From 0ce239509cfd49646b302f200f30d8bc53eecd2a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 5 Aug 2024 21:28:19 +0000 Subject: [PATCH 01/20] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0) - [github.com/pycqa/flake8: 7.1.0 → 7.1.1](https://github.com/pycqa/flake8/compare/7.1.0...7.1.1) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1831d7e..7b09e15 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: - id: check-case-conflict - id: check-merge-conflict - repo: https://github.com/psf/black - rev: 24.4.2 + rev: 24.8.0 hooks: - id: black - repo: https://github.com/pycqa/isort @@ -19,7 +19,7 @@ repos: hooks: - id: isort - repo: https://github.com/pycqa/flake8 - rev: 7.1.0 + rev: 7.1.1 hooks: - id: flake8 - repo: https://github.com/pycqa/pydocstyle From 730fb8d59d52014f86a6a9c491320dd967c510ab Mon Sep 17 00:00:00 2001 From: Marie-Eve Picard Date: Mon, 26 Aug 2024 17:33:14 -0400 Subject: [PATCH 02/20] Add contribution --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 06feda8..f0ac5c3 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -15,6 +15,11 @@ "orcid": "0000-0002-2553-3327", "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", "name": "Stefano Moia" + }, + { + "orcid": "0009-0001-2412-7829", + "affiliation": "Département de psychologie, Université de Montréal", + "name": "Marie-Eve Picard" } ], "access_right": "open" From ce23f7273b7e12a63070aa0186850b4e36e585d8 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 16:39:07 +0200 Subject: [PATCH 03/20] Update Zenodo (and hopefully not breaking it) --- .zenodo.json | 224 ++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 206 insertions(+), 18 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index f0ac5c3..23ba575 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -3,24 +3,212 @@ "title": "physiopy/peakdet: A python toolbox for reproducible physiological data analysis", "upload_type": "software", "creators": [ - { - "affiliation": "McGill University", - "name": "Elizabeth DuPre" - }, - { - "affiliation": "McGill University", - "name": "Ross Markello" - }, - { - "orcid": "0000-0002-2553-3327", - "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", - "name": "Stefano Moia" - }, - { - "orcid": "0009-0001-2412-7829", - "affiliation": "Département de psychologie, Université de Montréal", - "name": "Marie-Eve Picard" - } + { + "affiliations": [ + { + "name": "Stanford University" + } + ], + "person_or_org": { + "family_name": "DuPre", + "given_name": "Elizabeth", + "identifiers": [ + { + "identifier": "0000-0003-1358-196X", + "scheme": "orcid" + } + ], + "name": "DuPre, Elizabeth", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "National Institute of Mental Health" + } + ], + "person_or_org": { + "family_name": "Glen", + "given_name": "Daniel", + "identifiers": [ + { + "identifier": "0000-0001-8456-5647", + "scheme": "orcid" + } + ], + "name": "Glen, Daniel", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "02j61yw88", + "name": "Aristotle University of Thessaloniki" + } + ], + "person_or_org": { + "family_name": "Kikas", + "given_name": "Georgios", + "name": "Kikas, Georgios", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Markello", + "given_name": "Ross", + "identifiers": [ + { + "identifier": "0000-0003-1057-1336", + "scheme": "orcid" + } + ], + "name": "Markello, Ross", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "01pxwe438", + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Miedema", + "given_name": "Mary", + "identifiers": [ + { + "identifier": "0009-0008-3263-731X", + "scheme": "orcid" + } + ], + "name": "Miedema, Mary", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Maastricht University" + } + ], + "person_or_org": { + "family_name": "Moia", + "given_name": "Stefano", + "identifiers": [ + { + "identifier": "0000-0002-2553-3327", + "scheme": "orcid" + } + ], + "name": "Moia, Stefano", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Universit\u00e9 de