream release -- Carlo Segre Mon, 21 Jun 2004 22:55:21 -0500 horae (036-2) unstable; urgency=low * Changed to require libarchive-zip-perl (>=1.02). -- Carlo Segre Thu, 3 Jun 2004 11:55:21 -0500 horae (036-1) unstable; urgency=low * New upstream release -- Carlo Segre Wed, 2 Jun 2004 22:51:19 -0500 horae (035-1) unstable; urgency=low * New upstream release -- Carlo Segre Wed, 2 Jun 2004 01:05:45 -0500 horae (034-1) unstable; urgency=low * New upstream release -- Carlo Segre Thu, 20 May 2004 18:55:29 -0500 horae (033-2) unstable; urgency=low * Correct build dependencies to use pbuilder. -- root Fri, 16 Apr 2004 01:17:23 -0500 horae (033-1) unstable; urgency=low * New upstream release, fixed project file managment in Artemis -- Carlo Segre Fri, 9 Apr 2004 23:46:07 -0500 horae (031-1) unstable; urgency=low * New upstream release. Merged Atoms into package. -- Carlo Segre Sun, 14 Mar 2004 00:56:39 -0600 horae (027-2) unstable; urgency=low * Fine tune installation of ifeffit perl extensions. -- Carlo Segre Sun, 21 Dec 2003 11:11:45 -0600 horae (027-1) unstable; urgency=low * New upstream release -- Carlo Segre Sun, 7 Dec 2003 23:12:43 -0600 horae (026-1) unstable; urgency=low * New upstream release -- Carlo Segre Wed, 26 Nov 2003 15:59:28 -0600 horae (025-1) unstable; urgency=low * New upstream release -- Carlo Segre Tue, 4 Nov 2003 00:07:21 -0600 horae (024-2) unstable; urgency=low * New release of ifeffit, rebuild wrapper -- Carlo Segre Thu, 30 Oct 2003 23:32:08 -0600 horae (024-1) unstable; urgency=low * New upstream release -- Carlo Segre Sat, 27 Sep 2003 16:03:27 -0500 horae (021-1) unstable; urgency=low * New upstream release -- Carlo Segre Thu, 19 Jun 2003 23:02:04 -0500 horae (020-2) unstable; urgency=low * New release of ifeffit, rebuild wrapper -- root Fri, 30 May 2003 17:31:32 -0500 horae (020-1) unstable; urgency=low * New upstream release, removed horae-update -- Carlo Segre Fri, 16 May 2003 22:24:41 -0500 horae (019-1) unstable; urgency=low * New upstream release -- Carlo Segre Mon, 5 May 2003 00:48:14 -0500 horae (018-4) unstable; urgency=low * Added color icons -- Carlo Segre Wed, 30 Apr 2003 02:19:56 -0500 horae (018-3) unstable; urgency=low * Added menu entry and draft icons -- Carlo Segre Tue, 29 Apr 2003 14:01:17 -0500 horae (018-2) unstable; urgency=low * Restored FBox after finding file selection bug in stock version -- Carlo Segre Mon, 28 Apr 2003 09:02:31 -0500 horae (018-1) unstable; urgency=low * New upstream release -- Carlo Segre Wed, 23 Apr 2003 22:55:02 -0500 horae (017-1) unstable; urgency=low * New upstream release -- Carlo Segre Tue, 22 Apr 2003 10:10:16 -0500 horae (015-3) unstable; urgency=low * Removed Tie:Watch as it is in perl-tk -- Carlo Segre Wed, 2 Apr 2003 01:02:48 -0600 horae (015-2) unstable; urgency=low * Removed FBox, Elements and Tk-Pod which caused overwrite conflicts. -- Carlo Segre Fri, 28 Mar 2003 11:01:08 -0600 horae (015-1) unstable; urgency=low * New upstream release -- Carlo Segre Fri, 28 Mar 2003 01:44:24 -0600 horae (014-1) unstable; urgency=low * Initial Release. -- Carlo Segre Wed, 5 Mar 2003 14:01:16 -0600 debian/control0000644000000000000000000000422511577677124010615 0ustar Source: horae Section: contrib/science Priority: optional Maintainer: Carlo Segre Build-Depends: debhelper (>= 7) Build-Depends-Indep: perl (>= 5.6.0-16), libchemistry-elements-perl, perl-tk (>= 804), libifeffit-perl Homepage: http://cars9.uchicago.edu/~ravel/software/Welcome.html Standards-Version: 3.9.2 Package: horae Architecture: all Tag: field::biology, field::chemistry, field::physics, implemented-in::perl, interface::x11, legacy::science, scope::suite, uitoolkit::tk, x11::application Depends: ${perl:Depends}, perl-tk (>= 804), ifeffit (>= 1:1.2.5), libifeffit-perl, libarchive-zip-perl (>=1.02), libchemistry-elements-perl, libchemistry-formula-perl, libcompress-zlib-perl, libconfig-inifiles-perl, libmath-combinatorics-perl, libmath-derivative-perl, libmath-spline-perl, libmath-round-perl, libparse-recdescent-perl, libpod-escapes-perl, libpod-simple-perl, libspreadsheet-writeexcel-perl, libstatistics-descriptive-perl, libtext-glob-perl, libtie-ixhash-perl, libtime-stopwatch-perl, libtk-gbarr-perl, libtk-histentry-perl, libtk-pod-perl, libtk-splashscreen-perl, libtk-filedialog-perl, libxml-simple-perl, libxray-absorption-perl, libxray-scattering-perl, perlindex, libwwwbrowser-perl, ${misc:Depends} Recommends: horae-doc Suggests: libstar-parser-perl Homepage: http://cars9.uchicago.edu/~ravel/software/Welcome.html Description: interactive graphical processing and analysis of EXAFS data ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms. . ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis. . HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data. debian/copyright0000644000000000000000000000232311372367730011132 0ustar This package was debianized by Carlo Segre on Wed, 5 Mar 2003 14:01:16 -0600. It was downloaded from http://cars9.uchicago.edu/~ravel/software Upstream Author: Bruce Ravel Athena and Artemis are Copyright (c) 2001-2008 Bruce Ravel All rights reserved. This program is free software; you can redistribute it and/or modify it provided that the above notice of copyright, these terms of use, and the disclaimer of warranty below appear in the source code and documentation, and that none of the names of The Naval Research Laboratory, The University of Chicago, University of Washington, or the authors appear in advertising or endorsement of works derived from this software without specific prior written permission from all parties. 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 THIS SOFTWARE. debian/rules0000755000000000000000000000534111577700445010263 0ustar #!/usr/bin/make -f # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PACKAGE=$(shell dh_listpackages) ifndef PERL PERL = /usr/bin/perl endif TMP = $(CURDIR)/debian/$(PACKAGE) configure: configure-stamp configure-stamp: dh_testdir # Generate the Build script $(PERL) Build.PL destdir=$(TMP) touch configure-stamp build: build-arch build-indep build-arch: build-indep: build-stamp build-stamp: configure-stamp dh_testdir ./Build build --verbose=1 ./Build test --verbose=1 # Generate man pages for artemis only cd lib/Ifeffit/lib/artemis.doc ; ./make_doc --man cd examples && \ tar -czf artemis_examples.tar.gz artemis && \ tar -czf athena_examples.tar.gz athena touch build-stamp clean: dh_testdir dh_testroot dh_clean build-stamp configure-stamp [ ! -f Build ] || ./Build realclean --verbose=1 # rm -f */*.db # rm -f athena.pl artemis.pl diana.pl hephaestus.pl athena artemis diana hephaestus rm -f athena_parts/rc.pl artemis_parts/rc.pl rm -f lib/Ifeffit/lib/athena/athenarc \ lib/Ifeffit/lib/athena/athena.ini \ lib/Ifeffit/lib/athena/athenarcw rm -f lib/Ifeffit/lib/artemis/artemisrc \ lib/Ifeffit/lib/artemis/artemis.ini \ lib/Ifeffit/lib/artemis/artemisrcw \ lib/Ifeffit/lib/artemis.doc/artemis.1 \ lib/Ifeffit/lib/artemis.doc/artemisdoc.pod rm -f examples/*.tar.gz dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # Install package in temporary directory ./Build install --installdirs vendor --verbose=1 rm -rf $(CURDIR)/debian/horae/usr/share/man/man3 rm -rf $(CURDIR)/debian/horae/usr/lib rm -rf $(CURDIR)/debian/horae/usr/share/perl5/WWWBrowser.pm # Tidy up names to avoid lintian errors mv $(CURDIR)/debian/horae/usr/bin/ifeffit_shell.pl \ $(CURDIR)/debian/horae/usr/bin/ifeffit_shell mv $(CURDIR)/debian/horae/usr/share/man/man1/ifeffit_shell.pl.1p \ $(CURDIR)/debian/horae/usr/share/man/man1/ifeffit_shell.1p dh_install debian/athena.xpm usr/share/pixmaps dh_install debian/artemis.xpm usr/share/pixmaps dh_install debian/hephaestus.xpm usr/share/pixmaps dh_install debian/athena.desktop usr/share/applications dh_install debian/artemis.desktop usr/share/applications dh_install debian/hephaestus.desktop