From 35822051148ae2042ebd450c207170dd31b0291a Mon Sep 17 00:00:00 2001 From: Michael Denker Date: Thu, 8 Aug 2024 01:02:32 +0200 Subject: [PATCH] Housekeeping release for 0.2.0 (#78) * Update citaion * Update authors and zenodo * Update F.M. * Drafted release notes * Add release notes to TOC * Added codemeta.json for KG * Indicate version 0.1.0 as prior version * Corrected zenodo info * Update version numbers * Update .zenodo.json Co-authored-by: Cosimo Lupo <36234686+cosimolupo@users.noreply.github.com> * Update doc/source/authors.rst Co-authored-by: Cosimo Lupo <36234686+cosimolupo@users.noreply.github.com> * Update doc/source/authors.rst Co-authored-by: Cosimo Lupo <36234686+cosimolupo@users.noreply.github.com> * Fixed typos * Fixed typos * Updated release notes * Typos in release notes * Corrected zenodo entries for conformity * Corrected zenodo entries for conformity * Correct EBRAINS mirror --------- Co-authored-by: Cosimo Lupo <36234686+cosimolupo@users.noreply.github.com> --- .github/workflows/ebrains.yml | 6 +- .zenodo.json | 83 ++++++++++----- VERSION | 3 +- cobrawap/__init__.py | 2 +- codemeta.json | 186 ++++++++++++++++++++++++++++++++++ doc/source/authors.rst | 2 + doc/source/citation.rst | 3 +- doc/source/index.rst | 1 + doc/source/release_notes.rst | 51 ++++++++++ pyproject.toml | 2 +- 10 files changed, 306 insertions(+), 33 deletions(-) create mode 100644 codemeta.json create mode 100644 doc/source/release_notes.rst diff --git a/.github/workflows/ebrains.yml b/.github/workflows/ebrains.yml index 23545168..35162124 100644 --- a/.github/workflows/ebrains.yml +++ b/.github/workflows/ebrains.yml @@ -8,12 +8,12 @@ on: jobs: sync_to_ebrains: runs-on: ubuntu-latest - if: ${{ github.repository_owner == 'INM-6' }} + if: ${{ github.repository_owner == 'NeuralEnsemble' }} steps: - name: syncmaster uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 with: - source_repo: "INM-6/cobrawap" + source_repo: "NeuralEnsemble/cobrawap" source_branch: "master" destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/neuralensemble/cobrawap.git" destination_branch: "master" @@ -21,7 +21,7 @@ jobs: - name: synctags uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 with: - source_repo: "INM-6/cobrawap" + source_repo: "NeuralEnsemble/cobrawap" source_branch: "refs/tags/*" destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/neuralensemble/cobrawap.git" destination_branch: "refs/tags/*" diff --git a/.zenodo.json b/.zenodo.json index 1f9cdd65..986f4bcf 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,94 +2,106 @@ "creators": [ { "orcid": "0000-0001-7373-5962", - "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany", + "affiliation": "Department of Psychology and Center for Data Science, New York University, New York, USA", "name": "Gutzen, Robin", - "role": "Project member" + "type": "ProjectMember" }, { - "orcid": "0000-0001-7079-5724", + "orcid": "0000-0002-2651-1277", "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", - "name": "De Bonis, Giulia", - "role": "Project member" + "name": "Lupo, Cosimo", + "type": "ProjectMember" }, { - "orcid": "0000-0003-3488-0088", - "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland", - "name": "De Luca, Chiara", - "role": "Project member" + "orcid": "0000-0002-5933-2873", + "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", + "name": "Marmoreo, Federico", + "type": "ProjectMember" + }, + { + "orcid": "0000-0001-7079-5724", + "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", + "name": "De Bonis, Giulia", + "type": "ProjectMember" } ], "contributors": [ + { + "orcid": "0000-0003-3488-0088", + "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland", + "name": "De Luca, Chiara", + "type": "ProjectMember" + }, { "orcid": "0000-0003-0682-1232", "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", "name": "Pastorelli, Elena", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-9958-2551", "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", "name": "Capone, Cristiano", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-8489-0076", "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy", "name": "Allegra