* feat(opt): add model listing + registration

* refactor(opt): rename _api functions

* docs: update README and fig1 in joss draft

* style: pre-commit fixes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…_losses docstring (#74)

…ure wordcount < 1000 (#75)

* docs(paper): make summary less jargon-y, ensure wordcount < 1000, add joss github action

* fix: fix EOL in draft-pdf workflow

* docs: fix author affiliations and bib DOIs

* docs(paper): add country for affil 1

Bumps the actions group with 1 update: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi).


Updates `prefix-dev/setup-pixi` from 0.8.8 to 0.8.10
- [Release notes](https://github.com/prefix-dev/setup-pixi/releases)
- [Commits](prefix-dev/setup-pixi@v0.8.8...v0.8.10)

---
updated-dependencies:
- dependency-name: prefix-dev/setup-pixi
  dependency-version: 0.8.10
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* feat: add benchmarks for base matrix operations

* chore: add matrix benchmark tests in python

* fix (py): fix benchmark test names

updates:
- [github.com/python-jsonschema/check-jsonschema: 0.33.0 → 0.33.1](python-jsonschema/check-jsonschema@0.33.0...0.33.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* feat: port matrix operations to ndarray + rust-numpy

* refactor: re-vamp rust core

* Trigger Pre-Commit CI

* fix(demo): fix matrix dtype to float32

* feat: vcov and precision matrices + move float ops to f64

* style: pre-commit fixes

* docs(r): fix docs for new functions in R

* refactor(py): add legacy alias for to-be-deprecated metrics

* refactor(r/lib): remove deprecated f32 comment

* docs(py): fix docs in stats

* Update phylo2vec/src/matrix/graph.rs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* style: pre-commit fixes

* refactor: rename variance-covariance functions

* fix(r): fix vcv name in stats

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* feat: add incidence matrix functions

* style: pre-commit fixes

* feat(r): add incidence function and tests

* refactor: add coo/COO to codespell whitelist

* refactor: discard precommit codespell

* chore: add scipy to pixi dependencies for testing

* refactor(py/incidence): remove dok, make coo default and add tests

* refactor(rust): discard precommit codespell

* style: pre-commit fixes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* refactor(py): code cleaning

* refactor(rust): add more docstrings to public functions

* style: pre-commit fixes

* fix(py): fix error catching for io and simplify functions

* Update phylo2vec/src/vector/convert.rs

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* fix(py): handle the no-match case gracefully in update_version

* refactor(py): print real warnings for update_version and print runtimerror for git

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

updates:
- [github.com/python-jsonschema/check-jsonschema: 0.33.1 → 0.33.2](python-jsonschema/check-jsonschema@0.33.1...0.33.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Bumps the actions group with 1 update: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi).


Updates `prefix-dev/setup-pixi` from 0.8.10 to 0.8.11
- [Release notes](https://github.com/prefix-dev/setup-pixi/releases)
- [Commits](prefix-dev/setup-pixi@v0.8.10...v0.8.11)

---
updated-dependencies:
- dependency-name: prefix-dev/setup-pixi
  dependency-version: 0.8.11
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps the actions group with 1 update: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi).


Updates `prefix-dev/setup-pixi` from 0.8.11 to 0.8.14
- [Release notes](https://github.com/prefix-dev/setup-pixi/releases)
- [Commits](prefix-dev/setup-pixi@v0.8.11...v0.8.14)

---
updated-dependencies:
- dependency-name: prefix-dev/setup-pixi
  dependency-version: 0.8.14
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* feat: add a simple CLI for the python API

* style: pre-commit fixes

* refactor(cli): update pyproject.toml

* refactor(cli): remove unused deps from tests

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>