Montr\u00e9al" + } + ], + "person_or_org": { + "family_name": "Picard", + "given_name": "Marie-\u00c8ve", + "identifiers": [ + { + "identifier": "0000-0002-4316-2830", + "scheme": "orcid" + } + ], + "name": "Picard, Marie-\u00c8ve", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "University of Pennsylvania" + } + ], + "person_or_org": { + "family_name": "Salo", + "given_name": "Taylor", + "identifiers": [ + { + "identifier": "0000-0001-9813-3167", + "scheme": "orcid" + } + ], + "name": "Salo, Taylor", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "The Alan Turing Institute" + } + ], + "person_or_org": { + "family_name": "Stickland", + "given_name": "Rachael", + "identifiers": [ + { + "identifier": "0000-0003-3398-4272", + "scheme": "orcid" + } + ], + "name": "Stickland, Rachael", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "University of Geneva" + } + ], + "person_or_org": { + "family_name": "Tan", + "given_name": "Mi Xue", + "identifiers": [ + { + "identifier": "0000-0002-8214-2146", + "scheme": "orcid" + } + ], + "name": "Tan, Mi Xue", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "01a28zg77", + "name": "Basque Center on Cognition, Brain and Language" + } + ], + "person_or_org": { + "family_name": "Uru\u00f1uela", + "given_name": "Eneko", + "identifiers": [ + { + "identifier": "0000-0001-6849-9088", + "scheme": "orcid" + } + ], + "name": "Uru\u00f1uela, Eneko", + "type": "personal" + } + } ], "access_right": "open" } From 6b5fe5aed3f98e56ced9ee823f6a41b9f59199ea Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 16:57:28 +0200 Subject: [PATCH 04/20] Add @maestroque as a contributor --- .all-contributorsrc | 14 ++++++++++++++ README.md | 3 ++- 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 92a3dfb..a09d3ac 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -89,6 +89,20 @@ "contributions": [ "code" ] + }, + { + "login": "maestroque", + "name": "George Kikas", + "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", + "profile": "https://github.com/maestroque", + "contributions": [ + "bug", + "code", + "ideas", + "infra", + "review", + "test" + ] } ] } diff --git a/README.md b/README.md index 489b3f7..af8ff91 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-8-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -63,6 +63,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Mi-Xue Tan
Mi-Xue Tan
💻 📓 🔌 Eneko Uruñuela
Eneko Uruñuela
🚇 xl624
xl624
💻 + George Kikas
George Kikas
🐛 💻 🤔 🚇 👀 ⚠️ From 8daf87a430aac1180a33db78951cc1d049dc2242 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 16:58:25 +0200 Subject: [PATCH 05/20] Add @raystick as a contributor --- .all-contributorsrc | 9 +++++++++ README.md | 5 ++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index a09d3ac..7ac9912 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -103,6 +103,15 @@ "review", "test" ] + }, + { + "login": "RayStick", + "name": "Rachael Stickland", + "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", + "profile": "https://github.com/RayStick", + "contributions": [ + "doc" + ] } ] } diff --git a/README.md b/README.md index af8ff91..2d7b97e 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-8-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-9-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -65,6 +65,9 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d xl624
xl624
💻 George Kikas
George Kikas
🐛 💻 🤔 🚇 👀 ⚠️ + + Rachael Stickland
Rachael Stickland
📖 + From d48a9a8bcfc5e0e6aafe402a76b3afd455c6e218 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 16:59:03 +0200 Subject: [PATCH 06/20] Add @afni-dglen as a contributor --- .all-contributorsrc | 10 ++++++++++ README.md | 3 ++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 7ac9912..a6dcb72 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -112,6 +112,16 @@ "contributions": [ "doc" ] + }, + { + "login": "afni-dglen", + "name": "Daniel Glen", + "avatar_url": "https://avatars.githubusercontent.com/u/10454715?v=4", + "profile": "https://github.com/afni-dglen", + "contributions": [ + "bug", + "code" + ] } ] } diff --git a/README.md b/README.md index 2d7b97e..865a388 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-9-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -67,6 +67,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Rachael Stickland