Mascaro, Anna Letizia", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-9605-5852", "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy", "name": "Resta, Francesco", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-8306-0759", "affiliation": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain", "name": "Manasanch, Arnau", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-0675-3981", "affiliation": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, Italy", "name": "Pavone, Francesco Saverio", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-8437-9083", "affiliation": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain", "name": "Sanchez-Vives, Maria V.", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0002-2356-4509", "affiliation": "Natl. Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy", "name": "Mattia, Maurizio", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0003-2829-2220", - "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany", + "affiliation": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany", "name": "Grün, Sonja", - "role": "Project member" + "type": "ProjectMember" }, { "orcid": "0000-0003-1255-7300", - "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany", + "affiliation": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany", "name": "Denker, Michael", - "role": "Project leader" + "type": "ProjectLeader" }, { "orcid": "0000-0003-1937-6086", "affiliation": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy", "name": "Paolucci, Pier Stanislao", - "role": "Project leader" + "type": "ProjectLeader" } ], - "title": "Cobrawap 0.1.0", + "title": "Cobrawap 0.2.0", "keywords": [ "neuroscience", @@ -99,22 +111,43 @@ ], "license": { - "id": "GNU General Public License v3.0 or later" + "id": "GPL-3.0-or-later" }, "related_identifiers": [ + { + "scheme": "doi", + "identifier": "10.5281/zenodo.10198748", + "relation": "isVersionOf", + "resource_type": "software" + }, + + { + "scheme": "doi", + "identifier": "10.5281/zenodo.13134351", + "relation": "isNewVersionOf", + "resource_type": "software" + }, + { "scheme": "doi", "identifier": "10.48550/arXiv.2211.08527", "relation": "isDocumentedBy", "resource_type": "publication-preprint" + }, + + { + "scheme": "doi", + "identifier": "10.1016/j.crmeth.2023.100681", + "relation": "isDocumentedBy", + "resource_type": "publication-article" } ], "grants": [ {"id": "785907"}, {"id": "945539"}, - {"id": "MUR CUP B51E22000150006"} + {"id": "101147319"} ], "upload_type": "software" diff --git a/VERSION b/VERSION index 627f9b54..0ea3a944 100644 --- a/VERSION +++ b/VERSION @@ -1,2 +1 @@ -0.1.1 - +0.2.0 diff --git a/cobrawap/__init__.py b/cobrawap/__init__.py index a2d00ad6..e0b5366e 100644 --- a/cobrawap/__init__.py +++ b/cobrawap/__init__.py @@ -1,2 +1,2 @@ -__version__ = '0.1.0' +__version__ = '0.2.0' __author__ = 'Cobrawap authors and contributors ' diff --git a/codemeta.json b/codemeta.json new file mode 100644 index 00000000..f1220652 --- /dev/null +++ b/codemeta.json @@ -0,0 +1,186 @@ +{ + "@context": "https://w3id.org/codemeta/3.0", + "type": "SoftwareSourceCode", + "applicationCategory": "data analysis", + "author": [ + { + "id": "http://orcid.org/0000-0001-7373-5962", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Department of Psychology and Center for Data Science, New York University, New York, USA" + }, + "familyName": "Gutzen", + "givenName": "Robin" + }, + { + "id": "http://orcid.org/0000-0002-2651-1277", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "Lupo", + "givenName": "Cosimo" + }, + { + "id": "http://orcid.org/0000-0002-5933-2873", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "Marmoreo", + "givenName": "Federico" + }, + { + "id": "http://orcid.org/0000-0001-7079-5724", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "De Bonis", + "givenName": "Giulia" + } + ], + "codeRepository": "git+https://github.com/NeuralEnsemble/cobrawap/", + "contributor": [ + { + "id": "http://orcid.org/0000-0003-3488-0088", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland" + }, + "familyName": "De Luca", + "givenName": "Chiara" + }, + { + "id": "http://orcid.org/0000-0003-0682-1232", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "Pastorelli", + "givenName": "Elena" + }, + { + "id": "http://orcid.org/0000-0002-9958-2551", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "Capone", + "givenName": "Cristiano" + }, + { + "id": "http://orcid.org/0000-0002-8489-0076", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy" + }, + "familyName": "Allegra Mascaro", + "givenName": "Anna Letizia" + }, + { + "id": "http://orcid.org/0000-0002-9605-5852", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy" + }, + "familyName": "Resta", + "givenName": "Francesco" + }, + { + "id": "http://orcid.org/0000-0002-8306-0759", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain" + }, + "familyName": "Manasanch", + "givenName": "Arnau" + }, + { + "id": "http://orcid.org/0000-0002-0675-3981", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, Italy" + }, + "familyName": "Pavone", + "givenName": "Francesco Saverio" + }, + { + "id": "http://orcid.org/0000-0002-8437-9083", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain" + }, + "familyName": "Sanchez-Vives", + "givenName": "Maria V." + }, + { + "id": "http://orcid.org/0000-0002-2356-4509", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Natl. Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy" + }, + "familyName": "Mattia", + "givenName": "Maurizio" + }, + { + "id": "http://orcid.org/0000-0003-2829-2220", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany" + }, + "familyName": "Grün", + "givenName": "Sonja" + }, + { + "id": "http://orcid.org/0000-0003-1255-7300", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Institute for Advanced Simulation (IAS-6), Jülich Research Centre, Jülich, Germany" + }, + "familyName": "Denker", + "givenName": "Michael" + }, + { + "id": "http://orcid.org/0000-0003-1937-6086", + "type": "Person", + "affiliation": { + "type": "Organization", + "name": "Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy" + }, + "familyName": "Paolucci", + "givenName": "Pier Stanislao" + } + ], + "dateModified": "2024-07-24", + "datePublished": "2023-11-23", + "description": "Cobrawap is an adaptable and reusable analysis pipeline for the multi-scale, multi-methodology analysis of cortical wave activity. The pipeline ingests data from heterogeneous sources of spatially organized neuronal activity, such as ECoG or calcium imaging recordings, as well as the outcome of numerical simulations. The pipeline returns statistical measures to quantify the dynamic wave-like activity patterns found in the data.", + "downloadUrl": "https://pypi.org/project/cobrawap", + "identifier": "10.5281/zenodo.10198748; RRID:SCR_022966", + "keywords": "neuroscience; neurophysiology; statistics; data-analysis", + "license": "https://spdx.org/licenses/GPL-3.0-or-later", + "name": "Collaborative Brain Wave Analysis Pipeline (Cobrawap)", + "programmingLanguage": "Python", + "relatedLink": "https://cobrawap.readthedocs.io", + "releaseNotes": "https://cobrawap.readthedocs.io/en/latest/release_notes.html", + "version": "0.2.0", + "developmentStatus": "active", + "funding": "European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreements No. 945539 (Human Brain Project SGA3) and No. 785907 (Human Brain Project SGA2); the European Commission NextGeneration EU through grant MUR CUP B51E22000150006 (EBRAINS-Italy IR00011 PNRR); European Union’s Horizon Europe Programme under the Specific Grant Agreement No. 101147319 (EBRAINS 2.0 Project)", + "issueTracker": "https://github.com/NeuralEnsemble/cobrawap/issues", + "referencePublication": "https://doi.org/10.1016/j.crmeth.2023.100681" +} \ No newline at end of file diff --git a/doc/source/authors.rst b/doc/source/authors.rst index d2d8f960..ec690041 100644 --- a/doc/source/authors.rst +++ b/doc/source/authors.rst @@ -20,6 +20,8 @@ contribution, and may not be the current affiliation of a contributor. * Sonja Grün (orcid: 0000-0003-2829-2220) [1, 2] * Pier Stanislao Paolucci (orcid: 0000-0003-1937-6086) [3] * Michael Denker (orcid: 0000-0003-1255-7300) [1] +* Cosimo Lupo (orcid: 0000-0002-2651-1277) [3] +* Federico Marmoreo (orcid: 0000-0002-5933-2873) [3] 1. Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany 2. Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany diff --git a/doc/source/citation.rst b/doc/source/citation.rst index 70642fb9..55b40805 100644 --- a/doc/source/citation.rst +++ b/doc/source/citation.rst @@ -12,4 +12,5 @@ To cite a specific version of Cobrawap please see version-specific DOIs at: To cite Cobrawap, please use: -Gutzen, R., De Bonis, G., De Luca, C., Pastorelli, E., Capone, C., Allegra Mascaro, A. L., Resta, F., Manasanch, A., Pavone, F. S., Sanchez-Vives, M. V., Mattia, M., Grün, S., Paolucci, P. S., & Denker, M. (2022). *Comparing apples to apples—Using a modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets*. arXiv:2211.08527. `https://doi.org/10.48550/arXiv.2211.08527 `_ +Gutzen, R., De Bonis, G., De Luca, C., Pastorelli, E., Capone, C., Allegra Mascaro, A. L., Resta, F., Manasanch, A., Pavone, F. S., Sanchez-Vives, M. V., Mattia, M., Grün, S., Paolucci, P. S., & Denker, M. (2022). *A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets*. Cell Reports Methods 4, 100681. `https://doi.org/10.1016/j.crmeth.2023.100681 `_ + diff --git a/doc/source/index.rst b/doc/source/index.rst index b0c8b57c..0ed0a134 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -5,6 +5,7 @@ pipeline command_line_interface pipeline_stages + release_notes acknowledgments authors citation diff --git a/doc/source/release_notes.rst b/doc/source/release_notes.rst new file mode 100644 index 00000000..8331f845 --- /dev/null +++ b/doc/source/release_notes.rst @@ -0,0 +1,51 @@ +************* +Release Notes +************* + + +Release 0.2.0 +============= +New functionality and features +------------------------------ +* Ability to plot complete signal ranges using `TSTART` and `TSTOP` set to `None` (`#48 `_) +* New default value `None` for `MAXIMA_THRESHOLD_WINDOW` to indicate that the complete signal duration is considered (`#49 `_) +* Added additional keyword arguments to `cobrawap` command (`#76 `_) + +Bug fixes +--------- +* Fixed bug related to updating of AnalogSignal names (`#67 `_) +* Fixed issue where `roi_selection` and `spatial_derivative` incorrectly handled boolean arguments (`#65 `_) +* Fixed issue related to directly specifying a stage from the cobrawap interface (`#70 `_) +* Fixed issue with cyclic boundary conditions during phase convolution (`#66 `_) + +Documentation +------------- +* Updated `README` information (`#59 `_), (`#74 `_) + +Other changes +------------- +* Automated package distribution to PyPI (`#62 `_) + + +Release 0.1.1 +============= +Documentation +------------- +* Added help statement for CLI client + +Bug fixes +--------- +* Fixed install by disallowing Snakemake versions >=8.0.0, which are missing subworkflow support + +Selected dependency changes +--------------------------- +* snakemake >= 7.10.0, < 8.0.0 + + +Release 0.1.0 +============= +Initial release of Cobrawap accompanying the manuscript + +Gutzen, R., De Bonis, G., De Luca, C., Pastorelli, E., Capone, C., Allegra Mascaro, A. L., Resta, F., Manasanch, A., Pavone, F. S., Sanchez-Vives, M. V., Mattia, M., Grün, S., Paolucci, P. S., & Denker, M. (2022). *A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets*. Cell Reports Methods 4, 100681. `https://doi.org/10.1016/j.crmeth.2023.100681 `_ + + diff --git a/pyproject.toml b/pyproject.toml index 107715e1..42893cbc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "cobrawap" description = "Collaborative Brain Wave Analysis Pipeline (Cobrawap)" -version = "0.1.1" +version = "0.2.0" readme = "README.rst" authors = [ { name = "Cobrawap authors and contributors", email = "robin.gutzen@outlook.com" }