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Code Issues 14 Pull requests 2 Packages Activity Actions

[BUG]: Correct file reading for AFNI outputs #409

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synchon merged 6 commits from update/afni-impls into main 2024-12-03 10:54:18 +00:00
Conversation 5 Commits 6 Files changed 9 +79 -80
synchon commented 2024-12-02 12:52:01 +00:00 (Migrated from github.com)
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  • description of feature/fix
  • tests added/passed
  • add an entry for the latest changes

This PR updates the interface for AFNI-based markers and also fixes correct output suffices for AFNI outputs depending on NIfTI headers.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR updates the interface for AFNI-based markers and also fixes correct output suffices for AFNI outputs depending on NIfTI headers.
codecov[bot] commented 2024-12-02 12:56:30 +00:00 (Migrated from github.com)
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Codecov Report

Attention: Patch coverage is 0% with 28 lines in your changes missing coverage. Please review.

Project coverage is 0.01%. Comparing base (9ff17e6) to head (f26113c).
Report is 7 commits behind head on main.

Files with missing lines Patch % Lines
junifer/markers/falff/_afni_falff.py 0.00% 12 Missing ⚠️
junifer/markers/reho/_afni_reho.py 0.00% 11 Missing ⚠️
junifer/markers/falff/_junifer_falff.py 0.00% 3 Missing ⚠️
junifer/markers/reho/_junifer_reho.py 0.00% 2 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@           Coverage Diff            @@
##            main    #409      +/-   ##
========================================
- Coverage   0.01%   0.01%   -0.01%     
========================================
  Files        133     133              
  Lines       5609    5615       +6     
========================================
  Hits           1       1              
- Misses      5608    5614       +6
Flag Coverage Δ
docs 100.00% <ø> (ø)
junifer 0.00% <0.00%> (ø)

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

Files with missing lines Coverage Δ
junifer/markers/falff/falff_base.py 0.00% <ø> (ø)
junifer/markers/reho/reho_base.py 0.00% <ø> (ø)
junifer/markers/reho/_junifer_reho.py 0.00% <0.00%> (ø)
junifer/markers/falff/_junifer_falff.py 0.00% <0.00%> (ø)
junifer/markers/reho/_afni_reho.py 0.00% <0.00%> (ø)
junifer/markers/falff/_afni_falff.py 0.00% <0.00%> (ø)
## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/409?dropdown=coverage&src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report Attention: Patch coverage is `0%` with `28 lines` in your changes missing coverage. Please review. > Project coverage is 0.01%. Comparing base [(`9ff17e6`)](https://app.codecov.io/gh/juaml/junifer/commit/9ff17e655780f3a5e85f8d5898d2970205e0fe66?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) to head [(`f26113c`)](https://app.codecov.io/gh/juaml/junifer/commit/f26113c29b4c5a685e3fe96c8a0e1f81c5ce6eb2?dropdown=coverage&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml). > Report is 7 commits behind head on main. | [Files with missing lines](https://app.codecov.io/gh/juaml/junifer/pull/409?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Patch % | Lines | |---|---|---| | [junifer/markers/falff/\_afni\_falff.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffalff%2F_afni_falff.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL19hZm5pX2ZhbGZmLnB5) | 0.00% | [12 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/markers/reho/\_afni\_reho.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Freho%2F_afni_reho.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vX2FmbmlfcmVoby5weQ==) | 0.00% | [11 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/markers/falff/\_junifer\_falff.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffalff%2F_junifer_falff.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL19qdW5pZmVyX2ZhbGZmLnB5) | 0.00% | [3 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | | [junifer/markers/reho/\_junifer\_reho.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Freho%2F_junifer_reho.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vX2p1bmlmZXJfcmVoby5weQ==) | 0.00% | [2 Missing :warning: ](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | <details><summary>Additional details and impacted files</summary> [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/409/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/409?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #409 +/- ## ======================================== - Coverage 0.01% 0.01% -0.01% ======================================== Files 133 133 Lines 5609 5615 +6 ======================================== Hits 1 1 - Misses 5608 5614 +6 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/409/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/409/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)` | | | [junifer](https://app.codecov.io/gh/juaml/junifer/pull/409/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `0.00% <0.00%> (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/409?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/markers/falff/falff\_base.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffalff%2Ffalff_base.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL2ZhbGZmX2Jhc2UucHk=) | `0.00% <ø> (ø)` | | | [junifer/markers/reho/reho\_base.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Freho%2Freho_base.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vcmVob19iYXNlLnB5) | `0.00% <ø> (ø)` | | | [junifer/markers/reho/\_junifer\_reho.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Freho%2F_junifer_reho.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vX2p1bmlmZXJfcmVoby5weQ==) | `0.00% <0.00%> (ø)` | | | [junifer/markers/falff/\_junifer\_falff.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffalff%2F_junifer_falff.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL19qdW5pZmVyX2ZhbGZmLnB5) | `0.00% <0.00%> (ø)` | | | [junifer/markers/reho/\_afni\_reho.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Freho%2F_afni_reho.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL3JlaG8vX2FmbmlfcmVoby5weQ==) | `0.00% <0.00%> (ø)` | | | [junifer/markers/falff/\_afni\_falff.py](https://app.codecov.io/gh/juaml/junifer/pull/409?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffalff%2F_afni_falff.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL19hZm5pX2ZhbGZmLnB5) | `0.00% <0.00%> (ø)` | | </details>
github-actions[bot] commented 2024-12-02 13:07:26 +00:00 (Migrated from github.com)
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PR Preview Action v1.4.8
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2024-12-03 11:07 UTC
[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.8 :---: Preview removed because the pull request was closed. 2024-12-03 11:07 UTC <!-- Sticky Pull Request Commentpr-preview -->
fraimondo (Migrated from github.com) reviewed 2024-12-02 13:28:44 +00:00
junifer/markers/falff/falff_base.py
@ -148,3 +148,3 @@
alff, falff, alff_path, falff_path = estimator.compute( # type: ignore
data=input_data["data"],
input_path=input_data["path"],
highpass=self.highpass,
fraimondo (Migrated from github.com) commented 2024-12-02 13:28:33 +00:00
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Is there any reason why we move to paths instead of in-memory data?

Is there any reason why we move to paths instead of in-memory data?
synchon (Migrated from github.com) reviewed 2024-12-02 14:03:49 +00:00
junifer/markers/falff/falff_base.py
@ -148,3 +148,3 @@
alff, falff, alff_path, falff_path = estimator.compute( # type: ignore
data=input_data["data"],
input_path=input_data["path"],
highpass=self.highpass,
synchon (Migrated from github.com) commented 2024-12-02 14:03:48 +00:00
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Passing the path is easier to reason about inside the method and cheaper to hash for the LRU cache.

Passing the path is easier to reason about inside the method and cheaper to hash for the LRU cache.
fraimondo (Migrated from github.com) approved these changes 2024-12-03 10:29:04 +00:00
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