Rachael Stickland
📖 + Daniel Glen
Daniel Glen
🐛 💻 From 955f88f35598837ec4441bf39d0c685dbad0285d Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 16:59:16 +0200 Subject: [PATCH 07/20] Add @raystick as a contributor --- .all-contributorsrc | 4 +++- README.md | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index a6dcb72..54decf8 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -110,7 +110,9 @@ "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", "profile": "https://github.com/RayStick", "contributions": [ - "doc" + "doc", + "infra", + "test" ] }, { diff --git a/README.md b/README.md index 865a388..57f57ea 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d George Kikas
George Kikas
🐛 💻 🤔 🚇 👀 ⚠️ - Rachael Stickland
Rachael Stickland
📖 + Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ Daniel Glen
Daniel Glen
🐛 💻 From bae43b0555eb629d1800cd3fcf9414bc23885f08 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:00:07 +0200 Subject: [PATCH 08/20] Add @me-pic as a contributor --- .all-contributorsrc | 10 ++++++++++ README.md | 3 ++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 54decf8..4293469 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -124,6 +124,16 @@ "bug", "code" ] + }, + { + "login": "me-pic", + "name": "Marie-Eve Picard", + "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4", + "profile": "https://github.com/me-pic", + "contributions": [ + "doc", + "review" + ] } ] } diff --git a/README.md b/README.md index 57f57ea..01ea5c9 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-11-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -68,6 +68,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ Daniel Glen
Daniel Glen
🐛 💻 + Marie-Eve Picard
Marie-Eve Picard
📖 👀 From 4a2a8e34a8189fd1924de3b61f151f9fdee8084a Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:00:28 +0200 Subject: [PATCH 09/20] Update @me-pic as a contributor --- .all-contributorsrc | 3 ++- README.md | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 4293469..ac5d7a9 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -132,7 +132,8 @@ "profile": "https://github.com/me-pic", "contributions": [ "doc", - "review" + "review", + "mentoring" ] } ] diff --git a/README.md b/README.md index 01ea5c9..5283427 100644 --- a/README.md +++ b/README.md @@ -68,7 +68,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ Daniel Glen
Daniel Glen
🐛 💻 - Marie-Eve Picard
Marie-Eve Picard
📖 👀 + Marie-Eve Picard
Marie-Eve Picard
📖 👀 🧑‍🏫 From f887e7ee044e07ab5f9a16952307aff914981e4c Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:01:20 +0200 Subject: [PATCH 10/20] Add @m-miedema as a contributor --- .all-contributorsrc | 10 ++++++++++ README.md | 3 ++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index ac5d7a9..424abb5 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -135,6 +135,16 @@ "review", "mentoring" ] + }, + { + "login": "m-miedema", + "name": "m-miedema", + "avatar_url": "https://avatars.githubusercontent.com/u/39968233?v=4", + "profile": "https://github.com/m-miedema", + "contributions": [ + "review", + "mentoring" + ] } ] } diff --git a/README.md b/README.md index 5283427..051fb50 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-11-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-12-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -69,6 +69,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ Daniel Glen
Daniel Glen
🐛 💻 Marie-Eve Picard
Marie-Eve Picard
📖 👀 🧑‍🏫 + m-miedema
m-miedema
