From 9b7b930e5783d2faf943a6705c1aa45954ad8e64 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Tue, 17 Oct 2023 13:41:03 -0400 Subject: [PATCH 01/17] Add a minimal CITATION.cff --- CITATION.cff | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..e44c1935 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,15 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: Forest +message: >- + If you use this software, please cite it using the metadata from this file. +type: software +authors: + - name: Onnela Lab +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. +license: BSD-3-Clause From 589072bf96fafa23d89d2808236a6bb5df4ad076 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Tue, 17 Oct 2023 14:04:38 -0400 Subject: [PATCH 02/17] Add citation validation workflow to GitHub actions --- .github/workflows/citation.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .github/workflows/citation.yml diff --git a/.github/workflows/citation.yml b/.github/workflows/citation.yml new file mode 100644 index 00000000..5d3ae402 --- /dev/null +++ b/.github/workflows/citation.yml @@ -0,0 +1,16 @@ +on: + push: + paths: + - CITATION.cff + workflow_dispatch: + +name: CITATION.cff +jobs: + Validate-CITATION-cff: + runs-on: ubuntu-latest + name: Validate CITATION.cff + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Validate CITATION.cff + uses: dieghernan/cff-validator@v3 From 410c4db28594ecd1ab3ded82129e62d9fa668180 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Tue, 17 Oct 2023 17:56:12 -0400 Subject: [PATCH 03/17] Add a reference and cleanup CITATION.cff --- CITATION.cff | 31 +++++++++++++++++++++---------- 1 file changed, 21 insertions(+), 10 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index e44c1935..b77cae6a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,15 +1,26 @@ -# This CITATION.cff file was generated with cffinit. -# Visit https://bit.ly/cffinit to generate yours today! - cff-version: 1.2.0 title: Forest -message: >- - If you use this software, please cite it using the metadata from this file. +message: "If you use Forest, please cite it using the metadata from this file." type: software authors: - - name: Onnela Lab -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. + - name: "Onnela Lab" +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." license: BSD-3-Clause +references: + - authors: + - family-names: Straczkiewicz + given-names: M + - family-names: Huang + given-names: EJ + - family-names: Onnela + given-names: JP + 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 From 2185a5593e12fd7e3108e8e461a1f11cbef4674c Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Tue, 17 Oct 2023 18:42:12 -0400 Subject: [PATCH 04/17] Add another reference and cleanup CITATION.cff --- CITATION.cff | 54 +++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 49 insertions(+), 5 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index b77cae6a..0180a7c9 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,18 +4,24 @@ message: "If you use Forest, please cite it using the metadata from this file." type: software authors: - name: "Onnela Lab" -repository-code: https://github.com/onnela-lab/forest -url: https://forest.beiwe.org +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." license: BSD-3-Clause references: - authors: - family-names: Straczkiewicz - given-names: M + given-names: Marcin + affiliation: "Department of Biostatistics, Harvard University" + orcid: "https://orcid.org/0000-0002-8703-4451" - family-names: Huang - given-names: EJ + 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: JP + 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 @@ -24,3 +30,41 @@ references: type: article volume: 6 year: 2023 + - 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 From e2a396b8bb704a459d31d15ff9721571e0550519 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Tue, 17 Oct 2023 19:00:06 -0400 Subject: [PATCH 05/17] Add a badge showing the current status of validation of CITATION.cff --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 1dc9d610..15c74860 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 From ab7695a34db97d493482bcb4cba021a4d0e88eb6 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Wed, 18 Oct 2023 16:29:07 -0400 Subject: [PATCH 06/17] Add keywords --- CITATION.cff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 0180a7c9..3ce063bb 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,6 +7,9 @@ authors: 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 license: BSD-3-Clause references: - authors: From 9a5d2c55cf6e6473e8ed367c2c4e9fbc64b22ada Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Wed, 18 Oct 2023 16:33:50 -0400 Subject: [PATCH 07/17] Update citation GA workflow --- .github/workflows/citation.