Update from master #95
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* BinnedSpikeTrain optional CSC format * BinnedSpikeTrain.binarize() 'copy' arg is back
…#404) * accelerated pmat_neighbors function * cluster_matrix_entries with chunking
…386) Co-authored-by: Michael Denker <[email protected]>
* Changed to pytest and pytest-cov for running tests with coverage * Changed mpiexec test and added coveralls Co-authored-by: Cristiano Köhler <[email protected]>
Co-authored-by: Cristiano Köhler <[email protected]>
* Fix complexity annotation dtype * Adapt test name to new object name * Combine redundant type casts Co-authored-by: kleinjohann <[email protected]>
* bug fixed dealing with units * fixed same unit error in trial shuffling * added Bielefeld fim.so and adapted filtering and added window param to fpgrowth * removed max_occ test * further unit stuff * debugging for new fim version * enabled multithreading in fpgrowth * less verbose in spade * set equal number of bins in bin shuffling wrt spade * added tolerance to binning in spade everywhere * Added accelerated FIM algorithm sources by Florian Porrmann. * Enh/accelerated spade build (#82) * Added cibuildwheel action * Added Python requirements to wheel build * Build only on 64bit machines, otherwise overflow * Removed Windows for testing, as vc is not available * Removed MacOS for testing, as -fopenmp is not available * Removed pp- (pypy) builds since they lack C. * Fixed removing pp- (pypy) builds since they lack C. * Put Macos back in. * Windows Hack * Remove vcpython alltogether, ignore 2.7 Python * Removed extra compile option, which breaks on Windows * Removed more extra compile options, which breaks on Windows * Try C++ instead of Gnu++. * Try C++ instead of Gnu++ Windows style argument. * Remove linux build while testing windows. * Remove libraries. * Differentiate Windows and Linux. * Added missing import. * Last mile: MacOS * Remove openMP lib * Remove openMP lib * Add openMP lib * More brew installs * Mac is called mac on github * Make sure C is reinstalled. * Multilib * Next try, new options * Ignore warning about void type * Update newsest fim package * Revert "Ignore warning about void type" This reverts commit 3ff6b62 * Revert to prior fim, new compiler argument. * Revert "Update newsest fim package" This reverts commit f321f77 * Definitely, gnu++17, but new try. * Try C++ * Warning message * llvm maybe? * Added apple in source * Small fixes for MacOS, but not comprehensive * Limit to Windows and Linux for now * Remove MacOS entry * Fix fix from mindlessness * Testrun * Trying to include fim.so, despite its renaming by wheels * Added newest version of original module * Reverted previous breaking change commited by accident. * Reverted package name from testing. * Test focal as CI build * Test bionic as CI build * Understand installation issue on CI -- is importing elephant importing the installed version? * Spelling error only * Try to make sure travis loads the installed elephant, not the cwd. * One step further -- which version will nosetests use? * Switch to pytest as of PR #413 * Added authors of new FIM module and reference in new docs. * Added authors of new FIM module and reference in new docs. * Small text clarifications. * Test if entry for fim.so/pyd in MANIFEST is now redundant. * Update elephant/spade.py Co-authored-by: Alexander Kleinjohann <[email protected]> * Update elephant/spade.py Co-authored-by: Alexander Kleinjohann <[email protected]> * Added SPADE tutorial * Prevent wheel building on every push, and limit scipy version workaround * Pushed tutorial, removed file added in error * New attempt to make mybinder install requirements. * New attempt, dropping viziphant. * Avoid recursive elephant installation by viziphant in postBuild * Removed unit test that is fragile as it depends on the implementation of surrogate methods * Add viziphant to RTD environment * Typo in tutorial * Add viziphant to travis doc tests Co-authored-by: pbouss <[email protected]> Co-authored-by: stellalessandra <[email protected]> Co-authored-by: Alessandra Stella <[email protected]> Co-authored-by: Alexander Kleinjohann <[email protected]>
* First test to move viziphant to the environment.yml * Back to start * Update Python * Remove mpi4py * Remove pip * Add mpi4py, viziphant * Hopefully working version * Remove viziphant again * Added deprecated fake_neo objects from neo to allow neo 0.10.0+. * Fix imports to Python 3. * Another attempt to fix imports to Python 3. * Attempt relative import. * Cross-test with UE analysis test suite. * Next attempt.... * Remove viziphant to prevent elephant install and new attempt. * Remove viziphant to prevent elephant install and new attempt. * Try with a new version number * Stop trying to fix neo 0.10.0, must be separate. * Reintroduce viziphant in conda environment. * Introduce concurrent requirement for neo in environment and use pip install . * Final beautification measures