👀 🧑‍🏫 From b275d53fcffbabd6dbc74ef6b9ff2c14e1dd6c54 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:01:26 +0200 Subject: [PATCH 11/20] Update @smoia as a contributor --- .all-contributorsrc | 5 +---- README.md | 2 +- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 424abb5..664d325 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -46,10 +46,7 @@ "avatar_url": "https://avatars.githubusercontent.com/u/35300580?v=4", "profile": "https://github.com/smoia", "contributions": [ - "review", - "code", - "infra", - "projectManagement" + "review" ] }, { diff --git a/README.md b/README.md index 051fb50..755a4e4 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Elizabeth DuPre
Elizabeth DuPre
💻 🚇 Ross Markello
Ross Markello
🐛 💻 📖 🤔 🚇 🚧 📆 👀 ⚠️ ✅ - Stefano Moia
Stefano Moia
👀 💻 🚇 📆 + Stefano Moia
Stefano Moia
👀 Taylor Salo
Taylor Salo
🚇 From 2f93e80be63521cc0a5f3a28c54052a4403e84e4 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:05:57 +0200 Subject: [PATCH 12/20] Update @smoia as a contributor --- .all-contributorsrc | 8 +++++++- README.md | 2 +- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 664d325..df86789 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -46,7 +46,13 @@ "avatar_url": "https://avatars.githubusercontent.com/u/35300580?v=4", "profile": "https://github.com/smoia", "contributions": [ - "review" + "review", + "bug", + "code", + "ideas", + "infra", + "mentoring", + "projectManagement" ] }, { diff --git a/README.md b/README.md index 755a4e4..de6b9a2 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Elizabeth DuPre
Elizabeth DuPre
💻 🚇 Ross Markello
Ross Markello
🐛 💻 📖 🤔 🚇 🚧 📆 👀 ⚠️ ✅ - Stefano Moia
Stefano Moia
👀 + Stefano Moia
Stefano Moia
👀 🐛 💻 🤔 🚇 🧑‍🏫 📆 Taylor Salo
Taylor Salo
🚇 From f306a1e6a8c15249734933e59d07d059ccc60dea Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:06:08 +0200 Subject: [PATCH 13/20] Update @afni-dglen as a contributor --- .all-contributorsrc | 3 ++- README.md | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index df86789..3874bd5 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -125,7 +125,8 @@ "profile": "https://github.com/afni-dglen", "contributions": [ "bug", - "code" + "code", + "maintenance" ] }, { diff --git a/README.md b/README.md index de6b9a2..1313684 100644 --- a/README.md +++ b/README.md @@ -67,7 +67,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ - Daniel Glen
Daniel Glen
🐛 💻 + Daniel Glen
Daniel Glen
🐛 💻 🚧 Marie-Eve Picard
Marie-Eve Picard
📖 👀 🧑‍🏫 m-miedema
m-miedema
👀 🧑‍🏫 From 2c95155e0bd806d9e6c5c748af7643c579685bb0 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:08:26 +0200 Subject: [PATCH 14/20] Update contributors --- .all-contributorsrc | 115 ++++++++++++++++++++++---------------------- 1 file changed, 58 insertions(+), 57 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 3874bd5..e6b19fe 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -22,6 +22,31 @@ "infra" ] }, + { + "login": "afni-dglen", + "name": "Daniel Glen", + "avatar_url": "https://avatars.githubusercontent.com/u/10454715?v=4", + "profile": "https://github.com/afni-dglen", + "contributions": [ + "bug", + "code", + "maintenance" + ] + }, + { + "login": "maestroque", + "name": "George Kikas", + "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", + "profile": "https://github.com/maestroque", + "contributions": [ + "bug", + "code", + "ideas", + "infra", + "review", + "test" + ] + }, { "login": "rmarkello", "name": "Ross Markello", @@ -34,12 +59,23 @@ "ideas", "infra", "maintenance", + "mentoring", "projectManagement", "review", "test", "tutorial" ] }, + { + "login": "m-miedema", + "name": "m-miedema", + "avatar_url": "https://avatars.githubusercontent.com/u/39968233?v=4", + "profile": "https://github.com/m-miedema", + "contributions": [ + "review", + "mentoring" + ] + }, { "login": "smoia", "name": "Stefano Moia", @@ -55,6 +91,17 @@ "projectManagement" ] }, + { + "login": "me-pic", + "name": "Marie-Eve Picard", + "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4", + "profile": "https://github.com/me-pic", + "contributions": [ + "doc", + "review", + "mentoring" + ] + }, { "login": "tsalo", "name": "Taylor Salo", @@ -64,6 +111,17 @@ "infra" ] }, + { + "login": "RayStick", + "name": "Rachael Stickland", + "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", + "profile": "https://github.com/RayStick", + "contributions": [ + "doc", + "infra", + "test" + ] + }, { "login": "mixue-t", "name": "Mi-Xue Tan", @@ -92,63 +150,6 @@ "contributions": [ "code" ] - }, - { - "login": "maestroque", - "name": "George Kikas", - "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", - "profile": "https://github.com/maestroque", - "contributions": [ - "bug", - "code", - "ideas", - "infra", - "review", - "test" - ] - }, - { - "login": "RayStick", - "name": "Rachael Stickland", - "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", - "profile": "https://github.com/RayStick", - "contributions": [ - "doc", - "infra", - "test" - ] - }, - { - "login": "afni-dglen", - "name": "Daniel Glen", - "avatar_url": "https://avatars.githubusercontent.com/u/10454715?v=4", - "profile": "https://github.com/afni-dglen", - "contributions": [ - "bug", - "code", - "maintenance" - ] - }, - { - "login": "me-pic", - "name": "Marie-Eve Picard", - "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4", - "profile": "https://github.com/me-pic", - "contributions": [ - "doc", - "review", - "mentoring" - ] - }, - { - "login": "m-miedema", - "name": "m-miedema", - "avatar_url": "https://avatars.githubusercontent.com/u/39968233?v=4", - "profile": "https://github.com/m-miedema", - "contributions": [ - "review", - "mentoring" - ] } ] } From ebb2adda3606af78857db4f2b3e59a835757e621 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 17:10:00 +0200 Subject: [PATCH 15/20] Update readme --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 1313684..6b6b21f 100644 --- a/README.md +++ b/README.md @@ -55,21 +55,21 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Elizabeth DuPre
Elizabeth DuPre
💻 🚇 - Ross Markello
Ross Markello
🐛 💻 📖 🤔 🚇 🚧 📆 👀 ⚠️ ✅ + Daniel Glen
Daniel Glen
🐛 💻 🚧 + George Kikas
George Kikas
🐛 💻 🤔 🚇 👀 ⚠️ + Ross Markello
Ross Markello
🐛 💻 📖 🤔 🚇 🚧 🧑‍🏫 📆 👀 ⚠️ ✅ + + + m-miedema
m-miedema
👀 🧑‍🏫 Stefano Moia
Stefano Moia
👀 🐛 💻 🤔 🚇 🧑‍🏫 📆 + Marie-Eve Picard
Marie-Eve Picard
📖 👀 🧑‍🏫 Taylor Salo
Taylor Salo
🚇 + Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ Mi-Xue Tan
Mi-Xue Tan
💻 📓 🔌 Eneko Uruñuela
Eneko Uruñuela
🚇 xl624
xl624
💻 - George Kikas
George Kikas
🐛 💻 🤔 🚇 👀 ⚠️ - - - Rachael Stickland
Rachael Stickland
📖 🚇 ⚠️ - Daniel Glen
Daniel Glen
🐛 💻 🚧 - Marie-Eve Picard
Marie-Eve Picard
📖 👀 🧑‍🏫 - m-miedema
m-miedema
👀 🧑‍🏫 From fe4a6209d12b157f74299becce281bf29e61af79 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Fri, 23 Aug 2024 09:32:28 +0200 Subject: [PATCH 16/20] The added peak type is a standard python int --- peakdet/editor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/peakdet/editor.py b/peakdet/editor.py index e3cd0ba..c4d69b8 100644 --- a/peakdet/editor.py +++ b/peakdet/editor.py @@ -161,7 +161,7 @@ def on_edit(self, xmin, xmax, *, method): if method == "insert": tmp = np.argmax(self.data.data[tmin:tmax]) if tmin != tmax else 0 - newpeak = tmin + tmp + newpeak = int(tmin + tmp) if newpeak == tmin: self.plot_signals() return From 4d9523cc0a5eca2666ded1f8c968a2c57015e343 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Tue, 27 Aug 2024 15:20:51 +0000 Subject: [PATCH 17/20] Update CHANGELOG.md [skip ci] --- CHANGELOG.md | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f640380..97aea2e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,28 @@ +# 0.5.1 (Tue Aug 27 2024) + +:tada: This release contains work from a new contributor! :tada: + +Thank you, Marie-Eve Picard ([@me-pic](https://github.com/me-pic)), for all your work! + +#### 🐛 Bug Fix + +- Fix type errors in exporting history after manually adding peaks [#79](https://github.com/physiopy/peakdet/pull/79) ([@smoia](https://github.com/smoia)) + +#### 📝 Documentation + +- Update contributors [#82](https://github.com/physiopy/peakdet/pull/82) ([@smoia](https://github.com/smoia)) + +#### 🏠 Internal + +- Add contribution [#81](https://github.com/physiopy/peakdet/pull/81) ([@me-pic](https://github.com/me-pic)) + +#### Authors: 2 + +- Marie-Eve Picard ([@me-pic](https://github.com/me-pic)) +- Stefano Moia ([@smoia](https://github.com/smoia)) + +--- + # 0.5.0 (Fri Jul 19 2024) #### 🚀 Enhancement From a2b7e8c7c2a9bdc58e74d3aa3f4d794aa97a14b5 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Wed, 9 Oct 2024 12:26:32 +0200 Subject: [PATCH 18/20] Make sure peak detection works with negative signals --- peakdet/operations.