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Merged
IAmirKhani merged 12 commits into from
Jul 17, 2026
Merged

Joss review fixes #8

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30eed17
docs: fix PyPI wording, MyST {doc} roles, and stale test description
IAmirKhani Jul 1, 2026
8773f9b
paper: finalize AI-usage disclosure wording
IAmirKhani Jul 1, 2026
8c4c9e9
paper: scope AI-usage disclosure to documentation and style refactoring
IAmirKhani Jul 1, 2026
bbc9681
fix(packaging): declare matplotlib dependency and trim sdist bloat
IAmirKhani Jul 2, 2026
2cfc31f
Update acknowledgments
IAmirKhani Jul 15, 2026
ffd5c68
Merge branch 'main' into joss-review-fixes
IAmirKhani Jul 15, 2026
fba9e48
update the README
IAmirKhani Jul 16, 2026
5fa3134
docs: describe the real public API in the package docstring
IAmirKhani Jul 17, 2026
7603ede
remove unused stats.summaries module
IAmirKhani Jul 17, 2026
fffbc1f
fix(simulations): honor the rng argument when generating spikes
IAmirKhani Jul 17, 2026
0f0de8d
fix(simulations): use .item() for scalar firing rates
IAmirKhani Jul 17, 2026
3674f72
release: bump to 0.0.2 and single-source the version
IAmirKhani Jul 17, 2026
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2 changes: 0 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -155,8 +155,6 @@ If you use PyGPLA in your research, please cite the original GPLA method paper:
}
```

A dedicated software citation (JOSS) will be added here once the paper is published.

## License

BSD 2-Clause License. See `LICENSE`.
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2 changes: 0 additions & 2 deletions docs/api.md
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Expand Up @@ -49,8 +49,6 @@ pygpla.stats.jitter.interval_jitter
pygpla.stats.jitter.isi_preserved_jitter
pygpla.stats.jitter.group_preserved_jitter
pygpla.stats.jitter.population_jitter
pygpla.stats.summaries.summarize_gplv_results
pygpla.stats.summaries.summarize_plv_matrix
```

## Simulations
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2 changes: 1 addition & 1 deletion docs/conf.py
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Expand Up @@ -16,7 +16,7 @@
try:
release = version("pygpla")
except PackageNotFoundError:
release = "0.0.1"
release = "0.0.2"
version = release

extensions = [
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12 changes: 6 additions & 6 deletions docs/software_architecture.md
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Expand Up @@ -141,11 +141,11 @@ important QA step.

## Version Management

PyGPLA currently uses an explicit package version:
PyGPLA keeps its version in a single source:

- `project.version = "0.0.1"` in `pyproject.toml`
- `__version__ = "0.0.1"` in `src/pygpla/_version.py`
- `__version__` in `src/pygpla/_version.py`

The Hatch setting `tool.hatch.version.path = "src/pygpla/_version.py"` keeps the package's
runtime version source in one place. Version bumps are therefore currently a deliberate,
manual release action rather than git-tag-driven automation.
`pyproject.toml` declares `dynamic = ["version"]` and points Hatch at that file via
`tool.hatch.version.path = "src/pygpla/_version.py"`, so the build metadata and the runtime
`pygpla.__version__` are read from the same place. Version bumps are a deliberate, manual
release action (edit `_version.py`) rather than git-tag-driven automation.
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