usr/share/applications # Build architecture-independent files here. binary-indep: build install dh_testdir dh_testroot dh_installdocs dh_installexamples dh_installmenu dh_installman dh_installchangelogs dh_link dh_compress dh_fixperms dh_installdeb dh_perl dh_gencontrol dh_md5sums dh_builddeb # Build architecture-dependent files here. binary-arch: # We have nothing to do by default. binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install 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"Qt.iQtQtQtQtQtQtQtQtQtQtQtQtQtQt#W.La1#S.IbiQtQtQtQtQt.xbhbp#M#B", "Qt.S#MQtQtQtQtQtQtQtQtQtQtQtQtQtaUaY.n#lbE#sQt#gQtQtQtQt.F#iaL#X", "Qt#b#BQtQtQtQtQtQtQtQtQtQtQtQtQt.j#T#..7bsbF#g#4QtQtQtQt.F##a7aU"}; debian/atoms.10000644000000000000000000000337011372367730010407 0ustar .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .TH ATOMS 1 "May 1, 2006" .SH NAME atoms \- make lists of atomic coordinates from crystallographic data .SH SYNOPSIS .B atoms .RI [\-fu8gpsbaxF] [\-r#] [\-qvh] [\-t atptype \-o file] input_file .SH DESCRIPTION .IX Header DESCRIPTION Take crystallographic data from the input file given on the command line and write output as indicated by their contents. If no input file is given, F is used. If the input file specified at the command line is '-', then input is read from STDIN. If no output format is specified, an input file for feff will be written. Several command line switches can be used to override the contents of the input files. .PP .Vb 8 \& output file flags \& \-f feff6 input file \-u unit cell file \& \-8 feff8 input file \-g geometry file \& \-p P1 input file \-s symmetry file \& \-a alchemy atoms list \-x xyz atoms list \& \-b Protein Databank list \& \-F do not write feff file \-O write to STDOUT \& \-t s user supplied template \-o f output file name .Ve .PP .Vb 6 \& operational flags \& \-r # override the value of rmax with the given value \& \-A use a named file from the Atoms Database \& \-q suppress screen messages \& \-v write version information and exit \& \-h write this message and exit .Ve .PP .Vb 2 \& # = number f = file s = string .Ve .PP For complete information about Atoms, consult the documentation at: .br http://cars9.uchicago.edu/~ravel/software/doc/Atoms/ .SH AUTHOR .IX Header AUTHOR Atoms is copyright (c) 1998-2005 Bruce Ravel .br bravel@bnl.gov .br http://cars9.uchicago.edu/~ravel debian/README.Debian0000644000000000000000000000661511372401237011237 0ustar The horae tarball is distributed with all the CPAN modules that are required for the program. In order to save archive space and because one of the modules is non-free, the tarball has been modified from the original by completely removing the contents of the 0CPAN directory. The Ifeffit perl wrapper is not built as it is available as a separate package. The horae_update program is not included with the distribution as it is not used for Debian. Carlo U. Segre, June 26, 2006 ----- If you have visibility problems with the fixed fonts in artemis or athena or the fonts are so large that buttons are missing at the bottom of the window, you will need to edit ~/.horae/athenarc or ~/.horae/artemisrc to resolve the problem. The font information is a the bottom of these two files and the fonts most likely to need changes for visibility are those identified as "fixed" and "entry". Increasing or decreasing the point sizes by 2 should improve legibility or allow display of the buttons in the windows. Carlo U. Segre, July 29, 2007 ----- The freedesktop.org standards put all scientific software into a top level menu category called "Education". This is short-sighted and just plain wrong but until they change it, has to be rectified in the Window Manager configurations. KDE and Gnome already provide for a "Science" top level category but XFCE4 does not. It is relatively easy to make this change, however. 