From 2b483ac8a43033ac01976932495b2bec88a7d0d4 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 24 Feb 2025 08:42:32 +0100 Subject: [PATCH 1/3] doc: Update README (#153) Prettify links and other updates. --------- Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> --- README.md | 30 +++++++++++++++++++----------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 474fc7a..7ae1902 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,8 @@ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14183390.svg)](https://doi.org/10.5281/zenodo.14183390) -The PEtab extension for model selection, including additional file formats and library. +The [PEtab](https://petab.readthedocs.io/) extension for model selection, +including the additional file formats and package. ## Install @@ -18,24 +19,31 @@ Further documentation is available at ## Examples -There are example Jupyter notebooks covering the Python API, CLI, and visualization in the "doc/examples" directory. +There are example Jupyter notebooks covering visualization, custom non-SBML +models, and the CLI and Python API, in the `doc/examples` directory. The notebooks can be viewed at [https://petab-select.readthedocs.io/en/stable/examples.html](https://petab-select.readthedocs.io/en/stable/examples.html). ## Supported features -### Criterion +PEtab Select offers various methods and criteria for model selection, as well +as a variety of visualization options. -- `AIC`: https://en.wikipedia.org/wiki/Akaike_information_criterion#Definition -- `AICc`: https://en.wikipedia.org/wiki/Akaike_information_criterion#Modification_for_small_sample_size -- `BIC`: https://en.wikipedia.org/wiki/Bayesian_information_criterion#Definition +### Criteria + +- `AIC`: [Akaike information criterion](https://en.wikipedia.org/wiki/Akaike_information_criterion#Definition) +- `AICc`: [Corrected Akaike information criterion](https://en.wikipedia.org/wiki/Akaike_information_criterion#Modification_for_small_sample_size) +- `BIC`: [Bayesian information criterion](https://en.wikipedia.org/wiki/Bayesian_information_criterion#Definition) ### Methods -- `forward`: https://en.wikipedia.org/wiki/Stepwise_regression#Main_approaches -- `backward`: https://en.wikipedia.org/wiki/Stepwise_regression#Main_approaches -- `brute_force`: Optimize all possible model candidates, then return the model - with the best criterion value. -- `famos`: https://doi.org/10.1371/journal.pcbi.1007230 +- `forward`: + [Forward selection](https://en.wikipedia.org/wiki/Stepwise_regression#Main_approaches). + Iteratively increase model complexity. +- `backward`: [Backward selection](https://en.wikipedia.org/wiki/Stepwise_regression#Main_approaches). + Iteratively decrease model complexity. +- `brute_force`. Calibrate all models. +- `famos`: + [Flexible and dynamic Algorithm for Model Selection (FAMoS)](https://doi.org/10.1371/journal.pcbi.1007230) Note that the directional methods (forward, backward) find models with the smallest step size (in terms of number of estimated parameters). For example, From ba453606d4f454b5eb24d8263b498286734f12de Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 12 Aug 2025 07:21:03 +0000 Subject: [PATCH 2/3] Bump actions/checkout from 4 to 5 Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci.yml | 2 +- .github/workflows/deploy_release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ff747ac..314b1c9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: steps: - name: Check out repository - uses: actions/checkout@v4 + uses: actions/checkout@v5 - name: Prepare python ${{ matrix.python-version }} uses: actions/setup-python@v5 diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml index 29347a5..cf7dec9 100644 --- a/.github/workflows/deploy_release.yml +++ b/.github/workflows/deploy_release.yml @@ -20,7 +20,7 @@ jobs: with: python-version: "3.12" - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: fetch-depth: 20 From 9d37b0c066f09ef3a33e0f8962fd286408e048bf Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 8 Sep 2025 22:17:27 +0000 Subject: [PATCH 3/3] Bump actions/setup-python from 5 to 6 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/ci.yml | 2 +- .github/workflows/deploy_release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 314b1c9..a05dfd1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,7 +25,7 @@ jobs: uses: actions/checkout@v5 - name: Prepare python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml index cf7dec9..2f4ddf8 100644 --- a/.github/workflows/deploy_release.yml +++ b/.github/workflows/deploy_release.yml @@ -16,7 +16,7 @@ jobs: steps: - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: "3.12"