Display live output from running processes #474
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rhinoella
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Jan 12, 2024
* Changed window title to only show filename (#456) * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * Upgrade PySide version to 6.6.0 (#463) Co-authored-by: Spitz <[email protected]> * lint * Fix IDAaaS Setup Script (#471) * Install XCB cursor lib. * More RPM requirements. * Fixes November 2023 (#473) * Add window title modification placeholder. * Add detectorCalibrationFileName to GudPyFileLibray and harmonise name capitalisation to reflect UI. * Notify user that all files were found. * Fix file types for input file dialog. * Be more careful about raising that dialog. * Don't forget to re-enable GUI after failing to find gudrun_dcs binary. * Formatting. * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Display live output from running processes (#474) * Live output of processes * Change 'setText' to append for smoother experience + remove unecessary code * Remove comment --------- Co-authored-by: Spitz <[email protected]> * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]>
rhinoella
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Jan 25, 2024
* Adjusted handling of temp directory * Removed shutil.rmtree * Docstring update * Does not delete/replce existing outputs * Organised iterator files, fixed some bugs * Modified import statements to align with new directory structure * Stored strings in variables * Uniquify default parameter names * Created extra util functions for uniquifying names and filenames * Output file handling process change * Output file handling process change in main window * Modifying dialog functions as needed * Formatting * Removed debugging print statements * Removed debugging print statements * fixed duplication of sample background directory * Documentation and commenting * Documentation and commenting * Fixed iteration counting * Fixed wavelength subtraction iterator * Applied changes to batch processing * Attempting to fix windows build * Attempting to fix windows build * Fix windows build? Make sure dir exists * Creating gudrun file in temp directory * Comments * Gudrun runs in temporary directory, files are copied over * Organised and renamed, gave more responsibility to iterator objects * Fixed output handler resetting * Refactored and fixed output handler to work with new system * updated imports * updated imports * updated imports * Refactored mainwindow.py and fixed process * Moved dialogs to one module * Applied new changes to test * Removed unecessary parameter * removed unecessary import * Changed the way outputs work- directory now overwrites * Removed uneeded parameter * Removing previous output dir if exists * Combined naive organise and iterative into one function, changed the way files are moved over * Fixed spelling * Fixed issues, works as expected now * Updated docstrings and output handling function * Changed inelasticity menu name to be consistent * Better clarity of 'default' run, refactored code * Changed function naming to be private, updated to not require nCurrent * Added assertions and set run dir function * Updated parameters for new organiseoutput * Fixed and modified output tree * Updated inelasticity to be the only one that saves all iter outputs * removed unused import * Creating and asserting gudrun is run in tempdir * Fix bug * Bug fixes * Output file handler returns path information * Fixing nTotal in init composition * Fix tests * Fixing tests * Fixing tests * Formatting * Formatting * Bug fix * Fixing undeclared var issue * Fix write_out * Attempt to fix tests and improve iterators * Fixed errors * Fixed linting * Linting * WIP Fix * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * lint * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error * Outputs fix 2.5 (#461) * Changed window title to only show filename (#456) * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * Upgrade PySide version to 6.6.0 (#463) Co-authored-by: Spitz <[email protected]> * lint * Fix IDAaaS Setup Script (#471) * Install XCB cursor lib. * More RPM requirements. * Fixes November 2023 (#473) * Add window title modification placeholder. * Add detectorCalibrationFileName to GudPyFileLibray and harmonise name capitalisation to reflect UI. * Notify user that all files were found. * Fix file types for input file dialog. * Be more careful about raising that dialog. * Don't forget to re-enable GUI after failing to find gudrun_dcs binary. * Formatting. * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Display live output from running processes (#474) * Live output of processes * Change 'setText' to append for smoother experience + remove unecessary code * Remove comment --------- Co-authored-by: Spitz <[email protected]> * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]> * Fix purge and bugs * Output YAML file to project directory * Update main_window.py * Fix export dialog and remove inputfiledir var * Create loadFile variable-GudrunFile * Fix incorrect var name * Fix tests with new loadFile variable * Print dicts * Retrieve gudfile using function * Apply suggestions from code review * Remove blank line * Fix tests * Fix write-out paths * Fix path to loadfile * Fix test * Remove actions step debug * Remove print debugging * Fix test * Fix test * Update ui * Fix test to use abspath * Use abspath * Remove abspath * Remove assertion * Fix test * Do abspath * Fix * Undo * try fix again * Remove paths from assertion * Debugging * debug * debug * attempt to fix test * Specify encoding * Debug * Remove debugging and parse data file directory as abspath * Include trailling slash to path * Include trailling slash to path * Debug again * Fix path on water.txt * Remove debugging * Test everything --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]>
