Merge branch 'release-1.3.0'

Author: moritzlayer

docs/source/authors_and_contributors.rst

@@ -11,7 +11,8 @@ contribution, and may not be the current affiliation of a contributor.
 - Moritz Layer [1, 2]
 - Johanna Senk [1]
 - Simon Essink [1, 2]
-- Alexander van Meegen [1, 2]
+- Alexander van Meegen [1]
+- Aitor Morales-Gregorio [1]
 - Karolína Korvasova [1, 2]
 - Jari Pronold [1, 2]
 - Hannah Bos [1, 2]

docs/source/bib/nnmt.bib

@@ -40,6 +40,20 @@ @article{amit1997
   journal = {Network: Computation in Neural Systems}
 }
 
+@article{beaulieu2008,
+  doi = {10.1109/tcomm.2008.060123},
+  url = {https://doi.org/10.1109/tcomm.2008.060123},
+  year = {2008},
+  month = mar,
+  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
+  volume = {56},
+  number = {3},
+  pages = {331--333},
+  author = {N.C. Beaulieu},
+  title = {Fast convenient numerical computation of lognormal characteristic functions},
+  journal = {{IEEE} Transactions on Communications}
+}
+
 @article{bos2016,
   doi = {10.1371/journal.pcbi.1005132},
   url = {https://doi.org/10.1371/journal.pcbi.1005132},
@@ -55,6 +69,19 @@ @article{bos2016
   journal = {{PLOS} Computational Biology}
 }
 
+@article{brunel2000,
+  doi = {10.1023/a:1008925309027},
+  url = {https://doi.org/10.1023/a:1008925309027},
+  year = {2000},
+  publisher = {Springer Science and Business Media {LLC}},
+  volume = {8},
+  number = {3},
+  pages = {183--208},
+  author = {Nicolas Brunel},
+  title = {Dynamics of Sparsely Connected Networks of Excitatory and Inhibitory Spiking Neurons},
+  journal = {Journal of Computational Neuroscience}
+}
+
 @article{fourcaud2002,
   doi = {10.1162/089976602320264015},
   url = {https://doi.org/10.1162/089976602320264015},
@@ -69,6 +96,16 @@ @article{fourcaud2002
   journal = {Neural Computation}
 }
 
+@article{gewaltig2007,
+  author  = {Marc-Oliver Gewaltig and Markus Diesmann},
+  title   = {NEST (NEural Simulation Tool)},
+  journal = {Scholarpedia},
+  year    = {2007},
+  volume  = {2},
+  pages   = {1430},
+  number  = {4}
+}
+
 @article{grecco2018,
   title={Pint},
   author={Grecco, Hernan E.},
@@ -127,6 +164,18 @@ @article{layer2022
   doi = {10.3389/fninf.2022.835657},
 }
 
+@article{layer2023,
+  doi = {10.48550/ARXIV.2308.00421},
+  url = {https://arxiv.org/abs/2308.00421},
+  author = {Layer, Moritz and Helias, Moritz and Dahmen, David},
+  keywords = {Disordered Systems and Neural Networks (cond-mat.dis-nn),  Neurons and Cognition (q-bio.NC),  FOS: Physical sciences,  FOS: Physical sciences,  FOS: Biological sciences,  FOS: Biological sciences},
+  title = {Beyond-mean-field theory for the statistics of neural coordination},
+  publisher = {arXiv},
+  journal={arXiv},
+  year = {2023},
+  copyright = {Creative Commons Attribution 4.0 International}
+}
+
 @article{potjans2014,
   doi = {10.1093/cercor/bhs358},
   url = {https://doi.org/10.1093/cercor/bhs358},
@@ -141,6 +190,17 @@ @article{potjans2014
   journal = {Cerebral Cortex}
 }
 
+@article{Saberali2012,
+  doi = {10.1109/glocom.2012.6503436},
+  url = {https://doi.org/10.1109/glocom.2012.6503436},
+  year = {2012},
+  month = dec,
+  publisher = {{IEEE}},
+  author = {Seyed Ali Saberali and Norman C. Beaulieu},
+  title = {New approximations to the lognormal characteristic function},
+  booktitle = {2012 {IEEE} Global Communications Conference ({GLOBECOM})}
+}
+
 @article{sanzeni2020,
   doi = {10.1371/journal.pcbi.1008165},
   url = {https://doi.org/10.1371/journal.pcbi.1008165},

docs/source/conf.py

@@ -26,7 +26,7 @@
 author = 'Moritz Layer, Johanna Senk, Simon Essink, Alexander van Meegen, Hannah Bos, Moritz Helias'
 
