fix: GH workflow test #635

mihai-sysbio · 2023-06-13T01:31:30Z

Main improvements in this PR:

This PR is continuing #629 aimed to fix the GH workflow test of the import-export cycle, thus resolving #628.

I hereby confirm that I have:

Tested my code on my own computer for running the model
Selected develop as a target branch
Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

code/test/testYamlConversion.m

- This commit includes fixing typos, and reverting back to original way of extracting subsystem values

haowang-bioinfo · 2023-06-13T18:28:55Z

the reported error in yaml import/export cycle is fixed by correcting typos and reverting to original subsystem value extraction (e118e1d); while the issue with GH action remains, which might be resolved later?

haowang-bioinfo

I tested this PR by locally running testYamlConversion and tandemly import/export the yaml file, everything is fine.

would be good to have checks for unknown keys (caused by typos) in yaml, but have no idea how to reactivate the "idling" action

mihai-sysbio · 2023-06-14T06:06:02Z

I'm still working on getting the workflow to fail in a visible way.

feiranl

LGTM!

haowang-bioinfo · 2023-06-16T06:57:27Z

could this be merged, how's going with the workflow test? @mihai-sysbio

mihai-sysbio · 2023-06-16T08:54:55Z

could this be merged, how's going with the workflow test? @mihai-sysbio

The workflow still appears as passing in the latest workflow run even though it clearly prints out an error. I am having difficulties relaying the exit(1) from Matlab to bash. I've tried a few different things but none seemed to work. In the meantime, this PR is converted as to draft, since merging it would not resolve the intended issue.

haowang-bioinfo · 2023-06-16T13:29:06Z

In the meantime, this PR is converted as to draft, since merging it would not resolve the intended issue.

yes, let's do so

~~the aim of this PR can be reduced to only~~ will continue in #629 resolving import/export cycle, which is a bug of develop branch that is now jammed

The workflow still appears as passing in the latest workflow run even though it clearly prints out an error. I am having difficulties relaying the exit(1) from Matlab to bash. I've tried a few different things but none seemed to work.

this workflow problem can be temporarily substituted with checking these Matlab-based tasks locally before merging

code/test/testYamlConversion.m

mihai-sysbio · 2023-06-19T14:47:25Z

The workflow has been updated to fail in an obvious way if problems are encountered in commit 29113a1. The following commit 927fb07 removed the purposefully-introduced error, which resulted in all workflows passing. Therefore, the core issue is now resolved.

.github/workflows/check-metabolictasks.yml

mihai-sysbio · 2023-06-19T15:17:00Z

Due to significant changes and slight scope creep, reviews will be re-requested.

haowang-bioinfo · 2023-06-19T19:20:52Z

if I can re-introduce the bug happened in Yaml before and see what happens?

mihai-sysbio · 2023-06-20T02:42:15Z

if I can re-introduce the bug happened in Yaml before and see what happens?

good idea, please play around with different test cases

mihai-sysbio · 2023-06-20T15:09:24Z

Another idea, should the disp function calls be replaced with warn?

- Test if GH action really work

haowang-bioinfo · 2023-06-27T17:14:47Z

the bug re-troduced by 97d030b suppose to lead to failure of both yaml-validation and yaml-conversion actions. But the latter still gives a pass, therefore this workflow bug persists.

mihai-sysbio · 2023-06-28T09:45:53Z

@haowang-bioinfo the reintroduced but caused a failure higher up in the testing code, which was not caught by the same mechanism. The previous commit 6e5d66c address this.

mihai-sysbio · 2023-06-28T09:51:31Z

If there is any other bug you'd want to test with, please go ahead @haowang-bioinfo

mihai-sysbio · 2023-07-03T13:28:11Z

Oh how interesting, none of tests capture the bug introduced in 5f39c61. The actions are passing, because the tests are passing. I would be inclined to report this as separate bug - the workflows now seem to reflect the status of the tests, which was the original aim of this PR.

haowang-bioinfo · 2023-07-03T13:51:47Z

go ahead please

This type of bug (5f39c61) probably can be detected by Yaml lint checker by providing a finite set of keys, from which any unknown keys could thus be detected and reported.

mihai-sysbio · 2023-07-04T16:07:52Z

PR #671 is aimed at merging into this one, and will catch the bug introduced in 5f39c61.

