Merge pull request #322 from esi-neuroscience/dev

Dev merge

.github/workflows/cov_test_workflow.yml

@@ -1,4 +1,4 @@
-name: Run tests and determine coverage
+name: Run basic tests and determine coverage
 
 on:
   # Triggers the workflow on push or pull request events
@@ -22,20 +22,25 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
+    - name: Install poetry
+      run: |
+        pip install poetry
     - name: Install SyNCoPy
       run: |
-        pip install -e .[dev]
+        poetry install
     - 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
+        poetry run 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
+        poetry run 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
+        # run parallel tests only for base CR
+        poetry run pytest -k 'computationalroutine and parallel'
+        # don't run general parallel tests
+        poetry run pytest  -k 'not parallel' --color=yes --tb=short --verbose --cov=../../syncopy --cov-config=../../.coveragerc --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v2
       with:

.gitlab-ci.yml

@@ -44,6 +44,8 @@ powerlinux:
     - conda clean --all -y
     - conda env update -f syncopy.yml --prune
     - conda activate syncopy
+    # see https://github.com/conda/conda/issues/10178
+    - conda install ruamel.yaml
     - tox -p 0
 
 intelwin:
@@ -104,7 +106,7 @@ slurmtest:
     - srun -p DEV --mem=8000m -c 4 pytest --full test_specest.py -k 'para'
     - srun -p DEV --mem=8000m -c 4 pytest --full test_connectivity.py
     - srun -p DEV --mem=8000m -c 4 pytest --full --ignore=test_specest.py --ignore=test_connectivity.py
-
+    
 pypitest:
     stage: upload
     only:
@@ -115,22 +117,18 @@ pypitest:
     variables:
         GIT_FETCH_EXTRA_FLAGS: --tags
     script:
+    - rm -rf dist/
     - source $HOME/miniconda/etc/profile.d/conda.sh
-    - conda update --yes conda
-    - conda clean --all -y
-    - conda env update -f syncopy.yml --prune
-    - conda activate syncopy
-    - conda install --yes twine keyring rfc3986
-    - conda update --yes twine keyring rfc3986
-    - rm -rf dist/ build/ esi_syncopy.egg-info/
-    - python setup.py sdist bdist_wheel
-    - tarname="$(basename -- $(ls dist/*.tar.gz) .tar.gz)"
-    - version=$(sed -e 's/esi-syncopy-\(.*\)/\1/' <<< "$tarname")
-    - twine upload --repository testpypi --config-file=~/.esipypirc dist/*
+    # get poetry with python 3.8
+    - conda activate spy38
+    - poetry build
+    # needs config pypi credentials on runner
+    - poetry publish -r testpypi
     - sleep 300
     - conda create --yes --name piptest python=3.8
     - conda activate piptest
     - conda install --yes pip
+    - version=$(grep 'version =' pyproject.toml | awk -F "\"" '{print $2}')
     - pip --no-cache-dir install --extra-index-url https://test.pypi.org/simple esi-syncopy==$version
     - python -c "import syncopy as spy"
     - conda deactivate
@@ -146,13 +144,10 @@ pypideploy:
     variables:
         GIT_FETCH_EXTRA_FLAGS: --tags
     script:
+    - rm -rf dist/
     - 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
-    - conda update --yes twine keyring rfc3986
-    - rm -rf dist/ build/ esi_syncopy.egg-info/
-    - python setup.py sdist bdist_wheel
-    - twine upload --config-file=~/.esipypirc dist/*
+    # get poetry with python 3.8
+    - conda activate spy38
+    - poetry build
+    # needs config pypi credentials on runner
+    - poetry publish -r pypi

CHANGELOG.md

@@ -4,6 +4,31 @@ 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).
 
