add bb5-tests #197

ilkilic · 2024-07-26T09:46:02Z

This PR adds the bluecellulab-bb5-tests folder to the repository. This folder contains tests for bluecellulab on the large circuits located on bb5. Please note that these tests are not directly usable as they are due to dependencies. This module will continue to be part of the CI pipeline on GitLab until December 31, 2024. After this date, the tests will no longer be included in the CI pipeline.

bluecellulab-bb5-tests/.gitlab-ci.yml

codecov-commenter · 2024-07-26T09:52:00Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.24%. Comparing base (e24a512) to head (f9c73f6).
Report is 2 commits behind head on main.

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@@           Coverage Diff           @@
##             main     #197   +/-   ##
=======================================
  Coverage   91.24%   91.24%           
=======================================
  Files          95       95           
  Lines        5708     5708           
=======================================
  Hits         5208     5208           
  Misses        500      500

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…ts' folder

AurelienJaquier

Could you add the license comment block at the head of every script file (python and sh)? Also could you check the license of the circuits that have already been open sourced (@darshanmandge knew about them I think). If the license is different we'll have to mention it in the LICENSE.txt file I believe, like we did for the mod files.

bluecellulab-bb5-tests/Makefile

bluecellulab-bb5-tests/README.md

bluecellulab-bb5-tests/tests/test_ssim.py

bluecellulab-bb5-tests/tests/test_ssim_gpfs.py

AurelienJaquier · 2024-07-26T13:50:34Z

bluecellulab-bb5-tests/tests/test_synapse_parameters.py

+    assert len(series1) == len(series2), "The series have different lengths."
+
+    # Iterate over each pair of elements
+    for i in range(len(series1)):


should we use enumerate and zip here? or do you ~~not care enough to change it~~ think it is alright like that?

I have changed it to enumerate and zip ;)

darshanmandge · 2024-07-26T14:14:04Z

Could you add the license comment block at the head of every script file (python and sh)? Also could you check the license of the circuits that have already been open sourced (@darshanmandge knew about them I think). If the license is different we'll have to mention it in the LICENSE.txt file I believe, like we did for the mod files.

Some of the circuits are here. You might have check for the ones you want

darshanmandge · 2024-07-26T14:03:13Z

tests/mechanisms/IN_Ih_Halnes2011.mod

@@ -0,0 +1,62 @@
+:Ih current for thalamic interneurons


Can you add a note in README.md file of this folder with details of where these mod files come from, date added and which files are added.

I think Aurélien maybe already mentioned it -- Can you add licenses to each new file being added: hoc, mod, py. However, I am not sure about it if we need to do it for other files too?

done in the last commit

AurelienJaquier · 2024-07-26T14:26:13Z

Could you add the license comment block at the head of every script file (python and sh)? Also could you check the license of the circuits that have already been open sourced (@darshanmandge knew about them I think). If the license is different we'll have to mention it in the LICENSE.txt file I believe, like we did for the mod files.

Some of the circuits are here. You might have check for the ones you want

We only have example 2-cells circuit in this PR. I had a quick look at your link, I don't think they have been released yet. So I think we probably can apply BlueCelluLab's license to them also, meaning we don't need to do anything more for the licensing of the circuits.

darshanmandge · 2024-07-29T09:31:24Z

could add in PR description what is added here and what these tests do?

darshanmandge

thanks @ilkilic !

AurelienJaquier

The initial commit of this github repo is 2023, so files that were there in the initial commit should have 2023-2024 in their license

AurelienJaquier · 2024-08-06T11:00:54Z

.compile_mod.sh

@@ -1,12 +1,26 @@
 #!/bin/sh

+# Copyright 2012-2024 Blue Brain Project / EPFL


2012? I think it should be 2023-2024

AurelienJaquier · 2024-08-06T11:04:34Z

bluecellulab-bb5-tests/README.md

+
+## Description
+
+This folder contains tests for bluecellulab on the large circuits located on bb5. Please note that these tests are not directly usable as they are due to dependencies.


