Simulator CLI/GUI #368

lawhead · 2024-11-26T00:45:06Z

Overview

Created a command line interface and GUI to assist with configuring parameters for a simulation.

Ticket

https://www.pivotaltracker.com/story/show/188497024

Contributions

Added an interactive mode to the existing command line interface. bcipy-sim -i.
Added a GUI to run the simulator: bcipy-sim-gui
Both modes produce similar results but the GUI has better support for selecting data directories from more loosely structured data folders.
Added an argument to customize the output folder of the simulation.
Simulator bug fixes

Test

Ran all unit tests
Ran the simulator CLI and GUI code to confirm output as expected.

tab-cmd

Looks good! I haven't pulled it locally to try the new GUI yet, but will soon. We should demo with Dan after the next visit to get some feedback.

tab-cmd · 2024-11-26T19:46:33Z

scripts/python/update_params.py

@@ -0,0 +1,65 @@
+"""Update parameters files to latest."""


What versions of BciPy would this support?

I think this works for all versions.

tab-cmd · 2024-11-26T19:48:42Z

setup.py

@@ -110,6 +110,7 @@ def run(self):
            'bcipy = bcipy.main:bcipy_main',
            'bcipy-erp-viz = bcipy.helpers.visualization:erp',
            'bcipy-sim = bcipy.simulator:main',
+            'bcipy-sim-gui = bcipy.simulator.ui.gui:main',


This could be a flag on bcipy-sim? I was considering collapsing some of these scripts in the future.

I refactored to remove the setup script and include a command line flag instead.

tab-cmd · 2024-11-26T19:52:39Z

bcipy/simulator/ui/gui.py

+        return True
+
+
+class ChooseFileInput(QWidget):


We have similar code in the GUI module for getting files and directories. Could we leverage that here? We will be collapsing some of the GUI code (and likely passing around a single QApplication Instance) to package in the future, which is why I ask.

These widgets are a bit different in that they represent just the selection input and not the input, label, checkbox, and separator, all of which would affect the layout. These also have hooks for a change action, which is important for this form, but not the parameters GUI.

I do think our existing widgets could be updated to use these components as the underlying input, which would eliminate the duplicate code between the two. That would be a good refinement and when we do that work these could move to a common location.

tab-cmd · 2024-11-26T19:54:12Z

bcipy/simulator/ui/gui.py

+    command = panel.cli_output()
+    app.quit()
+    if command:
+        print(command, file=sys.stdout)


use the logger?

Since this starts executing a subprocess immediately in the console it's confusing to the user if this doesn't print to stdout. Also, this gives users the opportunity to run straight from the command line once the configuration is set, which can be faster than the GUI if you're doing this multiple times with only small variation.

tab-cmd · 2024-11-26T19:55:48Z

bcipy/simulator/task/copy_phrase.py

@@ -133,7 +133,7 @@ def compute_device_evidence(
            # This assumes that sampling is independent. Changes to the sampler API are needed if
            # we need to provide the trial context of the last sample.
            sampled_data = sampler.sample_data(current_state)
-            evidence = model.compute_class_probabilities(
+            evidence = model.compute_likelihood_ratio(


tab-cmd · 2024-11-26T19:56:41Z

bcipy/gui/main.py

        "Override. Another checkbox is needed for editable"
+        if value is None:


Update type to show it can be more than bool

tab-cmd · 2024-11-26T19:58:31Z

I think this can go to the base branch 2.0 unless you were hoping to release it with the patch.

codacy-production · 2024-12-10T23:49:38Z

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
Report missing for `b256aed`¹	❌ 24.05% (target: 70.00%)

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (`b256aed`)	Report Missing	Report Missing	Report Missing
Head commit (`34b7511`)	9071	6114	67.40%

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#368)	582	140	24.05%

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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_{Codacy stopped sending the deprecated coverage status on June 5th, 2024. Learn more}

Codacy didn't receive coverage data for the commit, or there was an error processing the received data. Check your integration for errors and validate that your coverage setup is correct. ↩

lawhead added 8 commits November 18, 2024 10:36

Fixed simulator regression

df089ee

Added temporary script to update parameters files to our latest format

25774e6

Added an interactive command line tool for running the simulator

516adfc

Initial implementation for simulator GUI

5a6482a

GUI Refactoring

3398802

Added parent widgets

23c8ec7

Fixes to output a command

d5be43a

Sim GUI cleanup; added a bcipy command; type fixes and linting

49c27cb

lawhead requested a review from tab-cmd November 26, 2024 00:45

Fix types for Python 3.8

8017f6d

tab-cmd approved these changes Nov 26, 2024

View reviewed changes

lawhead added 7 commits November 26, 2024 13:55

Bug fix in directory filter

ce38af7

Fix bug in data engine

f4b2356

Fix linting issue

847fa65

Added sim parameter for sampler

71729fa

Fix type issue

52dd8bd

Refactored to remove bcipy-sim-gui setup script

2d41f96

Updated type

cdfcb06

lawhead changed the base branch from 2.0.1rc4 to 2.0.0 December 3, 2024 01:15

lawhead changed the base branch from 2.0.0 to 2.0.1rc4 December 3, 2024 01:25

lawhead changed the base branch from 2.0.1rc4 to 2.0.0 December 10, 2024 00:58

Merged 2.0.0 changes

34b7511

Adjusted the coverage tools

9ee862f

lawhead merged commit dde7b50 into 2.0.0 Dec 11, 2024
0 of 10 checks passed

lawhead deleted the sim-cli branch December 11, 2024 00:06

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Simulator CLI/GUI #368

Simulator CLI/GUI #368

lawhead commented Nov 26, 2024

tab-cmd left a comment

tab-cmd Nov 26, 2024

lawhead Dec 3, 2024

tab-cmd Nov 26, 2024

lawhead Dec 3, 2024

tab-cmd Nov 26, 2024

lawhead Dec 3, 2024

tab-cmd Nov 26, 2024

lawhead Dec 3, 2024

tab-cmd Nov 26, 2024

tab-cmd Nov 26, 2024

tab-cmd commented Nov 26, 2024

codacy-production bot commented Dec 10, 2024

		"Override. Another checkbox is needed for editable"
		if value is None:

Simulator CLI/GUI #368

Simulator CLI/GUI #368

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lawhead commented Nov 26, 2024

Overview

Ticket

Contributions

Test

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tab-cmd commented Nov 26, 2024

codacy-production bot commented Dec 10, 2024

Coverage summary from Codacy

Footnotes