1. in /etc/xdg/menus edit xfce-applications.menu to have an entry which reads: Science xfce-science.directory Science and modify the Education entry to read: Education xfce-education.directory Education Science 2. in /usr/share/desktop-directories add a file called xfce-science.directory with contents as listed below. Icons are taken by default from the /usr/share/icons/gnome/32x32/categories directory and fortunately, there is an applications-science.png icon there. [Desktop Entry] Version=1.0 Encoding=UTF-8 Type=Directory Icon=applications-science Name=Science Name[ar]=العلوم Name[be]=Навука Name[bn]=বিজ্ঞান Name[bs]=Nauka Name[ca]=Ciència Name[cs]=Věda Name[da]=Videnskab Name[de]=Wissenschaft Name[dz]=ཚན་རིག Name[el]=Επιστημονικά Name[en_GB]=Science Name[eo]=Scienco Name[eu]=Zientzia Name[fi]=Tiede Name[fr]=Sciences Name[gl]=Ciencias Name[gu]=વિજ્ઞાન Name[he]=מדע Name[hi]=विज्ञान Name[hr]=Znanost Name[hu]=Tudomány Name[id]=IPTEK Name[it]=Scienza Name[ja]=科学 Name[km]=វិទ្យាសាស្ត្រ​ Name[ko]=과학 Name[ku]=Zanist Name[mk]=Наука Name[ml]=ശാസ്ത്രം Name[mr]=विज्ञान Name[nb]=Vitenskap Name[ne]=विज्ञान Name[nl]=Wetenschap Name[nn]=Vitskap Name[pt]=Ciência Name[ro]=Știință Name[sk]=Veda Name[sq]=Shkencë Name[th]=วิทยาศาสตร์ Name[tl]=Agham Name[tr]=Bilim Name[uk]=Наука Name[vi]=Khoa học Name[zh_TW]=科學 Comment=Scientific applications Comment[it]=Applicazioni scientifiche Comment[fr]=Applications scientifique Carlo Segre, July 3, 2009 debian/athena.10000644000000000000000000001767711372367730010543 0ustar .TH athena 1 "June 26, 2006" .SH NAME athena \- interactive \s-1XAS\s0 data processing .SH SYNOPSIS .B athena .RI " file" ... .SH DESCRIPTION This manpage documents the .B athena program, for interactive \s-1XAS\s0 data processing, including converting raw data to mu(E), aligning, merging, deglitching, Fourier transforming, and plotting. Basically, \fBAthena\fR is intended to handle all chores involving \s-1XAS\s0 data except for quantitative analysis by fitting to theoretical standards. \fBAthena\fR's sister program \&\fBArtemis\fR is the fitting program. .PP \&\fBAthena\fR has two interesting and unusual features. The first is that there are no buttons for explicitly removing the background from mu(E) data or for performing Fourier transforms. The only active buttons displayed on the main window are for plotting. \fBAthena\fR always knows when data requires a background removal or a Fourier transform and will perform the necessary analysis steps before displaying the plot. .PP The second interesting feature is that it is just as easy to perform analysis and plotting chores on multiple data sets as on an individual data set. \fBAthena\fR automates the most common data processing chores and automatically generates plots of one or more data sets. .SH "SYNOPSIS" .IX Header "SYNOPSIS" \&\fBAthena\fR is a graphical and interactive program written in the perl programming language, using the Tk display engine, the \s-1IFEFFIT\s0 \s-1EXAFS\s0 library, and the \s-1PGPLOT\s0 plotting library. (See below for a list of relevant URLs.) .PP When \fBAthena\fR starts, you are presented with a window whose layout looks something like this: .PP .RS +----------------------------------------+ .br | menubar | .br +---------------------------+------------+ .br | | | .br | | | .br | | Group | .br | Group | List | .br | Parameters | | .br | | | .br | | | .br | +------------+ .br | | Plot crrnt | .br | +------------+ .br | | Plot mrked | .br | +------------+ .br | | | .br | | Plot | .br | | Features | .br | | | .br | | | .br +---------------------------+------------+ .br | echo area | .br +----------------------------------------+ .RE .PP As you import data into \fBAthena\fR, \fIdata groups\fR are created and those groups are listed in the section labeled `Group List' . You select a group as the active one by clicking the left mouse button on its entry in the group list. When selected, the list entry is highlighted with an orange background and the