docs: fix API ref links, add an estimators page, and correct docstrings - #1990
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Included review availability: Your plan includes up to 3 reviews per rolling hour; 2 remain after this review. 📝 WalkthroughWalkthroughThe PR adds estimator API documentation, updates estimator docstrings, replaces obsolete documentation links, and expands FAQ and validation guidance for unconstrained estimators. ChangesDocumentation updates
Estimated code review effort: 2 (Simple) | ~10 minutes Merge Risk: ⚪ Minimal · up to This PR updates documentation links, FAQ navigation, and API reference coverage without any identified merge-blocking risk at the current head. Possibly related PRs
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@janfb I am sorry for making two pull requests at the same time. I will avoid doing this in the future to keep things clean. |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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+ Coverage 88.20% 89.15% +0.95%
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Builds on @pawank925's commit. - Replace the absolute readthedocs URLs in the reStructuredText pages with `:doc:` roles. Sphinx resolves those at build time and warns when a target moves, which is what the dead `sbi.html` link needed. Six notebook cells used the same dead target and now point at api_reference.html. The notebooks keep absolute URLs, because readers also open them on GitHub and in Colab, where MyST roles do not render. - Give the estimators their own page. Each section of the landing page pairs with a page in the toctree. The entries went into `api_reference/neural_nets`, so the sidebar filed the classes under "Neural nets". Also add `ConditionalVectorFieldEstimator`, which is the base class of the score and flow matching estimators and the type that `vector_field_estimator_based_potential` takes, plus `FlowMatchingEstimator` and `MixedDensityEstimator` for the FMPE, MNLE and MNPE methods that the Training section already lists. - Fix the FAQ page that becomes visible with the toctree entry. The code sample was missing a comma and raised a SyntaxError. The title was not phrased as a question like the other entries. The first sentence assumed the reader arrived from the leakage entry. The page also described the transform as zuko-only, although `mdn` supports it. Renumber the file to 04, because questions 04 to 07 went away in sbi-dev#1519.
`build_mdn` has supported `z_score_x="transform_to_unconstrained"` since sbi-dev#1888, which shipped in 0.27.0, but the error from the nflows builders still sent users to the zuko models only. Name `mdn` as well, and correct the same claim in the guard's docstring. The message stays as it is for the classifier, vector field and unconditional builders, which never named an alternative model. Documenting the estimator classes also turns on RST parsing for docstrings that nothing parsed before. That surfaced 19 warnings: shape tuples such as `(sample_dim, batch_dim, *input_shape)` without backticks, display equations indented below the prose, and two footnotes with no citation in the class docstring. The SDE in `ConditionalScoreEstimator` rendered glued to the sentence before it and is now a `.. math::` block. The branch builds with 56 warnings, one fewer than main. No control flow changes. The only runtime change is the error message.
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Thanks @pawank925, this closes #1982. All three parts were right: the two dead links, the FAQ toctree entry, and the estimator classes in the API reference. I pushed two commits on top instead of sending the PR back and forth. The docs commit gives the estimators their own API reference page, adds three more estimator classes, switches the internal links to Nothing needed from you here. |
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Inline comments:
In `@docs/faq/question_04_unconstrained.md`:
- Around line 19-27: Update the example around density_estimator_build_fun to
define a minimal prior before it is passed as x_dist and reused by NPE, or
explicitly state that an existing prior is required; ensure copied code does not
reference an undefined prior.
- Around line 43-44: Update the FAQ statement about supported transformations to
limit the Zuko claim to conditional builders, naming zuko_maf and zuko_nsf or
describing them as conditional Zuko estimators; do not imply support from the
unconditional builder build_zuko_unconditional_flow.
In `@sbi/neural_nets/estimators/base.py`:
- Around line 533-536: Align the Normal-distribution documentation with the
implementation’s scale convention: in sbi/neural_nets/estimators/base.py lines
533-536, update the perturbation-kernel equation to use std_fn() consistently;
in sbi/neural_nets/estimators/score_estimator.py lines 22-35, state the same
scale-versus-variance convention in the SDE marginal equation.