 # The full version, including alpha/beta/rc tags
-release = '1.2.0'
+release = '1.3.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/contributor_guide.rst

@@ -395,3 +395,9 @@ a :ref:`release note <sec_release_notes>` should be added, and the list of
 :ref:`authors and contributors <sec_authors_and_contributors>`, as well as the
 :ref:`acknowledgements <sec_acknowledgements>` should be updated if required.
 
+****************************
+How to publish a new release
+****************************
+
+Please follow our :ref:`step-by-step guide <sec_how_to_make_a_new_release>` for
+publishing a new release.

docs/source/examples.rst

@@ -15,3 +15,4 @@ Examples
    bos_2016_index.rst
    mapping_lif_rate_and_spatial_patterns_index.rst
    auto_examples/binary_rate_simulation/binary_sim_vs_thy.rst
+   auto_examples/prediction_of_simulation_results/prediction_and_simulation_EI_network.rst

docs/source/how_to_release_nnmt.rst

@@ -0,0 +1,216 @@
+.. _sec_how_to_make_a_new_release:
+
+====================================
+How to publish a new release of NNMT
+====================================
+
+1.  Checkout the develop branch
+
+    .. code::
+
+        git checkout develop
+        git pull
+
+
+2.  Check that the code is working
+
+    Make sure the new feature you implemented does what it is supposed to do.
+
+3.  Check that code is tested
+
+    The point above should be done by writing tests that ensure this.
+
+4.  Check that code is well documented
+
+    Follow the guidelines in the docs for this.
+
+5.  Check the release notes
+
+    All changes need to be documented in the release notes.
+
+6.  Check that all tests run
+
+    .. code::
+
+        cd tests/
+        pytest
+        cd ../
+
+7.  Create a release branch
+
+    .. code::
+
+        git checkout -b release-<release_number>
+
+
+8.  Fix anything left
+
+9.  Update version numbers to pre-format
+
+    In ``nnmt/__init__.py``, ``docs/source/conf.py``, and ``setup.py``.
+
+    **WARNING**: You can upload each file only once to testpypi, even if you delete them on testpypi. Therefore use version names like ``1.0.0a0``.
+
+10. Create new conda environment and check local installation
+
+    .. code::
+
+        conda create -n temp0
+        conda activate temp0
+        conda install setuptools
+        pip install .
+        cd tests/
+        pytest
+        cd ../
+
+11. Create sdist and wheel
+
+    Remove any old wheels
+
+    .. code::
+
+        rm -r dist/
+
+    Then check that ``setup.py`` contains all necessary data by running
+
+    .. code::
+
+        python setup.py check
+
+    If this works, you can create the sdist and wheel source distribution using
+
+    .. code::
+
+        python setup.py sdist bdist_wheel
+
+    which creates a new directory ``dist``.
+
+12. Upload to test.pypi
+
+    Then install ``twine`` and upload to testpypi
+
+    **WARNING**: You can upload each file only once, even if you delete them on
+    testpypi. Therefore use version names like ``1.0.0a``.
+
+    .. code::
+
+        conda install twine
+        twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+
+13. Create new conda env and test install from test.pyi
+
+    .. code::
+
+        conda create -n temp1
+        conda activate temp1
+        conda install pip
+        pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple nnmt==<release_number>
+        cd tests/
+        pytest
+        cd ../
+
+14. If this fails, fix problems, change version numbers to ``1.0.0b`` and repeat.
+
+15. Update version numbers to final format
+
+    In ``nnmt/__init__.py``, ``docs/source/conf.py``, and ``setup.py``,
+
+    and commit
+
+    .. code::
+
+        git add nnmt/__init__.py docs/source/conf.py setup.py
+        git commit -m 'Final update of version numbers'
+
+16. Merge into ``master`` and ``develop`` and delete release branch
+
+    .. code::
+
+        git checkout master
+        git pull
+        git merge --no-ff release-<release_number>
+        git push
+
+        git checkout develop
+        git pull
+        git merge --no-ff release-<release_number>
+        git push
+
+        git checkout master
+        git branch -d release-<release_number>
+
+17. Create sdist and wheel
+
+    .. code::
+
+        conda activate temp0
+        rm -r dist/
+        python setup.py check
+        python setup.py sdist bdist_wheel
+
+18. Upload to test.pypi
+
+    .. code::
+
+        twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+
+19. Create new conda env and test install from test.pypi
+
+    .. code::
+
+        conda create -n temp2
+        conda activate temp2
+        conda install pip
+        pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple nnmt==<release_number>
+        cd tests/
+        pytest
+        cd ../
+
+20. Upload to pypi
+
+    Finally, you can upload your package to pypi.
+
+    **WARNING**: This cannot be reversed, and the code cannot be changed
+    afterwards, so the package needs to be in a final state.
+
+    .. code::
+
+        conda activate temp0
+        twine upload dist/*
+
+21. Test pip install
+
+    .. code:
+
+        conda create -n temp3
+        conda activate temp3
+        conda install pip
+        pip install nnmt==<release_number>
+        cd tests/
+        pytest
+        cd ../
+
+22. Remove temporary conda environments
+
+    .. code::
+
+        conda activate base
+        conda env remove -n temp0
+        conda env remove -n temp1
+        conda env remove -n temp2
+        conda env remove -n temp3
+
+23. Create Release on GitHub
+
+    Optional: Create tag from command line
+
+    .. code::
+
+        git tag -a v<release_number>
+        git push origin --tags
+
+    Note that releases are a GitHub feature and can only be done on GitHub itself.
+
+24. Upload compressed compy of the repository to Zenodo
+
+25. Check readthedocs

