Merge branch 'jonescompneurolab:master' into delete_drive

.circleci/build_cache

@@ -0,0 +1,2 @@
+# Change the following version number to trigger a complete rebuild of the doc in CircleCI.
+v4

.circleci/config.yml

@@ -3,8 +3,9 @@ version: 2.1
 
 jobs:
     build_docs:
-      docker:
-          - image: circleci/python:3.8.1-buster
+      machine:
+        image: ubuntu-2004:current
+      resource_class: large
       steps:
           - checkout
 
@@ -14,7 +15,7 @@ jobs:
                   sudo apt-get install wget
                   wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh;
                   chmod +x ~/miniconda.sh;
-                  ~/miniconda.sh -b -p ~/miniconda;
+                  bash ~/miniconda.sh -b -p ~/miniconda;
 
           - run:
               name: Install openmpi
@@ -36,7 +37,7 @@ jobs:
               command: |
                   source ~/miniconda/bin/activate testenv
                   sudo apt-get install pandoc
-                  pip install sphinx numpydoc sphinx_bootstrap_theme pillow nbsphinx
+                  pip install sphinx numpydoc sphinx_bootstrap_theme sphinx-copybutton pillow nbsphinx
                   pip install --user -U https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
 
           - run:
@@ -50,8 +51,11 @@ jobs:
               command: |
                   source ~/miniconda/bin/activate testenv
                   pip install -U pip setuptools virtualenv
-                  pip install ipywidgets voila
-                  python setup.py install
+                  pip install '.[gui]'
+
+          - restore_cache:
+              keys:
+                - built-{{ checksum ".circleci/build_cache" }}
 
           - run:
               name: Build the documentation
@@ -63,6 +67,12 @@ jobs:
               root: doc/_build
               paths: html
 
+          - save_cache:
+              key: built-{{ checksum ".circleci/build_cache" }}
+              paths:
+                - doc/auto_examples
+                - doc/_build
+
           - store_artifacts:
               path: doc/_build/html/
               destination: html
@@ -103,4 +113,4 @@ workflows:
             - build_docs
           filters:
             branches:
-              only: master
+              only: master

.github/workflows/linkcheck.yml

@@ -27,9 +27,8 @@ jobs:
           sudo apt-get install pandoc
           python -m pip install --upgrade pip
           pip install numpy matplotlib scipy NEURON
-          pip install ipywidgets voila
-          pip install sphinx-gallery sphinx sphinx_bootstrap_theme numpydoc pillow nbsphinx
-          python setup.py install
+          pip install sphinx-gallery sphinx sphinx_bootstrap_theme sphinx-copybutton numpydoc pillow nbsphinx
+          pip install '.[gui]'
       - name: Linkcheck
         shell: bash -el {0}
         run: |

.github/workflows/unit_tests.yml

@@ -34,9 +34,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install flake8 pytest pytest-cov
-          pip install mne psutil joblib
-          pip install NEURON
-          pip install ipywidgets voila
+          pip install psutil joblib
           if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
             pip install mpi4py
           else
@@ -45,15 +43,15 @@ jobs:
       - name: Install HNN-core
         shell: bash -el {0}
         run: |
-          python setup.py --verbose install
+          pip install --verbose '.[gui]'
       - name: Lint with flake8
         shell: bash -el {0}
         run: |
           flake8 --count hnn_core
       - name: Test with pytest
         shell: bash -el {0}
         run: |
-          python -m py.test .  --cov=hnn_core hnn_core/tests/ --cov-report=xml
+          python -m pytest .  --cov=hnn_core hnn_core/tests/ --cov-report=xml
       - name: Upload code coverage
         shell: bash -el {0}
         run: |

