[ENH]: Enable `stdout` and `stderr` capturing for `AFNI` commands #234

Merged

synchon merged 3 commits from fix/afni-log-capture into main

2023-06-27 08:59:28 +00:00

synchon commented

2023-06-23 11:25:27 +00:00

(Migrated from github.com)

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

This PR enables support for stdout and stderr capturing for AFNI commands run via subprocess, specifically for ReHo and fALFF. This should allow us to understand #233 better.

* [x] description of feature/fix * [x] tests added/passed * [x] add an entry for the latest changes This PR enables support for `stdout` and `stderr` capturing for `AFNI` commands run via `subprocess`, specifically for `ReHo` and `fALFF`. This should allow us to understand #233 better.

github-actions[bot] commented

2023-06-23 11:30:49 +00:00

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2023-06-27 09:04 UTC

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.4.4 :---: Preview removed because the pull request was closed. 2023-06-27 09:04 UTC

codecov[bot] commented

2023-06-23 11:45:38 +00:00

(Migrated from github.com)

Codecov Report

Merging #234 (ef5f43d) into main (c811a65) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #234   +/-   ##
=======================================
  Coverage   93.61%   93.61%           
=======================================
  Files          82       82           
  Lines        3460     3460           
  Branches      644      644           
=======================================
  Hits         3239     3239           
  Misses        144      144           
  Partials       77       77

Flag	Coverage Δ
docs	`100.00% <ø> (ø)`
junifer	`93.61% <ø> (ø)`

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

Impacted Files	Coverage Δ
junifer/markers/falff/falff_estimator.py	`95.50% <ø> (ø)`
junifer/markers/reho/reho_estimator.py	`68.70% <ø> (ø)`

## [Codecov](https://app.codecov.io/gh/juaml/junifer/pull/234?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) Report > Merging [#234](https://app.codecov.io/gh/juaml/junifer/pull/234?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (ef5f43d) into [main](https://app.codecov.io/gh/juaml/junifer/commit/c811a65c451082252a48a1ddfb94b79161351cac?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) (c811a65) will **not change** coverage. > The diff coverage is `n/a`. [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/234/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/234?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #234 +/- ## ======================================= Coverage 93.61% 93.61% ======================================= Files 82 82 Lines 3460 3460 Branches 644 644 ======================================= Hits 3239 3239 Misses 144 144 Partials 77 77 ``` | Flag | Coverage Δ | | |---|---|---| | docs | `100.00% <ø> (ø)` | | | junifer | `93.61% <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. | [Impacted Files](https://app.codecov.io/gh/juaml/junifer/pull/234?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\_estimator.py](https://app.codecov.io/gh/juaml/junifer/pull/234?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2ZhbGZmL2ZhbGZmX2VzdGltYXRvci5weQ==) | `95.50% <ø> (ø)` | | | [junifer/markers/reho/reho\_estimator.py](https://app.codecov.io/gh/juaml/junifer/pull/234?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)` | |

fraimondo (Migrated from github.com) approved these changes

2023-06-27 08:59:22 +00:00