rhinoella
added a commit
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Feb 13, 2024
* Adjusted handling of temp directory * Removed shutil.rmtree * Docstring update * Does not delete/replce existing outputs * Organised iterator files, fixed some bugs * Modified import statements to align with new directory structure * Stored strings in variables * Uniquify default parameter names * Created extra util functions for uniquifying names and filenames * Output file handling process change * Output file handling process change in main window * Modifying dialog functions as needed * Formatting * Removed debugging print statements * Removed debugging print statements * fixed duplication of sample background directory * Documentation and commenting * Documentation and commenting * Fixed iteration counting * Fixed wavelength subtraction iterator * Applied changes to batch processing * Attempting to fix windows build * Attempting to fix windows build * Fix windows build? Make sure dir exists * Creating gudrun file in temp directory * Comments * Gudrun runs in temporary directory, files are copied over * Organised and renamed, gave more responsibility to iterator objects * Fixed output handler resetting * Refactored and fixed output handler to work with new system * updated imports * updated imports * updated imports * Refactored mainwindow.py and fixed process * Moved dialogs to one module * Applied new changes to test * Removed unecessary parameter * removed unecessary import * Changed the way outputs work- directory now overwrites * Removed uneeded parameter * Removing previous output dir if exists * Combined naive organise and iterative into one function, changed the way files are moved over * Fixed spelling * Fixed issues, works as expected now * Updated docstrings and output handling function * Changed inelasticity menu name to be consistent * Better clarity of 'default' run, refactored code * Changed function naming to be private, updated to not require nCurrent * Added assertions and set run dir function * Updated parameters for new organiseoutput * Fixed and modified output tree * Updated inelasticity to be the only one that saves all iter outputs * removed unused import * Creating and asserting gudrun is run in tempdir * Fix bug * Bug fixes * Output file handler returns path information * Fixing nTotal in init composition * Fix tests * Fixing tests * Fixing tests * Formatting * Formatting * Bug fix * Fixing undeclared var issue * Fix write_out * Attempt to fix tests and improve iterators * Fixed errors * Fixed linting * Linting * WIP Fix * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * lint * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error * Outputs fix 2.5 (#461) * Changed window title to only show filename (#456) * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * Upgrade PySide version to 6.6.0 (#463) Co-authored-by: Spitz <[email protected]> * lint * Fix IDAaaS Setup Script (#471) * Install XCB cursor lib. * More RPM requirements. * Fixes November 2023 (#473) * Add window title modification placeholder. * Add detectorCalibrationFileName to GudPyFileLibray and harmonise name capitalisation to reflect UI. * Notify user that all files were found. * Fix file types for input file dialog. * Be more careful about raising that dialog. * Don't forget to re-enable GUI after failing to find gudrun_dcs binary. * Formatting. * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Display live output from running processes (#474) * Live output of processes * Change 'setText' to append for smoother experience + remove unecessary code * Remove comment --------- Co-authored-by: Spitz <[email protected]> * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]> * Fix purge and bugs * Output YAML file to project directory * Update main_window.py * Fix export dialog and remove inputfiledir var * Create loadFile variable-GudrunFile * Fix incorrect var name * Fix tests with new loadFile variable * Print dicts * Retrieve gudfile using function * Apply suggestions from code review * Remove blank line * Fix tests * Fix write-out paths * Fix path to loadfile * Fix test * Remove actions step debug * Remove print debugging * Load from project, save as project, export input file * Merge branch 'develop' into load-project * Check if config is used * Refactor code * Refactor code * Advance GudPy exception handling, fix test failiure on empty path * Declare outpath as const * Fix outpath changes * Fix attribute error --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]>
rhinoella