* bug fixed dealing with units * fixed same unit error in trial shuffling * added Bielefeld fim.so and adapted filtering and added window param to fpgrowth * removed max_occ test * further unit stuff * debugging for new fim version * enabled multithreading in fpgrowth * less verbose in spade * added correction factor to rate estimation * only spiketrain with more than one spikes are corrected * started rearranging the spike train generation: equilibrium rp. and class structure * enable option equilibrium /ordinary * annotations * Fixed bugs for zero rate * added test of boundary correction * PEP8 * revert wrongly merged master * separate from firing rate correction * simplified recovered rate test * finished restructuring in classes * Added lognormal and inv-gaussian processes * Updated Tests, added Log-Normal, Inverse Gaussian * PEP8 * added test for invgauss and lognorm * PEP8 * updated hardcoded SPADE tests * update hardcoded UE test * update hardcoded UE test * update hard-coded spike train synchrony test * PEP8 * combined Poisson and PPD into one function * simplified compound poisson process, single interaction process * deleted unused hidden functions * added CV test * added test for CV and first spike & added more comments * PEP8 * simplified bib-tex entry * started working in Robins review * fix breaked test for Joint-ISI dithering * continued working on Robins review * fixed bug - in getting first spike function * finished working on Robins review, improved first-spike function * changed to return None for option in init Co-authored-by: stellalessandra <[email protected]> Co-authored-by: Alessandra Stella <[email protected]>
This is a fix related to issue #424: t_start was lost while transposing lfp, because t_start was not set in the redefinition of the new neo.analogSignal. Fixed by transposing the neo.Analogsignal directly. @ojoenlanuca , @rgutzen
* Replaced custom test build with unittest.main() in - test_cell_assembly_detection.py - test_cubic.py - test_gpfa.py - test_icsd.py - test_spade.py - test_spike_train_surrogates.py * Fixed deprecation warnings in test_cell_assembly_detection.py: - numpy.testing.utils -> numpy.testing - data -> binned_spiketrain - maxlag -> max_lag - min_occ -> min_occurrences * Fixed deprecation warning (ximax -> max_iteractions) in test_cubic.py * Fixed typo in test_cubic.py * removed redundant blank lines at the end of code blocks
The plots generated in the Granger causality tutorial had incorrect axis ranges. This was fixed by setting x- and y-axis bounds in both plots. - Fixed the figures in granger_causality.ipynb tutorial
* Updated zscore to change the units to dimensionless when performing in-place operations, and also to return the original object instead of a new AnalogSignal object pointing to the original array. * Changed to raise ValueError when the in-place operation is not valid. * New AnalogSignal object is created using Neo function. * Updated unit tests to check for same/different objects when doing in-place operation in zscore. * Changed test_zscore_single_inplace_int as the function now raises ValueError. Co-authored-by: Cristiano Köhler <[email protected]>
* Update README.md added zenodo batch with DOI * Update README.md Co-authored-by: Michael Denker <[email protected]> Co-authored-by: Michael Denker <[email protected]>
* fix for bug related to pytest 7.0.0, fixed version to 6.2.5 thus fixing errors when running pytest with `--import-mode=importlib` * Update .travis.yml Co-authored-by: Michael Denker <[email protected]>
New Feature: multitaper psd estimate. Tests include a comparison against nitime multitaper.
New Feature: multitaper psd estimate. Tests include a comparison against nitime multitaper. Co-authored-by: ackurth <[email protected]> Co-authored-by: Regimantas Jurkus <[email protected]> Co-authored-by: Aitor Morales-Gregorio <[email protected]> Co-authored-by: kleinjohann <[email protected]> Co-authored-by: pbouss <[email protected]> Co-authored-by: Danylo Ulianych <[email protected]> Co-authored-by: Alexander Kleinjohann <[email protected]> Co-authored-by: Andrew Davison <[email protected]> Co-authored-by: Anno Christopher Kurth <[email protected]>
added `discretise_spiketimes(spiketrains, sampling_rate)` to conversion
…ant (#447) * Handle SpikeTrainList as input for BinnedSpikeTrain * Add corresponding regression test * PEP 8; avoid universal try-except clause * Fixed SpikeTrainList issue in spike train synchrony class * Fixed SpikeTrainList issue in SPADE * Pep8 issue * This removes support of RrcordingChannelGroup in CSD methods. * Changed requirements to Neo >=0.10.0 * Fix spiketrain lists in instantaneous rate.
