From a5245382ee8120746ddd3787e3dae33b843ffb6a Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 16:22:28 -0500 Subject: [PATCH] Add citation file --- .github/workflows/build.yml | 2 + CITATION.cff | 165 ++++++++++++++++++++++++++++++++++++ README.md | 1 + docs/source/development.md | 7 +- pyproject.toml | 1 + 5 files changed, 173 insertions(+), 3 deletions(-) create mode 100644 CITATION.cff diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9c3106c5..895aca9a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -38,3 +38,5 @@ jobs: run: mypy -p forest - name: Run the test suite run: pytest + - name: Validate citation file + run: cffconvert -i CITATION.cff --validate diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..ba07c0d3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,165 @@ +cff-version: 1.2.0 +title: Forest +message: "If you use Forest, please cite it using the metadata from this file." +type: software +authors: + - family-names: Clement + given-names: Zachary + - family-names: Efstathiadis + given-names: Georgios + orcid: "https://orcid.org/0009-0006-2278-1882" + - family-names: Huang + given-names: Emily J. + orcid: "https://orcid.org/0000-0003-1964-5231" + - family-names: Karas + given-names: Marta + orcid: "https://orcid.org/0000-0001-5889-3970" + - family-names: Liu + given-names: Greyson + - family-names: Onnela + given-names: Jukka-Pekka + orcid: "https://orcid.org/0000-0001-6613-8668" + - family-names: Straczkiewicz + given-names: Marcin + orcid: "https://orcid.org/0000-0002-8703-4451" +repository-code: "https://github.com/onnela-lab/forest" +url: "https://forest.beiwe.org" +abstract: "Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data." +keywords: + - "digital phenotyping" + - smartphone + - statistics + - accelerometer + - GPS +license: BSD-3-Clause +references: + - authors: + - family-names: Straczkiewicz + given-names: Marcin + affiliation: "Department of Biostatistics, Harvard University" + orcid: "https://orcid.org/0000-0002-8703-4451" + - family-names: Huang + given-names: Emily J. + affiliation: "Department of Statistical Sciences, Wake Forest University" + orcid: "https://orcid.org/0000-0003-1964-5231" + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + doi: 10.1038/s41746-022-00745-z + journal: "npj Digital Medicine" + month: 2 + start: 29 + title: "A “one-size-fits-most” walking recognition method for smartphones, smartwatches, and wearable accelerometers" + type: article + volume: 6 + year: 2023 + - authors: + - family-names: Huang + given-names: Emily J. + affiliation: "Department of Mathematics and Statistics, Wake Forest University" + orcid: "https://orcid.org/0000-0003-1964-5231" + - family-names: Yan + given-names: Kebin + affiliation: "Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania" + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + doi: 10.3390/s22072618 + issue: 7 + journal: Sensors + start: 2618 + title: "Smartphone-Based Activity Recognition Using Multistream Movelets Combining Accelerometer and Gyroscope Data" + type: article + volume: 22 + year: 2022 + - authors: + - family-names: Liu + given-names: Guangyu + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + doi: 10.1093/jamia/ocab069 + issue: 8 + journal: "Journal of the American Medical Informatics Association" + start: 1777 + title: "Bidirectional imputation of spatial GPS trajectories with missingness using sparse online Gaussian Process" + type: article + volume: 28 + year: 2021 + - authors: + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + - family-names: Dixon + given-names: Caleb + affiliation: "Zagaran, Inc." + - family-names: Griffin + given-names: Keary + affiliation: "Rocket Farm Studios" + - family-names: Jaenicke + given-names: Tucker + affiliation: "Zagaran, Inc." + - family-names: Minowada + given-names: Leila + affiliation: "Zagaran, Inc." + - family-names: Esterkin + given-names: Sean + affiliation: "Zagaran, Inc." + - family-names: Siu + given-names: Alvin + affiliation: "Zagaran, Inc." + - family-names: Zagorsky + given-names: Josh + affiliation: "Zagaran, Inc." + - family-names: Jones + given-names: Eli + affiliation: "Zagaran, Inc." + doi: 10.21105/joss.03417 + issue: 68 + journal: "Journal of Open Source Software" + month: 12 + start: 3417 + title: "Beiwe: A data collection platform for high-throughput digital phenotyping" + type: article + volume: 6 + year: 2021 + - authors: + - family-names: Barnett + given-names: Ian + affiliation: "Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania" + orcid: "https://orcid.org/0000-0003-3256-5703" + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + doi: 10.1093/biostatistics/kxy059 + end: e112 + issue: 2 + journal: Biostatistics + start: e98 + title: "Inferring mobility measures from GPS with missing data" + type: article + volume: 21 + year: 2020 + - authors: + - family-names: Huang + given-names: Emily J. + affiliation: "Department of Mathematics and Statistics, Wake Forest University" + orcid: "https://orcid.org/0000-0003-1964-5231" + - family-names: Onnela + given-names: Jukka-Pekka + affiliation: "Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University" + orcid: "https://orcid.org/0000-0001-6613-8668" + doi: 10.3390/s20133706 + issue: 13 + journal: Sensors + start: 3706 + title: "Augmented movelet method for activity classification using smartphone gyroscope and accelerometer data" + type: article + volume: 20 + year: 2020 diff --git a/README.md b/README.md index fe937de3..0f3b2903 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![build](https://github.com/onnela-lab/forest/actions/workflows/build.yml/badge.svg)](https://github.com/onnela-lab/forest/actions/workflows/build.yml) [![Documentation Status](https://readthedocs.org/projects/forest-docs/badge/)](https://forest.beiwe.org/en/latest/) +[![CITATION.cff](https://github.com/onnela-lab/forest/actions/workflows/citation.yml/badge.svg)](https://github.com/onnela-lab/forest/actions/workflows/citation.yml) Forest logo diff --git a/docs/source/development.md b/docs/source/development.md index 8e46b8dc..da0b21b9 100644 --- a/docs/source/development.md +++ b/docs/source/development.md @@ -5,9 +5,10 @@ Information for contributors ## Quick start * Change current directory to the top level of your local Forest repository * Install Forest in editable mode along with development tools: `pip install -e ".[dev]"` -* Run code style checks: `flake8` -* Run type hint checks: `mypy` -* Run test suite: `pytest` +* Check code style: `flake8` +* Run static type checks: `mypy` +* Run the test suite: `pytest` +* Validate the citation file: `cffconvert -i CITATION.cff --validate` ### Documentation Install required dependencies: diff --git a/pyproject.toml b/pyproject.toml index 8c5a5f75..d4f28e9d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,6 +55,7 @@ Source = "https://github.com/onnela-lab/forest" [project.optional-dependencies] dev = [ "build", + "cffconvert", "flake8", "flake8-pytest-style", "mypy",