feat: add basic memote tests

mihai-sysbio · 2023-07-05T12:25:43Z

@haowang-bioinfo the purposefully introduced bug has now been caught and may be removed.

code/test/testMetabolicTasks.m

code/test/testYamlConversion.m

haowang-bioinfo · 2023-07-07T02:20:57Z

with #672, both yaml-conversion and yaml-validation actions can catch the typo in MAM1261m

haowang-bioinfo

looks very good - the previously idle yaml-conversion action in functioning, together with enhanced memote checks

mihai-sysbio mentioned this pull request Jun 13, 2023

fix-add a error report in the import/export cycle #629

Merged

mihai-sysbio commented Jun 13, 2023

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mihai-sysbio and others added 2 commits June 13, 2023 14:20

test: introduce a bug to see if it is picked up by the workflow

db8ca8c

fix: typos introduced in #606

e118e1d

- This commit includes fixing typos, and reverting back to original way of extracting subsystem values

test: revert back testYamlConversion to the original

3be0333

haowang-bioinfo approved these changes Jun 13, 2023

View reviewed changes

refactor: test yaml conversion

5410ebf

mihai-sysbio force-pushed the fix/importExportCycle branch 2 times, most recently from e9426a9 to b247c0b Compare June 15, 2023 04:21

feiranl approved these changes Jun 16, 2023

View reviewed changes

mihai-sysbio marked this pull request as draft June 16, 2023 08:52

haowang-bioinfo marked this pull request as ready for review June 16, 2023 13:30

haowang-bioinfo changed the title ~~fix: import export cycle and GH workflow test~~ fix: import export cycle bug Jun 16, 2023

haowang-bioinfo marked this pull request as draft June 16, 2023 13:47

haowang-bioinfo changed the title ~~fix: import export cycle bug~~ fix: GH workflow test Jun 16, 2023

haowang-bioinfo mentioned this pull request Jun 18, 2023

feat: add hart2015 essentiality suite #563

Merged

3 tasks

mihai-sysbio force-pushed the fix/importExportCycle branch 2 times, most recently from e822985 to 6ac87c4 Compare June 19, 2023 13:50

feat: fail action based on matlab exit code

29113a1

mihai-sysbio force-pushed the fix/importExportCycle branch from 6ac87c4 to 29113a1 Compare June 19, 2023 14:20

mihai-sysbio commented Jun 19, 2023

View reviewed changes

code/test/testYamlConversion.m Outdated Show resolved Hide resolved

revert: remove purposeful error

927fb07

fix: metabolic tasks fail visibly

ba6a1c7

mihai-sysbio commented Jun 19, 2023

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.github/workflows/check-metabolictasks.yml Outdated Show resolved Hide resolved

mihai-sysbio requested review from haowang-bioinfo and feiranl June 19, 2023 15:26

mihai-sysbio mentioned this pull request Jun 21, 2023

Merge Reactions With Same Stoichiometry But Different Genes #657

Merged

3 tasks

Devlin-Moyer mentioned this pull request Jun 21, 2023

add Alpha subunits of sodium channel genes to MAR01527 #664

Merged

3 tasks

test: re-introduce bug to Yaml file

97d030b

- Test if GH action really work

fix: catch all potential errors in yaml conversion workflow

6e5d66c

test: replicate Yaml bug reported in #6286

5f39c61

mihai-sysbio mentioned this pull request Jul 3, 2023

bug in test setup #671

Closed

feat: add basic memote test

b881243

Merge pull request #672 from SysBioChalmers/fix/yaml-test-bug

1b6f15c

feat: add basic memote tests

mihai-sysbio commented Jul 6, 2023

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mihai-sysbio and others added 2 commits July 7, 2023 02:02

refactor: use warning instead of disp in matlab tests

82c67a2

test: revert typo purposely introduced to the "metabolites" key

be2c34e

test: revert typo purposely introduced to id MAM01261m

a5da1e6

haowang-bioinfo approved these changes Jul 7, 2023

View reviewed changes

mihai-sysbio merged commit f4f99d7 into develop Jul 7, 2023

mihai-sysbio deleted the fix/importExportCycle branch July 7, 2023 03:49

haowang-bioinfo mentioned this pull request Sep 25, 2023

Human 1.17 #700

Merged

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fix: GH workflow test #635

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fix: GH workflow test #635

fix: GH workflow test #635

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Main improvements in this PR:

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