merge

Author: alejoe91

.github/workflows/io-test.yml

@@ -19,7 +19,7 @@ jobs:
       matrix:
         # "macos-latest", "windows-latest"
         os: ["ubuntu-latest", ]
-        python-version: ['3.8', ]
+        python-version: ['3.9', ]
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -37,7 +37,7 @@ jobs:
         # the key depend on the last commit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
         id: ephy_testing_data_hash
         run: |
-          echo "latest_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> GITHUB_OUTPUT
+          echo "latest_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
 
       - uses: actions/cache@v3
         # Loading cache of ephys_testing_dataset
@@ -59,7 +59,7 @@ jobs:
         id: cache-conda-env
         with:
           path: /usr/share/miniconda/envs/neo-test-env
-          key: ${{ runner.os }}-conda-env-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ hashFiles('**/environment_testing.txt') }}-${{ steps.date.outputs.date }}
+          key: ${{ runner.os }}-conda-env-${{ hashFiles('**/pyproject.toml') }}-${{ steps.date.outputs.date }}
 
       - name: Install testing dependencies
         # testing environment is only installed if no cache was found
@@ -75,6 +75,7 @@ jobs:
       - name: Install neo
         run: |
           pip install --upgrade -e .
+          pip install .[test]
 
       - name: Test with pytest
         run: |

.readthedocs.yaml

@@ -12,4 +12,6 @@ python:
   install:
     - method: pip
       path: .
-    - requirements: doc/requirements_docs.txt
+      extra_requirements:
+        - docs
+

doc/requirements_docs.txt

@@ -13,17 +13,16 @@
 
 import os
 import sys
+import re
 
 from packaging.version import Version
 
-with open("../../neo/version.py") as fp:
-    d = {}
-    exec(fp.read(), d)
-    neo_release = d['version']
+with open('../../pyproject.toml', mode='r') as f:
+    txt = f.read()
+    neo_release = re.findall('version = "(\S+)"', txt)[0]
 
 neo_version = '.'.join((str(e) for e in Version(neo_release).release[:2]))
 
-
 AUTHORS = 'Neo authors and contributors <[email protected]>'
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -51,7 +50,7 @@
 
 # General information about the project.
 project = 'Neo'
-copyright = '2010-2022, ' + AUTHORS
+copyright = '2010-2023, ' + AUTHORS
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/conf.py

@@ -40,14 +40,12 @@ Requirements
 
     * Python_ 3.8 or later
     * numpy_ >= 1.19.5
-    * quantities_ >= 0.12.1
-    * nose_ >= 1.1.2 (for running tests)
+    * quantities_ >= 0.14.1
+    * pytest (for running tests)
     * Sphinx_ (for building documentation)
-    * (optional) coverage_ >= 2.85 (for measuring test coverage)
-    * (optional) scipy >= 0.12 (for MatlabIO)
-    * (optional) h5py >= 2.5 (for KwikIO)
-    * (optional) nixio (for NixIO)
-    * (optional) pillow (for TiffIO)
+
+There are many optional dependencies for different IO modules (see below).
+If you don't install these, tests for those modules will be skipped.
 
 We strongly recommend you develop within a virtual environment (from virtualenv, venv or conda).
 
@@ -65,26 +63,20 @@ To get a local copy of the repository::
     $ git clone [email protected]:<username>/python-neo.git
 
 Now you need to make sure that the ``neo`` package is on your PYTHONPATH.
-You can do this either by installing Neo::
+You can do this by installing Neo with the *editable* option,
+which avoids reinstalling when there are changes in the code::
 
     $ cd python-neo
-    $ python3 setup.py install
-
-(if you do this, you will have to re-run ``setup.py install`` any time you make
-changes to the code) *or* by creating symbolic links from somewhere on your
-PYTHONPATH, for example::
-
-    $ ln -s python-neo/neo
-    $ export PYTHONPATH=/some/directory:${PYTHONPATH}
+    $ pip install -e .
 
-An alternate solution is to install Neo with the *develop* option, this avoids
-reinstalling when there are changes in the code::
+To install all dependencies needed for testing, including optional dependencies
+for IO modules, run::
 
-    $ sudo python setup.py develop
+    $ pip install -e .[test]
 
-or using the "-e" option to pip::
+or if using the zsh shell::
 
-    $ pip install -e python-neo
+    $ pip install -e ".[test]"
 
 To update to the latest version from the repository::
 
@@ -97,20 +89,15 @@ Running the test suite
 Before you make any changes, run the test suite to make sure all the tests pass
 on your system::
 
-    $ cd neo/test
-    $ python3 -m unittest discover
-
-If you have nose installed::
-
-    $ nosetests
+    $ pytest
 
 At the end, if you see "OK", then all the tests
 passed (or were skipped because certain dependencies are not installed),
 otherwise it will report on tests that failed or produced errors.
 