.github/workflows/windows_unit_tests.yml

@@ -0,0 +1,47 @@
+name: Unit test
+
+on:
+  push:
+    branches: ['**']
+  pull_request:
+    branches: ['**']
+
+env:
+    PYTHONPATH: C:\nrn_test\lib\python
+    NEURONHOME: C:\nrn_test
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        python-version: [3.7, 3.8]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+      - name: Install Neuron on Windows separately
+        shell: cmd
+        run: |
+          powershell -command "gh release download --repo https://github.com/neuronsimulator/nrn --pattern '*.exe' --output nrn-setup.exe"
+          start /b /wait .\nrn-setup.exe /S /D=C:\nrn_test
+          powershell -command "'C:\nrn_test\bin' >> $env:GITHUB_PATH"
+          python -c "import neuron"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Install dependencies and HNN
+        shell: cmd
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest pytest-cov
+          pip install psutil joblib
+          pip install --verbose .[gui]
+      - name: Test with pytest
+        shell: cmd
+        run: |
+          python -m pytest .  --cov=hnn_core hnn_core/tests/ --cov-report=xml

MANIFEST.in

@@ -5,8 +5,6 @@ recursive-include examples *.py
 recursive-include examples *.txt
 
 recursive-include hnn_core/mod *
-recursive-include hnn_core/mod/x86_64 *
-recursive-include hnn_core/mod/x86_64/.libs *
 
 recursive-include hnn_core *.py
 recursive-include hnn_core *.ipynb

Makefile

@@ -15,3 +15,16 @@ clean :
 
 check-manifest:
 	check-manifest
+
+test: flake
+	pytest .
+
+flake:
+	@if command -v flake8 > /dev/null; then \
+		echo "Running flake8"; \
+		flake8 hnn_core --count; \
+	else \
+		echo "flake8 not found, please install it!"; \
+		exit 1; \
+	fi;
+	@echo "flake8 passed"

README.rst

@@ -7,10 +7,12 @@ hnn-core
 
 This is a leaner and cleaner version of the code based off the `HNN repository <https://github.com/jonescompneurolab/hnn>`_.
 
-It is early Work in Progress. Contributors are very welcome.
+Contributors are very welcome. Please read our
+:doc:`contributing guide <contributing>` if you are interested.
 
 Dependencies
 ------------
+hnn-core requires Python (>=3.7) and the following packages:
 
 * numpy
 * scipy
@@ -23,8 +25,8 @@ Optional dependencies
 GUI
 ~~~
 
-* ipywidgets
-* voila
+* ipywidgets (<=7.7.1)
+* voila (<=0.3.6)
 
 Parallel processing
 ~~~~~~~~~~~~~~~~~~~
@@ -51,11 +53,11 @@ because the pip installer works better with virtual environments such as the one
 
 If you want to track the latest developments of ``hnn-core``, you can install the current version of the code (nightly) with::
 
-	$ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master
+   $ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master
 
 To check if everything worked fine, you can do::
 
-	$ python -c 'import hnn_core'
+   $ python -c 'import hnn_core'
 
 and it should not give any error messages.
 
@@ -64,6 +66,10 @@ and it should not give any error messages.
 To install the GUI dependencies along with ``hnn-core``, a simple tweak to the above command is needed::
 
    $ pip install hnn_core[gui]
+   
+Note if you are zsh in macOS the command is::
+
+   $ pip install hnn_core'[gui]'
 
 To start the GUI, please do::
 
@@ -76,17 +82,17 @@ than one CPU core, refer to our `parallel backend guide`_.
 
 **Note for Windows users**
 
-The pip installer for Neuron does not yet work for Windows. In this case, it is better to
-install ``hnn_core`` without the dependencies::
+Install Neuron using the `precompiled installers`_ **before** installing
+``hnn-core``. Make sure that::
 
-   $ pip install hnn_core --no-deps
+   $ python -c 'import neuron;'
 
-and then install the dependencies separately::
+does not throw any errors before running the install command.
+If you encounter errors, please get help from `NEURON forum`_.
+Finally, do::
 
-   $ pip install scipy numpy matplotlib
+   $ pip install hnn_core[gui]
 
-and install Neuron using the traditional package installer available here
-`https://neuron.yale.edu/neuron/ <https://neuron.yale.edu/neuron/>`_.
 
