update: add support for pre-commit #232

Merged

synchon merged 10 commits from enh/pre-commit into main 2023-06-21 10:48:42 +00:00

Conversation 7 Commits 10 Files changed 49 +195 -145

synchon commented 2023-05-22 16:09:38 +00:00 (Migrated from github.com)

Copy link

• description of feature/fix
• tests added/passed
• add an entry for the latest changes

This PR adds support for pre-commit in the codebase and makes necessary changes to adopt it.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR adds support for `pre-commit` in the codebase and makes necessary changes to adopt it.

codecov[bot] commented 2023-05-22 16:12:09 +00:00 (Migrated from github.com)

Copy link

Codecov Report

Merging #232 (e3c3792) into main (02a14ad) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

❗ Current head e3c3792 differs from pull request most recent head d031615. Consider uploading reports for the commit d031615 to get more accurate results

@@            Coverage Diff             @@
##             main     #232      +/-   ##
==========================================
- Coverage   93.62%   93.61%   -0.01%     
==========================================
  Files          82       82              
  Lines        3464     3460       -4     
  Branches      644      644              
==========================================
- Hits         3243     3239       -4     
  Misses        144      144              
  Partials       77       77              

Flag	Coverage Δ
docs	100.00% <ø> (ø)
junifer	93.61% <100.00%> (-0.01%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
docs/conf.py	100.00% <ø> (ø)
junifer/api/cli.py	69.14% <ø> (ø)
junifer/data/masks.py	96.42% <ø> (-0.04%)	⬇️
...r/external/nilearn/junifer_nifti_spheres_masker.py	93.33% <ø> (-0.08%)	⬇️
junifer/markers/reho/reho_estimator.py	68.70% <ø> (ø)
junifer/storage/pandas_base.py	95.55% <ø> (ø)
junifer/api/functions.py	96.23% <100.00%> (ø)
junifer/api/parser.py	94.87% <100.00%> (ø)
junifer/data/coordinates.py	100.00% <100.00%> (ø)
junifer/data/parcellations.py	98.08% <100.00%> (-0.01%)	⬇️
... and 19 more

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report > Merging [#232](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (e3c3792) into [main](https://app.codecov.io/gh/juaml/junifer/commit/02a14ad3a9642b704afdcdf3bcbe8461e027dc99?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (02a14ad) will **decrease** coverage by `0.01%`. > The diff coverage is `100.00%`. > :exclamation: Current head e3c3792 differs from pull request most recent head d031615. Consider uploading reports for the commit d031615 to get more accurate results [](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #232 +/- ## ========================================== - Coverage 93.62% 93.61% -0.01% ========================================== Files 82 82 Lines 3464 3460 -4 Branches 644 644 ========================================== - Hits 3243 3239 -4 Misses 144 144 Partials 77 77 ``` | Flag | Coverage Δ | | |---|---|---| | docs | `100.00% <ø> (ø)` | | | junifer | `93.61% <100.00%> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs/conf.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-ZG9jcy9jb25mLnB5) | `100.00% <ø> (ø)` | | | [junifer/api/cli.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvY2xpLnB5) | `69.14% <ø> (ø)` | | | [junifer/data/masks.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL21hc2tzLnB5) | `96.42% <ø> (-0.04%)` | :arrow_down: | | [...r/external/nilearn/junifer\_nifti\_spheres\_masker.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9leHRlcm5hbC9uaWxlYXJuL2p1bmlmZXJfbmlmdGlfc3BoZXJlc19tYXNrZXIucHk=) | `93.33% <ø> (-0.08%)` | :arrow_down: | | [junifer/markers/reho/reho\_estimator.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vcmVob19lc3RpbWF0b3IucHk=) | `68.70% <ø> (ø)` | | | [junifer/storage/pandas\_base.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9zdG9yYWdlL3BhbmRhc19iYXNlLnB5) | `95.55% <ø> (ø)` | | | [junifer/api/functions.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvZnVuY3Rpb25zLnB5) | `96.23% <100.00%> (ø)` | | | [junifer/api/parser.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9hcGkvcGFyc2VyLnB5) | `94.87% <100.00%> (ø)` | | | [junifer/data/coordinates.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL2Nvb3JkaW5hdGVzLnB5) | `100.00% <100.00%> (ø)` | | | [junifer/data/parcellations.py](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhL3BhcmNlbGxhdGlvbnMucHk=) | `98.08% <100.00%> (-0.01%)` | :arrow_down: | | ... and [19 more](https://app.codecov.io/gh/juaml/junifer/pull/232?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | |

github-actions[bot] commented 2023-05-22 16:16:03 +00:00 (Migrated from github.com)

