From bc1a603791cfecc429a3072b850dfabd7ae4c289 Mon Sep 17 00:00:00 2001 From: Werner Van Geit Date: Tue, 22 Aug 2023 11:18:44 +0200 Subject: [PATCH 1/3] Adding zenodo banner --- .zenodo.json | 48 +++++++++++++++++++++++++++ README.rst | 94 +++++++++++++++++++++++----------------------------- 2 files changed, 90 insertions(+), 52 deletions(-) create mode 100644 .zenodo.json diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 00000000..87b05270 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,48 @@ +{ + "title" : "BluePyOpt", + "license": "LGPLv3", + "upload_type": "software", + "description": "The Blue Brain Python Optimisation Library (BluePyOpt) is an extensible framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures.", + "creators": [ + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Van Geit, Werner", + "orcid": "0000-0002-2915-720X" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Gevaert, Michael", + "orcid": "0000-0002-7547-3297" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Damart, Tanguy", + "orcid": "0000-0003-2175-7304" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Rössert, Christian", + "orcid": "0000-0002-4839-2424" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Courcol, Jean-Denis", + "orcid": "0000-0002-9351-1461" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Chindemi, Guiseppe", + "orcid": "0000-0001-6872-2366" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Jaquier, Aurélien", + "orcid": "0000-0001-6202-6175" + }, + { + "affiliation": "Blue Brain Project, EPFL", + "name": "Muller, Eilif", + "orcid": "0000-0003-4309-8266" + } + ] +} diff --git a/README.rst b/README.rst index f4cb40a8..1692d408 100644 --- a/README.rst +++ b/README.rst @@ -3,59 +3,22 @@ BluePyOpt ========= -.. raw:: html - - - - - - - - - - - - - - - - - - - - - - - - - - -
Latest Release - - latest release - -
Documentation - - latest documentation - -
License - - license - -
Build Status - - Actions build status - -
Coverage - - coverage - -
Gitter - - -
++----------------+------------+ +| Latest Release | |pypi| | ++----------------+------------+ +| Documentation | |docs| | ++----------------+------------+ +| License | |license| | ++----------------+------------+ +| Build Status | |build| | ++----------------+------------+ +| Coverage | |coverage| | ++----------------+------------+ +| Gitter | |gitter| | ++----------------+------------+ +| Zenodo | |zenodo| | ++----------------+------------+ Introduction @@ -229,6 +192,33 @@ Copyright (c) 2016-2022 Blue Brain Project/EPFL The index.rst location is used for the docs README; index.rst also defined an end-marker, to skip content after the marker 'substitutions'. +.. |pypi| image:: https://img.shields.io/pypi/v/bluepyopt.svg + :target: https://pypi.org/project/bluepyopt/ + :alt: latest release + +.. |docs| image:: https://readthedocs.org/projects/bluepyopt/badge/?version=latest + :target: https://bluepyopt.readthedocs.io/ + :alt: latest documentation + +.. |license| image:: https://img.shields.io/pypi/l/bluepyopt.svg + :target: https://github.com/BlueBrain/bluepyopt/blob/main/LICENSE.txt + :alt: license + +.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=main + :target: https://github.com/BlueBrain/BluePyOpt/actions + :alt: actions build status + +.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=main + :target: https://codecov.io/gh/BlueBrain/bluepyopt + :alt: coverage + +.. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg + :target: https://gitter.im/BlueBrain/blueptopt + :alt: Join the chat at https://gitter.im/BlueBrain/BluePyOpt + +.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8135890.svg + :target: https://doi.org/10.5281/zenodo.8135890 + .. substitutions .. |banner| image:: docs/source/logo/BluePyOptBanner.png .. |landscape_example| image:: examples/simplecell/figures/landscape_example.png From d9b697a668c26ac9a8858a26280cc5a6face8648 Mon Sep 17 00:00:00 2001 From: Werner Van Geit Date: Tue, 22 Aug 2023 11:28:39 +0200 Subject: [PATCH 2/3] Fix build badge --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 1692d408..df747685 100644 --- a/README.rst +++ b/README.rst @@ -208,7 +208,7 @@ Copyright (c) 2016-2022 Blue Brain Project/EPFL :target: https://github.com/BlueBrain/BluePyOpt/actions :alt: actions build status -.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=main +.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master :target: https://codecov.io/gh/BlueBrain/bluepyopt :alt: coverage From 8696e4be21a2466c6026c51fdfe3a10f13dca601 Mon Sep 17 00:00:00 2001 From: Werner Van Geit Date: Tue, 22 Aug 2023 11:30:12 +0200 Subject: [PATCH 3/3] Fix build badge again --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index df747685..8c124b2f 100644 --- a/README.rst +++ b/README.rst @@ -201,10 +201,10 @@ Copyright (c) 2016-2022 Blue Brain Project/EPFL :alt: latest documentation .. |license| image:: https://img.shields.io/pypi/l/bluepyopt.svg - :target: https://github.com/BlueBrain/bluepyopt/blob/main/LICENSE.txt + :target: https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt :alt: license -.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=main +.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master :target: https://github.com/BlueBrain/BluePyOpt/actions :alt: actions build status