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sanghamitra-mukhopadhyayRastislavTuranyiTuranyieurydice76gonzalezma
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Merging release-next into main in preparation to the release 1.5.2 (#204)
* Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * 28 enhance simple help (#54) * Replaced plain text window by an HTML window for better reading experience of the simple help * Add superscipts * added a missing superscript in simple help html file Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add User Guide DOI to GUI help menu (#49) Co-authored-by: Turanyi <[email protected]> * Replace outputData reference with correct variables * Remove ability to plot non-meaningful data (#34) * Catch the TypeError and abort autofit * Notification is shown when user initiates invalid autofit * Handle TypeError in add_offset method * Partially clean up code to increase PEP8 compliance * Revert and instead stop before plotting * Remove certain variables from plotting * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Prevent plotting of new variables * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * filtered out the variables which are not of numeric type * Forbid remaining trajectory variables Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Update headers (#47) * Update copyright information inside headers * Revert ILL copyright to 2013-now Co-authored-by: Turanyi <[email protected]> * Implement velocity reading in Gromacs converter via TRR files (#44) * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Change gui label to 'xtc and trr file' * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Add tests * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Add tests * The coords, velocities and forces arrays are now casted to float64 * Clean up Gromacs.py of git dif lines * Update tests to check gradients Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Use existing vars to calculate tcf and rdf * Fixed bug in writing quaternions,com and fit variables in rbt job * Write units in trajectory files (#72) * Fixed typo in Converter.py file * Fixed typo in Converter.py file * Securized the code for writing units in the trajectory file Co-authored-by: eric pellegrini <[email protected]> * Added better securization around the adding of units in Converter.finalize method (#73) Co-authored-by: eric pellegrini <[email protected]> * MD compliant plotter (#61) * Added a new mode for viewing 3D data * Added brand new plugin for viewing trajectory related variables * Added support for unit in TrajectoryViewer plugin cosmetic change in DCDConverter file * Fix bug with 2D slice * Fixed windows-specific bug when doing scalar plot * Added the possibility to remove lines for the TrajectoryViewer plugin * Fixed buggy behavior with the legend Co-authored-by: eric pellegrini <[email protected]> * Make the names of output files more descriptive (#60) * Change output file default name in GUI * Implement incrementing filename for job output * Modified the algorithm for checking already existing filename * Added a mechanism for guessing the output filename for converter analysis * Removed print * Added a new configuration/widget for setting single output file * Update headers of new files to comply with #47 * Update configurator docstrings * Removed useless checking of datakey in set_data method * Renamed OutputFile configurator and widgets to SingleOutputFile Co-authored-by: eric pellegrini <[email protected]> * Add continuous integration using GitHub actions (#20) * Replace buggy py2app qt recipes with correct ones * Change the replacement qt files to always return None * Change qt5.py into a dummy function * Make qt6 a dummy too * Truly make qt6 a dummy too and add netcdf investigation * Place change_dylib_path.sh code into deploy_old.sh * Add investigation and ' to deploy_old.sh * Add more investigation * Add more investigation * Try using -fv with problematic command * Stop using wildcard with cp * Deploy for different ubuntus separately * Deploy for different ubuntus separately * Correct artifact name * Increase investigation * Copy libhdf5 files into artifacts * Try removing arguments from build.py * Restore arguments to build.py * Search ubuntu for libsz * Copy the whole x86_64-linux-gnu file * Use argparse in build.py * Only parse known arguments * Revert, instead hardcode py2app arg and change depends for deb * Try several things and fix syntax error * Correct paths and try sudo * Use source and include parameters * Add osx sphinx investigation and copy libnetcdf on ubuntu * Add more investigation about sphinx * Correct syntax and upload log * Fix yaml indentation * Correct path to sphinx logs * Add further investigation * Always run the copy of sphinx log * Disable the failing sphinx usage for now * Place ' around args * Remove args completely from build.py * Specify version of docutils * Move scripts to the same run as build.py * Create different installers for different versions of ubuntu * Enable ubuntu * Correct ubuntu and use getenv * Enable ubuntu * Use sys.argv * Try solutions to the build.py issue * Try using --argv-inject * Try ways to use --argv-inject correctly * Print sys.argv * Use argv correctly * Remove the extra MDANSE from icon path * Correct path to icons * Create directory before creating file inside it * Add postinst and create installer for ubuntu 21 * Correct postinst path and remove rm * Correct artifact name for ubuntu 21 * Add mising su privilege * Add missing su privileges * Correct ubuntu version, sed permanently and correct postinst * Create Contents/MacOS directory before symlinking into it * Add missing files * Expand amount of places where env vars are exported on ubuntu * Add missing ' * Correct postinst type of ' on ubuntu * Correct env var name * Copy dylibs * Add investigation * Add investigation and add files for fake osx deploy * Correct mistakes and add investigation * Correct path * Copy libwx * Correct typo and dist dir path * Remove unmounting and add sudo * Provide correct permissions and investigate * Add investigation * Add sudo everywhere in old * Use mv -T to force rename * Remove -T * Use matrix for osx CI and add investigation * Create bin in resources first * Add missing sudo * Add more sudos * Change python link name * Add more sudos * Add investigation and use the list rather than ls list * Use full path with GITHUB_WORKSPACE for wx dylibs * Remove quotes around the dylib path * Add investigation * Use complete full path * Use sudo inside script rather than sudo script * Add investigation and use * instead of @ * Use cd and then get the list * Add investigation, add files to fake and add sudo * Remove sudo and investigation and use more complete path * Correct paths * Correct paths * Add investigation * Use sudo hdiutil create * Remove unmount and -debug * Increase projected dmg size and remove untarred artifacts * Try ways to decrease disk size * Upload dist folder * Delete instead of uninstall and use df -h * Remove upload * Add investigation to create_dmg * Move dylibs rather than copy * Set -size to be 200 larger than expected * Add sudos * Remove deploy_osx and investigation and export mdanse_dmg * Search for libint* * Dont copy python dylib * Include libint dylib and deploy on macos 11 too * Correct yaml syntax * Correct artifact names * Change libintl path in libpython2.7.dylib * Comment out _boot_multiprocessing in __boot__ and add investigation * Correct python dylib pointer on macos11 * Relink dylibs amond each other, add investigation and cp not mv * Replace ls with find for investigation * Also change wx dylib links. Add investigation * Change dylib link for all wx dylibs * Remove ' from cp with wildcard * Change dylib links for libwx in lib-dynload * Search for libz and libc++ * Include missing dylibs and change rpath to executable path * Correct typos in dylib names * Actually correct typos in dylib names * Investigate hashlib and don't copy libz and libc++ on 11 * Try unlinking openssl and correct paths * Only unlink on