Dev #62
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Dev #62
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…meindex removes scipyen_desktop.sh; I now use the same script (scipyen) for launching scipyen from the terminal, or via a desktop file (Linux) envact: script which defined the 'scipyact' shell function which activates the python virtual environment for running scipyen and is sourced by the scipyen script. This ensures that scipyen can be called to launch Scipyen without having to activate the environment specifically (on can stil do it like this, but now one can type a single command) Upon first installation, or changing the python virtual environment under which Scipyen is supposed ot run, the script 'envact' must be edited manually so that the correct environment is activated. To activate the virtual environment WITHOUT launching Scipyen, the 'envact' script file also needs to be sourced in (or its contents copied to) the '.bashrc' file (or one of '.zshrc', '.cshrc', '.tcshrc' depending on what shell you actually use - read their corresponding UNIX man pages for more details) The script 'scipyen' needs to be made executable and a symbolic link to it created in a directory included in the PATH environment variable (usually, $HOME/bin) the preliminary invocation of the environment's activate script. Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
2) Add some documentation to the envact shell script; make clear it IS compatible ONLY with bash and the Z shell (this overrides my comments to the last commit) 3) gui.consoles.ScipyenInProcesKernel now also overrides execute_request (a coroutine) to await _abort_queues() (which is defined as a coroutine in the InProcessKernel superclass) Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
object created on the file_origin attribute of a neo object -> useful to inspect protocol epochs together with getABF function, this is beginning to leverage the pyabf functionality alongside neo framework core.pyabfbridge: clean up code in epochTable2DF; now outputs the DAC level and Delta level in the appropriate DAC units for the given channel ephys.membrane: analyse_AP_step_injection and analyse_AP_step_injection_series now accept Istart and Istop in samples (default False), and as times relative to the start of Vm signal (default True) the adaptation of these values tot the actual Vm signal times is delegated to extract_AP_train() Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
…y with Python 3.9 scipyen.py: small cosmetic rearrangement of import statements w/o functional impact Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
…dent configurations of Python and virtual Python environments Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
Adapted Scipyen configuration and launch scripts for the possibility of using virtual environments with different Python versions (>= 9.7) Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
ephys.membrane: fixed bug in allowing use of samples instead of times, for Istart, Istop in analyse_AP_step_injection_series INSTALL - hopefully, final update Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
Signed-off-by: ctigaret <cezar.tigaret@gmail.com>
must investigate Signed-off-by: ctigaret <cezar.tigaret@gmail.com>
seems like a "race" condition with the observed_vars in the DataBag workspace model that appears after some long list of variables (mileage varies of different computers and python versions) MUST DEFINITELY SORT THIS OUT - REDESIGN OF WORKSPACE MODEL? Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
…gone? Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
Signed-off-by: ctigaret <cezar.tigaret@gmail.com>
…ve shell (and inherited by Scipyen consoles) because the zmq one clear the system (OS) console where scipyen is launched, instead of the ipython console used by scipyen Signed-off-by: ctigaret <cezar.tigaret@gmail.com>
Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
core.quantities: removed obsolete function symbol_from_quantity 2) ephys.membrane: make vm_thr a parameter present to all functions from analyse_AP_step_injection_series down the call stack to detect_AP_rises TODO: streamline this code! 3) gui.mainwindow: 3.1) class WindowManager: call show() when matplotlib figure activated in workspace viewer (FIXME: if minimized it won't be restored! - using Qt5Agg) 3.2) class ScipyenWindow: 3.2.1) call plt.close() when matplotlib figure is removed 3.2.2) When choosing a neo DataObject to be plotted with matplotlib, we now introspect in order to: 3.2.2.1) plot data vs object's domain (the 'times' attribute) 3.2.2.2) get appropriate xlabel and ylabel 4) gui.pictgui class ItemsListDialog Fix bug in self.listWidget.setMinimumWidth which is ALWAYS expecting an int! (previously it was a float due to the fm.width(longestItem) * 1.1 call ) Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
class WindowManager - fixed bug calling get_window_title() on a matplotlib figure (the alleged returned stirng was nto used anyway) class ScipyenWindow - related to script management fix bug/update code to reflect that self.recentScripts is a plain old list and not a deque (as it was previously) This is because the confuse/YAML framework does not support deque objects) Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
class WindowManager FIXME: self._setCurrentWindow and self._raiseCurrentWindow do the same thing? Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
… ALL mpl Figure windows!!! gui.workspacemodel.WorkspaceModel.pre-execute begin dealing with mpl Figures c'ted at console Signed-off-by: Cezar M. Tigaret <cezar@w009.psych.cf.ac.uk>
setting current viewer (double vs single click in workspace viewer) Workspace model now generates "visible" bindings to mpl figures created at console (but ONLY direcly, and not via plt.plot...-like functions) TODO: add an observed of plt.get_fignums() to capture the latter condition This is somewhat contrived, as mpl figures generated by code executed INSIDE python, NOT the console (e.g. running a module cole) will NOT be captured Signed-off-by: Cezar M. Tigaret <cezar.tigaret@gmail.com>
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Bug fixes in window management for matplotlib figures (still some work in progress).
Scipyen console has CTRL+SHIFT+K shortcut for clearing the window.
Fixed bugs in ScipyenInprocessKernel: