Merge branch 'dev' into master

.github/workflows/cov_test_workflow.yml

@@ -0,0 +1,43 @@
+name: Run tests and determine coverage
+
+on:
+  # Triggers the workflow on push or pull request events
+  push:
+    branches:
+    - master
+    - dev
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install SyNCoPy
+      run: |
+        pip install -e .[dev]
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest and get coverage
+      run: |
+        cd syncopy/tests
+        pytest --color=yes --tb=short --verbose --cov=../../syncopy --cov-config=../../.coveragerc --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        name: syncopy-codecov
+        verbose: true

.gitlab-ci.yml

@@ -4,6 +4,9 @@ stages:
     - upload
     - deploy
 
+variables:
+    TEST_DIR: "$CI_PROJECT_DIR/syncopy/tests"
+
 intellinux:
     stage: tox
     allow_failure: true
@@ -19,6 +22,7 @@ intellinux:
     script:
     - rm -rf ~/.spy
     - source $HOME/miniconda/etc/profile.d/conda.sh
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - tox -p 0
@@ -37,6 +41,7 @@ powerlinux:
     script:
     - rm -rf ~/.spy
     - source /opt/conda/etc/profile.d/conda.sh
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - tox -p 0
@@ -53,6 +58,7 @@ intelwin:
         PYTEST_ADDOPTS: "--color=yes --tb=short --verbose"
         GIT_FETCH_EXTRA_FLAGS: --tags
     script:
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda.bat activate syncopy
     - tox
@@ -72,6 +78,7 @@ m1macos:
     - ulimit -n 25000
     - rm -rf ~/.spy
     - source /opt/conda/etc/profile.d/conda.sh
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - tox -p 0
@@ -92,7 +99,9 @@ slurmtest:
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - export PYTHONPATH=$CI_PROJECT_DIR
-    - srun -p DEV --mem=8000m -c 4 pytest
+    - srun -p DEV --mem=8000m -c 4 pytest --full $TEST_DIR/test_specest.py
+    - srun -p DEV --mem=8000m -c 4 pytest --full $TEST_DIR/test_connectivity.py
+    - srun -p DEV --mem=8000m -c 4 pytest --full --ignore=$TEST_DIR/test_specest.py --ignore=$TEST_DIR/test_connectivity.py
 
 pypitest:
     stage: upload
@@ -106,6 +115,7 @@ pypitest:
     script:
     - source $HOME/miniconda/etc/profile.d/conda.sh
     - conda update --yes conda
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - conda install --yes twine keyring rfc3986
@@ -136,6 +146,7 @@ pypideploy:
     script:
     - source $HOME/miniconda/etc/profile.d/conda.sh
     - conda update --yes conda
+    - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
     - conda install --yes twine keyring rfc3986

CHANGELOG.md

@@ -4,7 +4,63 @@ 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 follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [v0.2] - 2022-01-18
+## [v0.21] - 2022-04-13
+Feature update and bugfixes.
+
+### NEW
+- Added preprocessing functionality
+- Added experimental loading functionality for NWB 2.0 files
+- Added experimental loading functionality for Matlab mat files
+- Added support for "scalar" selections, i.e., things like `selectdata(trials=0)`
+  or `data.selectdata(channels='mychannel')`
+- Added command line argument "--full" for more granular testing: the new default
+  for running the testing pipeline is to execute a trimmed-down testing suite that
+  does not probe all possible input permutations but focuses on the core functionality
+  without sacrificing coverage.
+- New meta-function `taper_opt` parameter to control arbitrary taper (e.g. kaiser)
+  parameters
+
+### CHANGED
+- Renamed `_selection` class property to `selection`
+- Reworked plotting framework and made it matplotlib 3.5 compatible
+- The output of `show` is now automatically squeezed (i.e., singleton dimensions
+  are removed from the returned array).
+- Enhanced online documentation, now also covering connectivity analysis
+- Multi-tapering (`freqanalysis`, `connectivityanalysis`) now is switched on by
+  only specifying the `tapsmofrq` parameter, removed the need for the additional
+  and redundant setting of `taper='dpss'`
+- Granger-Geweke algorithm now matches the reference implementation (Dhamala 2008)
+  with machine precision
+
+### REMOVED
+- Do not parse scalars using `numbers.Number`, use `numpy.number` instead to
+  catch Boolean values
+- Do not raise a `SPYTypeError` if an arithmetic operation is performed using
+  objects of different numerical types (real/complex; closes #199)
+
+### DEPRECATED
+- Removed loading code for ESI binary format that is no longer supported
+- Repaired top-level imports: renamed `connectivity` to `connectivityanalysis`
+  and the "connectivity" module is now called "nwanalysis"
+- Included `conda clean` in CD pipeline to avoid disk fillup by unused conda
+  packages/cache
+- Inverted `selectdata` messaging policy: only actual on-disk copy operations
+  trigger a `SPYInfo` message (closes #197)
+- Matched selector keywords and class attribute names, i.e., selecting channels
+  is now done by using a `select` dictionary with key `'channel'` (not `'channels'`
+  as before). See the documentation of `selectdata` for details.
+- Retired Travis CI tests since free test runs are exhausted. Migrated to GitHub
+  actions (and re-included codecov)
+
+### FIXED
+- The `trialdefinition` arrays constructed by the `Selector` class were incorrect
+  for `SpectralData` objects without time-axis, resulting in "empty" trials. This
+  has been fixed (closes #207)
+- Repaired `array_parser` to adequately complain about mixed-type arrays (closes #211)
+- The `show` routine now consistently returns a list of trials if and only if
+  multiple trials are selected
+
+## [v0.20] - 2022-01-18
 Major Release
 