macos10.15 * Correct placements of conditional statement * Investigate openssl on mac11 * Try specifying openssl version * Link more dylibs and try copying libssl * Add investigation and try buildin app with --includes openssl * Investigate ssl locations * Relink _hashlib.so to correct dylibs * Relink vtk so files inside lib-dynload * Change vtk rpath instead * Try relinking other files, remove extra python and link dylibs rather than copy * Correct issue * Try different source for wxpython * Try different source for conda wx * Revert to previous provider and correct cp paths * Correct path * Revert to original provider * Investigate wx version * Use -r to copy egg info * Build wxpython from source * Use sudo * Only build from source on 10.15 * Try wx from travis on mac11 * Disable fail fast * Copy over files on mac11 * Move vtk and wx installation to deploy and use conda wx3 * Correct yaml syntax * Remove wx installation from ci_osx * Replace mdanse_gui test with running the app at the end of deploy * Correct copying and remove ln * Relink .so files in lib-dynload/wx * Make PlatformError in create_directory more descriptive * Correct yaml syntax * Test bundled python and add bash script to run it * Correct sed command syntax * Use echo >> instead of sed -i * Improve script and make executable and bundle bin/python * Remove extension from script * Correct script name * Make python2 behave like an actual python * Correct script and remove bin/python * Correct windows desktip shortcut icon path * Delete unused files * Try using for links in windows nsi * Copy the MDANSE shortcut to desktop * Clean up yaml and scripts * Try out cache action for vs2008 * Try removing ' from around path * Remove ' from around paths * Set VS90CMNTOOLS * Append PATH and use cmd * Cache sdk 5.0 too * Cache sdk 5 and 6 and set windowssdkdir * Correct mistakes and search for mingw * Correct yaml syntax * Use cmd for test * Use powershell ls for test * Try using mingw and editing vcvarsamd64 * Use custom vcvarsamd.bat and set env vars manually * Correct mistake and set python vars * Try vs for python2.7 * Add investigation * Cache separately * Correct yaml issues * Correct yaml issues * Run restore after retrieving from cache * Try full install after restoring cache * Try vc for python2.7 * Try using setuptools * Run vcvarsall too * Add paths * Remove restoring VS2008 * Correct name * Save the msi to github workspace * Remove id * Restore vs2008 from cache * Bring the experimental win CI to be official * Try removing .net framework from caching * Add postrm script for ubuntu * Run vcvars before scientific and cache CI result * Try replacing distutils with setuptools in scientific * Replace scientific setup.py with edited one * Install VS2008 if python could not be restored * Correct != into == * Change key name from python to mdanse * Remove old step * Use full path to python * Use ' * Put the problematic line on a separate line * Fix the yaml syntax * Use full path to all pythons * Try running macos tests directly * Unpack list for os.path.join in BuildJobTests * Correct BuildJobTests.py to get right path to ref data * Make AllTests.py be able to be run from anywhere * Use different approach * Create the test files inside Jobs/ * Put test file name as full path * Use os.chdir inside all test scripts * Add usage instructions to mac * Bring the README to workspace * Correct readme path and try different logic * Correct yaml indentation * Correct yaml syntax * Remove extra MDANSE build install step * Make mdanse scripts able to be run by themselves * Correct ubuntu dependencies and ensure LD_LIBRARY_PATH is set * Correct sed syntax * Remove superfluous netcdf caching * Correct python syntax edited into mdanse scripts * Correct windows netcdf download url * Use older py2app and try != true instead of == false * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Add sudo apt-get update on ubuntus * Update maintainer/publisher information * Remove this branch from deploy list * Remove dangerous MacOS parse_command_line.py * Remove the copying of removed script * Remove deployment on this branch * Fixed regression due to recent merge * Don't subtract 1 from pdf during tcf_intra calculation * Regenerate test reference file using current code * Fixed buggy DL_POLY trajectory * Added mdanse_job application for running a job through a stand-alone dialog (#65) * Added mdanse_job application for running a job through a stand-alone dialog * Added more info to mdanse_job script help Fixed typo with Doc/conf_api.py file * Revert changes to Doc Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix broken tests (#66) * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Change BuildJobTests to ignore T and KE * Use try finally when opening NetCDF files * Don't compare velocities in DFTB and Forcite * Make DFTB and Forcite tests proper by generating new references * Delete copies even when exception occurs * Fix issues due to output_file vs output_files * Fix bug with triclinic unit cells * Fixed regression in ConfigurationPanel (#84) Co-authored-by: eric pellegrini <[email protected]> * Use netCDF4 as the NetCDF dependency instead of Scientific.IO/NetCDF (#81) * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Install netCDF4 during CI/CD pipeline * Correct windows netCDF4 path * Copy netCDF4 contents on ubuntu ci * Add investigation to CI/CD * Set HOME env var before using it on win * Correct netCDF4 path on ubuntu and mac * Copy .so libraries on unixes * Add investigation to windows pipeline * Investigate RUNNER_TOOL_CACHE on win CI * Correct netCDF4 destination path on win * Separate conda calls on win and copy libmfhdf on unix * Copy over libdf.so on unix pipelines * Remove leadin \ from xcopy source on win pipeline * Create destination dirs on windows pipeline * Edit paths on ubuntu * Investigate KeyError on win pipeline * Copy netcdf and hdf5 libs on ubuntu * Try importing problematic configurator directly * Add investigation to pipelines * Correct yaml syntax * Correct yaml syntax * Copy msvc dlls from conda to main on win * Copy netcdf dlls into python\DLLs on win * Copy netcdf dlls into netCDF4 directory * Clean up pipelines * Fix broken tests * Handle possible IOError in tests * Handle IOError on monoprocessor too * Run AllTests.py with sudo * Relocate test output file for Test_dp * Add forgotten \n to BuildJobTests * Correct test generation for dp on linux * Use repo directory for dp output path on linux * Alter BuildJobTests to output to reference dir * Clean up pipeline and BuildJobTests * Use context manager in test_gromacs_trr * Use context manager in PlotterPlugin * Add forgotten context managers to test_trr Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fixed bug when closing partial charges plugin (#85) Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add advanced units manipulation and definition options (#78) * Added Units module for handling units * Advances in integration of Units module in the plotter * Added Units module for handling units * Advances in integration of Units module in the plotter * Added app for editing units The plotter accepts now equivalent units (e.g. THz/eV) Added icon ofr units * Removed external dependencyy to magnitude project * Fixed conflicts * Added the possibility to add an unit from the units editor * Fixed bug when closing the UnitsEditor dialog * Install pyyaml on CI/CD pipeline * Added docstrings and more unit tests to Units module * Added new equivalences Added warning when adding unit in the unit editor * Added new equivalences * Updated the units editor dialog * Big fixed when multiplying or dividing unit by another * Added J_per_mole unit * Change q unit from inv_nm to 1/nm Big fixed in the unit parser * Bug fix with inv_nm factor in Units.yml * Added unit test for prefixes * Bug fixed in __ipow__ function * Removed old dependencies to magnitude * Fixed regression in Forcite converter * Fixed bug in SFFSF analysis * Added akma_time in available units Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix script installation (#82) * Remove setuptools and enable CD * Correct branch name in CI.yml and try running VS9 vcvars * Call correct vcvars on CD too * Use setuptools on runners only, keep only distutils in default setup * Remove this branch from contains() calls * Add abstraction for plotter data (#86) * Added abstraction layer for NetCDF data * Added missing method for closing data properly * Added missing module * Added _IPlotterVariable interface and NetCDFPlotterVariable concrete class * Added comments to PlotterData module Fixed bug in load_data * Fixed bug with axis names * Fixed regression in PlotterPlugin.py * Flattened the name of the variable in PlotterData Added Path columns to datalist in Plotter * Implement context manager for PlotterData classes * Removed __del__ method of _IPlotterData class Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Update apt-get on ubuntu CD (#77) * Make MacOS CI fail when tests fail (#88) * Move MacOS tests to yaml * Add bug to test changes * Remove testing bug * Fix the installation of netCDF4 on MacOS CI/CD (#90) * Investigate the issue * Remove leading / when copying netcdf4 * Remove investigation * Correct MacOS CI artifact upload mechanism (#92) * Alter yaml syntax for MacOS if * Try different syntax change on MacOS CI * Use the working syntax everywhere * Add interpolation to ccf (#35) * Add interpolation to ccf * Bug fixed with velocities array * Use a sparse array for setting the velocities in case when interpolation is set * Bug fix when setting the velocities sparse array * Start rewriting * Implement slower but memory-efficient interpolation * Implement disk interpolation * Add another disk interpolation implementation * Introduce chunking * Add vel preloading to disk interpolation * Error out if 'preload' == 0 * Delete self._velocities at start of finalize() * Close netcdf at start of finalize() * Handle os.path.join error * Use unique name for each ccf instance * Improve name readability and change defaults * Fix bug caused by using old name * Add mode that selects appropriate mode Co-authored-by: eric pellegrini <[email protected]> * Fix lm and lux units (#96) * Fix AtomsListPlugin (#100) * Correct AtomsListWidget method name * Disable SpinCtrl instead of hiding it * Remove default value from msg_set_ud (#101) * Added support for HDF5 format for output files (#94) * Addd support for HDF5 format for output files * Install h5py and enable deploy win * Copy conda hdf dlls, libs etc * Alter PATH in win launcher.bat * Correct path in .bat and try setting path * Copy all conda dlls etc * Use conda only for win CD * Correct numpy installation on win CD * Use conda numpy in win CD * Add testing to win CD * Add more testing to win CD * Set paths on win CD * Use setup-miniconda action in win CD * Adapt win CD to setup-miniconda action * Add vcvars to PATH on win CD * Call vcvars in win CD * Use setuptools in ScientificPython win CD * Use setuptools for mmtk on win CD * Added hardcoded netcdf.h path to mmtk setup.py * Add investigation to win CD * Copy netcdf.h directly to include on win CD * Try copying Scientific\* to include * Look for missing header files * Try setuptools and distutils for Scientific * Remove investigations from win CD * Rework win CI/CD to use conda * Only use conda netcdf-c files * Alter Scientific setup.py to correct lib path * Split windows CI tests * Use full python path to run tests * Use setuptools and distutils for mmtk * Use different trajectory in TestConfigurator.py * Change caching key * Add investigation to win CD * Add investigation to windows CI * Try setting use-only-tar-bz2 on conda setup * Change setup-miniconda interaction with caching * Add investigation to windows CI * Try running 'conda activate' * Try different setup-miniconda configuration * Try different setup-miniconda configuration * Replace conda with mamba * Specifiy python 2.7.18 for mamba * Change conda and cache interaction * Cache only packages * Cache all of site-packages * Hardoce conda path for cache * Use conda only for h5py and netcdf4 * Change cache key * Remove python caching on Windows * Correct artifact name on win CD * Correct wrong shell usage * Clean up environment before packaging * Use -y with pip uninstall * Disable windows CD on this branch * Enable MacOS and Ubuntu CI Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Use only centre of masses selection for COM calculation (#102) * Use distutils in Ubuntu CI/CD * Restore if statements in CI.yml * Fix MacOS CD (#103) * Fix type in MacOS deploy.sh * Correct order of MacOS deploy instructions * Use -y with pip uninstall * Fix Toggle toolbar option (#108) * Use ToolBar.IsShown() * Keep the main window size constant * Update CHANGELOG (#104) * Update CHANGELOG * Update CHANGELOG to include #48 * Fixed bug when building clusters in XTD parser (#106) Co-authored-by: eric pellegrini <[email protected]> * Install psutil in CI/CD (#109) * Update authors information (#112) * Add path information to NetCDFInputData (#114) * Create Path column only in standalone plotter * Implement recursive var search in netcdf * Refactor to use variable wrappers * Refactor into multiple files * Set .nc and .h5 formats as default for browsing in plotter (#116) * Preparing for the Release 1.5.0 (#115) * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * 28 enhance simple help (#54) * Replaced plain text window by an HTML window for better reading experience of the simple help * Add superscipts * added a missing superscript in simple help html file Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add User Guide DOI to GUI help menu (#49) Co-authored-by: Turanyi <[email protected]> * Replace outputData reference with correct variables * Remove ability to plot non-meaningful data (#34) * Catch the TypeError and abort autofit * Notification is shown when user initiates invalid autofit * Handle TypeError in add_offset method * Partially clean up code to increase PEP8 compliance * Revert and instead stop before plotting * Remove certain variables from plotting * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Prevent plotting of new variables * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * filtered out the variables which are not of numeric type * Forbid remaining trajectory variables Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Update headers (#47) * Update copyright information inside headers * Revert ILL copyright to 2013-now Co-authored-by: Turanyi <[email protected]> * Implement velocity reading in Gromacs converter via TRR files (#44) * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Change gui label to 'xtc and trr file' * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Add tests * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remove unused parts of trr module * Add tests * The coords, velocities and forces arrays are now casted to float64 * Clean up Gromacs.py of git dif lines * Update tests to check gradients Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Use existing vars to calculate tcf and rdf * Fixed bug in writing quaternions,com and fit variables in rbt job * Write units in trajectory files (#72) * Fixed typo in Converter.py file * Fixed typo in Converter.py file * Securized the code for writing units in the trajectory file Co-authored-by: eric pellegrini <[email protected]> * Added better securization around the adding of units in Converter.finalize method (#73) Co-authored-by: eric pellegrini <[email protected]> * MD compliant plotter (#61) * Added a new mode for viewing 3D data * Added brand new plugin for viewing trajectory related variables * Added support for unit in TrajectoryViewer plugin cosmetic change in DCDConverter file * Fix bug with 2D slice * Fixed windows-specific bug when doing scalar plot * Added the possibility to remove lines for the TrajectoryViewer plugin * Fixed buggy behavior with the legend Co-authored-by: eric pellegrini <[email protected]> * Make the names of output files more descriptive (#60) * Change output file default name in GUI * Implement incrementing