* First fix for unittests missing fake_neo objects * Fixed all GetAllObjsTestCase unit tests * Started work on Events test case * Fixed Events test case * Fixed Epochs and Spiketrain tests * Starting to fix ExtractNeoAttrs * 7 more failing tests for ExtractNeoAttrs * All neo_tools tests fixed for Neo 0.10 * Enabled dataset generators from neo 0.10.0 * This PR adds SpikeTrainList as output of `get_all_spiketrains()`` * Use SpikeTrainList, work around SpikeTrainList.extend() bug. * Fix pandas_bridge tests to work without fake_neo() * PEP8 Line length corrections * More PEP8 finishes * Yet more PEP8 finishes * Last PEP8 finish * Update elephant/neo_tools.py
* added CI.yml containing workflows * added badge for CI tests to README.md * restructured requirements, environment.yml refactored to environment-docs.yml and environment-tests.yml. * adapted runners according to new new .yml files * update requirements in environment-*.yml to neo>=0.10.0
* initial draft for .zenodo.json, collected some authors for release 0.11.0 from commits since release 0.10.0 * added keywords * changed license id * corrected creator entry * added authors * corrected entry * added entry * Apply suggestions from code review added keyword, corrected affiliation for INM Co-authored-by: Michael Denker <[email protected]> * corrected INM affiliation in authors.rst and for all entries in .zenodo.json * added grants by id * added grant agreement no. 604102 (Human Brain Project, HBP) to .zenodo.json and acknowledgments.rst. * added "title" field * added orcid Pa. Da. * reformat Co-authored-by: Michael Denker <[email protected]>
* added Zenodo DOIs to docs, "how to cite elephant" * added links for DOIs * fix: added spade notebook to toctree * added description for DOIs * deleted extended description of different DOIs * added "doi:" to DOI links * typos * reformulate citation, fixed typo
…414) Co-authored-by: stellalessandra <[email protected]>
* added CI.yml containing workflows * added badge for CI tests to README.md * restructured requirements, environment.yml refactored to environment-docs.yml and environment-tests.yml. * adapted runners according to new new .yml files * re-add environment.yml for Travis, to be removed together with travis.yml * update requirements in environment-*.yml to neo>=0.10.0 * updated .yml files to python version 3.7 * removed python 3.6 from docs 'install.rst', added python version requirement to `setup.py` * rename travis conda 3.6 extras,opencl runner * updated build_wheels workflow to exclude python 3.6 * removed redundant line * changed structure of installation for docs runner * added extras to docs runner * added trigger for github actions CI: run tests after merged PR * added classifiers to setup.py (python >=3.7), removed classifiers for python 2 * add python 3.10 * update cibuildwheel version to 2.3.1
…5.0 (#441) * updated UE tutorial and requirements to use nixio 1.5.0 (#86) * updated links for datasets used in tutorials asset and UE * use 'read only' to assure backwards compatibility * reset outputs of notebook * remove permalinks from tutorials asset and UE * hotfix fixed jinja2 version to 3.0.3 * changed URLs to elephant-data master
* added function and environment variable to specifiy elephant-data download URLs * fixed errors * changed ASSET tutorial to work with nixio==1.5.0b3 * added docstrings * use return of download_elephant_data in tutorials * rename variable, update docstrings * fixed return of download_elephant_data * added version specific URL (depending on elephant version) * added in 'v' for versioning , e.g. v0.10.0 * changed check to see if version is available * Enh/data utils (#92) * added handling for SSL verification error * update ASSET and UE tutorials * Enh/data utils (#93) * allow download without verified certificate * rename data_utils to datasets, and download_elephant_data to download_datasets * fixed UE tutorial * fixed pep8 * removed download.py
* fixed deprecation warnings, replaced homogeneous_poisson_process with StationaryPoissonProcess * added import for scipy.signal * fixed size of output for instantaneous_rate, edited unittests accordingly * test to check length of outputs * added unittest to check consistency of rate times (should be multiple of sampling period), to get consistent ouput sizes, cutting of wings is done by fft convolve for center_kernel=True * fixed pep8, added comments, restructure * added include endpoint option * added notes to docstrings, reformat docstrings and code, removed endpoint option * fix docstrings * restructured unit tests, added regression tests * fixed pep8 * fixed indentation * fixed wrong return
* update copyright year to 2022 * fix PyPI description display and updated copyright year in `LICENSE.txt` * Bumped version number * clear outputs of gpfa notebook * fix pep8 * fix further pep8 * fixed CodeFactor issues * fixed further CodeFactor issues * removed maintainers_guide.rst * remove travis.yml * added release notes for release 0.11.0
* Update spike_train_correlation.py Improvement of Spike Time Tiling Coefficient (STTC) calculation by utilizing numpy function. Details: - use numpy.where to find overlapping tiles in run_T - some comments elaborated/changed - changed name of time_A to time_max for maximum time covered by tiles This enhancement was inspired by Thierry Nieus
* removed compilation of fim for darwin * compile only on Linux Windows
* added example to docstring, removed reference to annotations * fixed doctest for conversion
* removed compilation of fim for darwin * changed precision in asset to double, added 2 github action runners for macOS * removed viziphant from environment-tests.yml * Update setup.py Co-authored-by: Michael Denker <[email protected]>
* bumped version number to 0.11.1 * added doi for elephant 0.11.0 to citation * fixed typo in version * added initial draft of release note to release_notes.rst * fixed link to all versions of elephant * updated release notes * edited section to cite specific elephant version * update title in .zenodo.json
* added a test that compares the victor_purpura_distance results to the results of the oroginal matlab implementation Co-authored-by: Oliver Kloß <[email protected]>
Co-authored-by: Cristiano Köhler <[email protected]>
…he environment (#485) * added coverage to MPI runner, removed MPI from pip added function get_opencl_capability() to utils, to detect openCL devices * updated docstring, changed return logic * added unittest, regression Issue #481 Co-authored-by: Cristiano Köhler <[email protected]>
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update this branch to later include additions from NeuralEnsemble#491