diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3f73de1..6ab384f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -9,21 +9,25 @@ on: jobs: call-test-workflow: - uses: BlueBrain/BluePyOpt/.github/workflows/test.yml@master + uses: openbraininstitute/BluePyOpt/.github/workflows/test.yml@master build-tag-n-publish: name: Build, tag and publish on PyPI runs-on: ubuntu-latest needs: call-test-workflow + environment: # needed for pypi publication + name: pypi + url: https://pypi.org/p/bluepyopt permissions: contents: write + id-token: write # needed for pypi publication steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10 + - name: Set up Python 3.12 uses: actions/setup-python@v4 with: - python-version: "3.10" + python-version: "3.12" - name: Bump version and push tag uses: anothrNick/github-tag-action@1.64.0 @@ -54,7 +58,4 @@ jobs: generate_release_notes: true - name: Publish package to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - user: __token__ - password: ${{ secrets.PYPI_PASSWORD }} + uses: pypa/gh-action-pypi-publish@release/v1.12 diff --git a/.github/workflows/keep-alive.yml b/.github/workflows/keep-alive.yml index 493b8ee..071f28d 100644 --- a/.github/workflows/keep-alive.yml +++ b/.github/workflows/keep-alive.yml @@ -7,7 +7,7 @@ on: jobs: call-test-workflow: - uses: BlueBrain/BluePyOpt/.github/workflows/test.yml@master + uses: openbraininstitute/BluePyOpt/.github/workflows/test.yml@master keep-workflow-alive: name: Keep workflow alive diff --git a/.github/workflows/mirror-ebrains.yml b/.github/workflows/mirror-ebrains.yml deleted file mode 100644 index 0f47f7e..0000000 --- a/.github/workflows/mirror-ebrains.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: Mirror to Ebrains - -on: - push: - branches: [ master ] - -jobs: - to_ebrains: - runs-on: ubuntu-latest - steps: - - name: syncmaster - uses: wei/git-sync@v3 - with: - source_repo: "BlueBrain/BluePyOpt" - source_branch: "master" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/BlueBrain/bluepyopt.git" - destination_branch: "master" - - name: synctags - uses: wei/git-sync@v3 - with: - source_repo: "BlueBrain/BluePyOpt" - source_branch: "refs/tags/*" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/BlueBrain/bluepyopt.git" - destination_branch: "refs/tags/*" \ No newline at end of file diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a0414e0..f4dde8c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,14 +14,14 @@ jobs: os: [ubuntu-latest] python-version: ["3.9", "3.10", "3.11", "3.12"] include: - - os: macos-12 - python-version: "3.10" + - os: macos-13 + python-version: "3.12" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} @@ -34,7 +34,7 @@ jobs: run: tox - name: "Upload coverage to Codecov" - uses: codecov/codecov-action@v4 + uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: false diff --git a/README.rst b/README.rst index 9c97fca..c33e195 100644 --- a/README.rst +++ b/README.rst @@ -62,21 +62,21 @@ When you use the BluePyOpt software or method for your research, we ask you to c Publications that use or mention BluePyOpt ========================================== -The list of publications that use or mention BluePyOpt can be found on `the github wiki page `_. +The list of publications that use or mention BluePyOpt can be found on `the github wiki page `_. Support ======= -We are providing support using a chat channel on `Gitter `_, or the `Github discussion page `_. +We are providing support using a chat channel on `Gitter `_, or the `Github discussion page `_. News ==== - 2023/01: BluePyOpt now supports the Arbor simulator. - 2022/12: Support for LFPy models merged into master. Examples and preprint: https://github.com/alejoe91/multimodalfitting, https://www.biorxiv.org/content/10.1101/2022.08.03.502468v1.full -- 2022/12: BluePyOpt now has the ability to write out NeuroML files: https://github.com/BlueBrain/BluePyOpt/tree/master/bluepyopt/neuroml +- 2022/12: BluePyOpt now has the ability to write out NeuroML files: https://github.com/openbraininstitute/BluePyOpt/tree/master/bluepyopt/neuroml - 2021/08/30: BluePyOpt dropped Python 2.7 support. - 2017/01/04: BluePyOpt is now considered compatible with Python 3.6+. - 2016/11/10: BluePyOpt now supports NEURON point processes. This means we can fit parameters of Adex/GIF/Izhikevich models, and also synapse models. -- 2016/06/14: Started a wiki: https://github.com/BlueBrain/BluePyOpt/wiki +- 2016/06/14: Started a wiki: https://github.com/openbraininstitute/BluePyOpt/wiki - 2016/06/07: The BluePyOpt paper was published in Frontiers in Neuroinformatics (for link, see above) - 2016/05/03: The API documentation was moved to `ReadTheDocs `_ - 2016/04/20: BluePyOpt now contains the code of the IBEA selector, no need to install a BBP-specific version of DEAP anymore @@ -88,7 +88,7 @@ Requirements * `Python 3.9+ `_ * `Pip `_ (installed by default in newer versions of Python) * `Neuron 7.4+ `_ (compiled with Python support) -* `eFEL eFeature Extraction Library `_ (automatically installed by pip) +* `eFEL eFeature Extraction Library `_ (automatically installed by