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/peakdet/operations.py b/peakdet/operations.py index 480b0c0..61dd1c0 100644 --- a/peakdet/operations.py +++ b/peakdet/operations.py @@ -144,8 +144,15 @@ def peakfind_physio(data, *, thresh=0.2, dist=None): data = utils.check_physio(data, ensure_fs=ensure_fs, copy=True) # first pass peak detection to get approximate distance between peaks cdist = data.fs // 4 if dist is None else dist - thresh = np.squeeze(np.diff(np.percentile(data, [5, 95]))) * thresh - locs, heights = signal.find_peaks(data[:], distance=cdist, height=thresh) + + # check if data is negative, if so make it all positive and continue with signal + phys_signal = data.data - data.data.min() if data.data.min() < 0 else data.data + logger.debug( + f"Negative signal detected (min = {data.data.min()}), workgin with positive signal for peak detection." + ) + + thresh = np.squeeze(np.diff(np.percentile(phys_signal, [5, 95]))) * thresh + locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=thresh) logger.debug( f"First peak detection iteration. Acquiring approximate distance between peaks (Number of peaks: {len(locs)})" ) @@ -153,7 +160,7 @@ def peakfind_physio(data, *, thresh=0.2, dist=None): # second, more thorough peak detection cdist = np.diff(locs).mean() // 2 heights = np.percentile(heights["peak_heights"], 1) - locs, heights = signal.find_peaks(data[:], distance=cdist, height=heights) + locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=heights) data._metadata["peaks"] = locs logger.debug( f"Second peak detection iteration. Acquiring more precise peak locations (Number of peaks: {len(locs)})" From e99c7059169cf01722be90b666ad6094fec302fa Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Wed, 9 Oct 2024 10:29:54 +0000 Subject: [PATCH 19/20] Update CHANGELOG.md [skip ci] --- CHANGELOG.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 97aea2e..0ea063a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,20 @@ +# 0.5.2 (Wed Oct 09 2024) + +#### 🐛 Bug Fix + +- Make sure peak detection works with negative signals [#84](https://github.com/physiopy/peakdet/pull/84) ([@smoia](https://github.com/smoia)) + +#### 🏠 Internal + +- [pre-commit.ci] pre-commit autoupdate [#75](https://github.com/physiopy/peakdet/pull/75) ([@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])) + +#### Authors: 2 + +- [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) +- Stefano Moia ([@smoia](https://github.com/smoia)) + +--- + # 0.5.1 (Tue Aug 27 2024) :tada: This release contains work from a new contributor! :tada: From 90378c651238d5168c1deb38b3471f4dd0d2c8e8 Mon Sep 17 00:00:00 2001 From: Stefano Moia Date: Wed, 30 Oct 2024 20:39:03 +0100 Subject: [PATCH 20/20] Update peakdet/operations.py --- peakdet/operations.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/peakdet/operations.py b/peakdet/operations.py index 61dd1c0..36d0511 100644 --- a/peakdet/operations.py +++ b/peakdet/operations.py @@ -148,7 +148,7 @@ def peakfind_physio(data, *, thresh=0.2, dist=None): # check if data is negative, if so make it all positive and continue with signal phys_signal = data.data - data.data.min() if data.data.min() < 0 else data.data logger.debug( - f"Negative signal detected (min = {data.data.min()}), workgin with positive signal for peak detection." + f"Negative signal detected (min = {data.data.min()}), working with positive signal for peak detection." ) thresh = np.squeeze(np.diff(np.percentile(phys_signal, [5, 95]))) * thresh