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Feature/depandabot 20231030 #787

Merged
merged 28 commits into from
Feb 5, 2024
Merged

Feature/depandabot 20231030 #787

merged 28 commits into from
Feb 5, 2024

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enicolasgomez
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dependabot bot and others added 23 commits July 6, 2023 22:01
@dependabot
Bump scipy from 1.4.1 to 1.10.0
86df4a7 
Bumps [scipy](https://github.com/scipy/scipy) from 1.4.1 to 1.10.0.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.4.1...v1.10.0)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump restrictedpython from 5.0 to 6.1
77bebf9 
Bumps [restrictedpython](https://github.com/zopefoundation/RestrictedPython) from 5.0 to 6.1.
- [Changelog](https://github.com/zopefoundation/RestrictedPython/blob/6.1/CHANGES.rst)
- [Commits](zopefoundation/RestrictedPython@5.0...6.1)

---
updated-dependencies:
- dependency-name: restrictedpython
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@sanjayankur31
feat(neuroml): return output string on import failure
3db4241
@sanjayankur31
feat(neuroml): increase jvm memory
8c1f732
@sanjayankur31
chore(neuroml): cosmetic tweaks
b553349 
remove trailing white space, extra lines and so on
@dependabot
Bump word-wrap from 1.2.3 to 1.2.4 in /tests/frontend/e2e
47726bf 
Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump word-wrap from 1.2.3 to 1.2.4 in /webapp
351bd55 
Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
- [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
- [Commits](jonschlinkert/word-wrap@1.2.3...1.2.4)

---
updated-dependencies:
- dependency-name: word-wrap
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump pygments from 2.6.1 to 2.15.0
190d505 
Bumps [pygments](https://github.com/pygments/pygments) from 2.6.1 to 2.15.0.
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.6.1...2.15.0)

---
updated-dependencies:
- dependency-name: pygments
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump cryptography from 2.9.2 to 41.0.3
08d7f13 
Bumps [cryptography](https://github.com/pyca/cryptography) from 2.9.2 to 41.0.3.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@2.9.2...41.0.3)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
Bump tornado from 6.1.0 to 6.3.3
ef1bd58 
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.1.0 to 6.3.3.
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.1.0...v6.3.3)

---
updated-dependencies:
- dependency-name: tornado
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@enicolasgomez
Merge pull request #762 from MetaCell/dependabot/pip/tornado-6.3.3
36f5f82 
Bump tornado from 6.1.0 to 6.3.3
@enicolasgomez
Merge pull request #760 from MetaCell/dependabot/pip/cryptography-41.0.3
476d149 
Bump cryptography from 2.9.2 to 41.0.3
@enicolasgomez
Merge branch 'feature/depandabot_20231030' into dependabot/pip/pygmen…
9c3a325 
…ts-2.15.0
@enicolasgomez
Merge pull request #756 from MetaCell/dependabot/pip/pygments-2.15.0
b111968 
Bump pygments from 2.6.1 to 2.15.0
@enicolasgomez
Merge pull request #755 from MetaCell/dependabot/npm_and_yarn/webapp/…
69550df 
…word-wrap-1.2.4

Bump word-wrap from 1.2.3 to 1.2.4 in /webapp
@enicolasgomez
Merge branch 'feature/depandabot_20231030' into dependabot/npm_and_ya…
baa9a82 
…rn/tests/frontend/e2e/word-wrap-1.2.4
@enicolasgomez
Merge pull request #754 from MetaCell/dependabot/npm_and_yarn/tests/f…
86cc427 
…rontend/e2e/word-wrap-1.2.4

Bump word-wrap from 1.2.3 to 1.2.4 in /tests/frontend/e2e
@enicolasgomez
Merge pull request #746 from sanjayankur31/feat/show-neuroml-import-e…
516c841 
…rror

Show neuroml import error on failure, increase memory for jvm
@enicolasgomez
Merge pull request #737 from MetaCell/dependabot/pip/restrictedpython…
d8996b3 
…-6.1

Bump restrictedpython from 5.0 to 6.1
@enicolasgomez
Merge pull request #735 from MetaCell/dependabot/pip/scipy-1.10.0
5471bdb 
Bump scipy from 1.4.1 to 1.10.0
regenerating dependencies
0cab979
@enicolasgomez
fixed wrong scipy version
a288d9d
@enicolasgomez
Copied requirements file from dev
cf1650b
@SimaoBolota-MetaCell
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SimaoBolota-MetaCell commented Dec 4, 2023 •
edited
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I am not sure what is happening with the tests workflow. It errors out as soon as the tests start with the following error: Cannot read property 'jest' of undefined

I tried the exact same steps taken by the github actions locally for this branch and I was able to run the tests with no problem (also with this branch deployed in dev - https://g.codefresh.io/build/656e202f715ff3ea041a04e1). The tests fail but that's because these are outdated compared to the one's in development.

Steps taken:

  1. Clone repo
  2. Checkout this branch feature/depandabot_20231030
  3. cd tests/frontend/e2e
  4. npm ci
  5. npm run Tutorial_1_test (for example) - the tests start up with no jest undefined error while in github actions it immediately fails

@enicolasgomez @ddelpiano

@ddelpiano ddelpiano changed the base branch from development to master December 5, 2023 14:46
@ddelpiano ddelpiano changed the base branch from master to development December 5, 2023 14:46
@ddelpiano
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#746 (comment)
@enicolasgomez can we move to pyneuroml > 1.0.9 as per comment from @sanjayankur31, please?

@ddelpiano
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@SimaoBolota-MetaCell I don't see anything obvious for jest to fail, 2 suggestions:

  • remove the yarn lock since the dockerfile uses npm
  • regenerate the package-lock json so that we can see if this works.

@SimaoBolota-MetaCell
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SimaoBolota-MetaCell commented Dec 5, 2023 •
edited
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Did what you suggested @ddelpiano @enicolasgomez

  • removed the yarn.lock file
  • regenerated package-lock.json

and am still getting the same error on the tests workflow from github actions
image

Building the dockerfile locally leads me to the same error I am encountering through the github actions - Cannot read property 'jest' of undefined
image

Do any of you know any solution for this? @enicolasgomez @ddelpiano

@SimaoBolota-MetaCell
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Now the build runs locally
image
and the tests pass on github actions as can be seen in the details
@enicolasgomez @ddelpiano

@ddelpiano ddelpiano changed the base branch from development to master February 5, 2024 14:58
@ddelpiano ddelpiano changed the base branch from master to release/1.1.0 February 5, 2024 14:58
@ddelpiano ddelpiano merged commit a3a71b4 into release/1.1.0 Feb 5, 2024
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4 participants
@enicolasgomez @SimaoBolota-MetaCell @ddelpiano @sanjayankur31