In `@sbi/neural_nets/estimators/flowmatching_estimator.py`:
- Around line 384-387: The score equation documentation around score()
incorrectly labels the subtracted state as θ_0; align it with the method
contract and implementation by renaming that term to the current input/state
θ_t, unless score() is intended to use initial data, in which case update the
implementation consistently.
In `@sbi/neural_nets/ratio_estimators.py`:
- Around line 110-111: Update the input-shape contracts in combine_theta_and_x()
and unnormalized_log_ratio() so theta and x have matching prefixes accepted by
_get_shape_prefix(); implement the required sample-dimension expansion for x if
that is the intended API, otherwise revise both docstrings to require matching
prefixes. Add a regression test covering the documented sample-dimension case.
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docs/advanced_tutorials.rstdocs/advanced_tutorials/03_density_estimators.ipynbdocs/api_reference.rstdocs/api_reference/estimators.rstdocs/faq.rstdocs/faq/question_04_unconstrained.mddocs/how_to_guide/03_density_estimators.ipynbdocs/index.rstdocs/tutorials.rstdocs/tutorials/00_getting_started.ipynbdocs/tutorials/01_Bayesian_workflow.ipynbsbi/neural_nets/estimators/base.pysbi/neural_nets/estimators/flowmatching_estimator.pysbi/neural_nets/estimators/score_estimator.pysbi/neural_nets/net_builders/flow.pysbi/neural_nets/ratio_estimators.pysbi/utils/sbiutils.py
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- docs/index.rst
- docs/faq.rst
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MathJax rejects an underscore inside `\text{}`. `\text{mean_t}` therefore
printed "'_' allowed only in math mode" where the equation should be. Write
the subscript properly, as `\text{mean}_t`.
Five of the seven were already in `mean_t_fn` and `std_t_fn` in `base.py`.
Nothing rendered those docstrings before this branch documented the
estimator classes, so the broken output was invisible. The other two are in
`ConditionalScoreEstimator`, where the previous commit moved two plain-text
equations into `.. math::` blocks. As plain text the underscores were
harmless; as maths they were not.
Sphinx reports no warning for this, because it is MathJax that rejects the
TeX in the browser. Checked with a browser: both display equations on the
ConditionalScoreEstimator page typeset, and none of the seven estimator
pages has a MathJax error.
janfb
approved these changes
Aug 17, 2026
Follows a CodeRabbit review. All five findings were valid. Three are older mistakes in docstrings that this branch renders for the first time. Two are in text this branch added. - `combine_theta_and_x` and `unnormalized_log_ratio` documented `theta` with a sample dimension and `x` without one. `_get_shape_prefix` compares the two prefixes exactly and states that it does not broadcast, so the documented shapes raise a `ValueError`. Document the contract that the code enforces. - The perturbation kernel read `N(mean_t, std_t)` in `mean_t_fn` and `N(mean_t, std_t^2)` in `std_fn`. `std_fn` returns a standard deviation, and the marginal variance adds `std_fn(t)**2`, so the variance form is the correct one. Use it in both, and in the SDE marginal. - The flow matching score equations subtracted `\theta_0`, but `score()` subtracts `input`, which is `\theta_t`. Substituting the interpolation into the code gives `-\theta_1/t`, the score of `p(\theta_t|\theta_0)`, so the code is right and the symbol was wrong. - The FAQ example used `prior` without defining it. Define it, so the example runs as it is. - The FAQ claimed the transform works with the `zuko_*` estimators. The unconditional (marginal) zuko builder rejects it, so limit the claim to the conditional ones.
janfb
changed the title
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Closes #1982
docs/index.rstanddocs/tutorials.rst(the oldsbi.htmltarget returns 404).faq/question_08_unconstrainedpage to the FAQ toctree.DensityEstimator,RatioEstimatorandScoreEstimatorclasses to the API reference under a newEstimatorssection.