+
+
+## [Unreleased]
+
+### NEW
+- Added down- and resampling algorithms for the new meta-function `resampledata`
+- Added FOOOF method as a post-processing option for the freqanalysis method mtmfft.
+- new global `spy.copy()` function which copies entire Syncopy objects on disk
+- Added `.info` attribute for all data classes to store auxiliary meta information
+
+
+### CHANGED
+- the `out.cfg` attached to an analysis result now allows to replay all analysis methods
+- `connectivityanalysis` now has FT compliant output support for the coherence
+- `spy.cleanup` now has exposed `interactive` parameter
+- removed keyword `deep` from `copy()`, all our copies are in fact deep
+- demeaning after tapering for granger analysis
+
+### FIXED
+- `out.cfg` global side-effects (sorry again @kajal5888)
+- `CrossSpectralData` plotting
+- mixing of explicit keywords and `cfg` to control analysis
+- fixed error on initializing SpikeData with empty ndarray (#257)
+
+
 ## [2022.05] - 2022-05-13
 Bugfixes and features additions for `EventData` objects.
 

CITATION.cff

@@ -37,5 +37,5 @@ keywords:
 - spectral-methods
 - brain
 repository-code: https://github.com/esi-neuroscience/syncopy
-version: 0.3.dev187
-date-released: '2022-04-13'
+version: 2022.6.dev203
+date-released: '2022-07-21'

doc/source/README.rst

@@ -1,7 +1,7 @@
 .. Syncopy documentation master file
 
 .. title:: Syncopy Documentation
-   
+
 .. image:: _static/syncopy_logo.png
     :alt: Syncopy logo
     :height: 200px
@@ -11,14 +11,14 @@
 Welcome to the Documentation of SyNCoPy!
 ========================================
 
-SyNCoPy (**Sy**\stems **N**\euroscience **Co**\mputing in **Py**\thon, spelled Syncopy in the following) 
-is a Python toolkit for user-friendly, large-scale electrophysiology data analysis. 
+SyNCoPy (**Sy**\stems **N**\euroscience **Co**\mputing in **Py**\thon, spelled Syncopy in the following)
+is a Python toolkit for user-friendly, large-scale electrophysiology data analysis.
 We strive to achieve the following goals:
 
 1. Syncopy provides a full *open source* Python environment for reproducible
    electrophysiology data analysis.
-2. Syncopy is *scalable* to accommodate *very large* datasets. It automatically 
-   makes use of available computing resources and is developed with built-in 
+2. Syncopy is *scalable* to accommodate *very large* datasets. It automatically
+   makes use of available computing resources and is developed with built-in
    parallelism in mind.
 3. Syncopy is *compatible* with the MATLAB toolbox `FieldTrip <http://www.fieldtriptoolbox.org/>`_.
 
@@ -27,15 +27,19 @@ Getting Started
 - Prerequisites: :doc:`Install Syncopy </setup>`
 - Jumping right in: :doc:`Quickstart Guide <quickstart/quickstart>`
 
-Want to contribute or just curious how the sausage 
-is made? Take a look at our :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:`Basic Concepts <user/concepts>`
 * :doc:`Syncopy for FieldTrip Users <user/fieldtrip>`
 * :doc:`Handling Data <user/data>`
+* :doc:`Fooof <tutorials/fooof>`
+
+Auto-generate API Docs
+-----------------------
 * :doc:`User API <user/user_api>`
 
 Navigation
@@ -46,8 +50,8 @@ Navigation
 
 Contact
 -------
-To report bugs or ask questions please use our `GitHub issue tracker <https://github.com/esi-neuroscience/syncopy/issues>`_. 
-For general inquiries please contact syncopy (at) esi-frankfurt.de. 
+To report bugs or ask questions please use our `GitHub issue tracker <https://github.com/esi-neuroscience/syncopy/issues>`_.
+For general inquiries please contact syncopy (at) esi-frankfurt.de.
 
 .. Any sections to be included in the Documentation dropdown menu have to be in the toctree
 
@@ -60,4 +64,5 @@ For general inquiries please contact syncopy (at) esi-frankfurt.de.
    user/fieldtrip.rst
    user/data.rst
    user/user_api.rst
-   developer/developers.rst   
+   tutorials/fooof.rst
+   developer/developers.rst

doc/source/conf.py

@@ -96,7 +96,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.