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/citation.yml b/.github/workflows/citation.yml index 5d3ae402..fa6115fc 100644 --- a/.github/workflows/citation.yml +++ b/.github/workflows/citation.yml @@ -1,16 +1,17 @@ +name: CITATION.cff + on: push: paths: - CITATION.cff workflow_dispatch: -name: CITATION.cff jobs: Validate-CITATION-cff: runs-on: ubuntu-latest name: Validate CITATION.cff steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Validate CITATION.cff uses: dieghernan/cff-validator@v3 From 05ece96ef6888205587f671bf7952d8311ff1929 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Mon, 16 Dec 2024 16:28:46 -0500 Subject: [PATCH 08/17] Add keywords to CITATION.cff --- CITATION.cff | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 3ce063bb..24b9152a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -10,6 +10,9 @@ abstract: "Forest is a library for analyzing smartphone-based high-throughput di keywords: - digital phenotyping - smartphone + - statistics + - accelerometer + - GPS license: BSD-3-Clause references: - authors: From 24b90bec5689555389b3d606864ee64ca257e906 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Mon, 16 Dec 2024 16:33:47 -0500 Subject: [PATCH 09/17] Add validation for citation file --- .github/workflows/build.yml | 2 ++ pyproject.toml | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9c3106c5..a133738e 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 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", From b80d2fae9a2e39d3b9cd2e84599ef6dfb7572864 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Mon, 16 Dec 2024 16:38:16 -0500 Subject: [PATCH 10/17] Remove redundant validation --- .github/workflows/citation.yml | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 .github/workflows/citation.yml diff --git a/.github/workflows/citation.yml b/.github/workflows/citation.yml deleted file mode 100644 index fa6115fc..00000000 --- a/.github/workflows/citation.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: CITATION.cff - -on: - push: - paths: - - CITATION.cff - workflow_dispatch: - -jobs: - Validate-CITATION-cff: - runs-on: ubuntu-latest - name: Validate CITATION.cff - steps: - - name: Checkout - uses: actions/checkout@v4 - - name: Validate CITATION.cff - uses: dieghernan/cff-validator@v3 From a92712adb790b9ba25e38daa0e2cfc6d7e52a0dd Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Mon, 16 Dec 2024 16:41:12 -0500 Subject: [PATCH 11/17] Update the dev docs --- docs/source/development.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/source/development.md b/docs/source/development.md index 8e46b8dc..ce379a77 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` ### Documentation Install required dependencies: From 3714a7947092ce3da33ec9a2c6ebff37c317438c Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Mon, 16 Dec 2024 16:43:17 -0500 Subject: [PATCH 12/17] Add missing flag --- .github/workflows/build.yml | 2 +- docs/source/development.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index a133738e..895aca9a 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -39,4 +39,4 @@ jobs: - name: Run the test suite run: pytest - name: Validate citation file - run: cffconvert -i CITATION.cff + run: cffconvert -i CITATION.cff --validate diff --git a/docs/source/development.md b/docs/source/development.md index ce379a77..da0b21b9 100644 --- a/docs/source/development.md +++ b/docs/source/development.md @@ -8,7 +8,7 @@ Information for contributors * Check code style: `flake8` * Run static type checks: `mypy` * Run the test suite: `pytest` -* Validate the citation file: `cffconvert -i CITATION.cff` +* Validate the citation file: `cffconvert -i CITATION.cff --validate` ### Documentation Install required dependencies: From 692f25f5fd60c92e4f4f32215d4a3fa4a7bbe6d8 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 14:13:06 -0500 Subject: [PATCH 13/17] Add publication --- CITATION.cff | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 24b9152a..4c54e43c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -36,6 +36,26 @@ references: 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: Onnela given-names: Jukka-Pekka From 0748148122660a0b27a33dc4a940cba39bdf60cb Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 14:20:34 -0500 Subject: [PATCH 14/17] Add publication --- CITATION.cff | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 4c54e43c..730275ae 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -56,6 +56,22 @@ references: 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 From 85c937902cb2a412a5c848c89882a7c6e9a6b417 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 14:37:41 -0500 Subject: [PATCH 15/17] Add publication --- CITATION.cff | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 730275ae..2e2b54b8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -110,3 +110,21 @@ references: 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 From 900604f18b7726de104e4a2e42babf10f168b56f Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 14:41:58 -0500 Subject: [PATCH 16/17] Add publication --- CITATION.cff | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 2e2b54b8..141f8075 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -128,3 +128,20 @@ references: 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 From e0cca5ecf04f41a525a61bb8c046484b08889b98 Mon Sep 17 00:00:00 2001 From: Ilya Sytchev Date: Thu, 19 Dec 2024 14:59:14 -0500 Subject: [PATCH 17/17] Add authors --- CITATION.cff | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 141f8075..ba07c0d3 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -3,12 +3,30 @@ title: Forest message: "If you use Forest, please cite it using the metadata from this file." type: software authors: - - name: "Onnela Lab" + - 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 + - "digital phenotyping" - smartphone - statistics - accelerometer