 To run tests from an individual file::
 
-    $ python3 test_analogsignal.py
+    $ pytest test_analogsignal.py
 
 
 Writing tests
@@ -123,7 +110,7 @@ check that the test now passes.
 
 To see how well the tests cover the code base, run::
 
-    $ nosetests --with-coverage --cover-package=neo --cover-erase
+    $ pytest --cov=neo
 
 
 Working on the documentation
@@ -221,11 +208,11 @@ Making a release
 
 Add a section in :file:`/doc/source/whatisnew.rst` for the release.
 
-First check that the version string (in :file:`neo/version.py`) is correct.
+First check that the version string (in :file:`pyproject.toml`) is correct.
 
-To build a source package::
+To build source and wheel packages::
 
-    $ python setup.py sdist
+    $ python -m build
 
 
 Tag the release in the Git repository and push it::
@@ -237,7 +224,7 @@ Tag the release in the Git repository and push it::
 
 To upload the package to `PyPI`_ (the members of the `maintainers team`_ have the necessary permissions to do this)::
 
-    $ twine upload dist/neo-0.X.Y.tar.gz
+    $ twine upload dist/neo-0.X.Y.tar.gz dist/neo-0.X.Y-py3-none-any.whl
 
 .. talk about readthedocs
 

doc/source/developers_guide.rst

@@ -0,0 +1,63 @@
+========================
+Neo 0.12.0 release notes
+========================
+
+17th February 2022
+
+.. currentmodule:: neo.io
+
+Change of packaging system
+--------------------------
+
+We have updated our tooling for building and installing Neo to follow the
+`latest recommendations`_ of the Python community (using pyproject.toml, etc.)
+
+For users, this means you should always use `pip` to install Neo,
+unless you're using another package manager such as `conda`, `spack`,
+or a Linux package manager.
+
+
+Improved file format detection
+------------------------------
+
+In addition to the existing :func:`get_io()` function, there is now an additional utility function
+for finding a suitable IO for a given dataset.
+
+:func:`list_candidate_ios()` provides a list of all IOs supporting the formats detected in a given path.
+This list is generated based on the file extension of the file
+or the extensions of the matching files in a given folder,
+potentially also scanning subfolders if required.
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to
+:class:`OpenEphysBinaryIO` and :class:`NWBIO`.
+
+
+Other changes
+-------------
+
+- The IO test suite has been greatly improved, with a substantial speed-up.
+
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+Updated dependencies
+--------------------
+
+We have dropped support for Python 3.7 and added support for 3.11.
+Neo now requires NumPy version >=1.19.5 and Quantities >=v0.14.1.
+
+
+Acknowledgements
+----------------
+
+Thanks to Julia Sprenger, Andrew Davison, and Samuel Garcia for their contributions to this release.
+
+.. generated with git shortlog --since=2022-10-21 -sne then checking Github for PRs merged since the last release but with commits before then
+
+.. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+milestone%3A0.12.0+is%3Aclosed
+.. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+merged%3A%3E2022-10-21+milestone%3A0.12.0
+.. _`latest recommendations`: https://packaging.python.org/en/latest/

doc/source/releases/0.12.0.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.12.0.rst
    releases/0.11.1.rst
    releases/0.11.0.rst
    releases/0.10.2.rst

doc/source/whatisnew.rst

@@ -4,5 +4,3 @@ channels:
 dependencies:
   - datalad
   - pip
-  - pip:
-    - -r requirements_testing.txt

environment_testing.yml

@@ -2,6 +2,9 @@
 Neo is a package for representing electrophysiology data in Python,
 together with support for reading a wide range of neurophysiology file formats
 '''
+import importlib.metadata
+# this need to be at the begining because some sub module will need the version
+__version__ = importlib.metadata.version("neo")
 
 import logging
 
@@ -10,4 +13,3 @@
 from neo.core import *
 from neo.io import *
 
-from neo.version import version as __version__

neo/__init__.py

@@ -272,12 +272,14 @@ def _merge_array_annotations(self, other):
         # Return the merged array_annotations
         return merged_array_annotations
 
-    def rescale(self, units):
+    def rescale(self, units, dtype=None):
         '''
-        Return a copy of the object converted to the specified
-        units
+        Return a copy of the object converted to the specified units.
+        The `dtype` argument exists only for backward compatibility within quantities, see
+        https://github.com/python-quantities/python-quantities/pull/204
         :return: Copy of self with specified units
         '''
+
         # Use simpler functionality, if nothing will be changed
         dim = pq.quantity.validate_dimensionality(units)
         if self.dimensionality == dim: