bluecellulab 1.0.2__tar.gz → 1.1.0__tar.gz

bluecellulab-1.1.0/.github/workflows/release.yml

@@ -0,0 +1,60 @@
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  call-test-workflow:
+    uses: BlueBrain/BlueCelluLab/.github/workflows/test.yml@main
+
+  build-and-publish:
+    name: Build, publish on PyPI and make a GitHub release
+    runs-on: ubuntu-latest
+    needs: call-test-workflow
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Fetch the tag, if any. If not tagged, create a patch tag
+        uses: anothrNick/github-tag-action@1.64.0
+        if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+        id: tag
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          WITH_V: false
+          DEFAULT_BUMP: patch
+
+
+      - name: Build a source tarball and wheel
+        run: |
+            pip install wheel
+            python setup.py sdist bdist_wheel
+
+      - name: Get and store tag from 'Bump version and push tag' step
+        if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+        run: echo "TAG_NAME=${{ steps.tag.outputs.new_tag }}" >> $GITHUB_ENV
+      - name: Get and store tag from triggered tag push
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        run: echo "TAG_NAME=${{ github.ref_name }}" >> $GITHUB_ENV
+
+      - name: Release
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: ${{ env.TAG_NAME }}
+          name: ${{ env.TAG_NAME }}
+          generate_release_notes: true
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

{bluecellulab-1.0.2 → bluecellulab-1.1.0}/.github/workflows/test.yml

@@ -2,6 +2,8 @@ name: CI Testing
 
 on:
     pull_request:
+    # allows this workflow to be reusable (e.g. by the build workflow)
+    workflow_call:
     push:
       branches:
         - main

bluecellulab-1.1.0/.zenodo.json

@@ -0,0 +1,32 @@
+{
+  "title" : "BlueCelluLab",
+  "license": "Apache-2.0",
+  "upload_type": "software",
+  "description": "BlueCelluLab is designed to do simulation and experiment on a single cell or a group of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally.",
+  "creators": [
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Van Geit, Werner",
+      "orcid": "0000-0002-2915-720X"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Tuncel, Anil",
+      "orcid": "0000-0003-0317-2556"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Gevaert, Mike"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Torben-Nielsen, Benjamin",
+      "orcid": "0000-0003-4203-9942"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Muller, Eilif",
+      "orcid": "0000-0003-4309-8266"
+    }
+  ]
+}

{bluecellulab-1.0.2 → bluecellulab-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.0.2
+Version: 1.1.0
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
@@ -33,6 +33,8 @@ BlueCelluLab
 +----------------+------------+
 | Gitter         | |gitter|   |
 +----------------+------------+
+| Citation       | |zenodo|   |
++----------------+------------+
 
 
 BlueCelluLab is designed to do simulation and experiment on a single cell or a group of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally.
@@ -44,7 +46,15 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 
 .. code-block:: 
 
-    @article {TBD Zenodo}
+    @software{bluecellulab_zenodo,
+      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      title        = {BlueCelluLab},
+      month        = jul,
+      year         = 2023,
+      publisher    = {Zenodo},
+      doi          = {10.5281/zenodo.8113483},
+      url          = {https://doi.org/10.5281/zenodo.8113483}
+    }
 
 Support
 =======
@@ -77,7 +87,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     from bluecellulab import Simulation
 
     cell = create_ball_stick()
-    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=1.5)
+    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=0.1)
     sim = Simulation()
     sim.add_cell(cell)
 
@@ -85,7 +95,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     time, voltage = cell.get_time(), cell.get_soma_voltage()
     # plotting time and voltage ...
 
-.. image:: docs/images/voltage-readme.png
+.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
    :alt: Voltage plot
 
 Tutorial
@@ -134,3 +144,6 @@ For MOD files for which the original source is available on ModelDB, any specifi
 .. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
                  :target: https://gitter.im/BlueBrain/BlueCelluLab
                  :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
+
+.. |zenodo| image:: https://zenodo.org/badge/640805129.svg
+                 :target: https://zenodo.org/badge/latestdoi/640805129

{bluecellulab-1.0.2 → bluecellulab-1.1.0}/README.rst

@@ -14,6 +14,8 @@ BlueCelluLab
 +----------------+------------+
 | Gitter         | |gitter|   |
 +----------------+------------+
+| Citation       | |zenodo|   |
++----------------+------------+
 
