Update version for release by cpaniaguam · Pull Request #933 · lnccbrown/HSSM

cpaniaguam · 2026-03-12T12:58:07Z

This pull request updates the project version in the pyproject.toml file to reflect a new release.

Project version updated from 0.2.12 to 0.3.0 in pyproject.toml.

digicosmos86 · 2026-03-12T13:44:12Z

There's a few other things that we need to do before release:

Update the changelog in the docs
Update the announcements in the docs
Run the documentation building process locally just to be sure that all documentation builds
Create a draft release with release note

This workflow seems to be a good use case for AI automation. We could write a skill or an agentic workflow for it on Github

- Claude Code skill (.claude/skills/prepare-release/SKILL.md) that automates the pre-release checklist: changelog update, announcement banner update, local docs build verification, and draft GitHub release creation - GitHub Actions workflow (.github/workflows/prepare-release.yml) as an alternative agentic approach using claude-code-action with workflow_dispatch Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add v0.3.0 changelog entry to docs/changelog.md - Update announcement banner to v0.3.0 - Fix mkdocs.yml: rename `import` to `inventories` for mkdocstrings-python 2.0 - Add poisson_race.ipynb to mkdocs execute_ignore list - Add notebook check workflow step to prepare-release skill Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- bayesflow_lre_integration: rename classifier_network → inference_network for bayesflow dev branch API compatibility - initial_values: add cores=1, chains=1 to fix multiprocessing EOFError - plotting: fix missing comma after sampler="numpyro" - poisson_race: fix kernel spec hssm-dev → python3 - CI: add workshop_1 and workshop_2 notebooks to skip list - pyproject.toml: move bayesflow+keras to notebook dep group, remove bayesflow optional extra (not yet released on PyPI) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Provides project-scoped context: structure, tooling, dependency management, common commands, key API patterns, CI workflows, and known issues for better Claude Code assistance. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

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AlexanderFengler · 2026-03-17T01:37:32Z

@cpaniaguam @digicosmos86 please give this a glance for any final adjustments if necessary.

Made a few improvements to tests, ran notebooks, docs adjusted and added a publication skill (that we likely want to iterate on a bit to perfect it) as well as a corresponding workflow (but I actually used the skill, workflow is just a placeholder for now).

I also added a first version of a CLAUDE.md file. Let's improve the project level skill infrastructure step by step, there's a lot of potential for optimization still.

digicosmos86

LGTM! Just minor comments

digicosmos86 · 2026-03-17T13:47:20Z

CLAUDE.md

+uv run pytest tests/
+
+# Run slow tests (marked with @pytest.mark.slow)
+uv run pytest tests/ --runslow


I think this might have been hallucinated? Don't remember a --runslow handle here

For this one uses the -m flag passing the "slow" value. So uv run pytest -m "slow".

digicosmos86 · 2026-03-17T13:47:44Z

CLAUDE.md

+uv sync --group dev --group notebook --group docs
+
+# Run tests
+uv run pytest tests/


We should add instructions about running fast tests here

digicosmos86 · 2026-03-17T13:48:59Z

CLAUDE.md

+## Known Issues / Notes
+
+- **Multiprocessing in notebooks:** PyMC's NUTS sampler with `cores>1` can cause `EOFError` in notebook execution contexts. Fix by adding `cores=1, chains=1` to `sample()` calls.
+- **bayesflow:** Currently installed from dev branch (`git+https://github.com/bayesflow-org/bayesflow@dev`) in the notebook group only, because PyPI release (2.0.8) doesn't yet include `RatioApproximator`. Not exposed as a user-facing optional extra until a stable release is available.


I don't think this should be in CLAUDE.md

digicosmos86 · 2026-03-17T13:50:14Z

docs/changelog.md

+
+This version includes the following changes:
+
+1. Support for **choice-only models**: the HSSM class, data validator, distributions, and model configs now handle models without reaction times, including a softmax likelihood family.


"a softmax likelihood family" sounds very AI...

digicosmos86 · 2026-03-17T13:50:47Z

docs/changelog.md

+3. **Poisson Race model**: initial implementation of the Poisson race model.
+4. **Hidden Markov Model (HMM-SSM)** example notebook.
+5. **BayesFlow LRE integration** through HSSM for likelihood ratio estimation.
+6. **RLSSM config system**: new `RLSSMConfig` and `BaseModelConfig` classes with comprehensive validation, plus a generalized RL likelihood builder supporting multiple computed parameters.


I think we should leave this out until RLSSM is out

digicosmos86 · 2026-03-17T13:54:34Z

.github/workflows/prepare-release.yml

+            You are preparing release v${{ inputs.version }} of the HSSM package.
+
+            ## Task 1: Update the changelog
+
+            1. Find the latest git tag: `git tag --list 'v*' --sort=-version:refname | head -1`
+            2. Gather changes: `git log <tag>..HEAD --oneline`
+            3. Read `docs/changelog.md` to see the existing format
+            4. Insert a new section after the `# Changelog` heading with this format:
+
+            ```
+            ### ${{ inputs.version }}
+
+            This version includes the following changes:
+
+            1. Human-readable description of change
+            2. ...
+            ```
+
+            Synthesize commits into user-facing descriptions. Focus on features, bug fixes,
+            and breaking changes. Skip CI-only changes.
+
+            ## Task 2: Update the announcement banner
+
+            Edit `docs/overrides/main.html`. Find the line with the version announcement
+            (pattern: `vX.Y.Z is released!`) and replace the version with v${{ inputs.version }}.
+
+            ## Important
+            - Changelog headings use NO "v" prefix (e.g., ### 0.3.0)
+            - Git tags use "v" prefix (e.g., v0.3.0)
+            - Only modify docs/changelog.md and docs/overrides/main.html


Should we just tell Claude to use the skill rather than providing a different context here?

cpaniaguam · 2026-03-17T14:02:49Z

CLAUDE.md

+
+```bash
+# Install all dev dependencies
+uv sync --group dev --group notebook --group docs


Here one can just use --all-groups.

Suggested change

uv sync --group dev --group notebook --group docs

uv sync --all-groups

Update version for release

63d34cc

cpaniaguam requested a review from AlexanderFengler March 12, 2026 12:58

AlexanderFengler and others added 4 commits March 15, 2026 12:26

Add CLAUDE.md with project context for Claude Code

82cf776

Provides project-scoped context: structure, tooling, dependency management, common commands, key API patterns, CI workflows, and known issues for better Claude Code assistance. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

slight improvements to tests

b4b709f

digicosmos86 previously approved these changes Mar 17, 2026

View reviewed changes

cpaniaguam commented Mar 17, 2026

View reviewed changes

bump lanfactory and ssm-simulators versions

e8e6eb8

AlexanderFengler dismissed digicosmos86’s stale review via e8e6eb8 March 19, 2026 22:17

bump bayesflow version

c815a4f

AlexanderFengler merged commit a34eb79 into main Mar 20, 2026
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Update version for release#933

Update version for release#933
AlexanderFengler merged 8 commits intomainfrom
update-version-0.3.0-for-release

cpaniaguam commented Mar 12, 2026

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		This version includes the following changes:

		1. Support for choice-only models: the HSSM class, data validator, distributions, and model configs now handle models without reaction times, including a softmax likelihood family.

	uv sync --group dev --group notebook --group docs
	uv sync --all-groups

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cpaniaguam commented Mar 12, 2026

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