filename for job output * Modified the algorithm for checking already existing filename * Added a mechanism for guessing the output filename for converter analysis * Removed print * Added a new configuration/widget for setting single output file * Update headers of new files to comply with #47 * Update configurator docstrings * Removed useless checking of datakey in set_data method * Renamed OutputFile configurator and widgets to SingleOutputFile Co-authored-by: eric pellegrini <[email protected]> * Add continuous integration using GitHub actions (#20) * Replace buggy py2app qt recipes with correct ones * Change the replacement qt files to always return None * Change qt5.py into a dummy function * Make qt6 a dummy too * Truly make qt6 a dummy too and add netcdf investigation * Place change_dylib_path.sh code into deploy_old.sh * Add investigation and ' to deploy_old.sh * Add more investigation * Add more investigation * Try using -fv with problematic command * Stop using wildcard with cp * Deploy for different ubuntus separately * Deploy for different ubuntus separately * Correct artifact name * Increase investigation * Copy libhdf5 files into artifacts * Try removing arguments from build.py * Restore arguments to build.py * Search ubuntu for libsz * Copy the whole x86_64-linux-gnu file * Use argparse in build.py * Only parse known arguments * Revert, instead hardcode py2app arg and change depends for deb * Try several things and fix syntax error * Correct paths and try sudo * Use source and include parameters * Add osx sphinx investigation and copy libnetcdf on ubuntu * Add more investigation about sphinx * Correct syntax and upload log * Fix yaml indentation * Correct path to sphinx logs * Add further investigation * Always run the copy of sphinx log * Disable the failing sphinx usage for now * Place ' around args * Remove args completely from build.py * Specify version of docutils * Move scripts to the same run as build.py * Create different installers for different versions of ubuntu * Enable ubuntu * Correct ubuntu and use getenv * Enable ubuntu * Use sys.argv * Try solutions to the build.py issue * Try using --argv-inject * Try ways to use --argv-inject correctly * Print sys.argv * Use argv correctly * Remove the extra MDANSE from icon path * Correct path to icons * Create directory before creating file inside it * Add postinst and create installer for ubuntu 21 * Correct postinst path and remove rm * Correct artifact name for ubuntu 21 * Add mising su privilege * Add missing su privileges * Correct ubuntu version, sed permanently and correct postinst * Create Contents/MacOS directory before symlinking into it * Add missing files * Expand amount of places where env vars are exported on ubuntu * Add missing ' * Correct postinst type of ' on ubuntu * Correct env var name * Copy dylibs * Add investigation * Add investigation and add files for fake osx deploy * Correct mistakes and add investigation * Correct path * Copy libwx * Correct typo and dist dir path * Remove unmounting and add sudo * Provide correct permissions and investigate * Add investigation * Add sudo everywhere in old * Use mv -T to force rename * Remove -T * Use matrix for osx CI and add investigation * Create bin in resources first * Add missing sudo * Add more sudos * Change python link name * Add more sudos * Add investigation and use the list rather than ls list * Use full path with GITHUB_WORKSPACE for wx dylibs * Remove quotes around the dylib path * Add investigation * Use complete full path * Use sudo inside script rather than sudo script * Add investigation and use * instead of @ * Use cd and then get the list * Add investigation, add files to fake and add sudo * Remove sudo and investigation and use more complete path * Correct paths * Correct paths * Add investigation * Use sudo hdiutil create * Remove unmount and -debug * Increase projected dmg size and remove untarred artifacts * Try ways to decrease disk size * Upload dist folder * Delete instead of uninstall and use df -h * Remove upload * Add investigation to create_dmg * Move dylibs rather than copy * Set -size to be 200 larger than expected * Add sudos * Remove deploy_osx and investigation and export mdanse_dmg * Search for libint* * Dont copy python dylib * Include libint dylib and deploy on macos 11 too * Correct yaml syntax * Correct artifact names * Change libintl path in libpython2.7.dylib * Comment out _boot_multiprocessing in __boot__ and add investigation * Correct python dylib pointer on macos11 * Relink dylibs amond each other, add investigation and cp not mv * Replace ls with find for investigation * Also change wx dylib links. Add investigation * Change dylib link for all wx dylibs * Remove ' from cp with wildcard * Change dylib links for libwx in lib-dynload * Search for libz and libc++ * Include missing dylibs and change rpath to executable path * Correct typos in dylib names * Actually correct typos in dylib names * Investigate hashlib and don't copy libz and libc++ on 11 * Try unlinking openssl and correct paths * Only unlink on macos10.15 * Correct placements of conditional statement * Investigate openssl on mac11 * Try specifying openssl version * Link more dylibs and try copying libssl * Add investigation and try buildin app with --includes openssl * Investigate ssl locations * Relink _hashlib.so to correct dylibs * Relink vtk so files inside lib-dynload * Change vtk rpath instead * Try relinking other files, remove extra python and link dylibs rather than copy * Correct issue * Try different source for wxpython * Try different source for conda wx * Revert to previous provider and correct cp paths * Correct path * Revert to original provider * Investigate wx version * Use -r to copy egg info * Build wxpython from source * Use sudo * Only build from source on 10.15 * Try wx from travis on mac11 * Disable fail fast * Copy over files on mac11 * Move vtk and wx installation to deploy and use conda wx3 * Correct yaml syntax * Remove wx installation from ci_osx * Replace mdanse_gui test with running the app at the end of deploy * Correct copying and remove ln * Relink .so files in lib-dynload/wx * Make PlatformError in create_directory more descriptive * Correct yaml syntax * Test bundled python and add bash script to run it * Correct sed command syntax * Use echo >> instead of sed -i * Improve script and make executable and bundle bin/python * Remove extension from script * Correct script name * Make python2 behave like an actual python * Correct script and remove bin/python * Correct windows desktip shortcut icon path * Delete unused files * Try using for links in windows nsi * Copy the MDANSE shortcut to desktop * Clean up yaml and scripts * Try out cache action for vs2008 * Try removing ' from around path * Remove ' from around paths * Set VS90CMNTOOLS * Append PATH and use cmd * Cache sdk 5.0 too * Cache sdk 5 and 6 and set windowssdkdir * Correct mistakes and search for mingw * Correct yaml syntax * Use cmd for test * Use powershell ls for test * Try using mingw and editing vcvarsamd64 * Use custom vcvarsamd.bat and set env vars manually * Correct mistake and set python vars * Try vs for python2.7 * Add investigation * Cache separately * Correct yaml issues * Correct yaml issues * Run restore after retrieving from cache * Try full install after restoring cache * Try vc for python2.7 * Try using setuptools * Run vcvarsall too * Add paths * Remove restoring VS2008 * Correct name * Save the msi to github workspace * Remove id * Restore vs2008 from cache * Bring the experimental win CI to be official * Try removing .net framework from caching * Add postrm script for ubuntu * Run vcvars before scientific and cache CI result * Try replacing distutils with setuptools in scientific * Replace scientific setup.py with edited one * Install VS2008 if python could not be restored * Correct != into == * Change key name from python to mdanse * Remove old step * Use full path to python * Use ' * Put the problematic line on a separate line * Fix the yaml syntax * Use full path to all