parameters associated with that group are displayed in the large area on the left labeled `Group Parameters'. When you pass the mouse over a label in the group parameters section, you will notice that the label changes color. This indicates that a mouse click on the label will have an effect. Clicking the left mouse button will display a hint in the echo area as to the function of that parameter. See the section on group operations for the effect of a right mouse click. .PP The view of the group parameters is replaced when certain features of \&\fBAthena\fR are used. Choosuing any of the options from the Data, Align, Diff, or Analysis menus will temporarily replace the group parameters with views of parameters relevant to the chosen task. For example, when the log-ratio option is chosen from the Analysis menu, the view of group parameters is replaced by a view of the interface to \&\fBAthena\fR's log\-ratio/phase\-difference analysis. .PP Below the group list are two rows of button for plotting data. The red buttons are for plotting the selected data group. The purple buttons are for plotting multiple data groups. These buttons are labeled according to the data space of the plot. \fIE\fR, \fIk\fR, \fIR\fR, and \fIq\fR refer to \fIenergy\fR, \fIphotoelectron k\fR, \fIreal space R\fR, and \&\fIbacktransform k\fR, respectively. .PP Below the plot buttons are a set of tabs for specifying the details of the plots in each space. For each space you can specify the range of the x\-axis. For energy plots, you can select whether the background function is plotted along with the data and whether the data and background are normalized. For k\-space plots, you can select the amount of k\-weighting. For R\- and q\-space plots, you can select which part of those complex functions are plotted. There are also tabs for setting up stacked plots and for establishing plot indicators. For a complete discussion see the section on plotting. .PP Finally, at the bottom of the page is the \fIecho area\fR. \fBAthena\fR uses this area to display hints, brief help messages, warnings, and updates about recently performed analysis or plotting actions. A few features of \fBAthena\fR will prompt the user for a text string. In those situations, the echo area is temporarily replaced by text string dialog. .PP Throughout \fBAthena\fR the right mouse button serves to post \fIcontext sensitive menus\fR. These include parameter labels, groups list entries, and other elements on the screen. You should try clicking the right mouse button in different places to see what usefuls things might pop up. .SH "REFERENCES" .IX Header "REFERENCES" Here are the relevant URLs: .IP "\s-1IFEFFIT\s0" 4 .IX Item "IFEFFIT" .RS http://cars.uchicago.edu/ifeffit .RE .IP "\s-1PGPLOT\s0" 4 .IX Item "PGPLOT" .RS http://www.astro.caltech.edu/~tjp/pgplot/ .RE .IP "Perl" 4 .IX Item "Perl" .RS http://www.perl.com .RE .IP "perl/Tk" 4 .IX Item "perl/Tk" .RS http://www.lehigh.edu/~sol0/ptk/ .RE .IP "Central atom phase shifts" 4 .IX Item "Central atom phase shifts" .RS http://leonardo.phys.washington.edu/~ravel/software/feff_tables/ .RE .SH "MISSING FEATURES" .IX Header "MISSING FEATURES" You betcha! Lots! Here's a partial list: .IP "*" 4 Principal Component Analysis on the set of marked groups .IP "*" 4 \&\s-1XANES\s0 analysis by fitting a sum of scans to an unknown .IP "*" 4 Dead-time and self-absorption corrections .IP "*" 4 Handle dispersive data sets, i.e. data sets wherein the I0 and \s-1IT\s0 measurements are in separate data files becuase the data were obtained sequentially .IP "*" 4 Calibrate dispersive data to a trusted standard .IP "*" 4 Handle \s-1SPEC\s0 files. An independent perl module would be ideal. This is a project some eager contributor could tackle without having to delve into \s-1ATHENA\s0's source code. .IP "*" 4 Alignment of scans using a reference, either of the same edge or of a nearby edge. (Any