 ### NEW

MANIFEST.in

@@ -2,6 +2,5 @@ exclude .gitignore
 exclude .gitlab-ci.yml
 exclude MANIFEST.in
 exclude .readthedocs.yml
-exclude .travis.yml
 recursive-exclude .github *
 recursive-exclude doc *

README.rst

@@ -8,11 +8,25 @@ Systems Neuroscience Computing in Python
 |Conda Version| |PyPi Version| |License|
 
 .. |Conda Version| image:: https://img.shields.io/conda/vn/conda-forge/esi-syncopy.svg
-   :target: https://anaconda.org/conda-forge/esi-syncopy 
-.. |PyPI version| image:: https://badge.fury.io/py/esi-syncopy.svg 
+   :target: https://anaconda.org/conda-forge/esi-syncopy
+.. |PyPI version| image:: https://badge.fury.io/py/esi-syncopy.svg
    :target: https://badge.fury.io/py/esi-syncopy
 .. |License| image:: https://img.shields.io/github/license/esi-neuroscience/syncopy
 
+master branch status: |Master Tests| |Master Coverage|
+
+.. |Master Tests| image:: https://github.com/esi-neuroscience/syncopy/actions/workflows/cov_test_workflow.yml/badge.svg?branch=master
+   :target: https://github.com/esi-neuroscience/syncopy/actions/workflows/cov_test_workflow.yml
+.. |Master Coverage| image:: https://codecov.io/gh/esi-neuroscience/syncopy/branch/master/graph/badge.svg?token=JEI3QQGNBQ
+   :target: https://codecov.io/gh/esi-neuroscience/syncopy
+
+dev branch status: |Dev Tests| |Dev Coverage|
+
+.. |Dev Tests| image:: https://github.com/esi-neuroscience/syncopy/actions/workflows/cov_test_workflow.yml/badge.svg?branch=dev
+   :target: https://github.com/esi-neuroscience/syncopy/actions/workflows/cov_test_workflow.yml
+.. |Dev Coverage| image:: https://codecov.io/gh/esi-neuroscience/syncopy/branch/dev/graph/badge.svg?token=JEI3QQGNBQ
+   :target: https://codecov.io/gh/esi-neuroscience/syncopy
+
 Syncopy aims to be a user-friendly toolkit for *large-scale*
 electrophysiology data-analysis in Python. We strive to achieve the following goals:
 

doc/README.md

@@ -0,0 +1,10 @@
+
+# (Online-) Documentation
+
+## Build Requirements
+
+Install (debian based packages):
+- `sphinx-common`
+- `python3-sphinx-bootstrap-theme`
+
+then run `make html` from this folder

doc/source/README.rst

@@ -24,15 +24,16 @@ We strive to achieve the following goals:
 