pythons * Try running macos tests directly * Unpack list for os.path.join in BuildJobTests * Correct BuildJobTests.py to get right path to ref data * Make AllTests.py be able to be run from anywhere * Use different approach * Create the test files inside Jobs/ * Put test file name as full path * Use os.chdir inside all test scripts * Add usage instructions to mac * Bring the README to workspace * Correct readme path and try different logic * Correct yaml indentation * Correct yaml syntax * Remove extra MDANSE build install step * Make mdanse scripts able to be run by themselves * Correct ubuntu dependencies and ensure LD_LIBRARY_PATH is set * Correct sed syntax * Remove superfluous netcdf caching * Correct python syntax edited into mdanse scripts * Correct windows netcdf download url * Use older py2app and try != true instead of == false * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Add sudo apt-get update on ubuntus * Update maintainer/publisher information * Remove this branch from deploy list * Remove dangerous MacOS parse_command_line.py * Remove the copying of removed script * Remove deployment on this branch * Fixed regression due to recent merge * Don't subtract 1 from pdf during tcf_intra calculation * Regenerate test reference file using current code * Fixed buggy DL_POLY trajectory * Added mdanse_job application for running a job through a stand-alone dialog (#65) * Added mdanse_job application for running a job through a stand-alone dialog * Added more info to mdanse_job script help Fixed typo with Doc/conf_api.py file * Revert changes to Doc Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix broken tests (#66) * Fix CASTEP test by removing gradients variable * Temporarily disable pdf tests * Change BuildJobTests to ignore T and KE * Use try finally when opening NetCDF files * Don't compare velocities in DFTB and Forcite * Make DFTB and Forcite tests proper by generating new references * Delete copies even when exception occurs * Fix issues due to output_file vs output_files * Fix bug with triclinic unit cells * Fixed regression in ConfigurationPanel (#84) Co-authored-by: eric pellegrini <[email protected]> * Use netCDF4 as the NetCDF dependency instead of Scientific.IO/NetCDF (#81) * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Replaced Scientific.IO.NetCDF dep by netCDF4 * Fixed regression * Install netCDF4 during CI/CD pipeline * Correct windows netCDF4 path * Copy netCDF4 contents on ubuntu ci * Add investigation to CI/CD * Set HOME env var before using it on win * Correct netCDF4 path on ubuntu and mac * Copy .so libraries on unixes * Add investigation to windows pipeline * Investigate RUNNER_TOOL_CACHE on win CI * Correct netCDF4 destination path on win * Separate conda calls on win and copy libmfhdf on unix * Copy over libdf.so on unix pipelines * Remove leadin \ from xcopy source on win pipeline * Create destination dirs on windows pipeline * Edit paths on ubuntu * Investigate KeyError on win pipeline * Copy netcdf and hdf5 libs on ubuntu * Try importing problematic configurator directly * Add investigation to pipelines * Correct yaml syntax * Correct yaml syntax * Copy msvc dlls from conda to main on win * Copy netcdf dlls into python\DLLs on win * Copy netcdf dlls into netCDF4 directory * Clean up pipelines * Fix broken tests * Handle possible IOError in tests * Handle IOError on monoprocessor too * Run AllTests.py with sudo * Relocate test output file for Test_dp * Add forgotten \n to BuildJobTests * Correct test generation for dp on linux * Use repo directory for dp output path on linux * Alter BuildJobTests to output to reference dir * Clean up pipeline and BuildJobTests * Use context manager in test_gromacs_trr * Use context manager in PlotterPlugin * Add forgotten context managers to test_trr Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fixed bug when closing partial charges plugin (#85) Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add advanced units manipulation and definition options (#78) * Added Units module for handling units * Advances in integration of Units module in the plotter * Added Units module for handling units * Advances in integration of Units module in the plotter * Added app for editing units The plotter accepts now equivalent units (e.g. THz/eV) Added icon ofr units * Removed external dependencyy to magnitude project * Fixed conflicts * Added the possibility to add an unit from the units editor * Fixed bug when closing the UnitsEditor dialog * Install pyyaml on CI/CD pipeline * Added docstrings and more unit tests to Units module * Added new equivalences Added warning when adding unit in the unit editor * Added new equivalences * Updated the units editor dialog * Big fixed when multiplying or dividing unit by another * Added J_per_mole unit * Change q unit from inv_nm to 1/nm Big fixed in the unit parser * Bug fix with inv_nm factor in Units.yml * Added unit test for prefixes * Bug fixed in __ipow__ function * Removed old dependencies to magnitude * Fixed regression in Forcite converter * Fixed bug in SFFSF analysis * Added akma_time in available units Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Fix script installation (#82) * Remove setuptools and enable CD * Correct branch name in CI.yml and try running VS9 vcvars * Call correct vcvars on CD too * Use setuptools on runners only, keep only distutils in default setup * Remove this branch from contains() calls * Add abstraction for plotter data (#86) * Added abstraction layer for NetCDF data * Added missing method for closing data properly * Added missing module * Added _IPlotterVariable interface and NetCDFPlotterVariable concrete class * Added comments to PlotterData module Fixed bug in load_data * Fixed bug with axis names * Fixed regression in PlotterPlugin.py * Flattened the name of the variable in PlotterData Added Path columns to datalist in Plotter * Implement context manager for PlotterData classes * Removed __del__ method of _IPlotterData class Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Update apt-get on ubuntu CD (#77) * Make MacOS CI fail when tests fail (#88) * Move MacOS tests to yaml * Add bug to test changes * Remove testing bug * Fix the installation of netCDF4 on MacOS CI/CD (#90) * Investigate the issue * Remove leading / when copying netcdf4 * Remove investigation * Correct MacOS CI artifact upload mechanism (#92) * Alter yaml syntax for MacOS if * Try different syntax change on MacOS CI * Use the working syntax everywhere * Add interpolation to ccf (#35) * Add interpolation to ccf * Bug fixed with velocities array * Use a sparse array for setting the velocities in case when interpolation is set * Bug fix when setting the velocities sparse array * Start rewriting * Implement slower but memory-efficient interpolation * Implement disk interpolation * Add another disk interpolation implementation * Introduce chunking * Add vel preloading to disk interpolation * Error out if 'preload' == 0 * Delete self._velocities at start of finalize() * Close netcdf at start of finalize() * Handle os.path.join error * Use unique name for each ccf instance * Improve name readability and change defaults * Fix bug caused by using old name * Add mode that selects appropriate mode Co-authored-by: eric pellegrini <[email protected]> * Fix lm and lux units (#96) * Fix AtomsListPlugin (#100) * Correct AtomsListWidget method name * Disable SpinCtrl instead of hiding it * Remove default value from msg_set_ud (#101) * Added support for HDF5 format for output files (#94) * Addd support for HDF5 format for output files * Install h5py and enable deploy win * Copy conda hdf dlls, libs etc * Alter PATH in win launcher.bat * Correct path in .bat and try setting path * Copy all conda dlls etc * Use conda only for win CD * Correct numpy installation on win CD * Use conda numpy in win CD * Add testing to win CD * Add more testing to win CD * Set paths on win CD * Use setup-miniconda action in win CD * Adapt win CD to setup-miniconda action * Add vcvars to PATH on win CD * Call vcvars in win CD * Use