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Update documentation for cuPhoton 0.1.3 - #53

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release-readme-updates
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@tpn tpn commented Sep 24, 2026 •

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The guides had fallen behind the upcoming 0.1.3 release: shared FITS reader selection, direct FITS candidate workflows, persistent GPU execution, and native packaging were missing or described inconsistently. Update the README, changelog, component guides, CLI help, installation instructions, and artifact contracts against the current implementation. Clarify reader fallback, device/host result boundaries, xRay fit granularity and units, and what the documented validation commands actually exercise.

Preserve this PR's component-name cleanup and removal of the README maturity disclaimer and outdated roadmap, including the removal requested in #58. The reviewed imaging walkthrough from #67 is preserved. Python changes affect documentation, comments, and user-facing names; identifiers, algorithms, artifact schemas, and notebook executable content are unchanged. Replaces #52.

Validation:

  • CPU suite: 2,755 passed, 188 skipped; five-component CPU quickstart passed.
  • Final xFit/Core CLI checks: 51 passed; ten documented xRay CPU commands and the iterative-fitting example passed.
  • All 135 relative links, 44 documented CLI commands, and 134 Python/shell examples passed structural checks.
  • make ci-lint includes the all-files pre-commit run; make package-check and git diff --check pass.
  • AST comparison confirms the 53 changed Python files contain only docstring/comment or component-name text changes; notebook code and metadata match main and outputs remain empty.

GPU, native-GDS, and multi-node execution were not rerun for this documentation pass. Release installation instructions remain conditional on publication.

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📥 Commits

Reviewing files that changed from the base of the PR and between 2d29b60 and d473b69.

📒 Files selected for processing (68)
  • README.md
  • ROADMAP.md
  • THIRD_PARTY_NOTICES.md
  • docs/README.md
  • docs/architecture.md
  • docs/cli.md
  • docs/components/xdr.md
  • docs/components/xfit.md
  • docs/components/xpois.md
  • docs/components/xscan.md
  • docs/data-artifacts.md
  • docs/glossary.md
  • docs/quickstarts.md
  • docs/references.md
  • docs/xray/ENVIRONMENT.md
  • docs/xray/GPU-FIRST.md
  • docs/xray/README.md
  • docs/xray/VALIDATION-VIZ.md
  • examples/imaging-pipeline/run_imaging_pipeline.ipynb
  • examples/imaging-pipeline/run_imaging_pipeline.py
  • examples/run_quickstarts.py
  • examples/xpois/dragon_batch.py
  • examples/xscan/hsc-benchmark.blackwell.example.yaml
  • src/cuphoton/xdr/prefetch.py
  • src/cuphoton/xfit/api.py
  • src/cuphoton/xpois/batch.py
  • src/cuphoton/xpois/commands.py
  • src/cuphoton/xpois/data.py
  • src/cuphoton/xpois/dragon.py
  • src/cuphoton/xpois/mpi.py
  • src/cuphoton/xpois/ois.py
  • src/cuphoton/xpois/review_bokeh.py
  • src/cuphoton/xpois/solver_options.py
  • src/cuphoton/xpois/workflows.py
  • src/cuphoton/xray/_types.py
  • src/cuphoton/xray/commands.py
  • src/cuphoton/xray/gpu.py
  • src/cuphoton/xray/linear_prediction.py
  • src/cuphoton/xray/phonon_viz.py
  • src/cuphoton/xray/templates/__init__.py
  • src/cuphoton/xray/templates/report.html
  • src/cuphoton/xray/validation_viz.py
  • src/cuphoton/xray/workflow_viz.py
  • src/cuphoton/xscan/alard_lupton_experiment_review.py
  • src/cuphoton/xscan/butler.py
  • src/cuphoton/xscan/commands.py
  • src/cuphoton/xscan/config.py
  • src/cuphoton/xscan/dataset.py
  • src/cuphoton/xscan/des.py
  • src/cuphoton/xscan/device_pipeline.py
  • src/cuphoton/xscan/dragon_pipeline.py
  • src/cuphoton/xscan/hsc.py
  • src/cuphoton/xscan/metrics.py
  • src/cuphoton/xscan/raw_compare_review.py
  • src/cuphoton/xscan/review.py
  • src/cuphoton/xscan/training.py
  • src/cuphoton/xscan/types.py
  • src/cuphoton/xscan/workflows.py
  • src/cuphoton/xscan/xfit_features.py
  • tests/xdr/test_project_structure.py
  • tests/xdr/test_reader.py
  • tests/xdr/test_reader_concurrency.py
  • tests/xray/test_phonon_viz.py
  • tests/xray/test_validation_viz.py
  • tests/xscan/test_cli.py
  • tests/xscan/test_dragon_pipeline.py
  • tests/xscan/test_xfit_features.py
  • tests/xscan/test_xfit_fusion.py
💤 Files with no reviewable changes (1)
  • ROADMAP.md

