tabdgp 0.2.0__tar.gz → 0.3.0__tar.gz

{tabdgp-0.2.0 → tabdgp-0.3.0}/.gitignore

@@ -9,15 +9,14 @@ dist/
 .ipynb_checkpoints/
 .DS_Store
 .claude/
-# local agent instructions (docs/conventions.md is the public part) and the roadmap
+# private files kept out of the repo
 CLAUDE.md
 ROADMAP.md
 next.md
-# design notes kept local: the lab notes and the prior-art survey
 lab/
 docs/prior-art.md
 docs/scamd-audit.md
 docs/related-simulators.md
 docs/frontier-priors.md
-# the model reports the survey read, kept local for their licences
+# the model reports the survey read, kept local for their licenses
 docs/reports/

{tabdgp-0.2.0 → tabdgp-0.3.0}/CITATION.cff

@@ -5,7 +5,7 @@ authors:
   - family-names: Kipnis
     given-names: Alex
 repository-code: https://github.com/adkipnis/tabdgp
-license: MIT
-version: 0.2.0
-date-released: 2026-10-14
+license: Apache-2.0
+version: 0.3.0
+date-released: 2026-10-23
 doi: 10.5281/zenodo.23322845

{tabdgp-0.2.0 → tabdgp-0.3.0}/CONTEXT.md

@@ -13,12 +13,12 @@ factor, family, link) are not redefined.
 **Covariate generator**:
 The process that draws a dataset's grouping structure and its typed covariate columns,
 continuous, binary, categorical or ordered, each within-group or group-level, with the quirks
-of real tables. TabDGP is one; it draws an outcome only as the optional outcome node.
+of real tables. TabDGP is one; it draws an outcome only as the outcome node.
 _Avoid_: predictor simulation, feature matrix, X generator, design-matrix generator
 
 **Design matrix**:
 The coding of the covariates the linear predictor sees: an intercept column, z-scored
-continuous columns, 0/1 binary columns, K − 1 treatment-coded columns per categorical.
+continuous columns, 0/1 binary columns, k − 1 treatment-coded columns per categorical.
 Derived from the covariates, never drawn; the hyperprior's design-column budget counts its
 columns besides the intercept.
 _Avoid_: X for the uncoded covariates, features
@@ -47,12 +47,12 @@ _Avoid_: edge case, noise, messiness
 
 **Node**:
 One variable of a dataset's structural causal model (SCM): a grouping factor, a group-level or
-within-group covariate, time, treatment, or the outcome node. A node has a parent set and a
-mechanism; a node without parents is a root.
+within-group covariate, a latent node, time, treatment, or the outcome node.
+A node has a parent set and a mechanism; a node without parents is a root.
 _Avoid_: feature, variable unqualified, neuron (of an MLP)
 
 **Grouping factor**:
-A root node whose values assign every row to one of its G groups, in metabeta's words "a
+A root node whose values assign every row to one of its m groups, in metabeta's words "a
 categorical variable whose levels index random effects"; a dataset has none (a flat table),
 one or several. Two grouping factors are **crossed** when their groups combine freely and
 **nested** when each group of the subordinate one lies within one group of the superior one,
@@ -67,8 +67,8 @@ _Avoid_: coarser and finer, parent and child (the graph's edges), higher and low
 
 **Unit**:
 What a node is drawn once per: the row, or one grouping factor, in which case the node takes
-one value per group of that factor, repeated across the group's rows (broadcast). A column at
-the row unit is a within-group covariate; one at a grouping factor's unit is group-level. A
+one value per group of that factor, repeated across the group's rows (broadcast). A covariate at
+the row unit is within-group; one at a grouping factor's unit is group-level. A
 nested grouping factor is a unit subordinate to the one it nests in; crossed ones are units
 without an order between them.
 _Avoid_: level (a factor level, or the multilevel literature's level 1 and 2), hierarchy
@@ -91,18 +91,24 @@ _Avoid_: hidden unit, confounder (a role a latent node can play)
 
 **Column**:
 A node observed in the table, with its metadata: type (continuous, binary, categorical,
-ordered), levels, role (grouping factor, covariate, time, treatment, outcome), and the
+ordered, count), levels, role (grouping factor, covariate, time, treatment, outcome), and the
 parameters its values were drawn with.
 _Avoid_: feature, variable unqualified
 