 Getting Started
 ---------------
-Our :doc:`Quickstart Guide <quickstart>` covers installation and basic usage. 
-More in-depth information relevant to Syncopy users can be found in our 
-:doc:`User Guide <user/users>`. Want to contribute or just curious how the sausage 
-is made? Take a look at our :doc:`Developer Guide <developer/developers>`. Once again
-in order of brevity:
+- Prerequisites: :doc:`Install Syncopy </setup>`
+- Jumping right in: :doc:`Quickstart Guide <quickstart/quickstart>`
 
-* :doc:`Quickstart Guide <quickstart>`
-* :doc:`User Guide <user/users>`
-* :doc:`Developer Guide <developer/developers>`
+Want to contribute or just curious how the sausage 
+is made? Take a look at our :doc:`Developer Guide <developer/developers>`. 
+
+
+In depth Guides and Tutorials
+-----------------------------
+* :doc:`General User Guide <user/users>`
 
 Navigation
 ----------
@@ -50,6 +51,8 @@ For general inquiries please contact syncopy (at) esi-frankfurt.de.
 .. toctree::
    :hidden:
 
-   quickstart
-   user/users.rst    
+   quickstart/quickstart.rst
+   setup
+   user/users.rst
+   user/user_api.rst
    developer/developers.rst   

doc/source/_static/esi-style.css

@@ -8,4 +8,10 @@ a.reference.external{
 
 p.rubric {
     font-size: 16px;
-}
+}
+
+p {
+    font-size: 1.1em
+}
+
+

doc/source/conf.py

@@ -22,7 +22,7 @@
 
 project = 'Syncopy'
 copyright = '2020, Joscha Schmiedt and Stefan Fuertinger'
-author = 'Joscha Schmiedt and Stefan Fuertinger'
+author = 'Joscha Schmiedt, Stefan Fuertinger and Gregor Mönke'
 
 # The short X.Y version
 version = syncopy.__version__
@@ -129,7 +129,9 @@ def setup(app):
     # Global TOC depth for "site" navbar tab. (Default: 1)
     # Switching to -1 shows all levels.
     'globaltoc_depth': 2,
-    'bootswatch_theme': "lumen",
+    # Currently, the supported themes are:
+    # - Bootstrap 3: https://bootswatch.com/3
+    'bootswatch_theme': "simplex",
     'navbar_links': [
         ("GitHub", "https://www.github.com/esi-neuroscience/syncopy", True),
     ],
@@ -195,7 +197,7 @@ def setup(app):
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'Syncopy.tex', 'Syncopy Documentation',
-     'Gregor Moenke, Joscha Schmiedt and Stefan Fuertinger', 'manual'),
+     'Gregor Mönke, Joscha Schmiedt and Stefan Fuertinger', 'manual'),
 ]
 
 

doc/source/quickstart/ar2_nw.py

@@ -0,0 +1,19 @@
+import numpy as np
+import syncopy as spy
+from syncopy.tests import synth_data
+
+nTrials = 50
+nSamples = 1500
+trls = []
+# 2x2 Adjacency matrix to define coupling
+AdjMat = np.zeros((2, 2))
+# coupling 0 -> 1
+AdjMat[0, 1] = 0.2
+
+for _ in range(nTrials):
+
+    trl = synth_data.AR2_network(AdjMat, nSamples=nSamples)
+    trls.append(trl)
+
+data = spy.AnalogData(trls, samplerate=500)
+spec = spy.freqanalysis(data, tapsmofrq=3, keeptrials=False)

doc/source/quickstart/damped_harm.py

@@ -0,0 +1,29 @@
+import numpy as np
+import syncopy as spy
+
+
+nTrials = 50
+nSamples = 1000
+nChannels = 2
+samplerate = 500   # in Hz
+
+# the sampling times vector needed for construction
+tvec = np.arange(nSamples) * 1 / samplerate
+# the 30Hz harmonic
+harm = np.cos(2 * np.pi * 30 * tvec)
+# dampening down to 10% of the original amplitude
+dampening = np.linspace(1, 0.1, nSamples)
+signal = dampening * harm
+
+# collect trials
+trials = []
+for _ in range(nTrials):
+
+    # start with the noise
+    trial = np.random.randn(nSamples, nChannels)
+    # now add the damped harmonic on the 1st channel
+    trial[:, 0] += signal
+    trials.append(trial)
+
+# instantiate Syncopy data object
+data = spy.AnalogData(trials, samplerate=samplerate)