docs/source/release_notes.rst

@@ -4,6 +4,30 @@
 Release notes
 =============
 
+**********
+NNMT 1.3.0
+**********
+
+- The option to use a lognormal delay distribution has been added to the
+  calcultion of the delay distribution matrix in ``nnmt.network_properties``.
+  As the characteristic function of a lognormal distribution has no closed
+  analytic form, the numerical integration proposed in :cite:t:`beaulieu2008`
+  has been implemented.
+- Add functions for computing the cvs of lif neurons: :func:`nnmt.lif.exp.cvs`,
+  :func:`nnmt.lif.exp._cvs`, and :func:`nnmt.lif.exp._cvs_single_population`.
+- Add functions for computing pairwise_effective_connectivity in linear
+  response approximation: :func:`nnmt.lif.exp.pairwise_effective_connectivity`,
+  :func:`nnmt.lif.exp._pairwise_effective_connectivity`.
+- Add functions for computing the spectral bound of the pairwise effective
+  connectivity matrix: :func:`nnmt.lif.exp.spectral_bound`,
+  :func:`nnmt.lif.exp._spectral_bound`.
+- Add functions for computing the pairwise covariances in linear response
+  approximation: :func:`nnmt.lif.exp.pairwise_covariances`,
+  :func:`nnmt.lif.exp._pairwise_covariances`.
+- Add an example on how to use NNMT to predict the firing rates, CVs, and
+  pair-wise covariances of a simple E-I network. The results are then compared
+  to a NEST simulation.
+
 **********
 NNMT 1.2.0
 **********

docs/source/tests.rst

@@ -12,18 +12,18 @@ environment specified in the provided ``environment.yaml`` file, and running
 
     pytest
 
-from the root directory (the one containing ``tests/`` and ``nnmt/``). If you
-want to be more specific, you can, for example, only run the unit tests:
+from the ``test/`` directory. If you want to be more specific, you can, for
+example, only run the unit tests:
 
 .. code::
 
-    pytest tests/unit/
+    pytest unit/
 
 Or just a single test:
 
 .. code::
 
-    pytest tests/unit/lif/test_exp.py::Test_firing_rate_shift::test_correct_output
+    pytest unit/lif/test_exp.py::Test_firing_rate_shift::test_correct_output
 
 See the `pytest documentation <https://docs.pytest.org/en/6.2.x/#>`_ for all
 available options.