suggestions? I am lacking a good idea about how to implement this...) .IP "*" 4 Formulas for the energy axis (useful for converting encoder readings to energy values) .IP "*" 4 R and q space records, that is to be able to read and write data in R and q space just as easily as E or k space. .IP "*" 4 Internationalization. That is, build a framework for having text strings read from external files and for the language to be a configuration option. .IP "*" 4 Documentation, documentation, documentation .SH "WHAT'S IN A NAME?" .IX Header "WHAT'S IN A NAME?" Athena was the goddess of wisdom and is also associated with skill and justice. Those are all good qualities for a data analysis program! .PP .SH OPTIONS This program requires no options. .SH SEE ALSO This program is part of the horae XAS analysis suite which can be obtained at .br http://cars9.uchicago.edu/~ravel/software/ .SH "AUTHOR" .IX Header "AUTHOR" Bruce Ravel (c) 2001 - 2003 .PP Ifeffit is copyright (c) 1992 - 2003 Matt Newville .br newville@cars.uchicago.edu .br http://cars9.uchicago.edu/~newville/ifeffit/ debian/horae.menu0000644000000000000000000000104011372367730011156 0ustar ?package(horae):needs="X11" \ section="Applications/Science/Data Analysis" \ title="Athena" \ command="/usr/bin/athena" \ icon="/usr/share/pixmaps/athena.xpm" ?package(horae):needs="X11" \ section="Applications/Science/Data Analysis" \ title="Artemis" \ command="/usr/bin/artemis" \ icon="/usr/share/pixmaps/artemis.xpm" ?package(horae):needs="X11" \ section="Applications/Science/Data Analysis" \ title="Hephaestus" \ command="/usr/bin/hephaestus" \ icon="/usr/share/pixmaps/hephaestus.xpm" debian/artemis.10000644000000000000000000000150711372367730010730 0ustar .TH ARTEMIS 1 "june 26, 2006" .SH NAME artemis \- interactive EXAFS data fitting and modeling .SH SYNOPSIS .B artemis .RI " file" ... .SH DESCRIPTION This manpage documents briefly the .B artemis program, an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis. .br This manual page was written for the Debian distribution because the original program does not have a manual page. .PP .SH OPTIONS This program requires no options. .SH SEE ALSO This program is part of the horae XAS analysis suite which can be obtained at .br http://cars9.uchicago.edu/~ravel/software/ .SH AUTHOR This manual page was written by Carlo Segre , for the Debian GNU/Linux system (but may be used by others). debian/watch0000644000000000000000000000013311372367730010225 0ustar version=3 http://cars9.uchicago.edu/~ravel/software/packages/horae-(\d{3})\.tar\.gz debian debian/athena.xpm0000644000000000000000000000250611372367730011170 0ustar /* XPM */ static char *dummy[]={ "32 32 10 1", ". c #000000", "h c #1c1c1c", "a c #393939", "c c #555555", "# c #717171", "g c #8e8e8e", "e c #aaaaaa", "b c #c6c6c6", "d c #e3e3e3", "f c #ffffff", "........#a#a##bcde..............", ".........a.e#dffda..............", "........a#gcffffffch............", ".........acfffffffbg............", "........adfffffffffge...........", "........adffffffffffda..........", "........cbffffffdebfd#..........", "........gffffffgdecfea..........", ".......affffffddffffff..........", ".......agfffffddffffgf#.........", ".......#fbgfffffffffbcgh........", "......aecgfffffffffffggh........", ".......eaebffffffgcbgfde........", ".......aaabffffgffffffde........", "......aacbeeffbgae..aaaee.....cb", "........ffaecchc........e.....hg", ".......afffbhh..hhggcc...#..aa.#", "......adcbgcgg.#bbffff..........", "......aa...#...##.edbbea........", "...................abc..........", "......hh......cghhaae...........", "......hh.....#cfggeee...........", "......e.hc..hcgbbfbfffe.........", "......a.hc..hcgbbgbfbca.........", "..........aahhgg##eee#..........", "............ghgg###.a#..........", "..............###.a.............", "..............aeeaa..#..........", "..........e#..aahhcc............", "..........a#.#..gggg............", "..........bge.a...