+**Count**:
+A column type for non-negative integers: a Poisson outcome's today, a covariate's once the
+measurement pass admits count covariates. In the design matrix a count is a continuous column.
+_Avoid_: integer column, discrete column (an ordered one)
+
 **Factor level**:
-One of the K categories of a binary, categorical or ordered column, or one group of a
+One of the k categories of a binary, categorical or ordered column, or one group of a
 grouping factor; R's `levels()`.
 _Avoid_: level unqualified, category, class
 
 **Marginal**:
-The distribution a continuous column's values are mapped onto after the SCM, from a catalogue
-of families (skewed, heavy-tailed, bounded, zero-inflated), keeping their ranks.
+The distribution a continuous or count column's values are mapped onto after the SCM, keeping
+their ranks: a family from a catalog (skewed, heavy-tailed, bounded, zero-inflated) for a
+continuous column, the Poisson for a count.
 _Avoid_: noise distribution (the root's), prior
 
 **Post-hoc type**:
@@ -126,7 +132,8 @@ _Avoid_: rng, random state, seed alone
 **Dataset**:
 What a draw returns: the columns as named arrays in their natural dtype, their metadata, the
 generating graph, the latent nodes' values, the hyperparameters every field resolved to except
-those each column or node draws for itself, and the key. Never padded, never a file.
+those each column or node draws for itself, and the key with the versions it reproduces under.
+Never padded, never a file.
 _Avoid_: batch, table (the columns alone), sample, corpus (the consumer's set of keys)
 
 **Hyperprior**:
@@ -137,9 +144,9 @@ proofs certify.
 _Avoid_: prior (the fitter's, over parameters), config unqualified, meta-distribution
 
 **Preset**:
-A named hyperprior for one kind of table, grouped or flat today, item response, survival or
-causal later: a choice of fields, never a new mechanism. Every draw starts from one; metabeta
-draws from the grouped preset.
+A named hyperprior for one kind of table, grouped, flat or glmm today, item response, survival
+or causal later: a choice of fields, never a new mechanism. Every draw starts from one; metabeta
+draws from the glmm preset, the grouped preset with the outcome node in its glmm form.
 _Avoid_: dataset type, kind, mode
 
 **Override**:
@@ -149,22 +156,44 @@ study, an ablation or a size outside the preset.
 _Avoid_: setting, parameter, hyperparameter
 
 **Quirk axis**:
-One field of the hyperprior that controls one quirk of the catalogue, granted only when
+One field of the hyperprior that controls one quirk of the catalog, granted only when
 mixedbench's measurement pass shows that real tables have the quirk strongly enough.
 _Avoid_: noise, perturbation, augmentation
 
 **Outcome node**:
-An optional node whose parents are drawn from the covariates, with a family, a link, the
-random effects per grouping factor and terms a GLMM lacks, that builds white-box
-misspecified datasets. Just another node; never drawn unless asked for.
-_Avoid_: y, target, label, response unqualified
+The node `y`, role `outcome`, drawn by default: a sink at the row unit, last in the generating
+graph, whose parents are drawn like any node's. Its form says how y follows from them. A
+dataset has at most one.
+_Avoid_: target, label, response unqualified, dependent variable
+
+**Form**:
+How the outcome node draws y, one per dataset: `scm`, a node like the others with a marginal
+or a post-hoc type, matched to real responses; or `glmm`, a generalized linear mixed model on
+the design matrix, with a family, a link, fixed effects, random effects per grouping factor
+and, when asked for, a deviation, what metabeta trains on and what builds white-box
+misspecified datasets.
+_Avoid_: mode, kind, outcome type (its column type)
+
+**Deviation**:
+The SCM mechanism over the outcome node's parents, latent ones included, added to a glmm
+form's linear predictor at a drawn scale, zero by default: what makes a dataset misspecified
+for every GLMM while its fixed and random effects stay the exact truth. A latent group-level
+parent in it is an endogeneity.
+_Avoid_: perturbation, nonlinearity, misspecification (the fitter's view of it), noise
+
+**Prior context**:
+The resolved hyperparameters of a glmm form's priors, recorded with the dataset: the scales
+and families its fixed effects, random-effect standard deviations and residual scale were
+drawn with, the correlation prior's shape, and the signal share and split that set the scales.
+What metabeta's posterior is conditioned on.
+_Avoid_: hyperparameters unqualified (the hyperprior's), prior unqualified (the fitter's)
 
