Merge branch 'master' into dependabot/github_actions/softprops/action…

…-gh-release-2

.github/workflows/build-wheels.yml

@@ -10,11 +10,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-latest, windows-latest]
+        os: [ubuntu-22.04, macos-12, windows-latest]
         python: [cp39, cp310, cp311, cp312]
         arch: [x86_64, amd64]
         exclude:
-          - os: macos-latest
+          - os: macos-12
             arch: amd64
           - os: ubuntu-22.04
             arch: amd64

.github/workflows/test.yml

@@ -84,6 +84,10 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install tox tox-gh-actions
+    - name: Install pandoc  # needed by nbconvert
+      uses: pandoc/actions/setup@main
+      with:
+        version: 2.19
     - name: Run tox
       run: tox -e docs
 

.gitignore

@@ -16,10 +16,17 @@ cpp_coverage.xml
 docs/bin
 docs/lib
 docs/source/lib
+docs/source/sonata-network.rst
+docs/source/sonata-network_files/
+docs/source/nmc-portal.rst
+docs/source/L5TTPC2_files/
+docs/source/load_nwb.rst
+docs/source/load_nwb_files/
 bin
 *.tox-info.json
 *.ipynb_checkpoints
 lib
 fllog.txt
 *.DS_Store
 pyvenv.cfg
+x86_64

.readthedocs.yaml

@@ -10,6 +10,9 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
+  jobs:
+    pre_build:
+      - sh docs/examples_to_rst.sh
 
 python:
   # Install our python package before building the docs

CHANGELOG.rst

@@ -5,6 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_,
 and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
+5.6.6 - 2024-04
+---------------
+
+- Adding AP_height to documentation
+
 5.6.0 - 2024-02
 ----------------
 

README.md

@@ -156,10 +156,10 @@ import efel
 To get a list with all the available feature names
 
 ```python
-efel.getFeatureNames()
+efel.get_feature_names()
 ```
 
-The python function to extract features is getFeatureValues(...).
+The python function to extract features is get_feature_values(...).
 Below is a short example on how to use this function. The code and example
 trace are available
 [here](https://github.com/BlueBrain/eFEL/blob/master/examples/basic/basic_example1.py)
@@ -207,7 +207,7 @@ def main():
 
     # Now we pass 'traces' to the efel and ask it to calculate the feature
     # values
-    traces_results = efel.getFeatureValues(traces,
+    traces_results = efel.get_feature_values(traces,
                                            ['AP_amplitude', 'voltage_base'])
 
     # The return value is a list of trace_results, every trace_results

docs/examples_to_rst.sh

@@ -0,0 +1,22 @@
+# to call from root
+
+# clean up
+rm docs/source/sonata-network.rst
+rm -rf docs/source/sonata-network_files
+rm docs/source/nmc-portal.rst
+rm -rf docs/source/L5TTPC2_files
+rm docs/source/load_nwb.rst
+rm -rf docs/source/load_nwb_files
+
+# convert
+jupyter nbconvert --to rst examples/sonata-network/sonata-network.ipynb
+jupyter nbconvert --to rst examples/nmc-portal/L5TTPC2.ipynb
+jupyter nbconvert --to rst examples/neo/load_nwb.ipynb
+
+# move
+mv examples/sonata-network/sonata-network.rst docs/source/
+mv examples/sonata-network/sonata-network_files docs/source/
+mv examples/nmc-portal/L5TTPC2.rst docs/source/nmc-portal.rst
+mv examples/nmc-portal/L5TTPC2_files docs/source/
+mv examples/neo/load_nwb.rst docs/source/
+mv examples/neo/load_nwb_files docs/source/

docs/source/conf.py

@@ -55,7 +55,8 @@
 
 # General information about the project.
 project = u'eFEL'
-copyright = u'2015-2024, BBP, EPFL'
+# do not define copyright here, in order to use the default Blue Brain project copyright
+# copyright = u'2015-2024, BBP, EPFL'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -108,7 +109,8 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx-bluebrain-theme"
+# html_theme = 'sphinx_rtd_theme'
 # html_theme = 'haiku-bbp'
 
 # Theme options are theme-specific and customize the look and feel of a theme

docs/source/deap_optimisation.rst

@@ -98,7 +98,7 @@ This translates into the following file (let's call it 'deap_efel_eval1.py')::
         trace['stim_end'] = [stim_end]
         traces = [trace]
 
-        features = efel.getFeatureValues(traces, ["voltage_base",
+        features = efel.get_feature_values(traces, ["voltage_base",
                                                  "steady_state_voltage"])
         voltage_base = features[0]["voltage_base"][0]
         steady_state_voltage = features[0]["steady_state_voltage"][0]