setuptools in ScientificPython win CD * Use setuptools for mmtk on win CD * Added hardcoded netcdf.h path to mmtk setup.py * Add investigation to win CD * Copy netcdf.h directly to include on win CD * Try copying Scientific\* to include * Look for missing header files * Try setuptools and distutils for Scientific * Remove investigations from win CD * Rework win CI/CD to use conda * Only use conda netcdf-c files * Alter Scientific setup.py to correct lib path * Split windows CI tests * Use full python path to run tests * Use setuptools and distutils for mmtk * Use different trajectory in TestConfigurator.py * Change caching key * Add investigation to win CD * Add investigation to windows CI * Try setting use-only-tar-bz2 on conda setup * Change setup-miniconda interaction with caching * Add investigation to windows CI * Try running 'conda activate' * Try different setup-miniconda configuration * Try different setup-miniconda configuration * Replace conda with mamba * Specifiy python 2.7.18 for mamba * Change conda and cache interaction * Cache only packages * Cache all of site-packages * Hardoce conda path for cache * Use conda only for h5py and netcdf4 * Change cache key * Remove python caching on Windows * Correct artifact name on win CD * Correct wrong shell usage * Clean up environment before packaging * Use -y with pip uninstall * Disable windows CD on this branch * Enable MacOS and Ubuntu CI Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Use only centre of masses selection for COM calculation (#102) * Use distutils in Ubuntu CI/CD * Restore if statements in CI.yml * Fix MacOS CD (#103) * Fix type in MacOS deploy.sh * Correct order of MacOS deploy instructions * Use -y with pip uninstall * Fix Toggle toolbar option (#108) * Use ToolBar.IsShown() * Keep the main window size constant * Update CHANGELOG (#104) * Update CHANGELOG * Update CHANGELOG to include #48 * Fixed bug when building clusters in XTD parser (#106) Co-authored-by: eric pellegrini <[email protected]> * Install psutil in CI/CD (#109) * Update authors information (#112) * Add path information to NetCDFInputData (#114) * Create Path column only in standalone plotter * Implement recursive var search in netcdf * Refactor to use variable wrappers * Refactor into multiple files * Set .nc and .h5 formats as default for browsing in plotter (#116) Co-authored-by: RastislavTuranyi <[email protected]> Co-authored-by: Turanyi <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> Co-authored-by: gonzalezma <[email protected]> Co-authored-by: franzlang <[email protected]> * Update README.md * Update README.md * Update README.md * Fix version names in installers (#120) * Correct branch names in setup_ci scripts * Fix release-next case * Merge develop into release-next (#121) * Update README.md * Update README.md * Update README.md * Fix version names in installers (#120) * Correct branch names in setup_ci scripts * Fix release-next case Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> Co-authored-by: gonzalezma <[email protected]> Co-authored-by: franzlang <[email protected]> * Fix the version name in fully released installers (#122) * Merge develop into release-next (#123) * Fix the version name in fully released installers (#122) Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> Co-authored-by: gonzalezma <[email protected]> Co-authored-by: franzlang <[email protected]> * Fix windows installer version (#124) * Try using /Y in move command * Correct test branch name * Don't use qoutes in if statement * Correct testing * Remove ' from comparison * Remove testing * Improve the parsing error messages (#128) * Improve the parsing error messages * Update CHANGELOG * Reformat and expand README (#134) * Decrease the minimum size of Quick View (#130) * Decrease Quick view min size * Use default size of 300 but keep 100 min size * Update CHANGELOG * Add CI/CD pipeline for Ubuntu 22 (#132) * Add Ubuntu 22 to CI matrix * Create separate CI for Ubuntu 22 * Remove python-dev from Ubuntu 22 CI * Use full python path to run tests * Investigate issue on Ubuntu 22 CI * Correct mistake in previous investigation * Use -n with conda install * Add CD to Ubuntu 22 CI * Try using ${{CONDA}} to downl/upload artifacts * Try saving $CONDA to $GITHUB_ENV * Fix yaml syntax * Hardcode conda path * Correct path syntax * Alter deploy.sh with sed to correct paths * Run new CD only on certain branches * Update CHAGELOG * Fix command line MDANSE on Windows (#133) * Set paths in MDANSE_command_shell.bat * Swap pip and conda installations in win CI * Enable Windows deploy on this branch * Reverse previous swap * Alter PATH in site.py instead of batch files * Remove Windows site.py and use .pth instead * Remove deployment on this branch and update CHANGELOG * Update setup_ci.bat * Update setup_ci.bat * Update setup_ci.bat * Update setup_ci.bat * Merge develop into release-next (#125) * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * 28 enhance simple help (#54) * Replaced plain text window by an HTML window for better reading experience of the simple help * Add superscipts * added a missing superscript in simple help html file Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: Turanyi <[email protected]> * Add User Guide DOI to GUI help menu (#49) Co-authored-by: Turanyi <[email protected]> * Replace outputData reference with correct variables * Remove ability to plot non-meaningful data (#34) * Catch the TypeError and abort autofit * Notification is shown when user initiates invalid autofit * Handle TypeError in add_offset method * Partially clean up code to increase PEP8 compliance * Revert and instead stop before plotting * Remove certain variables from plotting * Fix Elements Database Editor bug (#33) * Correct bug and change sizer and panel usage * Clean up code to PEP8 standard * Reorganise changed code to match the previous style Co-authored-by: Turanyi <[email protected]> * Correct macro name (#37) Co-authored-by: Turanyi <[email protected]> * Update AUTHORS * Update AUTHORS * Use forces instead of gradients (#39) Co-authored-by: Turanyi <[email protected]> * Implement rdf and tcf inside pdf (#40) Co-authored-by: Turanyi <[email protected]> * Fix normalisation in GACF and PACF (#36) * Fix gacf and pacf normalisation * Use normalize funtion in gacf and pacf * Fix bug by removing intermediary variable Co-authored-by: Turanyi <[email protected]> * Prevent plotting of new variables * only the congiguration (and velocities and gradients when available) are written in the output trajectory * bug fixed with the output of a few trajectory converters * added info method to NetCDFInputData added info about the variables stored in a trajectory in MMTKTrajectoryInputData * added time to the variables to be written in output trajectory * bug fix with missing time as output variable for a few converters * Add time to Gromacs and fix typo * 42 improve pane layout in plotter (#55) * Added a splitter window between the dataset and data list of the data panel * added a minimum size for the dataset and data panels of the splitter windows of the plotter * Removed frame sizing * Set back code to previous state Co-authored-by: eric pellegrini <[email protected]> * filtered out the variables which are not of numeric type * Forbid remaining trajectory variables Co-authored-by: Turanyi <[email protected]> Co-authored-by: Sanghamitra Mukhopadhyay <[email protected]> Co-authored-by: eric pellegrini <[email protected]> Co-authored-by: eurydice76 <[email protected]> * Update headers (#47) * Update copyright information inside headers * Revert ILL copyright to 2013-now Co-authored-by: Turanyi <[email protected]> * Implement velocity reading in Gromacs converter via TRR files (#44) * Implement velocity reading from trr * Update .gitignore to exclude trr.c and xtc.c after build * Remove problematic double import and unpack correctly * Fix read method by redefining a constant * Enable reading trr files not containing vels/forces * Remov…
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‎.github/workflows/CI.yml