Copy link

PR Preview Action v1.4.4
Preview removed because the pull request was closed.
2023-06-21 10:53 UTC

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.4 :---: Preview removed because the pull request was closed. 2023-06-21 10:53 UTC <!-- Sticky Pull Request Commentpr-preview -->

fraimondo commented 2023-06-20 10:23:59 +00:00 (Migrated from github.com)

Copy link

can you explain what's the goal behind this PR?

can you explain what's the goal behind this PR?

synchon commented 2023-06-21 06:15:59 +00:00 (Migrated from github.com)

Copy link

can you explain what's the goal behind this PR?

It enables the use of Git hooks specifically pre-commit via https://pre-commit.com . The pre-commit checks include everything from spellcheck to linting thus reducing the need for separate lint or spell-check commits and making contribution easy.

> can you explain what's the goal behind this PR? It enables the use of [Git hooks](https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks) specifically `pre-commit` via https://pre-commit.com . The pre-commit checks include everything from spellcheck to linting thus reducing the need for separate lint or spell-check commits and making contribution easy.

fraimondo commented 2023-06-21 07:08:00 +00:00 (Migrated from github.com)

Copy link

Is this optional? Or it will not allow to commit if something is off?

Is this _optional_? Or it will not allow to commit if something is off?

synchon commented 2023-06-21 08:48:41 +00:00 (Migrated from github.com)

Copy link

Is this optional? Or it will not allow to commit if something is off?

Once you do pre-commit install, it becomes mandatory. If you want to bypass a commit, you need to pass --no-verify flag to git commit. The docs include the instructions.

> Is this _optional_? Or it will not allow to commit if something is off? Once you do `pre-commit install`, it becomes mandatory. If you want to bypass a commit, you need to pass `--no-verify` flag to `git commit`. The docs include the instructions.

fraimondo commented 2023-06-21 08:51:45 +00:00 (Migrated from github.com)

Copy link

perfect!

Fix conflicts and LGTM

perfect! Fix conflicts and LGTM

Sign in to join this conversation.

Reviewers

No reviewers

Labels

Clear labels   

CRITICAL

High Priority Issue

  

Stale

  

WIP

Work in progress

  

bug

Something isn't working

  

concept

Design/Implementation concepts

  

coordinate

Issues or pull requests related to coordinates (ROIs)

  

dataset

Issues or pull requests related to datagrabbers or datasets

  

dependencies

Pull requests that update a dependency file

  

documentation

Improvements or additions to documentation

  

duplicate

This issue or pull request already exists

  

enhancement

New feature or request

  

github_actions

Pull requests that update GitHub Actions code

  

good first issue

Good for newcomers

  

help wanted

Extra attention is needed

  

invalid

This doesn't seem right

  

maintenance

Issues or pull requests related to maintenance

  

maps

Issues or pull requests related to maps (probabilistic atlases)

  

marker

Issues or pull requests related to markers

  

mask

Issues or pull requests related to masks

  

on hold

Issue waiting on other issue(s)

  

parcellation

Issues or pull requests related to parcellations (deterministic atlases)

  

preprocess

Issues or pull requests related to preprocessors

  

question

Further information is requested

  

ready

Pull request is ready for review and merge

  

storage

Issues or pull requests related to marker storage or retrieval

  

template-space

Issues or pull requests related to template spaces

  

triage

New issues waiting to be reviewed

  

wontfix

This will not be worked on

No labels

CRITICAL

Stale

WIP

bug

concept

coordinate

dataset

dependencies

documentation

duplicate

enhancement

github_actions

good first issue

help wanted

invalid

maintenance

maps

marker

mask

on hold

parcellation

preprocess

question

ready

storage

template-space

triage

wontfix

Milestone

Clear milestone

No items

No milestone

Assignees

Clear assignees

No assignees

1 participant

Notifications

Subscribe

Due date

The due date is invalid or out of range. Please use the format "yyyy-mm-dd".

No due date set.

Dependencies

No dependencies set

Reference

juaml/junifer!232

No description provided.