structboost 0.1.0__tar.gz → 0.1.2__tar.gz

structboost-0.1.2/CHANGELOG.md

@@ -0,0 +1,66 @@
+## Changelog
+
+Releases follow [semantic versioning](https://semver.org). While the project is
+pre-1.0, a minor bump may break API.
+
+### [0.1.2] - 2026-08-03
+
+Project metadata gains `Documentation` and `Changelog` links. PyPI renders
+`project.urls` as the sidebar next to the project description, and it carried
+only the repository and the issue tracker — so the documentation site, where
+every substantive explanation lives, was reachable from the README body but not
+from the navigation beside it. Both targets are verified live.
+
+As with 0.1.1, nothing in the package changed: `project.urls` reaches users only
+through an upload, so correcting it in the repository has no effect until a
+release carries it.
+
+### [0.1.1] - 2026-08-03
+
+A metadata release. No code in `structboost` changed; every difference is in
+what the package says about itself.
+
+The PyPI page is the reason for it. A project's long description is baked into
+the uploaded artifacts and is immutable per release, so 0.1.0 shipped with a
+README announcing "Not on PyPI yet" and directing readers to a pinned TestPyPI
+install. Correcting the file in git does not touch the published page — only a
+new release does. A `0.1.0.post1` would have expressed "packaging only" more
+precisely, but post-releases are handled inconsistently by downstream tooling
+and the versioning policy here is plain `MAJOR.MINOR.PATCH`.
+
+Python 3.13 is tested and advertised. `requires-python = ">=3.10"` never had an
+upper bound, so pip already installed on 3.13 while the CI matrix stopped at
+3.12 — support permitted but never exercised. The matrix now covers it, and the
+classifier list says what the requirement already allowed. 3.14 is left out
+until the `[bae]` extra's wheels are dependably available there.
+
+`CITATION.cff` gains `version` and `date-released`, which a citation file for a
+released version cannot do without, plus a `url` for the documentation site.
+
+### [0.1.0] - 2026-07-31
+
+First public release.
+
+Batch integration is one argument. `BAE.fit(batch_key=...)` names the covariate,
+following scVI's spelling, and `batch_integration_mode` chooses between
+`"decoder"`, `"encoder"` and `"both"`, defaulting to `"both"`. No `batch_key`
+means no integration, and naming a mode without one raises rather than quietly
+integrating nothing.
+
+`"encoder"` names the half of the model the mechanism protects, not a tensor the
+covariate is fed to: it enters the boosting design as a mandatory regressor so
+gene selection is not confounded by it. `transform` remains gene-only and needs
+no covariate labels under any mode.
+
+The ridge that stabilizes near-collinear covariates is `BAEConfig.nuisance_ridge`.
+It is a numerical knob rather than a modelling one, so it sits with the other
+algorithm settings.
+
+The `test` extra pulls the runtime dependencies. The sdist carries `tests/` and
+`conftest.py` so that downstream packagers can run the suite at build time, and
+with pytest alone that did not work: 360 of the 411 test functions sit behind an
+`importorskip` for torch or anndata, so `pip install .[test] && pytest` ran ~51
+tests, skipped the rest and reported success. Installing `[test]` now brings in
+`[bae]`, so a green build means the suite actually ran. Documenting the
+requirement in `CONTRIBUTING.md` instead was rejected, because the reader who
+needs it is an automated build script rather than a person.

{structboost-0.1.0 → structboost-0.1.2}/CITATION.cff

@@ -2,8 +2,11 @@ cff-version: 1.2.0
 message: "If you use structboost in your research, please cite it."
 title: "structboost"
 type: software
+version: "0.1.2"
+date-released: "2026-08-03"
 license: MIT
 authors:
   - family-names: Brunn
     given-names: Niklas
 repository-code: "https://github.com/NiklasBrunn/structboost"
+url: "https://niklasbrunn.github.io/structboost"

{structboost-0.1.0 → structboost-0.1.2}/PKG-INFO

@@ -1,10 +1,12 @@
 Metadata-Version: 2.4
 Name: structboost
-Version: 0.1.0
+Version: 0.1.2
 Summary: Boosting Autoencoders (BAE) and componentwise L2 boosting utilities for scverse-style workflows.
 Project-URL: Homepage, https://github.com/NiklasBrunn/structboost
+Project-URL: Documentation, https://niklasbrunn.github.io/structboost
 Project-URL: Repository, https://github.com/NiklasBrunn/structboost
 Project-URL: Issues, https://github.com/NiklasBrunn/structboost/issues
+Project-URL: Changelog, https://niklasbrunn.github.io/structboost/changelog.html
 Author: Niklas Brunn
 License: MIT License
         
@@ -37,6 +39,7 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.10
@@ -127,15 +130,6 @@ pip install structboost                 # allboost only, NumPy-only
 | `plot` | matplotlib | the `plot_*` functions |
 | `io` | pyarrow | Parquet encoder-weight files |
 
-Not on PyPI yet. Until it is, install from source or from TestPyPI. Pin the
-version: TestPyPI also carries older pre-release builds under this name, and an
-unpinned install resolves to one of those rather than to the current code.
-
-```bash
-pip install --index-url https://test.pypi.org/simple/ \
-            --extra-index-url https://pypi.org/simple/ "structboost[bae]==0.1.0"
-```
-
 See [Installation](https://niklasbrunn.github.io/structboost/installation.html)
 for the from-source and development setups.
 

{structboost-0.1.0 → structboost-0.1.2}/README.md

@@ -55,15 +55,6 @@ pip install structboost                 # allboost only, NumPy-only
 | `plot` | matplotlib | the `plot_*` functions |
 | `io` | pyarrow | Parquet encoder-weight files |
 
-Not on PyPI yet. Until it is, install from source or from TestPyPI. Pin the
-version: TestPyPI also carries older pre-release builds under this name, and an
-unpinned install resolves to one of those rather than to the current code.
-
-```bash
-pip install --index-url https://test.pypi.org/simple/ \
-            --extra-index-url https://pypi.org/simple/ "structboost[bae]==0.1.0"
-```
-
 See [Installation](https://niklasbrunn.github.io/structboost/installation.html)
 for the from-source and development setups.
 

{structboost-0.1.0 → structboost-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "structboost"
-version = "0.1.0"
+version = "0.1.2"
 description = "Boosting Autoencoders (BAE) and componentwise L2 boosting utilities for scverse-style workflows."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -20,6 +20,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering :: Bio-Informatics",
   "Topic :: Scientific/Engineering :: Artificial Intelligence",
 ]
@@ -72,8 +73,10 @@ docs = [
 
 [project.urls]
 Homepage = "https://github.com/NiklasBrunn/structboost"
+Documentation = "https://niklasbrunn.github.io/structboost"
 Repository = "https://github.com/NiklasBrunn/structboost"
 Issues = "https://github.com/NiklasBrunn/structboost/issues"
+Changelog = "https://niklasbrunn.github.io/structboost/changelog.html"
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/structboost"]

structboost-0.1.0/CHANGELOG.md

@@ -1,32 +0,0 @@
-## Changelog
-
-Releases follow [semantic versioning](https://semver.org). While the project is
-pre-1.0, a minor bump may break API.
-
-### [0.1.0] - 2026-07-31
-
-First public release.
-
-Batch integration is one argument. `BAE.fit(batch_key=...)` names the covariate,
-following scVI's spelling, and `batch_integration_mode` chooses between
-`"decoder"`, `"encoder"` and `"both"`, defaulting to `"both"`. No `batch_key`
-means no integration, and naming a mode without one raises rather than quietly
-integrating nothing.
-
-`"encoder"` names the half of the model the mechanism protects, not a tensor the
-covariate is fed to: it enters the boosting design as a mandatory regressor so
-gene selection is not confounded by it. `transform` remains gene-only and needs
-no covariate labels under any mode.
-
-The ridge that stabilizes near-collinear covariates is `BAEConfig.nuisance_ridge`.
-It is a numerical knob rather than a modelling one, so it sits with the other
-algorithm settings.
-
-The `test` extra pulls the runtime dependencies. The sdist carries `tests/` and
-`conftest.py` so that downstream packagers can run the suite at build time, and
-with pytest alone that did not work: 360 of the 411 test functions sit behind an
-`importorskip` for torch or anndata, so `pip install .[test] && pytest` ran ~51
-tests, skipped the rest and reported success. Installing `[test]` now brings in
-`[bae]`, so a green build means the suite actually ran. Documenting the
-requirement in `CONTRIBUTING.md` instead was rejected, because the reader who
-needs it is an automated build script rather than a person.