Add detailed step reference docs - #104
Merged
Merged
Conversation
Hand-written reference for all 28 steps plus combine_runs. One index page (step contract, array-shape vocabulary, master table) and four category pages: loading & filtering, detector & spatial, binning, spectra & reductions. Each entry lists what the step reads, what it writes, and every tunable parameter with its default. Wire a Step reference nav section into mkdocs.yml after the YAML guide; keep source_analysis.md as the source-linked API.
There was a problem hiding this comment.
Pull request overview
Adds a new hand-written “Step reference” section to the MkDocs site, providing a structured reference for all registered pipeline steps (and the combine_runs reduction) including read/write contracts, shapes, and YAML parameters.
Changes:
- Adds five new reference pages under
docs/steps/, grouped by step category. - Adds a “Step reference” section to
mkdocs.ymlnavigation linking the new pages. - Documents per-step reads/writes and parameter defaults, plus a master index/table of all steps.
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| mkdocs.yml | Adds “Step reference” nav entries pointing to the new docs pages. |
| docs/steps/index.md | Introduces the step contract, shape vocabulary, and a master step table with intra-doc links. |
| docs/steps/loading_filtering.md | Documents loading + filtering steps and their YAML parameters. |
| docs/steps/detector.md | Documents detector correction/geometry/spatial reduction steps and parameters. |
| docs/steps/binning.md | Documents axis/index steps and binned-reduction steps and parameters. |
| docs/steps/spectra.md | Documents spectrum finishing steps plus the combine_runs cross-run reduction. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+24
to
+27
| A step that can't find its input (`on` missing, or the attribute is `None`) | ||
| returns quietly and logs a status message rather than raising. This lets the | ||
| same pipeline run on a parent that has no detector loaded (batched path) and on | ||
| each batch that does. |
Comment on lines
+75
to
+76
| - **Reads (per run):** `<detector_key><laser_on_suffix>`, | ||
| `<detector_key><laser_off_suffix>`, and their `_bincount` arrays. |
| | `laser_on_suffix` | `"_simultaneous_laser_time_binned"` | laser-on data suffix | | ||
| | `laser_off_suffix` | `"_xray_not_laser_time_binned"` | laser-off data suffix | | ||
|
|
||
| Results land in `pipe.results` under the reduction name. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
What changed
Expands the "Analysis steps" docs from five raw docstring dumps into a
hand-written reference covering every registered step, organized by category.
New pages under
docs/steps/:index.md— step contract, array-shape vocabulary, and a master table of all 28 steps +combine_runs, each linking to its category anchor.loading_filtering.md— loading and shot-selection steps (10).detector.md— correction, geometry, spatial reduction (7).binning.md— axes, bin indices, binned reductions (8).spectra.md— normalize, background subtraction, purge, and thecombine_runsreduction.Each entry documents what the step reads (input shape: nothing / 1D / 2D / 3D),
what it writes, and every tunable parameter with its default.
mkdocs.ymlgets a "Step reference" nav section after the YAML guide.source_analysis.mdstays as the source-linked API.Test
mkdocs build(non-strict, same as CI) renders all five pages, resolves thenav, and produces no broken-link warnings. Remaining griffe warnings are
pre-existing on legacy
XSpect_*.pyfiles.