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📝 Walkthrough

Walkthrough

The pull request standardizes component-name capitalization across documentation, examples, source text, generated labels, and tests. It also adds detail to xPois input and xDR setup descriptions, updates xScan feature-bundle documentation, and deletes ROADMAP.md.

Changes

Component name standardization

Layer / File(s) Summary
Documentation and example descriptions
README.md, THIRD_PARTY_NOTICES.md, docs/*, examples/imaging-pipeline/*, examples/xpois/*, examples/xscan/*
Component names use consistent capitalization. The README clarifies xPois inputs. The imaging notebook describes xDR setup requirements. Artifact documentation adds detail about feature-bundle loading and detector artifact versions.
xPois and xScan source text
src/cuphoton/xpois/*, src/cuphoton/xscan/*, src/cuphoton/xfit/api.py, tests/xscan/*
Docstrings, command descriptions, generated headings, review titles, validation messages, and test expectations use the standardized names. Existing validation checks and execution behavior are unchanged.
xRay and xDR labels
src/cuphoton/xray/*, src/cuphoton/xdr/prefetch.py, examples/run_quickstarts.py, tests/xray/*, tests/xdr/*
Default visualization titles, error messages, source descriptions, and matching test expectations use consistent capitalization. Failure conditions remain unchanged.

Roadmap removal

Layer / File(s) Summary
Remove roadmap document
ROADMAP.md
The document listing planned CI, performance, packaging, interface, and reproducibility work is deleted.

Priority: ⬇️ Low

Merge Risk: ⚪ Minimal · up to d473b

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@tpn
tpn marked this pull request as ready for review September 24, 2026 03:16
@tpn
tpn requested a review from melo-gonzo as a code owner September 24, 2026 03:16
@tpn tpn changed the title Remove the README maturity disclaimer Remove the README maturity disclaimer and stale roadmap Sep 24, 2026
@tpn tpn changed the title Remove the README maturity disclaimer and stale roadmap Refresh documentation and standardize component names Sep 24, 2026
@tpn
tpn force-pushed the release-readme-updates branch from ec942a5 to d473b69 Compare September 24, 2026 22:54
@tpn

tpn commented Sep 25, 2026

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@tpn
tpn force-pushed the release-readme-updates branch 2 times, most recently from 4ce31fd to 8ca3452 Compare September 28, 2026 20:55
@tpn
tpn changed the base branch from main to codex/imaging-fit-visualizations-20260928 September 28, 2026 20:55
@tpn
tpn force-pushed the release-readme-updates branch from 8ca3452 to 234b934 Compare September 28, 2026 21:22
@tpn
tpn changed the base branch from codex/imaging-fit-visualizations-20260928 to main September 28, 2026 21:22
@tpn
tpn force-pushed the release-readme-updates branch from 234b934 to 9e6a5e7 Compare September 28, 2026 22:11
tpn added 4 commits September 28, 2026 20:24
Keep the introduction focused on the reference workflows and their
integration points before the workflow chooser.

Signed-off-by: Trent Nelson <trentn@nvidia.com>
Retire the v0.1.0 roadmap as part of the release documentation cleanup.
Track planned work in GitHub issues instead of maintaining a separate
list of release intentions.

Signed-off-by: Trent Nelson <trentn@nvidia.com>
Spell component names with a lowercase x across guides, examples,
CLI help, reports, and diagnostic messages. Update matching test
expectations while preserving identifiers and artifact contracts.

Signed-off-by: Trent Nelson <trentn@nvidia.com>
Align the guides with FITS reader policies, candidate inputs, device
execution, native packaging, and xRay analysis contracts. Add release
notes and correct installation, citation, and command examples.

Signed-off-by: Trent Nelson <trentn@nvidia.com>
@tpn tpn changed the title Refresh documentation and standardize component names Update documentation for cuPhoton 0.1.3 Sep 29, 2026
@tpn
tpn force-pushed the release-readme-updates branch from 9e6a5e7 to c82949e Compare September 29, 2026 03:38

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