Support pscalar and pconn files by tsalo · Pull Request #44 · PennLINC/ModelArrayIO

tsalo · 2026-04-01T13:19:37Z

Closes #38.

codecov-commenter · 2026-04-01T13:20:44Z

Codecov Report

❌ Patch coverage is 59.68992% with 52 lines in your changes missing coverage. Please review.
✅ Project coverage is 63.82%. Comparing base (5fc9a3f) to head (5bfa284).

Files with missing lines	Patch %	Lines
src/modelarrayio/utils/cifti.py	67.21%	10 Missing and 10 partials ⚠️
src/modelarrayio/storage/tiledb_storage.py	6.66%	14 Missing ⚠️
src/modelarrayio/cli/cifti_to_h5.py	45.00%	9 Missing and 2 partials ⚠️
src/modelarrayio/cli/h5_to_cifti.py	80.00%	3 Missing and 2 partials ⚠️
src/modelarrayio/cli/utils.py	75.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #44      +/-   ##
==========================================
+ Coverage   61.14%   63.82%   +2.67%     
==========================================
  Files          17       17              
  Lines        1045     1150     +105     
  Branches      170      207      +37     
==========================================
+ Hits          639      734      +95     
- Misses        360      362       +2     
- Partials       46       54       +8

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Copilot

Pull request overview

Adds support for parcellated CIFTI file types so ModelArrayIO can ingest and emit .pscalar.nii and .pconn.nii in addition to existing .dscalar.nii behavior (closes #38).

Changes:

Extend extract_cifti_scalar_data to handle ParcelsAxis (pscalar) and ParcelsAxis+ParcelsAxis (pconn, flattened) inputs.
Update h5_to_cifti to preserve output CIFTI type/extension and reshape outputs appropriately for pconn matrices.
Add/expand unit tests covering dscalar/pscalar/pconn roundtrips and error cases.

Reviewed changes

Copilot reviewed 5 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`src/modelarrayio/utils/cifti.py`	Adds parsing/validation logic for pscalar and pconn axes in `extract_cifti_scalar_data`.
`src/modelarrayio/cli/h5_to_cifti.py`	Infers output extension from template axes and reshapes output data for pconn vs scalar-like outputs.
`test/test_cifti_utils.py`	Adds unit tests for pscalar/pconn behavior in `extract_cifti_scalar_data`.
`test/test_cifti_cli_comprehensive.py`	New comprehensive CLI coverage for cifti↔h5 conversions across dscalar/pscalar/pconn.
`.github/workflows/tox.yml`	Changes CI push trigger filtering (now only runs on pushes to `main`).

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/modelarrayio/utils/cifti.py

src/modelarrayio/cli/h5_to_cifti.py

.github/workflows/tox.yml

src/modelarrayio/utils/cifti.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 7 out of 9 changed files in this pull request and generated 1 comment.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/modelarrayio/utils/cifti.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 7 out of 9 changed files in this pull request and generated 3 comments.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

src/modelarrayio/cli/utils.py

src/modelarrayio/utils/cifti.py

src/modelarrayio/storage/tiledb_storage.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Agent-Logs-Url: https://github.com/PennLINC/ModelArrayIO/sessions/0c2a8a88-c40b-4df1-80c4-d56a959932f8 Co-authored-by: tsalo <8228902+tsalo@users.noreply.github.com>

mattcieslak

Looks great!

mattcieslak · 2026-04-01T18:41:32Z

src/modelarrayio/utils/cifti.py

    cifti_scalar_data: :obj:`numpy.ndarray`
-        The scalar data from the cifti file
+        The scalar data from the cifti file, always 1-D.  For pconn files
+        this is the row-major flattened connectivity matrix.


Does cifti already have the data flattened in row-major order or does this happen in nibabel?

It should be done by ModelArrayIO. It'll be 2D (parcels x parcels) in both the CIFTI and the loaded nibabel data array.

Support pscalar and pconn files.

d9a5f8d

tsalo added the enhancement New feature or request label Apr 1, 2026

tsalo added 5 commits April 1, 2026 09:22

Run ruff.

aca9bc7

Add tests.