added a commit
that referenced
this pull request
Mar 14, 2024
* Changed function naming to be private, updated to not require nCurrent * Added assertions and set run dir function * Updated parameters for new organiseoutput * Fixed and modified output tree * Updated inelasticity to be the only one that saves all iter outputs * removed unused import * Creating and asserting gudrun is run in tempdir * Fix bug * Bug fixes * Output file handler returns path information * Fixing nTotal in init composition * Fix tests * Fixing tests * Fixing tests * Formatting * Formatting * Bug fix * Fixing undeclared var issue * Fix write_out * Attempt to fix tests and improve iterators * Fixed errors * Fixed linting * Linting * WIP Fix * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * lint * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error * Outputs fix 2.5 (#461) * Changed window title to only show filename (#456) * Changing temp directory control * Debug * Cwd change * Fix prev commit * Debugging * Attempt to fix test * Upgrade PySide version to 6.6.0 (#463) Co-authored-by: Spitz <[email protected]> * lint * Fix IDAaaS Setup Script (#471) * Install XCB cursor lib. * More RPM requirements. * Fixes November 2023 (#473) * Add window title modification placeholder. * Add detectorCalibrationFileName to GudPyFileLibray and harmonise name capitalisation to reflect UI. * Notify user that all files were found. * Fix file types for input file dialog. * Be more careful about raising that dialog. * Don't forget to re-enable GUI after failing to find gudrun_dcs binary. * Formatting. * Create base class for output handler * Run purge in temp dir * Output organising fixes- proper gudfile path * Iterator fixes * Make each iteration run in new temp dir * Composition iterator * Iterate by composition * Iterate by composition * Formatting * Fix progress bar * Fix merge * Fixing tests * Display live output from running processes (#474) * Live output of processes * Change 'setText' to append for smoother experience + remove unecessary code * Remove comment --------- Co-authored-by: Spitz <[email protected]> * Fix wavelength iterator * Fix asserion- invalid use of try except * Use POpen instead of run * Remove print * Refactor purge file * Fix composition iterator * Fix wavelength iteration process * Create gudrun worker * Create gudrun worker * Fix iterator * Fix assertions * Improve purge running and fix issue * Removing unecessary organise output * Used threading instead of qprocess, altered purge dialog, secured temp dir * Refactor * Refactor * Fixes for new changes * Fixes for new changes * Fixes for new changes * Remove print * Linting * Verbose test * Verbose test * Verbose test * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix hanging tests by manually error checking gudrun and stop using popen.wait() * Fix exception for windows * Fixing tests * Debugging * Fix test error * Fix test error --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]> * Fix purge and bugs * Output YAML file to project directory * Update main_window.py * Fix export dialog and remove inputfiledir var * Create loadFile variable-GudrunFile * Fix incorrect var name * Fix tests with new loadFile variable * Print dicts * Retrieve gudfile using function * Apply suggestions from code review * Remove blank line * Fix tests * Fix write-out paths * Fix path to loadfile * Fix test * Remove actions step debug * Remove print debugging * Fix test * Load from project, save as project, export input file * Fix test * Create class * Merge branch 'develop' into load-project * Check if config is used * Refactor code * Refactor code * Advance GudPy exception handling, fix test failiure on empty path * Declare outpath as const * Fix purge calls * Separate gudrun gui from backend- make gudpy module to handle processes * Check for errors * Remove unused imports * Support error handling * Merge * Check for errors * Remove unused imports * Create gudpy class and put iterators into single module * Merge branch 'gudpy-class' of https://github.com/disorderedmaterials/GudPy into gudpy-class * Update imports for iterators * Update imports for iterators * change config_ to config * Moving funcs from main window to control, removing responsibilities from gudrunFile * Update workers to thread, add progression functions * Remove use of gudrunFile from OutputHandler * Delete gui.gudpy * Move running processes to control class * Create process module, remove errorOccured, return exitcodes from runs * Create gui.py to initialise application (rename gui.gudpy to gui.gui) * Remove 'errorOccured' from gudpy process classes * Delete process.py * Create gudrun iterator * Remove iteration functions from iterators * Improve and updat composition iterator * Add compositioniterate function * Removed update from file * Add iterators, start batch processing * Move run containers & run individual files to gudpy class * Update Composition Iterations * Add iterate to GUI and connect signals & slots * Move over main window functions to control * Delete uneeded atributes from worker classes * Update batch processing, finalise * Simplify iteration dialog, return kwargs for iterator initialisation * Update iterators in