 **Random effect**:
-A per-group parameter of the outcome, an intercept or a slope, drawn jointly per group of a
-grouping factor in metabeta's parameterisation; metabeta's term. Only the outcome node draws
-random effects; a group-level node, latent or observed, is covariate structure, which a GLMM
-takes as given.
-_Avoid_: group effect, random intercept for a latent group-level node
+A per-group parameter of the outcome, α, an intercept or a slope, drawn jointly per group of a
+grouping factor in metabeta's parameterization and counted in design columns, a slope on a
+categorical column taking k − 1; metabeta's term. Only the outcome node draws random effects;
+a group-level node, latent or observed, is covariate structure, which a GLMM takes as given.
+_Avoid_: group effect, b (an earlier letter), random intercept for a latent group-level node
 
 ### The proofs
 

{tabdgp-0.2.0 → tabdgp-0.3.0}/CONTRIBUTING.md

@@ -6,7 +6,7 @@ Thank you for your interest. TabDGP is early stage and help is welcome.
 
 - **A real-data quirk the generator misses.** Open an issue naming the property, a public
   table that shows it and, if you can, how to measure it per column or per grouping factor;
-  the quirk catalogue grows through the measurement pass, never by hand.
+  the quirk catalog grows through the measurement pass, never by hand.
 - **A bug in a mechanism or a proof.** Open an issue with the smallest example that shows it,
   or a pull request with a failing test and the fix.
 - **A use case.** A model family or a simulation study that needs something the hyperprior
@@ -24,7 +24,7 @@ git clone https://github.com/adkipnis/tabdgp
 cd tabdgp
 uv sync
 uv run pytest               # the fast tests
-uv run pytest -m slow       # the proofs against mixedbench's registry, from roadmap item 3
+uv run pytest -m slow       # the proofs against mixedbench's registry, once they exist
 ```
 
 ## Find your way
@@ -33,7 +33,7 @@ uv run pytest -m slow       # the proofs against mixedbench's registry, from roa
 src/tabdgp/     the package; each module's docstring says what it defines and how
 tests/          mirrors src/, fixtures beside the tests
 docs/adr/       the design decisions and why they were taken
-docs/           the conventions, and from roadmap item 3 the proofs' method
+docs/           the conventions, and later the proofs' method
 ```
 
 [`CONTEXT.md`](CONTEXT.md) defines the words (node, mechanism, hyperprior, override, quirk
@@ -56,6 +56,6 @@ Three rules keep the generator trustworthy:
 - **Nothing from downstream.** TabDGP imports nothing from metabeta or mixedbench; the proofs
   read mixedbench's registry as a test dependency only.
 
-## Licence
+## License
 
-By contributing, you agree that your changes are released under [MIT](LICENSE).
+By contributing, you agree that your changes are released under [Apache-2.0](LICENSE).

tabdgp-0.3.0/LICENSE

@@ -0,0 +1,202 @@
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{tabdgp-0.2.0 → tabdgp-0.3.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.5
 Name: tabdgp
-Version: 0.2.0
+Version: 0.3.0
 Summary: A data-generating process for grouped and flat tables, to be matched to a registry of real tables
 Project-URL: Repository, https://github.com/adkipnis/tabdgp
 Project-URL: Issues, https://github.com/adkipnis/tabdgp/issues
 Author-email: Alex Kipnis <adkipnis@users.noreply.github.com>
-License-Expression: MIT
+License-Expression: Apache-2.0
 License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
@@ -21,8 +21,6 @@ Description-Content-Type: text/markdown
 
 [![CI](https://github.com/adkipnis/tabdgp/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/adkipnis/tabdgp/actions/workflows/ci.yml)
 [![PyPI](https://img.shields.io/pypi/v/tabdgp)](https://pypi.org/project/tabdgp/)
-[![Python](https://img.shields.io/pypi/pyversions/tabdgp)](https://github.com/adkipnis/tabdgp/blob/main/pyproject.toml)
-[![Licence](https://img.shields.io/badge/licence-MIT-blue)](https://github.com/adkipnis/tabdgp/blob/main/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23322845.svg)](https://doi.org/10.5281/zenodo.23322845)
 
 # TabDGP
@@ -33,14 +31,16 @@ TabDGP simulates tabular datasets from a random structural causal model (SCM) an
 reproduce the quirks of real data. Each table comes with the graph and the settings that
 generated it.
 
