Production & publication readiness: hardening, reproducibility, packaging, examples, docs, tests - #2

Merged

dmighty007 merged 14 commits into

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claude/autosampler-analysis-plan-jj0n1q

Jun 30, 2026

Commits on Jun 30, 2026

fix: restore green suite + repair documented conda env
claude
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cb3c4f3
fix: robust delta-checkpoint resume + tolerate walker failure (local backend)
claude
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abde0dc
packaging + docs: PyPI metadata, CITATION.cff, de-risk AlaD example, doc fixes
claude
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1e857c7
docs: add structured production-readiness review report (PDF + generator)
claude
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429a848
repro: thread config seed into CV training + enable torch determinism
claude
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9ce0282
robustness: add MD-walker timeout to the local backend (hang guard)
claude
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5abf593
fix: target-mode spawn crash + deep-tica device mismatch
claude
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fbdde53
packaging: make OpenMM optional + lazily imported (pip-installable base)
claude
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f410e92
ci: lint whole tree, add py3.12 + docs build + PyPI release workflow
claude
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ad54479
examples: add self-contained CPU-only alanine-dipeptide hello-world + index
claude
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e5640c7
examples: add configs for the undemoed features (spib, deep-tica, we, target, pbs)
claude
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33cde45
tests: cover the untested spawners (voronoi/lof/fps) and paths lineage helpers
claude
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0beb744
docs: add API reference, references/citations, and full CLI reference
claude
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59da318
docs: record the production-readiness hardening pass in the changelog
claude
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53d7ff1