Could you add a comma here?
not directly usable as they are, due to dependencies

bluecellulab-bb5-tests/tests/test_ssim_gpfs.py

AurelienJaquier · 2024-08-06T11:17:47Z

tests/helpers/os_utils.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:18:40Z

tests/test_analysis/test_inject_sequence.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:21:43Z

tests/test_synapse/test_synapse_factory.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:22:20Z

tests/test_tools.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:22:25Z

tests/test_ttx.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:22:30Z

tests/test_utils.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier · 2024-08-06T11:22:35Z

tests/test_verbosity.py

@@ -1,3 +1,16 @@
+# Copyright 2012-2024 Blue Brain Project / EPFL


AurelienJaquier

looks good, thanks!

* add cvode argument to apply_multiple_stimuli (#191) Co-authored-by: Jaquier Aurélien Tristan <[email protected]> * Feat: support custom node sets defined in simulation config (#192) * Add holding current to apply_multiple_stimuli (#193) Co-authored-by: Jaquier Aurélien Tristan <[email protected]> * Correct 'projections' for get_syn_descriptions (#187) * add contributing guidelines (#190) * replace amp_cv with relative_skew (#195) * remove double CircuitSimulation (#196) Co-authored-by: Jaquier Aurélien Tristan <[email protected]> * CI(dependabot): Bump anothrNick/github-tag-action from 1.69.0 to 1.70.0 (#198) Bumps [anothrNick/github-tag-action](https://github.com/anothrnick/github-tag-action) from 1.69.0 to 1.70.0. - [Release notes](https://github.com/anothrnick/github-tag-action/releases) - [Commits](anothrNick/github-tag-action@1.69.0...1.70.0) --- updated-dependencies: - dependency-name: anothrNick/github-tag-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add bb5-tests (#197) * add bb5-tests * remove gitlab-ci.yml * remove duplicate mod files for bb5-tests and merge them into the 'tests' folder * mod files info * add license header * update Makefile * update readme * Fix: Add missing 'units' attribute to timestamp in example test HDF5 file (#200) * add gh action for paper draft * add paper markdown * update draft-pdf.yml * fix yaml error in paper.md * add explanation to draft-pdf.yml * delete .gitlab-ci.yml for joss-paper * reword draft-pdf rule * trigger draft-pdf in any push * add doi for the unix programming env * add doi for agile software development Martin * add doi for parnas1972criteria * add explanation for figure1 --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Aurélien Jaquier <[email protected]> Co-authored-by: Jaquier Aurélien Tristan <[email protected]> Co-authored-by: ilkilic <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

add bb5-tests

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ilkilic requested review from darshanmandge and AurelienJaquier July 26, 2024 09:46

ilkilic self-assigned this Jul 26, 2024

AurelienJaquier reviewed Jul 26, 2024

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ilkilic added 2 commits July 26, 2024 11:54

remove gitlab-ci.yml

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remove duplicate mod files for bb5-tests and merge them into the 'tes…

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…ts' folder

AurelienJaquier reviewed Jul 26, 2024

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darshanmandge reviewed Jul 26, 2024

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ilkilic added 5 commits July 26, 2024 16:37

mod files info

661a342

add license header

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update Makefile

6eeae3f

code cleanup

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update readme

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darshanmandge approved these changes Jul 29, 2024

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AurelienJaquier reviewed Aug 6, 2024

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minor fix

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AurelienJaquier approved these changes Aug 6, 2024

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ilkilic merged commit 511ea26 into main Aug 6, 2024
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ilkilic deleted the bb5-tests branch August 6, 2024 12:06

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add bb5-tests #197

add bb5-tests #197

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		@@ -1,12 +1,26 @@
		#!/bin/sh

		# Copyright 2012-2024 Blue Brain Project / EPFL


		## Description

		This folder contains tests for bluecellulab on the large circuits located on bb5. Please note that these tests are not directly usable as they are due to dependencies.

		@@ -1,3 +1,16 @@
		# Copyright 2012-2024 Blue Brain Project / EPFL

add bb5-tests #197

add bb5-tests #197

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ilkilic commented Jul 26, 2024 •

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