-> **Alpha.** Release 0.2 draws grouped and flat tables from defaults that are round guesses;
-> the rest is planned below. Before 1.0, a release may change the dataset a key draws.
+> **Alpha.** Release 0.3 draws grouped and flat tables with an outcome `y`, from defaults that
+> are round guesses; the rest is planned below. Before 1.0, a release may change the dataset a key draws.
 
 ## Highlights
 
 - **Grouped or flat.** One to three grouping factors by default, nested or crossed, with 2 to
   400 groups each. A covariate varies by row or is constant within the groups of one factor.
   `Hyperprior.flat()` draws none.
+- **An outcome.** One node `y`, drawn by default as the last node of the SCM: continuous,
+  binary, categorical, ordered or count, with its own noise scale. `outcome_form='none'` draws none.
 - **White-box.** Each dataset carries its graph, latent nodes, column metadata and hyperparameters.
 - **Reproducible.** A dataset is a pure function of its key (a seed and an index) and the
   hyperprior, whatever batch or worker draws it.
@@ -69,37 +69,28 @@ print(len(dataset.latent), 'latent nodes,', dataset.graph.parents.sum(), 'edges'
 g0 categorical g0 [4 5 2]
 g1 categorical g1 [ 6 22 29]
 g2 categorical g2 [7 7 5]
-x0 binary g0 [1 1 1]
-x1 binary row [1 1 1]
-x2 continuous row [0.36 0.69 0.15]
-x3 binary row [0 0 0]
-x4 binary row [0 1 0]
-7 latent nodes, 16 edges
+x0 binary row [1 0 1]
+x1 binary row [0 1 0]
+x2 continuous g2 [1.77 1.77 2.66]
+x3 binary row [0 0 1]
+x4 binary g2 [0 0 1]
+y continuous row [0.76 0.62 0.93]
+7 latent nodes, 18 edges
 ```
 
 ## Planned
 
+- **Model-based outcomes:** exact or with a drawn deviation for white-box misspecified datasets.
 - **Quirk axes:** group confounding, rare levels, ties, bounds, near dependence and more.
-- **Matched defaults**, fitted to and checked against
-  [mixedbench](https://github.com/adkipnis/mixedbench)'s real grouped tables, then widened.
-- **An outcome node**, optional, for white-box misspecified datasets, with within-group time and
-  a binary treatment.
-
-## Learn more
-
-[`CONTEXT.md`](https://github.com/adkipnis/tabdgp/blob/main/CONTEXT.md) defines the vocabulary.
+- **Finetuning** the hyperprior's parameters to any batch of datasets.
+  Group presets are tuned against [mixedbench](https://github.com/adkipnis/mixedbench).
+- **Within-group time and a binary treatment.**
 
 ## Contributing
 
 Issues and pull requests are welcome; see
 [`CONTRIBUTING.md`](https://github.com/adkipnis/tabdgp/blob/main/CONTRIBUTING.md).
 
-## Citing
-
-Please cite the release you used, from
-[`CITATION.cff`](https://github.com/adkipnis/tabdgp/blob/main/CITATION.cff) or GitHub's "Cite
-this repository".
-
-## Licence
+## License
 
-[MIT](https://github.com/adkipnis/tabdgp/blob/main/LICENSE).
+[Apache-2.0](https://github.com/adkipnis/tabdgp/blob/main/LICENSE).

{tabdgp-0.2.0 → tabdgp-0.3.0}/README.md

@@ -1,7 +1,5 @@
 [![CI](https://github.com/adkipnis/tabdgp/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/adkipnis/tabdgp/actions/workflows/ci.yml)
 [![PyPI](https://img.shields.io/pypi/v/tabdgp)](https://pypi.org/project/tabdgp/)
-[![Python](https://img.shields.io/pypi/pyversions/tabdgp)](https://github.com/adkipnis/tabdgp/blob/main/pyproject.toml)
-[![Licence](https://img.shields.io/badge/licence-MIT-blue)](https://github.com/adkipnis/tabdgp/blob/main/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23322845.svg)](https://doi.org/10.5281/zenodo.23322845)
 
 # TabDGP
@@ -12,14 +10,16 @@ TabDGP simulates tabular datasets from a random structural causal model (SCM) an
 reproduce the quirks of real data. Each table comes with the graph and the settings that
 generated it.
 
-> **Alpha.** Release 0.2 draws grouped and flat tables from defaults that are round guesses;
-> the rest is planned below. Before 1.0, a release may change the dataset a key draws.
+> **Alpha.** Release 0.3 draws grouped and flat tables with an outcome `y`, from defaults that
+> are round guesses; the rest is planned below. Before 1.0, a release may change the dataset a key draws.
 
 ## Highlights
 
 - **Grouped or flat.** One to three grouping factors by default, nested or crossed, with 2 to
   400 groups each. A covariate varies by row or is constant within the groups of one factor.
   `Hyperprior.flat()` draws none.
+- **An outcome.** One node `y`, drawn by default as the last node of the SCM: continuous,
+  binary, categorical, ordered or count, with its own noise scale. `outcome_form='none'` draws none.
 - **White-box.** Each dataset carries its graph, latent nodes, column metadata and hyperparameters.
 - **Reproducible.** A dataset is a pure function of its key (a seed and an index) and the
   hyperprior, whatever batch or worker draws it.
@@ -48,37 +48,28 @@ print(len(dataset.latent), 'latent nodes,', dataset.graph.parents.sum(), 'edges'
 g0 categorical g0 [4 5 2]
 g1 categorical g1 [ 6 22 29]
 g2 categorical g2 [7 7 5]
-x0 binary g0 [1 1 1]
-x1 binary row [1 1 1]
-x2 continuous row [0.36 0.69 0.15]
-x3 binary row [0 0 0]
-x4 binary row [0 1 0]
-7 latent nodes, 16 edges
+x0 binary row [1 0 1]
+x1 binary row [0 1 0]
+x2 continuous g2 [1.77 1.77 2.66]
+x3 binary row [0 0 1]
+x4 binary g2 [0 0 1]
+y continuous row [0.76 0.62 0.93]
+7 latent nodes, 18 edges
 ```
 