 
 BlueCelluLab is designed to do simulation and experiment on a single cell or a group of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally.
@@ -25,7 +27,15 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 
 .. code-block:: 
 
-    @article {TBD Zenodo}
+    @software{bluecellulab_zenodo,
+      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      title        = {BlueCelluLab},
+      month        = jul,
+      year         = 2023,
+      publisher    = {Zenodo},
+      doi          = {10.5281/zenodo.8113483},
+      url          = {https://doi.org/10.5281/zenodo.8113483}
+    }
 
 Support
 =======
@@ -58,7 +68,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     from bluecellulab import Simulation
 
     cell = create_ball_stick()
-    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=1.5)
+    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=0.1)
     sim = Simulation()
     sim.add_cell(cell)
 
@@ -66,7 +76,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     time, voltage = cell.get_time(), cell.get_soma_voltage()
     # plotting time and voltage ...
 
-.. image:: docs/images/voltage-readme.png
+.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
    :alt: Voltage plot
 
 Tutorial
@@ -115,3 +125,6 @@ For MOD files for which the original source is available on ModelDB, any specifi
 .. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
                  :target: https://gitter.im/BlueBrain/BlueCelluLab
                  :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
+
+.. |zenodo| image:: https://zenodo.org/badge/640805129.svg
+                 :target: https://zenodo.org/badge/latestdoi/640805129

{bluecellulab-1.0.2 → bluecellulab-1.1.0}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 1.0.2
+Version: 1.1.0
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL
@@ -33,6 +33,8 @@ BlueCelluLab
 +----------------+------------+
 | Gitter         | |gitter|   |
 +----------------+------------+
+| Citation       | |zenodo|   |
++----------------+------------+
 
 
 BlueCelluLab is designed to do simulation and experiment on a single cell or a group of cells. Use cases for which bluecellulab is well suited include: scripting and statistics across single or pairs of cells, light-weight detailed reporting on a few state variables post-simulation, development of synaptic plasticity rules, dynamics validations of e.g. synaptic properties, automation of in-silico whole-cell patching experiments, debugging both scientifically and computationally.
@@ -44,7 +46,15 @@ When you use this BlueCelluLab software for your research, we ask you to cite th
 
 .. code-block:: 
 
-    @article {TBD Zenodo}
+    @software{bluecellulab_zenodo,
+      author       = {Van Geit, Werner and Tuncel, Anil and Gevaert, Mike and Torben-Nielsen, Benjamin and Muller, Eilif},
+      title        = {BlueCelluLab},
+      month        = jul,
+      year         = 2023,
+      publisher    = {Zenodo},
+      doi          = {10.5281/zenodo.8113483},
+      url          = {https://doi.org/10.5281/zenodo.8113483}
+    }
 
 Support
 =======
@@ -77,7 +87,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     from bluecellulab import Simulation
 
     cell = create_ball_stick()
-    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=1.5)
+    stimulus = cell.add_step(start_time=15.0, stop_time=20.0, level=0.1)
     sim = Simulation()
     sim.add_cell(cell)
 
@@ -85,7 +95,7 @@ The following example shows how to create a cell, add a stimulus and run a simul
     time, voltage = cell.get_time(), cell.get_soma_voltage()
     # plotting time and voltage ...
 
-.. image:: docs/images/voltage-readme.png
+.. image:: https://raw.githubusercontent.com/BlueBrain/BlueCelluLab/main/docs/images/voltage-readme.png
    :alt: Voltage plot
 
 Tutorial
@@ -134,3 +144,6 @@ For MOD files for which the original source is available on ModelDB, any specifi
 .. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
                  :target: https://gitter.im/BlueBrain/BlueCelluLab
                  :alt: Join the chat at https://gitter.im/BlueBrain/BlueCelluLab
+
+.. |zenodo| image:: https://zenodo.org/badge/640805129.svg
+                 :target: https://zenodo.org/badge/latestdoi/640805129

{bluecellulab-1.0.2 → bluecellulab-1.1.0}/bluecellulab.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 .compile_mod.sh
 .gitattributes
 .gitignore
+.zenodo.json
 AUTHORS.txt
 CHANGELOG.rst
 CONTRIBUTORS.txt
@@ -11,6 +12,7 @@ README.rst
 pyproject.toml
 setup.py
 tox.ini
+.github/workflows/release.yml
 .github/workflows/test.yml
 bluecellulab/__init__.py
 bluecellulab/connection.py