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Joss submission - #5
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Pull Request Overview
This pull request prepares the repository for JOSS (Journal of Open Source Software) submission by bringing changes from the joss-submission branch to dev. The main purpose is to update the submission materials and make the repository ready for re-submission as requested by the JOSS editor.
- Updates JOSS paper content with expanded mathematical framework and field comparison sections
- Enables previously disabled advection/diffusion tests with improved analytical solutions
- Prepares repository structure and metadata for JOSS requirements
Reviewed Changes
Copilot reviewed 16 out of 17 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/test_1100_AdvDiffCartesian.py | Major refactor replacing 1D numerical comparison with analytical solution verification |
| test.sh | Re-enables previously commented out advection/diffusion test suites |
| src/underworld3/_version.py | Version bump from 0.98.1b to 0.99.0b with release preparation comment |
| paper.md | Creates symbolic link to actual JOSS paper location |
| paper.bib | Creates symbolic link to JOSS bibliography file |
| docs/user/NextSteps.qmd | Updates API documentation URL and fixes syntax |
| docs/joss-paper/paper.md | Extensive content updates including expanded mathematical framework |
| docs/joss-paper/paper.crossref | Updates timestamps and adds author affiliations |
| docs/joss-paper/paper.bib | Major bibliography expansion with corrected citation keys |
| docs/joss-paper/JOSS_Checklist.md | Updates checklist items to completed status |
| docs/developer/CodingStyle.md | Reformats text and adds clarification about pytest independence |
| README.md | Adds build status badge and formatting improvements |
| LICENCE.md | Corrects reference to license file name |
| CONTRIBUTING.md | Adds comprehensive contribution guidelines |
| .zenodo.json | Reorders authors and fixes JSON syntax |
| .github/workflows/draft-pdf.yml | Updates action version from v3 to v4 |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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lmoresi added a commit
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Apr 29, 2026
Updated headline status from "Phase D delivers BDF-class fault mechanics" to honest scope: Phase B ships for VE / mild VEP; Phase D and Phase E investigations land on the branch as documented experiments but are NOT shipping features for deep-yield VEP. TL;DR rewritten to call out the three regime distinctions and the structural physics mismatch that ETD-as-designed cannot close without rebuilding from the ground up. API section split into "production" (Phase B integrator='etd' on existing classes) and "experimental — DO NOT USE for production" (Phase D split class, Phase E hybrid mode). Added Phase E section under Implementation phasing (DONE), with killer-test numbers and the slip-drift diagnosis. Renamed "generic TimeIntegrator refactor" to Phase F (deferred). New lessons: 8. The diagnostic that mattered: |σ_∥|, not |σ_xy| 9. The structural BDF-vs-ETD slip-rate difference is physics 10. Phase D recommendations checklist (rec #1, #4, #5 implemented; #2, #3 not; raw-E rejected; back-derived η rejected; Min cap rejected) 11. Phase E hybrid drifts because of shared σ* history 12. Investigation closed — ETD for VE / mild VEP, BDF for deep yield Underworld development team with AI support from Claude Code (https://claude.com/claude-code)
lmoresi added a commit
that referenced
this pull request
May 4, 2026
Updated headline status from "Phase D delivers BDF-class fault mechanics" to honest scope: Phase B ships for VE / mild VEP; Phase D and Phase E investigations land on the branch as documented experiments but are NOT shipping features for deep-yield VEP. TL;DR rewritten to call out the three regime distinctions and the structural physics mismatch that ETD-as-designed cannot close without rebuilding from the ground up. API section split into "production" (Phase B integrator='etd' on existing classes) and "experimental — DO NOT USE for production" (Phase D split class, Phase E hybrid mode). Added Phase E section under Implementation phasing (DONE), with killer-test numbers and the slip-drift diagnosis. Renamed "generic TimeIntegrator refactor" to Phase F (deferred). New lessons: 8. The diagnostic that mattered: |σ_∥|, not |σ_xy| 9. The structural BDF-vs-ETD slip-rate difference is physics 10. Phase D recommendations checklist (rec #1, #4, #5 implemented; #2, #3 not; raw-E rejected; back-derived η rejected; Min cap rejected) 11. Phase E hybrid drifts because of shared σ* history 12. Investigation closed — ETD for VE / mild VEP, BDF for deep yield Underworld development team with AI support from Claude Code (https://claude.com/claude-code)
lmoresi added a commit
that referenced
this pull request
May 10, 2026
- _rss_mb(): switch from resource.ru_maxrss (peak/high-water RSS) to psutil.Process().memory_info().rss (current RSS), with /proc/self/statm Linux fallback and ru_maxrss kept only as a last resort. Current RSS is preferred so freed memory shows as a negative delta. (Copilot #1, #6) - diff(): apply 0.01 MiB threshold before including rss_mb in the delta. Smaller noise prints as "+0.00 MiB" and defeats the "no change" fast path. (Copilot #2) - dump_petsc_leaks_at_finalize(): drop leading "-" from PETSc option keys (codebase convention is no dash; "-malloc_dump" was a no-op), and align docstring with what the function actually sets. (Copilot #3) - Remove unused `os` import from test module. (Copilot #4) - Soften ckdtree.pyx comment claiming Cython "guarantees deterministic destruction" — that's CPython refcounting, which can lag for objects trapped in reference cycles until cyclic GC runs. (Copilot #5) - Test: assert KDTree count deltas relative to immediate before/after, never to absolute baselines. Earlier tests in the same pytest session can leave KDTree refs alive that the cyclic GC may collect at any time, shifting the absolute count. CI surfaced this with "assert 332 == 338" — six trees from earlier tests collected during our gc.collect(). Underworld development team with AI support from Claude Code
lmoresi added a commit
that referenced
this pull request
May 10, 2026
- _rss_mb(): switch from resource.ru_maxrss (peak/high-water RSS) to psutil.Process().memory_info().rss (current RSS), with /proc/self/statm Linux fallback and ru_maxrss kept only as a last resort. Current RSS is preferred so freed memory shows as a negative delta. (Copilot #1, #6) - diff(): apply 0.01 MiB threshold before including rss_mb in the delta. Smaller noise prints as "+0.00 MiB" and defeats the "no change" fast path. (Copilot #2) - dump_petsc_leaks_at_finalize(): drop leading "-" from PETSc option keys (codebase convention is no dash; "-malloc_dump" was a no-op), and align docstring with what the function actually sets. (Copilot #3) - Remove unused `os` import from test module. (Copilot #4) - Soften ckdtree.pyx comment claiming Cython "guarantees deterministic destruction" — that's CPython refcounting, which can lag for objects trapped in reference cycles until cyclic GC runs. (Copilot #5) - Test: assert KDTree count deltas relative to immediate before/after, never to absolute baselines. Earlier tests in the same pytest session can leave KDTree refs alive that the cyclic GC may collect at any time, shifting the absolute count. CI surfaced this with "assert 332 == 338" — six trees from earlier tests collected during our gc.collect(). Underworld development team with AI support from Claude Code
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Bring the joss-submission information across to dev.
We will need to update the joss-submission branch to reflect the current state of the code (request from editor to re-submit)
L