617f9f9

Run ruff.

bc7df03

Fix warnings.

7600e3c

Limit push trigger to main.

468ae2b

tsalo marked this pull request as ready for review April 1, 2026 13:43

tsalo requested a review from Copilot April 1, 2026 13:43

Copilot started reviewing on behalf of tsalo April 1, 2026 13:44 View session

Copilot AI reviewed Apr 1, 2026

View reviewed changes

src/modelarrayio/utils/cifti.py Outdated Show resolved Hide resolved

src/modelarrayio/cli/h5_to_cifti.py Show resolved Hide resolved

.github/workflows/tox.yml Show resolved Hide resolved

src/modelarrayio/utils/cifti.py Show resolved Hide resolved

tsalo and others added 6 commits April 1, 2026 10:10

Merge branch 'main' into pciftis

1cff996

Update src/modelarrayio/cli/h5_to_cifti.py

2d11517

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Address some stuff.

9724bc6

Add parcel_id attributes.

06796c9

Fix up some stuff.

fd61b9f

Update cifti.py

2efdfd8

tsalo requested a review from Copilot April 1, 2026 16:23

Copilot started reviewing on behalf of tsalo April 1, 2026 16:24 View session

Copilot AI reviewed Apr 1, 2026

View reviewed changes

src/modelarrayio/utils/cifti.py Outdated Show resolved Hide resolved

tsalo and others added 2 commits April 1, 2026 12:36

Update src/modelarrayio/utils/cifti.py

bdc733a

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Run ruff.

a028972

tsalo requested a review from Copilot April 1, 2026 16:42

Copilot started reviewing on behalf of tsalo April 1, 2026 16:43 View session

Copilot AI reviewed Apr 1, 2026

View reviewed changes

src/modelarrayio/cli/utils.py Outdated Show resolved Hide resolved

src/modelarrayio/utils/cifti.py Show resolved Hide resolved

src/modelarrayio/storage/tiledb_storage.py Show resolved Hide resolved

Apply suggestions from code review

542d3e7

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot started work on behalf of tsalo April 1, 2026 16:49 View session

Fix write_parcel_names to raise ValueError for empty names

9b20bb3

Agent-Logs-Url: https://github.com/PennLINC/ModelArrayIO/sessions/0c2a8a88-c40b-4df1-80c4-d56a959932f8 Co-authored-by: tsalo <8228902+tsalo@users.noreply.github.com>

Copilot finished work on behalf of tsalo April 1, 2026 16:51

tsalo added 2 commits April 1, 2026 12:53

Run ruff.

9fd5f65

Merge branch 'main' into pciftis

5bfa284

tsalo requested a review from mattcieslak April 1, 2026 17:44

mattcieslak approved these changes Apr 1, 2026

View reviewed changes

mattcieslak merged commit f311120 into main Apr 1, 2026
8 checks passed

mattcieslak deleted the pciftis branch April 1, 2026 18:43

This was referenced Apr 1, 2026

Update ModelArray roxygen PennLINC/ModelArray#118

Merged

Update documentation adding recommendations for using pconns PennLINC/ModelArray#124

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Support pscalar and pconn files#44

Support pscalar and pconn files#44
mattcieslak merged 18 commits intomainfrom
pciftis

tsalo commented Apr 1, 2026 •

edited

Loading

Uh oh!

codecov-commenter commented Apr 1, 2026 •

edited

Loading

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

mattcieslak left a comment

Uh oh!

mattcieslak Apr 1, 2026

Uh oh!

tsalo Apr 1, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

Conversation

tsalo commented Apr 1, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov-commenter commented Apr 1, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Uh oh!

Uh oh!

Uh oh!

Uh oh!

mattcieslak left a comment

Choose a reason for hiding this comment

Uh oh!

mattcieslak Apr 1, 2026

Choose a reason for hiding this comment

Uh oh!

tsalo Apr 1, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

tsalo commented Apr 1, 2026 •

edited

Loading

codecov-commenter commented Apr 1, 2026 •

edited

Loading