add progress bars #4072

SophiaRuan · 2023-03-14T07:49:19Z

Changes made in this Pull Request:

add progress bars to _conclude()

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

SophiaRuan · 2023-03-14T19:56:43Z

Hi @orbeckst @hmacdope, I tried to add progress bars to _conclude_simple and _conclude_fft. I installed the module progressbar locally and the code pass the msd_test locally. How can I install the progressbar for remote repo here or is there any other solution?

hmacdope · 2023-03-14T20:19:57Z

@SophiaRuan normally we use the tqdm package for progress bars rather than "progress bars" You will need to test on your local machines

codecov · 2023-03-14T22:14:15Z

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (1207578) 93.58% compared to head (6421c00) 93.58%.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #4072   +/-   ##
========================================
  Coverage    93.58%   93.58%           
========================================
  Files          192      192           
  Lines        25132    25133    +1     
  Branches      4056     4056           
========================================
+ Hits         23519    23520    +1     
  Misses        1093     1093           
  Partials       520      520

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/msd.py	`100.00% <100.00%> (ø)`

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orbeckst · 2023-03-14T22:56:01Z

@hmacdope sorry to butt in... we do indeed have our own ProgressBar! The question is if the customizations in ProgressBar makes sense, it's a thin wrapper around tqdm.

SophiaRuan · 2023-03-14T22:59:47Z

Hi @hmacdope @orbeckst, I am wondering how to pass the dark_lint test. I am not sure if the current code aligns with the requirement.

RMeli · 2023-03-15T07:19:50Z

@SophiaRuan the dark_lint test is optional, see #4067. Here it seems that it is only asking to add a blank line after the from tqdm import tqdm.

hmacdope · 2023-03-15T07:29:13Z

@RMeli is correct. @SophiaRuan would you be able to share a screenshot showing that the progress bars work? Otherwise looks good to me!

package/MDAnalysis/analysis/msd.py

SophiaRuan · 2023-03-15T20:26:24Z

@RMeli is correct. @SophiaRuan would you be able to share a screenshot showing that the progress bars work? Otherwise looks good to me!

Hi @hmacdope, I am wondering how to check if progress bars work. I only used the pytest on my local machine to check if the code pass the test, but I can't see the progress bars.

hmacdope · 2023-03-15T22:49:32Z

@RMeli is correct. @SophiaRuan would you be able to share a screenshot showing that the progress bars work? Otherwise looks good to me!

Hi @hmacdope, I am wondering how to check if progress bars work. I only used the pytest on my local machine to check if the code pass the test, but I can't see the progress bars.

You should set up an example piece of code (copying one of the tests is fine) and then run it to see if progress bars appear.

hmacdope · 2023-03-15T22:50:30Z

You may need to use the verbose=True flag to run I can't remember.

SophiaRuan · 2023-03-16T19:06:27Z

Hi @hmacdope, I tried to run the test_msd.py in Pycharm. Does this look good to you?

hmacdope

Could you add a CHANGELOG entry?

03/20/23 SophiaRuan * 2.5.0 Changes * Add progress bar to track the progress of _conclude() functions (_conclude_simple() and _conclude_fft()) in msd.py (PR MDAnalysis#4072)

SophiaRuan · 2023-03-20T22:57:16Z

#4070
Hi @hmacdope, I just changed the CHANGELOG. Could you have a look? Thank you!
[(https://github.com/MDAnalysis/mdanalysis/compare/develop...SophiaRuan:mdanalysis:patch-1)]

hmacdope · 2023-03-21T00:07:10Z

@SophiaRuan you need to add them in this same PR

hmacdope · 2023-03-21T01:06:30Z

package/CHANGELOG

@@ -13,7 +13,15 @@ The rules for this file:
  * release numbers follow "Semantic Versioning" http://semver.org

 ------------------------------------------------------------------------------
-
+
+03/20/23 SophiaRuan


This needs to go with the other 2.5.0 entries, just add it to the list.

Hi @hmacdope, I just added the change to the 2.5.0 entries.

hmacdope

Would you also be able to addd your name to AUTHORS if you havn't already. other than that looks good!

IAlibay

Just a couple of small review comments on changelog formatting from me please.