control.py * Update iterators * Move export and missingfilesdialog to io.py * Get rid of gudpyGUI class, add names * Autosave and initialise view with gudrunfile object * Update imports * Fix errors * Fix output charts- use gudrunOutput obj * Minor fixes, file reorganising * Fix output organising and output reporting * Use gudrunOutput for plotting * Sort flow and updating widgets * Remove organise output func: * Fix output updating to only if results are there * Update mainwidget to ui name change * Minor update, restructuring, fixing outputChanged() signal * Fix plotting & chart * Creat test project dir * Update tests * Save gudrun outputs, return correct exitcodes, save exitcodes in process * Update tests * Fix missing data files import * Remove unused imports * Remove unused imports * Load missing files dialog * Load missing files dialog * remove uneeded imports * remove uneeded imports * remove uneeded imports * Lint * Fix gudpy spelling, tests * Fix gudrunfile initialisation assertion * Fix errors * Fix test errors, add output handling to iterators * Remove whitespace from test sample names * Debug * Fix finding binaries * Fix sample name whitespace * Fix test errors * Remove old purge function * Give gudrun access to purge * Fix runPurge -> pass in purge file correctly * Fix bugs in tests * Fix iterators, gui, rename class * reinitialize yaml? * Add exclude to iterator output organise * Remove self.gudrunfile from composition * Add gudrunfile to iteration dialog * Add gudrunfile to iteration dialog * Fix: GUI iterators * Fix: in worker classes change progress signal/func to progressChanged to avoid naming conflict with progress attribute * Fix: pass gudrunFile to iterators.organiseOutput() * Fix: make IterationBaseWorker inherrit from QThread so run() function is properly called on thread start. Remove invalid gudrunFile.gudrunOutput variable from iterator.performIteration() * Fix: iterators. Ensure init is properly called, results to include iterator name, stop execution if dialog is cancelled * Delete accidental file * Lint: remove whitespace * Fix: iterators for test. Wavelength iter not appending outputs, wrong composition class used * Fix: Properly report iterator results * Fix: progress bar. Move updateProgressBar to view, rewrite variable instead of adding to it * Debug messages for tests * Fix: Remove correct filepath in teardown(), grab correct gudrunOutput in test inelasticity subtraction iterator * Debugging- print the .gudw file * Fix: Remove correct filepath in teardown(), grab correct gudrunOutput in test inelasticity subtraction iterator Debugging- print the .gudw file Debugging- print the .gudw file * Update gitignore * Debugging- print the .gudw file * Revert good_water to previous state * Refactor: Use context in gudfile tests & create one function for loading gudFiles * Fix: composition iterator initialisation, iterator to inherrit from base class * Lint: remove unused import * Fix: composition iterator * Fix: composition iterator tests & iterator to have sample args passed in * Fix: output tree construction, check whether or not iterator is used * Fix: composition iterator. Change process to be managed by gudpy.CompositionIterator * Fix: gudrunoutput to construct GudFile object and return it instead of just the path, to prevent effects of overriding * Fix: save loadfile location in GudrunFile * Docs: add docstrings to gudpy.GudPy * Fix: GUI processes, reinitialise gudpy object on new loads, checkPurge function to not wipe purgeLocation, check workerThread object for process type * Feat: allow gudfile path to be specified in write_out() * Fix: capitalise iterator names, modify inelastic iterator to set proper names * Feat: save original gudrun file * Fix: pass around purge object instead of purgeLocationPath * Fix: check save location before running, fix iterator workflow * Fix: overwrite in output handler to wipe out existing Gudrun folder * Fix: management of purge object, startProcess() function to check and run purge, GUI iteration workflow * Fix: check that prev exists in output_tree before using * Feat: return if results are empty- don't show an empty results dialog * Feat: display 'Default run' indicator * Feat: tests to implement new gudrunOutput gudfiles, use context managers to avoid writing test files to home directory * Refactor: remove underscores from functions * Lint: reduce line length * Fix: pass purge into iterators, remove underscores from functions * Fix: only check if user wants to save if gudrunfile is initialised * Fix: configuration dialog initialisation * Fix: remove setPurgeLocation() function call * Update gudpy/gui/widgets/core/control.py Co-authored-by: Tristan Youngs <[email protected]> * Comments * Ask to save only if file is modified * Stronger purge warning message * Change 'appendDfs' to 'appendDataFiles' * Feat: Create standard stripping function * Fix: stripping function --------- Co-authored-by: Spitz <[email protected]> Co-authored-by: Tristan Youngs <[email protected]>
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Currently GudPy only displays outputs once the running process is complete. This PR enabled live outputs of Gudrun and Purge which will aid in debugging.