Update to 0.6.0

[Gab-D-G]

Summary by CodeRabbit

• Chores

  • Bumped project version to 0.6.0 and updated release date in metadata.

• Documentation

  • Updated documentation release identifier and docs dependency to match 0.6.0.

• User-facing fixes

  • Clarified CLI help for timeseries interval format (now uses "0-80" style).

• Improvements

  • Enhanced QC processing: increased memory allocation and explicit cleanup to improve QC report/video reliability and reduce runtime memory pressure.

[coderabbitai]

📝 Walkthrough

Walkthrough

Bump package release from 0.5.5 → 0.6.0 across metadata, docs, and dependency, update CLI help text formatting, and change HMC QC code: memory allocation increase, modified HMC_derivatives return signature, updated caller uses, and added explicit deletions for intermediates.

Changes

Cohort / File(s)	Summary
Version Management rabies/__version__.py	Updated VERSION tuple from (0, 5, 5) → (0, 6, 0), changing exported __version__ string.
Citation & Documentation Metadata CITATION.cff, docs/conf.py	Bumped software version 0.5.5 → 0.6.0 and date-released 2025-12-19 → 2026-03-26; updated Sphinx release.
Documentation Dependencies docs/requirements.txt	Bumped rabies dependency version from 0.5.5 → 0.6.0.
CLI Help Text rabies/parser.py	Adjusted --timeseries_interval help example formatting from 0,80 → 0-80 (help string only).
Preprocessing — HMC QC rabies/preprocess_pkg/hmc.py	Increased hmc_qc_node memory allocation (multiplied by 20 when QC report applied); changed HMC_derivatives(...) to return (img_preHMC, img_postHMC, derivatives_dict) instead of embedding images in the dict; updated HMC_QC._run_interface to consume the new tuple, added status prints and explicit del statements to release intermediates.

Sequence Diagram(s)

(Skipped — changes do not meet the multi-component sequence diagram criteria.)

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• switched to version 0.5.2 #430: Prior version-bump changes touching CITATION.cff, docs/conf.py, docs/requirements.txt, and rabies/__version__.py.
• Version0.5.5 #465: Another release update that modifies the same version/metadata files and may overlap with this bump.
• Optional masks and version 0.5.4 #447: Version/metadata updates plus edits to rabies/parser.py, related at the code-level to the CLI help change.

Poem

🐰 I hopped through lines of version and doc,
Swapped dates and numbers — a tidy small shock.
I nudged the HMC to free bits it keeps,
Memory grows, old intermediates fall asleep.
A tiny release dance — nibble, thump, and clock. 🥕

🚥 Pre-merge checks | ✅ 1 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 40.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The title 'Update to 0.6.0' is vague and lacks specificity about the actual changes made beyond the version number.	Consider a more descriptive title that clarifies the scope of changes, such as 'Release version 0.6.0' or 'Bump version to 0.6.0 and update documentation'.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ 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 version_0.6.0

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[coderabbitai]

🧹 Nitpick comments (2)

rabies/preprocess_pkg/hmc.py (2)

61-63: Avoid baking the 20x QC memory bump into the workflow.

opts.scale_min_memory is already the scheduler-facing scaling input, so another unconditional *20 makes this node's footprint cluster-specific and hard to tune. Please move this multiplier into config/CLI instead of hard-coding it here.

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@rabies/preprocess_pkg/hmc.py` around lines 61 - 63, The hmc_qc_node currently
hard-codes a 20x memory multiplier (mem_gb=1.1*opts.scale_min_memory*20), which
should be moved to configuration/CLI; remove the unconditional *20 in the
hmc_qc_node creation so mem_gb uses 1.1*opts.scale_min_memory, add a new
config/CLI option (e.g. opts.hmc_qc_memory_multiplier or
opts.scale_memory_multiplier) and apply that multiplier when the user sets it
(mem_gb = 1.1 * opts.scale_min_memory * opts.hmc_qc_memory_multiplier), and
update the CLI/config parsing and documentation to expose and default this
multiplier rather than baking it into the HMC_QC/hmc_qc_node instantiation.

---

275-277: Close the Matplotlib figure after writing it.

plot_motion_QC() creates the figure through matplotlib.pyplot, so it stays registered until explicitly closed. In this already RAM-sensitive node, releasing it right after savefig() will help keep worker memory flatter.

Proposed fix

         print('Creating QC figure...')
         fig = plot_motion_QC(derivatives_dict, self.inputs.ref_file, plot_R2=False)
         fig.savefig(figure_path, bbox_inches='tight')
+        import matplotlib.pyplot as plt
+        plt.close(fig)

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@rabies/preprocess_pkg/hmc.py` around lines 275 - 277, The Matplotlib figure
created by plot_motion_QC remains registered after savefig causing memory to
accumulate; after fig.savefig(figure_path, bbox_inches='tight') call, close and
release the figure (e.g., call matplotlib.pyplot.close(fig) or fig.close()) to
free memory; ensure matplotlib.pyplot is imported in the module if not present
and add the close call immediately after the savefig line in the same block
where plot_motion_QC is used.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In `@rabies/preprocess_pkg/hmc.py`:
- Around line 61-63: The hmc_qc_node currently hard-codes a 20x memory
multiplier (mem_gb=1.1*opts.scale_min_memory*20), which should be moved to
configuration/CLI; remove the unconditional *20 in the hmc_qc_node creation so
mem_gb uses 1.1*opts.scale_min_memory, add a new config/CLI option (e.g.
opts.hmc_qc_memory_multiplier or opts.scale_memory_multiplier) and apply that
multiplier when the user sets it (mem_gb = 1.1 * opts.scale_min_memory *
opts.hmc_qc_memory_multiplier), and update the CLI/config parsing and
documentation to expose and default this multiplier rather than baking it into
the HMC_QC/hmc_qc_node instantiation.
- Around line 275-277: The Matplotlib figure created by plot_motion_QC remains
registered after savefig causing memory to accumulate; after
fig.savefig(figure_path, bbox_inches='tight') call, close and release the figure
(e.g., call matplotlib.pyplot.close(fig) or fig.close()) to free memory; ensure
matplotlib.pyplot is imported in the module if not present and add the close
call immediately after the savefig line in the same block where plot_motion_QC
is used.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: e309d8d3-0f8a-4925-bfbe-6fc05b1eb4d5

📥 Commits

Reviewing files that changed from the base of the PR and between 3adcf9e and 39ed5b8.

📒 Files selected for processing (2)

• rabies/parser.py
• rabies/preprocess_pkg/hmc.py

✅ Files skipped from review due to trivial changes (1)

• rabies/parser.py