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# OSX
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ci_osx:
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runs-on: ${{ matrix.os }}
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contains( github.ref, 'hotfix-' ) ||
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contains( github.ref, 'build-' ) ||
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contains( github.ref, 'tags' )
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contains( github.ref, 'tags' )
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run: |
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cd /D %CONDA%\envs
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tar -czf mdanse.tar.gz mdanse
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contains( github.ref, 'release-' ) ||
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contains( github.ref, 'hotfix-' ) ||
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contains( github.ref, 'build-' ) ||
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contains( github.ref, 'tags' )
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contains( github.ref, 'tags' )
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uses: actions/upload-artifact@v2
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with:
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name: windows_artifacts

‎BuildServer/Unix/Debian/Resources/DEBIAN/control

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Package: mdanse
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Version: 1.5.0
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Version: 1.5.2
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Architecture: amd64
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Depends: netcdf-bin, libnetcdf-dev, libgtk2.0-0
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Section: Science
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Priority: optional
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Installed-Size: 1000
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Homepage: https://mdanse.org
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Homepage: https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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Maintainer: S. Mukhopadhyay <[email protected]>
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Description: MDANSE - Molecular Dynamics Analysis for Neutron Scattering Experiments.
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MDANSE (Molecular Dynamics Analysis for Neutron Scattering Experiments) is a python application designed for computing properties that can be directly compared with neutron scattering experiments such as the coherent and incoherent intermediate scattering functions and their Fourier transforms, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function. Moreover, it can also compute quantities such as the mean-square displacement, the velocity autocorrelation function as well as its Fourier Transform (the so-called vibrational density of states) enlarging the scope of the program to a broader range of physico-chemical properties.

