[BUG]: `DataladDataGrabber` is not using the `WorkDirManager` #386

Merged

fraimondo merged 3 commits from fix/386 into main

2024-11-11 15:03:21 +00:00

fraimondo commented

2024-11-11 10:32:18 +00:00

(Migrated from github.com)

Is there an existing issue for this?

I have searched the existing issues

Current Behavior

When using any DataladBase datagrabber, I observed that it was being cloned in a directory outside what I've set in the workdir manager.

Expected Behavior

The datasets should be cloned within the workdir manager path

Steps To Reproduce

Run any yaml with debug logging and set the workdir to something else than /tmp
Check where the dataset is being cloned

Environment

junifer:
  version: 0.0.6.dev176
python:
  version: 3.12.6
  implementation: CPython
dependencies:
  click: 8.1.7
  numpy: 1.26.4
  scipy: 1.14.1
  datalad: 1.1.3
  pandas: 2.2.2
  nibabel: 5.2.1
  ruamel.yaml: 0.17.40
  looseversion: None
system:
  platform: Linux-6.6.13+bpo-amd64-x86_64-with-glibc2.36
environment:
  PATH:
    /data/group/appliedml/tools/ants_2.5.0/binaries:/home/fraimondo/miniconda3/envs/junifer/bin:/home/fraimondo/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/games

Relevant log output

No response

Anything else?

Check this:

github.com/juaml/junifer@299b4549c8/junifer/datagrabber/datalad_base.py (L81-L82)

### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior When using any DataladBase datagrabber, I observed that it was being cloned in a directory outside what I've set in the workdir manager. ### Expected Behavior The datasets should be cloned within the workdir manager path ### Steps To Reproduce 1. Run any yaml with debug logging and set the workdir to something else than `/tmp` 2. Check where the dataset is being cloned ### Environment ```markdown junifer: version: 0.0.6.dev176 python: version: 3.12.6 implementation: CPython dependencies: click: 8.1.7 numpy: 1.26.4 scipy: 1.14.1 datalad: 1.1.3 pandas: 2.2.2 nibabel: 5.2.1 ruamel.yaml: 0.17.40 looseversion: None system: platform: Linux-6.6.13+bpo-amd64-x86_64-with-glibc2.36 environment: PATH: /data/group/appliedml/tools/ants_2.5.0/binaries:/home/fraimondo/miniconda3/envs/junifer/bin:/home/fraimondo/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/games ``` ### Relevant log output _No response_ ### Anything else? Check this: https://github.com/juaml/junifer/blob/299b4549c87b98c809c5f3cae18443e0ad364e13/junifer/datagrabber/datalad_base.py#L81-L82

codecov[bot] commented

2024-11-11 10:35:28 +00:00

(Migrated from github.com)

All modified and coverable lines are covered by tests ✅

Project coverage is 87.53%. Comparing base (36a61da) to head (9968bf6).
Report is 4 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #386   +/-   ##
=======================================
  Coverage   87.52%   87.53%           
=======================================
  Files         129      129           
  Lines        5332     5328    -4     
  Branches      857      857           
=======================================
- Hits         4667     4664    -3     
+ Misses        492      491    -1     
  Partials      173      173

Flag	Coverage Δ
docs	`100.00% <ø> (ø)`

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

Files with missing lines	Coverage Δ
junifer/datagrabber/datalad_base.py	`90.07% <ø> (+0.44%)`	⬆️

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/386?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report All modified and coverable lines are covered by tests :white_check_mark: > Project coverage is 87.53%. Comparing base [(`36a61da`)](https://app.codecov.io/gh/juaml/junifer/commit/36a61da0669d7f0943fd068c7ef66df3886f95d3?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) to head [(`9968bf6`)](https://app.codecov.io/gh/juaml/junifer/commit/9968bf64e036d3b802e031a6b45d7ea95868fd0d?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml). > Report is 4 commits behind head on main. <details><summary>Additional details and impacted files</summary> [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/386/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://app.codecov.io/gh/juaml/junifer/pull/386?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #386 +/- ## ======================================= Coverage 87.52% 87.53% ======================================= Files 129 129 Lines 5332 5328 -4 Branches 857 857 ======================================= - Hits 4667 4664 -3 + Misses 492 491 -1 Partials 173 173 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/386/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs](https://app.codecov.io/gh/juaml/junifer/pull/386/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `100.00% <ø> (ø)` | | 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. | [Files with missing lines](https://app.codecov.io/gh/juaml/junifer/pull/386?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [junifer/datagrabber/datalad\_base.py](https://app.codecov.io/gh/juaml/junifer/pull/386?src=pr&el=tree&filepath=junifer%2Fdatagrabber%2Fdatalad_base.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9kYXRhZ3JhYmJlci9kYXRhbGFkX2Jhc2UucHk=) | `90.07% <ø> (+0.44%)` | :arrow_up: | </details>

github-actions[bot] commented

2024-11-11 10:48:02 +00:00

(Migrated from github.com)

PR Preview Action v1.4.8
Preview removed because the pull request was closed.
2024-11-11 15:16 UTC

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.8 :---: Preview removed because the pull request was closed. 2024-11-11 15:16 UTC

synchon (Migrated from github.com) approved these changes

2024-11-11 14:42:38 +00:00