 Documentation and examples
 ==========================
@@ -117,10 +123,15 @@ report bugs. For user questions and scientific discussions, please join the
 Interested in Contributing?
 ===========================
 
-Read our `contributing guide`_.
+Read our :doc:`contributing guide <contributing>`.
+
+Roadmap
+=======
+
+Read our `roadmap`_.
 
-.. _parallel backend guide: https://jonescompneurolab.github.io/hnn-core/dev/parallel.html
-.. _contributing guide: https://jonescompneurolab.github.io/hnn-core/dev/contributing.html
+.. _precompiled installers: https://www.neuron.yale.edu/neuron/download
+.. _NEURON forum: https://www.neuron.yale.edu/phpbb/
 
 .. |tests| image:: https://github.com/jonescompneurolab/hnn-core/actions/workflows/unit_tests.yml/badge.svg?branch=master
    :target: https://github.com/jonescompneurolab/hnn-core/actions/?query=branch:master+event:push
@@ -129,12 +140,12 @@ Read our `contributing guide`_.
    :target: https://circleci.com/gh/jonescompneurolab/hnn-core
 
 .. |Codecov| image:: https://codecov.io/gh/jonescompneurolab/hnn-core/branch/master/graph/badge.svg
-	:target: https://codecov.io/gh/jonescompneurolab/hnn-core
+   :target: https://codecov.io/gh/jonescompneurolab/hnn-core
 
 .. |PyPI| image:: https://img.shields.io/pypi/dm/hnn-core.svg?label=PyPI%20downloads
-	:target: https://pypi.org/project/hnn-core/
+   :target: https://pypi.org/project/hnn-core/
 
-.. |HNN-GUI| image:: https://user-images.githubusercontent.com/11160442/178095018-35d2619a-6a82-4e27-91c9-ff2796fab435.png
+.. |HNN-GUI| image:: https://user-images.githubusercontent.com/11160442/197026635-39b6564a-f529-4caf-870e-af9ca4d2fb75.png
 
 .. |Gitter| image:: https://badges.gitter.im/jonescompneurolab/hnn_core.svg
    :target: https://gitter.im/jonescompneurolab/hnn-core?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge

doc/Dockerfile

@@ -44,7 +44,7 @@ RUN pip install numpy && \
     pip install scipy && \
     pip install matplotlib && \
     pip install pyqt5 && \
-	pip install ipywidgets && \
+	pip install 'ipywidgets<=7.7.1' && \
     pip install pillow && \
     pip install https://api.github.com/repos/mne-tools/mne-python/zipball/master
 

doc/Makefile

@@ -37,7 +37,7 @@ clean:
 	rm -rf modules/*
 
 html-noplot:
-	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) -D plot_gallery=0 -D nbsphinx_execute=never -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/api.rst

@@ -55,12 +55,12 @@ Dipole (:py:mod:`hnn_core.dipole`):
 
 ExtracellularArray (:py:mod:`hnn_core.extracellular`):
 ------------------------------------------------------
-   
+
 .. currentmodule:: hnn_core.extracellular
-   
+
 .. autosummary::
    :toctree: generated/
- 
+
    ExtracellularArray
 
 Visualization (:py:mod:`hnn_core.viz`):
@@ -80,6 +80,8 @@ Visualization (:py:mod:`hnn_core.viz`):
    plot_tfr_morlet
    plot_cell_connectivity
    plot_connectivity_matrix
+   plot_laminar_lfp
+   plot_laminar_csd
 
 Parallel backends (:py:mod:`hnn_core.parallel_backends`):
 ---------------------------------------------------------
@@ -113,4 +115,3 @@ GUI (:py:mod:`hnn_core.gui`):
    :toctree: generated/
 
    HNNGUI
-