‎BuildServer/Unix/Debian/Resources/DEBIAN/copyright

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Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0
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Upstream-Name: mdanse
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Upstream-Contact: Sanghamitra Mukhopadhyay <[email protected]>
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Source: https://mdanse.org/
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Source: https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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Files: *
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Copyright: Copyright 2016, Eric Pellegrini <[email protected]>; Copyright 2021, Sanghamitra Mukhopadhyay <[email protected]>

‎BuildServer/Windows/Resources/nsis/MDANSE_installer.nsi

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ShowUnInstDetails show
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!define PUBLISHER "ISIS Neutron and Muon Source"
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!define WEB_SITE "http://www.mdanse.org"
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!define WEB_SITE "https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx"
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!define UNINST_KEY "Software\Microsoft\Windows\CurrentVersion\Uninstall\MDANSE"
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!define UNINST_ROOT_KEY "HKLM"
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‎Doc/index.rst

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Introduction
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============
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Molecular Dynamics Analysis for Neutron Scattering Experiments
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MDANSE is a python application designed for computing neutron observables
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`MDANSE Project Website <https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx>`_
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`MDANSE GitHub Page <https://github.com/ISISNeutronMuon/MDANSE>`_
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**MDANSE** (**Molecular Dynamics Analysis for Neutron Scattering Experiments**)
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is a python application designed for computing neutron observables
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from molecular dynamics (MD) trajectories that can be directly compared with
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neutron scattering experiments, particularly inelastic and quasi-elastic
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neutron scattering spectroscopies.

‎Doc/pages/references.rst

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.. [Ref7] “The HDF Group.” https://www.hdfgroup.org/.
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.. [Ref8] “MDANSE.” https://mdanse.org/.
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.. [Ref8] “MDANSE.” https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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.. [Ref9] “MDANSE GitHub Issues.”
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https://github.com/ISISNeutronMuon/MDANSE/issues.

‎Extensions/setup.py

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# @file Extensions/setup.py
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# @brief Implements module/class/test setup
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎README.md

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## Quick start
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The easiest way to start using MDANSE is to download a built installer from out latest [github release](https://github.com/ISISNeutronMuon/MDANSE/releases/).
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The easiest way to start using MDANSE is to download a built installer from [MDANSE website](https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx)
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or our latest [github release](https://github.com/ISISNeutronMuon/MDANSE/releases/).
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There, we provide installers for the major operating systems, Windows, Linux and MacOS, which can be downloaded and installed
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any other software on that OS. After that, we recommend starting by using the GUI. The typical workflow will look as follows:
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The most complete user documentation of MDANSE can be found on [our Read the Docs page](https://mdanse.readthedocs.io). At the same time, it is still possible to access the original **[MDANSE User Guide](https://epubs.stfc.ac.uk/work/51935555)** \
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Other information including example scripts can be found on the MDANSE website [mdanse.org](https://mdanse.org/)
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Other information including example scripts can be found on the [MDANSE website](https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx)
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## Installing from source
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‎Scripts/mdanse

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_elements_database

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_gui

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_job

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_periodic_table

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_plotter

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_ud_editor

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Scripts/mdanse_units_editor

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# @file Src/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Core/ClassRegistry.py

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# @file Src/Core/ClassRegistry.py
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# @brief Implements module/class/test ClassRegistry
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Core/Error.py

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# @file Src/Core/Error.py
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# @brief Implements module/class/test Error
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Core/Platform.py

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# @file Src/Core/Platform.py
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# @brief Implements module/class/test Platform
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Core/Singleton.py

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# @file Src/Core/Singleton.py
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# @brief Implements module/class/test Singleton
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Core/__init__.py

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# @file Src/Core/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Data/ElementsDatabase.py

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# @file Src/Data/ElementsDatabase.py
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# @brief Implements module/class/test ElementsDatabase
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Data/__init__.py

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# @file Src/Data/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/DistributedComputing/MasterSlave.py

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# @file Src/DistributedComputing/MasterSlave.py
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# @brief Implements module/class/test MasterSlave
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/DistributedComputing/Slave.py

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# @file Src/DistributedComputing/Slave.py
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# @brief Implements module/class/test Slave
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/DistributedComputing/__init__.py

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# @file Src/DistributedComputing/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Extensions/__init__.py

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# @file Src/Extensions/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/__init__.py

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# @file Src/Externals/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/__init__.py

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# @file Src/Externals/pubsub/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/autosetuppubsubv1.py

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# @file Src/Externals/pubsub/autosetuppubsubv1.py
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# @brief Implements module/class/test autosetuppubsubv1
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/__init__.py

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# @file Src/Externals/pubsub/core/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/__init__.py

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# @file Src/Externals/pubsub/core/arg1/__init__.py
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# @brief Implements module/class/test __init__
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/listenerimpl.py

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# @file Src/Externals/pubsub/core/arg1/listenerimpl.py
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# @brief Implements module/class/test listenerimpl
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/publisher.py

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# @file Src/Externals/pubsub/core/arg1/publisher.py
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# @brief Implements module/class/test publisher
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/publishermixin.py

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# @file Src/Externals/pubsub/core/arg1/publishermixin.py
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# @brief Implements module/class/test publishermixin
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/topicargspecimpl.py

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# @file Src/Externals/pubsub/core/arg1/topicargspecimpl.py
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# @brief Implements module/class/test topicargspecimpl
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/arg1/topicmgrimpl.py

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# @file Src/Externals/pubsub/core/arg1/topicmgrimpl.py
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# @brief Implements module/class/test topicmgrimpl
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/callables.py

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# @file Src/Externals/pubsub/core/callables.py
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# @brief Implements module/class/test callables
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

‎Src/Externals/pubsub/core/datamsg.py

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# @file Src/Externals/pubsub/core/datamsg.py
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# @brief Implements module/class/test datamsg
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#
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# @homepage https://mdanse.org
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# @homepage https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
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# @license GNU General Public License v3 or higher (see LICENSE)
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# @copyright Institut Laue Langevin 2013-now
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# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now

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