 ## Planned
 
+- **Model-based outcomes:** exact or with a drawn deviation for white-box misspecified datasets.
 - **Quirk axes:** group confounding, rare levels, ties, bounds, near dependence and more.
-- **Matched defaults**, fitted to and checked against
-  [mixedbench](https://github.com/adkipnis/mixedbench)'s real grouped tables, then widened.
-- **An outcome node**, optional, for white-box misspecified datasets, with within-group time and
-  a binary treatment.
-
-## Learn more
-
-[`CONTEXT.md`](https://github.com/adkipnis/tabdgp/blob/main/CONTEXT.md) defines the vocabulary.
+- **Finetuning** the hyperprior's parameters to any batch of datasets.
+  Group presets are tuned against [mixedbench](https://github.com/adkipnis/mixedbench).
+- **Within-group time and a binary treatment.**
 
 ## Contributing
 
 Issues and pull requests are welcome; see
 [`CONTRIBUTING.md`](https://github.com/adkipnis/tabdgp/blob/main/CONTRIBUTING.md).
 
-## Citing
-
-Please cite the release you used, from
-[`CITATION.cff`](https://github.com/adkipnis/tabdgp/blob/main/CITATION.cff) or GitHub's "Cite
-this repository".
-
-## Licence
+## License
 
-[MIT](https://github.com/adkipnis/tabdgp/blob/main/LICENSE).
+[Apache-2.0](https://github.com/adkipnis/tabdgp/blob/main/LICENSE).

{tabdgp-0.2.0 → tabdgp-0.3.0}/pyproject.toml

@@ -1,9 +1,9 @@
 [project]
 name = "tabdgp"
-version = "0.2.0"
+version = "0.3.0"
 description = "A data-generating process for grouped and flat tables, to be matched to a registry of real tables"
 readme = "README.md"
-license = "MIT"
+license = "Apache-2.0"
 license-files = ["LICENSE"]
 authors = [{ name = "Alex Kipnis", email = "adkipnis@users.noreply.github.com" }]
 requires-python = ">=3.12"
@@ -34,12 +34,15 @@ dev = [
 ]
 
 [build-system]
-requires = ["hatchling>=1.27"]  # PEP 639 licence expression and licence files
+requires = ["hatchling>=1.27"]  # PEP 639 license expression and license files
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/tabdgp"]
 
+[tool.hatch.build.targets.sdist]
+exclude = ["/docs"]  # the ADRs and conventions are read on GitHub, not in the sdist
+
 [tool.ruff]
 line-length = 100