remove pdf documentation (#412)

* remove pdf documentation

* add bap and ais check to feature doc

* add condition on mypy version for the tests

* add tests for python 3.13

* use pyproject for cibuildwheel env variables

* add indices features to doc

* new example: settings

* updated changelog

---------

Co-authored-by: Jaquier Aurélien Tristan <aurelien.jaquier@epfl.ch>

Author: AurelienJaquier

.github/workflows/build-wheels.yml

@@ -22,8 +22,6 @@ jobs:
             arch: x86_64
     env:
       CIBW_BUILD: ${{ matrix.python }}*${{ matrix.arch }}
-      CIBW_TEST_REQUIRES: pytest neo[neomatlabio]>=0.5.1 pytest-xdist>=3.3.1
-      CIBW_TEST_COMMAND: pytest -sx -n auto {project}/tests
       CIBW_SKIP: "*-musllinux_*"
     steps:
       - uses: actions/checkout@v4

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4

CHANGELOG.rst

@@ -5,6 +5,38 @@ 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>`_.
 
+5.7.11 - 2024-11
+----------------
+
+- Removed pdf documentation file. Reason: There was no substantial information in the pdf that were not already present in the official doc.
+- added an example for using settings, and added this example to the docs
+- added the (already implemented) following features to docs:
+
+  * check_ais_initiation
+  * bpap_attenuation
+  * peak_indices
+  * AP_rise_indices
+  * AP_end_indices
+  * AP_fall_indices
+  * min_AHP_indices
+  * AP_begin_indices
+  * min_between_peaks_indices
+  * burst_begin_indices
+  * burst_end_indices
+  * ADP_peak_indices
+  * interburst_min_indices
+  * postburst_min_indices
+  * postburst_slow_ahp_indices
+  * postburst_fast_ahp_indices
+  * postburst_adp_peak_indices
+  * interburst_15percent_indices
+  * interburst_20percent_indices
+  * interburst_25percent_indices
+  * interburst_30percent_indices
+  * interburst_40percent_indices
+  * interburst_60percent_indices
+  * burst_ISI_indices
+
 5.7.9 - 2024-09
 ---------------
 

docs/examples_to_rst.sh

@@ -11,6 +11,8 @@ rm docs/source/extrafeats_example.rst
 rm docs/source/multiprocessing_example.rst
 rm docs/source/voltage_clamp.rst
 rm -rf docs/source/voltage_clamp_files
+rm docs/source/settings.rst
+rm -rf docs/source/settings_notebook_files
 
 # convert
 jupyter nbconvert --to rst examples/sonata-network/sonata-network.ipynb
@@ -19,6 +21,7 @@ jupyter nbconvert --to rst examples/neo/load_nwb.ipynb
 jupyter nbconvert --to rst examples/extracellular/extrafeats_example.ipynb
 jupyter nbconvert --to rst examples/parallel/multiprocessing_example.ipynb
 jupyter nbconvert --to rst examples/voltage_clamp/voltage_clamp.ipynb
+jupyter nbconvert --to rst examples/settings/settings_notebook.ipynb
 
 # move
 mv examples/sonata-network/sonata-network.rst docs/source/
@@ -30,4 +33,6 @@ mv examples/neo/load_nwb_files docs/source/
 mv examples/extracellular/extrafeats_example.rst docs/source/
 mv examples/parallel/multiprocessing_example.rst docs/source/
 mv examples/voltage_clamp/voltage_clamp.rst docs/source/
-mv examples/voltage_clamp/voltage_clamp_files docs/source/
+mv examples/voltage_clamp/voltage_clamp_files docs/source/
+mv examples/settings/settings_notebook.rst docs/source/settings.rst
+mv examples/settings/settings_notebook_files docs/source/