build: replace system c3d dependency with picsl-c3d by tomboulier · Pull Request #93 · tomboulier/oxytcmri-dti-processing

tomboulier · 2026-03-24T21:17:43Z

Summary

replace the system c3d subprocess dependency with picsl-c3d
remove the non-reproducible wget/sudo install path from the makefile
pin picsl-c3d==1.4.6.0 and refresh the lockfile

Verification

uv sync --group dev
./.venv/bin/pytest -q
result: 75 passed

Summary by CodeRabbit

Chores
- Simplified installation by removing an external CLI dependency from the build/install flow.
- Added a new integrated library dependency to handle internal processing previously delegated to that external tool.
Bug Fixes
- Ensure generated output files end with a trailing newline for consistency.

coderabbitai · 2026-03-24T21:18:00Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: 6016e708-18d0-420b-9733-711da2523de9

📥 Commits

Reviewing files that changed from the base of the PR and between d3a5356 and 460337c.

📒 Files selected for processing (1)

oxytcmri/interface/mri/staple_segmenter.py

🚧 Files skipped from review as they are similar to previous changes (1)

oxytcmri/interface/mri/staple_segmenter.py

Walkthrough

Replaces external c3d CLI usage with the Python picsl-c3d library, updates Makefile to remove the c3d target and its fallback install logic, and adds picsl-c3d==1.4.6.0 to project dependencies. Staple segmenter now calls the library API and adapts error handling.

Changes

Cohort / File(s)	Summary
Build System `makefile`	Removed the `c3d` target and its system-install fallback; removed `c3d` from `install` and `install-dev` dependencies; switched dev install invocation from `uv pip install --group dev` to `uv sync --group dev`; added trailing newline in `compute-dti-normative-values` output file.
Library Migration `oxytcmri/interface/mri/staple_segmenter.py`	Replaced subprocess-based `c3d` CLI invocation with `picsl_c3d.Convert3D().execute()` using `io.StringIO` to capture output; removed `subprocess` import, added `picsl_c3d` and `io` imports; updated logged messages and error handling to raise `RuntimeError` with `picsl-c3d`-prefixed messages.
Project Dependencies `pyproject.toml`	Added runtime dependency `picsl-c3d==1.4.6.0`.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'build: replace system c3d dependency with picsl-c3d' accurately and specifically describes the main objective of the pull request, which is to replace the system c3d subprocess dependency with the picsl-c3d Python package.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

Create stacked PR
Commit on current branch

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch codex/picsl-c3d-staple

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Copilot

Pull request overview

This PR makes the build and runtime environment more reproducible by removing reliance on a system-installed c3d binary and switching the STAPLE merge implementation to use the Python package picsl-c3d instead.

Changes:

Add picsl-c3d==1.4.6.0 as a pinned runtime dependency.
Replace subprocess execution of c3d with picsl_c3d.Convert3D().execute() in the STAPLE segmentation merger.
Remove the Makefile’s non-reproducible wget/sudo installation path for c3d and simplify install / install-dev.

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

File	Description
`pyproject.toml`	Pins and adds `picsl-c3d` as a project dependency to eliminate system `c3d` requirements.
`oxytcmri/interface/mri/staple_segmenter.py`	Switches STAPLE merging execution from `subprocess` to `picsl-c3d`’s Python API.
`makefile`	Removes the system-level `c3d` install target and updates install workflows to use `uv sync`.

Copilot · 2026-03-24T21:21:08Z

+            logger.info(f"Running c3d command: {cmd}")
+            picsl_c3d.Convert3D().execute(cmd, out=stdout, err=stderr)
            logger.info(f"c3d command completed successfully, output saved to {output_path}")
-        except subprocess.CalledProcessError as e:
-            raise RuntimeError(f"c3d command failed: {e.stderr}")
+        except RuntimeError as e:
+            error_details = stderr.getvalue().strip() or stdout.getvalue().strip() or str(e)
+            raise RuntimeError(f"c3d command failed: {error_details}") from e


The log and raised error text still refer to a “c3d command”, but this code now executes via picsl_c3d.Convert3D(). Updating these messages to mention picsl-c3d/Convert3D would avoid confusion when debugging failures.

@copilot open a new pull request to apply changes based on this feedback

Copilot · 2026-03-24T21:52:18Z

@tomboulier I've opened a new pull request, #94, to work on those changes. Once the pull request is ready, I'll request review from you.

* Initial plan * fix: update log and error messages to reference picsl-c3d Convert3D Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com> Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/3a05aa71-12b5-4555-8c93-5eaf8e8575e9 * fix: update remaining c3d STAPLE log message to picsl-c3d Convert3D Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com> Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/3a05aa71-12b5-4555-8c93-5eaf8e8575e9 * Update oxytcmri/interface/mri/staple_segmenter.py * fix: simplify redundant picsl-c3d Convert3D wording Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com> Agent-Logs-Url: https://github.com/tomboulier/oxytcmri-dti-processing/sessions/f4f6fb26-bca3-4f32-afc2-b01ebec4c101 * Update oxytcmri/interface/mri/staple_segmenter.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update oxytcmri/interface/mri/staple_segmenter.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tomboulier <14161960+tomboulier@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

sonarqubecloud · 2026-03-24T22:19:59Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

build: replace system c3d dependency with picsl-c3d

d3a5356

Copilot AI review requested due to automatic review settings March 24, 2026 21:17

Copilot started reviewing on behalf of tomboulier March 24, 2026 21:18 View session

Copilot AI reviewed Mar 24, 2026

View reviewed changes

Copilot AI mentioned this pull request Mar 24, 2026

fix: update stale "c3d command" references to "picsl-c3d" #94

Merged

tomboulier merged commit fc7fab4 into dev Mar 24, 2026
4 checks passed

tomboulier deleted the codex/picsl-c3d-staple branch March 24, 2026 22:22

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build: replace system c3d dependency with picsl-c3d#93

build: replace system c3d dependency with picsl-c3d#93
tomboulier merged 2 commits into
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codex/picsl-c3d-staple

tomboulier commented Mar 24, 2026 •

edited by coderabbitai Bot

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tomboulier commented Mar 24, 2026 •

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