pip) * `Numpy `_ (automatically installed by pip) * `Pandas `_ (automatically installed by pip) * The instruction below are written assuming you have access to a command shell on Linux / UNIX / MacOSX / Cygwin @@ -116,7 +116,7 @@ Cloud infrastructure We provide instructions on how to set up an optimisation environment on cloud infrastructure or cluster computers -`here `_ +`here `_ Quick Start =========== @@ -127,8 +127,8 @@ Single compartmental model An iPython notebook with an introductory optimisation of a one compartmental model with 2 HH channels can be found at -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb (NEURON) -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell_arbor.ipynb (Arbor) +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb (NEURON) +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/simplecell/simplecell_arbor.ipynb (Arbor) |landscape_example| @@ -139,39 +139,39 @@ https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecel Neocortical Layer 5 Pyramidal Cell ---------------------------------- Scripts for a more complex neocortical L5PC are in -`this directory `__ +`this directory `__ With a notebook: -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb (NEURON) -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC_arbor.ipynb (Arbor) +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb (NEURON) +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/l5pc/L5PC_arbor.ipynb (Arbor) Thalamocortical Cells --------------------- Scripts for 2 thalamocortical cell types are in -`this directory `__ +`this directory `__ With a notebook: -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/thalamocortical-cell/thalamocortical-cell_opt.ipynb +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/thalamocortical-cell/thalamocortical-cell_opt.ipynb Tsodyks-Markram Model of Short-Term Plasticity ---------------------------------------------- Scripts for 2 version of fitting the Tsodyks-Markram model to synaptic traces are in -`this directory `__ +`this directory `__ With 2 notebooks: -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp.ipynb -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp_multiplefreqs.ipynb +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp.ipynb +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/tsodyksmarkramstp/tsodyksmarkramstp_multiplefreqs.ipynb Exporting cell in neuroml format -------------------------------- An iPython notebook showing how to export a BluePyOpt cell in the neuroml format, how to create a LEMS simulation, and how to run the LEMS simulation with the neuroml cell can be found at: -https://github.com/BlueBrain/BluePyOpt/blob/master/examples/neuroml/neuroml.ipynb +https://github.com/openbraininstitute/BluePyOpt/blob/master/examples/neuroml/neuroml.ipynb API documentation @@ -185,6 +185,8 @@ This project/research was supported by funding to the Blue Brain Project, a rese Copyright (c) 2016-2024 Blue Brain Project/EPFL +Copyright (c) 2025 Open Brain Institute + .. The following image is also defined in the index.rst file, as the relative path is different, depending from where it is sourced. @@ -201,20 +203,20 @@ Copyright (c) 2016-2024 Blue Brain Project/EPFL :alt: latest documentation .. |license| image:: https://img.shields.io/pypi/l/bluepyopt.svg - :target: https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt + :target: https://github.com/openbraininstitute/bluepyopt/blob/master/LICENSE.txt :alt: license -.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master - :target: https://github.com/BlueBrain/BluePyOpt/actions +.. |build| image:: https://github.com/openbraininstitute/BluePyOpt/workflows/Build/badge.svg?branch=master + :target: https://github.com/openbraininstitute/BluePyOpt/actions :alt: actions build status -.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master - :target: https://codecov.io/gh/BlueBrain/bluepyopt +.. |coverage| image:: https://codecov.io/github/openbraininstitute/BluePyOpt/coverage.svg?branch=master + :target: https://codecov.io/gh/openbraininstitute/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 + :target: https://gitter.im/openbraininstitute/blueptopt + :alt: Join the chat at https://gitter.im/openbraininstitute/BluePyOpt .. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8135890.svg :target: https://doi.org/10.5281/zenodo.8135890 diff --git a/pyproject.toml b/pyproject.toml index e289b1f..9a317df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,10 +47,10 @@ lfpy = ["LFPy>=2.3"] arbor = ["arbor>=0.10"] [project.urls] -Homepage = "https://github.com/BlueBrain/BluePyOpt" -Source = "https://github.com/BlueBrain/BluePyOpt" -Repository = "https://github.com/BlueBrain/BluePyOpt.git" -Tracker = "https://github.com/BlueBrain/BluePyOpt/issues" +Homepage = "https://github.com/openbraininstitute/BluePyOpt" +Source = "https://github.com/openbraininstitute/BluePyOpt" +Repository = "https://github.com/openbraininstitute/BluePyOpt.git" +Tracker = "https://github.com/openbraininstitute/BluePyOpt/issues" Documentation = "https://bluepyopt.readthedocs.io/en/latest" [project.scripts]