IAlibay · 2023-03-22T06:51:11Z

package/CHANGELOG

+  * Add progress bars to track the progress of _conclude() functions
+    (_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)


Entries should be newest first (please see line 7 in the instructions at the top of the file). This helps us easily scan the ordered history of changes in the repository.

IAlibay · 2023-03-22T06:53:01Z

package/CHANGELOG

@@ -50,6 +50,9 @@ Changes
    analysis.nucleicacids' NucPairDist and WatsonCrickDist classes has been
    removed. Please use the `results.pair_distances` and `times` attributes
    instead (Issue #3744)
+  * Add progress bars to track the progress of _conclude() functions
+    (_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)
+


Suggested change

Sorry this might look overly pedantic but we try to keep the empty line formatting fixed in this file.

hmacdope · 2023-03-23T04:02:24Z

package/CHANGELOG

 ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
         ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
-         xhgchen, jaclark5, DrDomenicoMarson
+         xhgchen, jaclark5, DrDomenicoMarson, SophiaRuan
+


I know this is annoying @SophiaRuan but this should show no diff except your name

Hi @hmacdope, I just made some changes. Could you help me check a bit? Thank you for your help!

SophiaRuan · 2023-03-27T20:05:27Z

Hi @hmacdope, I made some changes to the Author and CHANGELOG recently. Could you help me check on this?
Also, I find there are some conflicts in Author and CHANGELOG constantly. Should I solve the conflicts remotely or on my local machine? Previously, I find I need to solve conflicts both remotely and locally in order to push my next change. Sorry for asking so many questions. Thank you for your help!

hmacdope

Apply this suggestion and should be good to go.

package/CHANGELOG

Co-authored-by: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>

github-actions · 2023-03-27T22:06:17Z

Linter Bot Results:

Hi @SophiaRuan! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/4549141753/jobs/8020908277

Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

SophiaRuan · 2023-03-28T01:11:59Z

Apply this suggestion and should be good to go.

Hi @hmacdope, I have made the change! Thank you!

hmacdope

Looks good to me !

hmacdope · 2023-03-28T01:23:01Z

@SophiaRuan resolve conflicts and then good to go.

SophiaRuan · 2023-03-28T19:00:22Z

@SophiaRuan resolve conflicts and then good to go.

Hi @hmacdope @IAlibay, I have solved the conflicts. Thank you for your help!

github-actions bot added the Component-Analysis label Mar 14, 2023

IAlibay requested changes Mar 15, 2023

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SophiaRuan force-pushed the msd_pbar branch from 2ae90f3 to 6f691e0 Compare March 15, 2023 20:34

hmacdope requested changes Mar 19, 2023

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SophiaRuan force-pushed the msd_pbar branch from b455e10 to c5a5a8c Compare March 21, 2023 00:14

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SophiaRuan force-pushed the msd_pbar branch from c5a5a8c to 08719d6 Compare March 21, 2023 06:07

hmacdope requested changes Mar 22, 2023

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SophiaRuan force-pushed the msd_pbar branch from d99f651 to 8a1c0cf Compare March 23, 2023 00:22

orbeckst assigned hmacdope Mar 23, 2023

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SophiaRuan added 4 commits March 23, 2023 14:22

add progress bars

7c36d7c

update pbar maxval

f41138b

fix format

b3055ef

use tqdm

5e66445

SophiaRuan added 3 commits March 23, 2023 14:22

move import of tqdm up

3b2ac29

changelog

27c4972

author and changelog

b0493ef

SophiaRuan force-pushed the msd_pbar branch from c8b72b2 to b0493ef Compare March 23, 2023 21:41

hmacdope requested changes Mar 27, 2023

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Update package/CHANGELOG

2648773

Co-authored-by: Hugo MacDermott-Opeskin <hugomacdermott@gmail.com>

hmacdope approved these changes Mar 28, 2023

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Merge branch 'develop' into msd_pbar

481e6cf

hmacdope requested a review from IAlibay March 28, 2023 22:40

IAlibay approved these changes Mar 29, 2023

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Merge branch 'develop' into msd_pbar

6421c00

hmacdope merged commit 75f0fb9 into MDAnalysis:develop Mar 29, 2023

SophiaRuan deleted the msd_pbar branch March 29, 2023 07:19

IAlibay added the enhancement label Sep 21, 2023

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		* Add progress bars to track the progress of _conclude() functions
		(_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)

add progress bars #4072

add progress bars #4072

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