#.............", "..........cga#a.aa.............."}; debian/hephaestus.xpm0000644000000000000000000000231511372367730012077 0ustar /* XPM */ static char *dummy[]={ "32 32 2 1", "# c #000000", ". c #ffffff", "................................", "................................", "................######..........", "............##########..........", "........##############..........", "......################..........", "....##################..........", "....##################..........", "....#################...........", "....################............", "....#############...............", "....############................", "............####................", ".............###................", "..............##................", "..............##................", "..............##................", "..............##................", "..............###...............", "..............###...............", "..............####..............", "..............####..............", "..............#######...........", "..............#######...........", "..............########..........", "..............########..........", ".............##########.........", "............############........", "...........#############........", "..........##############........", "..........##############........", "..........##############........"}; debian/hephaestus.desktop0000644000000000000000000000046311372367730012746 0ustar [Desktop Entry] Type=Application Encoding=UTF-8 Name=Hephaestus Comment=The x-ray absorption spectroscopist's periodic table GenericName=X-ray Absorption Data Tables Icon=/usr/share/pixmaps/hephaestus.xpm Exec=hephaestus %F Terminal=False StartupNotify=true Categories=Education;Science;DataVisualization; debian/horae.manpages0000644000000000000000000000017011372367730012010 0ustar debian/athena.1 lib/Ifeffit/lib/artemis.doc/artemis.1 debian/hephaestus.1 debian/findatp.1 debian/atoms.1 debian/rdaj.1 debian/horae.dirs0000644000000000000000000000005111372367730011154 0ustar usr/share/applications usr/share/pixmaps debian/artemis.desktop0000644000000000000000000000040711372367730012237 0ustar [Desktop Entry] Type=Application Encoding=UTF-8 Name=Artemis Comment=Interactive EXAFS data analysis GenericName=EXAFS Analysis Icon=/usr/share/pixmaps/artemis.xpm Exec=artemis %F Terminal=False StartupNotify=true Categories=Education;Science;DataVisualization; debian/athena.desktop0000644000000000000000000000040711372367730012033 0ustar [Desktop Entry] Type=Application Encoding=UTF-8 Name=Athena Comment=Interactive EXAFS data processing GenericName=EXAFS Processing Icon=/usr/share/pixmaps/athena.xpm Exec=athena %F Terminal=False StartupNotify=true Categories=Education;Science;DataVisualization; debian/hephaestus.10000644000000000000000000000147211372367730011436 0ustar .TH HEPHAESTUS 1 "June 26, 2006" .SH NAME hephaestus \- a periodic table for the spectroscopist .SH SYNOPSIS .B hephaestus .RI " file" ... .SH DESCRIPTION This manpage documents briefly the .B hephaestus program, a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data. .br This manual page was written for the Debian distribution because the original program does not have a manual page. .PP .SH OPTIONS This program requires no options. .SH SEE ALSO This program is part of the horae XAS analysis suite which can be obtained at .br http://cars9.uchicago.edu/~ravel/software/ .SH AUTHOR This manual page was written by Carlo Segre , for the Debian GNU/Linux system (but may be used by others). debian/rdaj.10000644000000000000000000000063611372367730010206 0ustar .TH RDAJ 1 "May 1, 2006" .SH NAME rdaj \- echo the journal entry Athena/Artemis projects to the screen .SH SYNOPSIS .IX Header SYNOPSIS .B rdaj .RI [\-h] project_file .SH DESCRIPTION .IX Header DESCRIPTION This little program grabs the journal entry from your Athena or Artemis project files and echos it to the screen. .SH AUTHOR .IX Header AUTHOR Bruce Ravel, bravel@anl.gov .br http://cars9.uchicago.edu/~ravel debian/diana.10000644000000000000000000000147711372367730010346 0ustar .TH DIANA 1 "June 26, 2006" .SH NAME diana \- interactive EXAFS data fitting and modeling .SH SYNOPSIS .B diana .RI " file" ... .SH DESCRIPTION This manpage documents briefly the .B diana program, an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis. .br This manual page was written for the Debian distribution because the original program does not have a manual page. .PP .SH OPTIONS This program requires no options. .SH SEE ALSO This program is part of the horae XAS analysis suite which can be obtained at .br http://cars9.uchicago.edu/~ravel/software/ .SH AUTHOR This manual page was written by Carlo Segre , for the Debian GNU/Linux system (but may be used by others). debian/findatp.10000644000000000000000000000135611372367730010713 0ustar .TH FINDATP 1 "June 26, 2006" .SH NAME findatp \- find atoms template files .SH SYNOPSIS .B findatp .RI " file" ... .SH DESCRIPTION This manpage documents briefly the .B findatp program, a program which searchers for atoms template files. This program is mostly called internally by components of artemis. .br This manual page was written for the Debian distribution because the original program does not have a manual page. .PP .SH OPTIONS This program requires no options. .SH SEE ALSO This program is part of the horae XAS analysis suite which can be obtained at .br http://cars9.uchicago.edu/~ravel/software/ .SH AUTHOR This manual page was written by Carlo Segre , for the Debian GNU/Linux system (but may be used by others). debian/compat0000644000000000000000000000000211372367730010375 0ustar 7 debian/NEWS0000644000000000000000000000032111372367730007672 0ustar horae (064-1) unstable; urgency=low The dependency on libtk-filedialog-perl has been dropped by upstream, you may delete the package. -- Carlo Segre Thu, 28 Dec 2006 12:36:48 -0600 debian/horae.examples0000644000000000000000000000010111372367730012025 0ustar examples/artemis_examples.tar.gz examples/athena_examples.tar.gz debian/patches/0000755000000000000000000000000011424224067010617 5ustar debian/patches/series0000644000000000000000000000005111372367730012037 0ustar change-athena-fonts change-artemis-fonts debian/patches/change-athena-fonts0000644000000000000000000000101611424224067014352 0ustar --- a/lib/Ifeffit/lib/athena/athena.config +++ b/lib/Ifeffit/lib/athena/athena.config @@ -2491,7 +2491,7 @@ variable=fixed type=font -default=Courier 12 +default=Courier 14 windows=Courier 10 variable_width=no restart=1 @@ -2501,7 +2501,7 @@ variable=entry type=font -default=Courier 10 +default=Courier 12 windows=Courier 9 variable_width=no restart=1 @@ -2510,7 +2510,7 @@ variable=entrybold type=font -default=Courier 10 bold +default=Courier 12 bold windows=Courier 9 bold variable_width=no restart=1 debian/patches/change-artemis-fonts0000644000000000000000000000144211372367730014570 0ustar --- a/lib/Ifeffit/lib/artemis/artemis.config +++ b/lib/Ifeffit/lib/artemis/artemis.config @@ -1704,7 +1704,7 @@ variable=fixedsm type=font -default=Courier 10 +default=Courier 12 variable_width=no restart=1 description @@ -1713,8 +1713,8 @@ variable=fixed type=font -default=Courier 12 -windows=Courier 10 +default=Courier 14 +windows=Courier 12 variable_width=no restart=1 description @@ -1724,8 +1724,8 @@ variable=fixedit type=font -default=Courier 12 italic -windows=Courier 10 italic +default=Courier 14 italic +windows=Courier 12 italic variable_width=no restart=1 description @@ -1735,8 +1735,8 @@ variable=fixedbold type=font -default=Courier 12 bold -windows=Courier 10 bold +default=Courier 14 bold +windows=Courier 12 bold variable_width=no restart=1 description debian/source/0000755000000000000000000000000011372373760010477 5ustar debian/source/format0000644000000000000000000000001411372373760011705 0ustar 3.0 (quilt)