Fixing typos and alignments/spacings #61

cosimolupo · 2024-02-15T11:50:42Z

Fixes some typos here and there.
Adds or removes spaces and blank lines, where necessary for a more homogeneous formatting across similar files.

rgutzen

Thank you for cleaning up the formatting and spelling in so many files. I just added a few comments where the fix is not too obvious.

cobrawap/pipeline/stage02_processing/scripts/frequency_filter.py

cobrawap/pipeline/stage02_processing/scripts/logMUA_estimation.py

rgutzen · 2024-02-20T15:34:51Z

cobrawap/pipeline/stage03_trigger_detection/Snakefile

@@ -102,6 +102,7 @@ use rule template as minima with:
               'plot_channels', 'plot_tstart', 'plot_tstop',
                img_name='minima_channel0.'+config.PLOT_FORMAT, config=config)

+


Comment headings are not preceded by two blank lines.

We should instead use two blank lines before comment headings, so to better distinguish rules belonging to different "groups", given that rules from the same group are separated by double blank lines anyway. Let's decide a norm, and then let's stick to it.

cobrawap/pipeline/stage03_trigger_detection/Snakefile

rgutzen · 2024-02-20T15:43:25Z

cobrawap/pipeline/stage05_channel_wave_characterization/Snakefile

-               / f'{config.EVENT_NAME}_spatial_derivative.{config.PLOT_FORMAT}'
+                         / f'{config.EVENT_NAME}_spatial_derivative.{config.PLOT_FORMAT}'


This line is purposefully under-indented to fit in a 79-character line bound.

rgutzen · 2024-02-20T15:47:58Z

cobrawap/pipeline/stage05_channel_wave_characterization/configs/config_template.yaml

-STAGE_OUTPUT: 'channel-wise_measures.csv'
+STAGE_OUTPUT: 'channel_wise_measures.csv'


I don't think this should be changed. We would need to evaluate if this is helpful or more consistent in any way.

We previously changed the stage name, by using "channel_wave" instead of "channel-wave". So I was acting here coherently.

The naming convention for the stage names requires no use of '-' since it can cause issues when chaining together the pipeline from the stages. However, this is separate from conventions for file names. I think with the current naming conventions, this change in file names wouldn't make it more consistent. However, we could think about standardizing the naming of stages and their output files some more, also for the other stages.
For the stage05 this may entail also adapting the stage names. One possibility would be, for example, stage05_wave_wise_characterization :-> wave_wise_characterization.csv and stage05_channel_wise_characaterization :-> channel_wise_characterization.csv.
Such changes may, however, influence existing pipeline applications. Therefore, I would postpone such improvements of the naming conventions to version 0.2.

rgutzen · 2024-02-20T15:48:09Z

cobrawap/pipeline/stage05_wave_characterization/configs/config_template.yaml

-STAGE_OUTPUT: 'wave-wise_measures.csv'
+STAGE_OUTPUT: 'wave_wise_measures.csv'


I don't think this should be changed. We would need to evaluate if this is helpful or more consistent in any way.

We previously changed the stage name, by using "channel_wave" instead of "channel-wave". So I was acting here coherently.

see comment above

cobrawap/pipeline/utils/Snakefile

cobrawap/pipeline/utils/neo_utils.py

gulpgiulia · 2024-02-21T15:23:57Z

cobrawap/pipeline/stage04_wave_detection/scripts/plot_waves.py

+CLI.add_argument("--data", nargs='?', type=str,
+                 help="path to input data in neo format")
+CLI.add_argument("--output_dir", nargs='?', type=str,
+                 help="path to output directory")
 CLI.add_argument("--img_name", nargs='?', type=str)


very very minor, just to be consistent with other changes introduced above, assume that each argument line has a "help" option

(I inserted a suggestion, with the "empty" help option in a new line, to be coherent with what done above, but for short lines can also be put in the same line)

Yes, right. I could add help="" where still missing, so to have it for every single command-line arg.

gulpgiulia · 2024-02-21T15:25:27Z

cobrawap/pipeline/stage04_wave_detection/scripts/plot_waves.py

+CLI.add_argument("--data", nargs='?', type=str,
+                 help="path to input data in neo format")
+CLI.add_argument("--output_dir", nargs='?', type=str,
+                 help="path to output directory")
 CLI.add_argument("--img_name", nargs='?', type=str)


Suggested change

CLI.add_argument("--img_name", nargs='?', type=str)

CLI.add_argument("--img_name", nargs='?', type=str)

help="")

gulpgiulia · 2024-02-21T15:31:39Z

cobrawap/pipeline/stage04_wave_detection/scripts/plot_waves.py

 CLI.add_argument("--img_name", nargs='?', type=str)
 CLI.add_argument("--time_window", nargs='?', type=float, default=0.4,
-                    help="size of the plotted window in seconds.")
+                 help="size of the plotted window in seconds.")
 CLI.add_argument("--colormap", nargs='?', type=str, default='viridis')


"help" also here, but maybe not needed to be present each time...?

rgutzen

Looks all fine now.
I just added a comment to postpone the changes to file naming conventions to a later separate PR.

cosimolupo · 2024-02-28T16:08:53Z

Ok then, I will provide a new commit right now, following @rgutzen's suggestion of postponing changes in naming conventions to a future PR.

Postponing this change to a future PR

mdenker · 2024-03-07T13:49:18Z

New issue #63 is used to collect ideas for naming conventions.

mdenker

I could not spot any remaining issues -- all good from my side.

* Updates the PR according to the presence of robust_t novel function in neo_utils * Adding "None" as a permitted value in all plotting scripts * Minor change in config template files * Fix for extra spacings added when merging PR #61

Fixing typos and alignments/spacings

63190ec

cosimolupo requested review from rgutzen, mdenker and gulpgiulia and removed request for rgutzen February 15, 2024 11:50

rgutzen reviewed Feb 20, 2024

View reviewed changes

cosimolupo added 3 commits February 20, 2024 22:33

Adjusting indentation in CLI args definition

8d082ad

Further changing indentation

647d228

Fix

c011f82

cosimolupo requested a review from rgutzen February 21, 2024 13:23

gulpgiulia reviewed Feb 21, 2024

View reviewed changes

Adding help for CLI args where still missing

249489b

mdenker assigned mdenker and unassigned mdenker Feb 22, 2024

rgutzen reviewed Feb 28, 2024

View reviewed changes

rgutzen added the formatting improvement of code style and structure label Feb 28, 2024

Rolling back to previous naming convention

b2a2b9f

Postponing this change to a future PR

rgutzen approved these changes Feb 28, 2024

View reviewed changes

cosimolupo self-assigned this Mar 20, 2024

mdenker approved these changes Mar 22, 2024

View reviewed changes

mdenker merged commit a1c0579 into NeuralEnsemble:master Mar 22, 2024

cosimolupo added a commit to APE-group/cobrawap that referenced this pull request Mar 22, 2024

Fix for extra spacings added when merging PR NeuralEnsemble#61

3ff1ad7

cosimolupo mentioned this pull request Mar 22, 2024

New logic for plot limits #48

Merged

cosimolupo deleted the bugfix/typos branch June 21, 2024 13:35

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Fixing typos and alignments/spacings #61

Fixing typos and alignments/spacings #61

cosimolupo commented Feb 15, 2024

rgutzen left a comment

rgutzen Feb 20, 2024

cosimolupo Feb 20, 2024

rgutzen Feb 20, 2024

cosimolupo Feb 20, 2024

rgutzen Feb 20, 2024

cosimolupo Feb 20, 2024

rgutzen Feb 28, 2024

rgutzen Feb 20, 2024

cosimolupo Feb 20, 2024

rgutzen Feb 28, 2024

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gulpgiulia Feb 21, 2024

cosimolupo Feb 21, 2024

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gulpgiulia Feb 21, 2024

rgutzen left a comment

cosimolupo commented Feb 28, 2024

mdenker commented Mar 7, 2024

mdenker left a comment

		@@ -102,6 +102,7 @@ use rule template as minima with:
		'plot_channels', 'plot_tstart', 'plot_tstop',
		img_name='minima_channel0.'+config.PLOT_FORMAT, config=config)

		/ f'{config.EVENT_NAME}_spatial_derivative.{config.PLOT_FORMAT}'
		/ f'{config.EVENT_NAME}_spatial_derivative.{config.PLOT_FORMAT}'

		STAGE_OUTPUT: 'channel-wise_measures.csv'
		STAGE_OUTPUT: 'channel_wise_measures.csv'

		STAGE_OUTPUT: 'wave-wise_measures.csv'
		STAGE_OUTPUT: 'wave_wise_measures.csv'

	CLI.add_argument("--img_name", nargs='?', type=str)
	CLI.add_argument("--img_name", nargs='?', type=str)
	help="")

Fixing typos and alignments/spacings #61

Fixing typos and alignments/spacings #61

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cosimolupo commented Feb 28, 2024

mdenker commented Mar 7, 2024

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