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‎.github/workflows/caches_cron_job.yml‎

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Original file line numberDiff line numberDiff line change
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jobs:
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create-conda-env-cache-if-missing:
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name: Caching conda env
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runs-on: "ubuntu-latest"
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strategy:
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fail-fast: true
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defaults:
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# by default run in bash mode (required for conda usage)
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- name: Get current year-month
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id: date
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run: |
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echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
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- name: Get current dependencies hash
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id: dependencies
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run: |
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echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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- uses: actions/cache@v3
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# the cache for python package is reset:
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# * every month
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# * when package dependencies change
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id: cache-conda-env
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with:
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path: /usr/share/miniconda/envs/neo-test-env
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key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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- name: Cache found?
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run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
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# activate environment if not restored from cache
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- uses: conda-incubator/[email protected]
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if: steps.cache-conda-env.outputs.cache-hit != 'true'
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with:
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activate-environment: neo-test-env
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environment-file: environment_testing.yml
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python-version: 3.9
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- name: Create the conda environment to be cached
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if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# create conda env, configure git and install pip, neo and test dependencies from master
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# for PRs that change dependencies, this environment will be updated in the test workflow
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run: |
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git config --global user.email "neo_ci@fake_mail.com"
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git config --global user.name "neo CI"
62-
python -m pip install -U pip # Official recommended way
63-
pip install --upgrade -e .[test]
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# create-conda-env-cache-if-missing:
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# name: Caching conda env
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# runs-on: "ubuntu-latest"
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# strategy:
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# fail-fast: true
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# defaults:
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# # by default run in bash mode (required for conda usage)
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# run:
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# shell: bash -l {0}
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# steps:
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# - uses: actions/checkout@v3
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# - name: Get current year-month
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# id: date
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# run: |
28+
# echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
29+
30+
# - name: Get current dependencies hash
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# id: dependencies
32+
# run: |
33+
# echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
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35+
# - uses: actions/cache@v3
36+
# # the cache for python package is reset:
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# # * every month
38+
# # * when package dependencies change
39+
# id: cache-conda-env
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# with:
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# path: /usr/share/miniconda/envs/neo-test-env
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# key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
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# - name: Cache found?
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# run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
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# # activate environment if not restored from cache
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# - uses: conda-incubator/[email protected]
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# if: steps.cache-conda-env.outputs.cache-hit != 'true'
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# with:
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# activate-environment: neo-test-env
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# environment-file: environment_testing.yml
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# python-version: 3.9
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55+
# - name: Create the conda environment to be cached
56+
# if: steps.cache-conda-env.outputs.cache-hit != 'true'
57+
# # create conda env, configure git and install pip, neo and test dependencies from master
58+
# # for PRs that change dependencies, this environment will be updated in the test workflow
59+
# run: |
60+
# git config --global user.email "neo_ci@fake_mail.com"
61+
# git config --global user.name "neo CI"
62+
# python -m pip install -U pip # Official recommended way
63+
# pip install --upgrade -e .[test]
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create-data-cache-if-missing:
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name: Caching data env

‎.github/workflows/core-test.yml‎

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Original file line numberDiff line numberDiff line change
@@ -24,27 +24,44 @@ jobs:
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strategy:
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fail-fast: true
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matrix:
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os: ["ubuntu-latest", "windows-latest"]
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# "macos-latest",
29-
python-version: ['3.8', '3.9', '3.10', '3.11']
30-
numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1']
27+
os: ["ubuntu-latest", "windows-latest", "macos-latest"]
28+
python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
29+
numpy-version: ['1.22.4', '1.23.5', '1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1']
30+
# numpy 1.22: 3.10, 1.23: 3.11, 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
3131
exclude:
32-
- python-version: '3.8'
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numpy-version: '1.25.1'
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- python-version: '3.10'
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numpy-version: '1.20.3'
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- python-version: '3.11'
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numpy-version: '1.20.3'
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- python-version: '3.9'
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numpy-version: '2.1'
3834
- python-version: '3.11'
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numpy-version: '1.21.6'
35+
numpy-version: '1.22.4'
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- python-version: '3.12'
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numpy-version: '1.22.4'
38+
- python-version: '3.12'
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numpy-version: '1.23.5'
40+
- python-version: '3.12'
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numpy-version: '1.24.4'
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- python-version: '3.12'
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numpy-version: '1.25.1'
44+
- python-version: '3.13'
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numpy-version: '1.22.4'
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- python-version: '3.13'
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numpy-version: '1.23.5'
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- python-version: '3.13'
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numpy-version: '1.24.4'
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- python-version: '3.13'
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numpy-version: '1.25.1'
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- python-version: '3.13'
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numpy-version: '1.26.4'
54+
- python-version: '3.13'
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numpy-version: '2.0.2'
56+
4057
steps:
4158
- name: Set up Python ${{ matrix.python-version }}
42-
uses: actions/setup-python@v4
59+
uses: actions/setup-python@v5
4360
with:
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python-version: ${{ matrix.python-version }}
4562

4663
- name: Checkout repository
47-
uses: actions/checkout@v3
64+
uses: actions/checkout@v4
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4966
- name: Install numpy ${{ matrix.numpy-version }}
5067
run: |

‎.github/workflows/io-test.yml‎

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Original file line numberDiff line numberDiff line change
@@ -13,20 +13,21 @@ concurrency: # Cancel previous workflows on the same pull request
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jobs:
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build-and-test:
16-
name: Test on (${{ inputs.os }})
16+
name: Test on (${{ inputs.os }}) (${{ matrix.python-version}}) (${{ matrix.numpy-version }})
1717
runs-on: ${{ inputs.os }}
1818
strategy:
1919
fail-fast: true
2020
matrix:
21-
python-version: ['3.9', ]
21+
python-version: ['3.9', '3.12']
22+
numpy-version: ['1.26', '2.0']
2223
defaults:
2324
# by default run in bash mode (required for conda usage)
2425
run:
2526
shell: bash -l {0}
2627
steps:
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2829
- name: Checkout repository
29-
uses: actions/checkout@v3
30+
uses: actions/checkout@v4
3031

3132
- name: Get current year-month
3233
id: date
@@ -38,7 +39,7 @@ jobs:
3839
run: |
3940
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
4041
41-
- uses: actions/cache/restore@v3
42+
- uses: actions/cache/restore@v4
4243
# Loading cache of ephys_testing_dataset
4344
id: cache-datasets
4445
with:
@@ -48,33 +49,36 @@ jobs:
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4950
- uses: conda-incubator/setup-miniconda@v3
5051
with:
51-
activate-environment: neo-test-env
52+
activate-environment: neo-test-env-${{ matrix.python-version }}
5253
python-version: "${{ matrix.python-version }}"
53-
54-
- name: Get current dependencies hash
55-
id: dependencies
56-
run: |
57-
echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
58-
59-
- uses: actions/cache/restore@v3
54+
55+
# TEST NOT USING CACHE
56+
#- name: Get current dependencies hash
57+
# id: dependencies
58+
# run: |
59+
# echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
60+
61+
#- uses: actions/cache/restore@v3
6062
# the cache for python package is reset:
6163
# * every month
6264
# * when package dependencies change
63-
id: cache-conda-env
64-
with:
65-
path: /usr/share/miniconda/envs/neo-test-env
66-
key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
65+
# id: cache-conda-env
66+
# with:
67+
# path: /usr/share/miniconda/envs/neo-test-env-${{ matrix.python-version }}
68+
# key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
6769
# restore-keys match any key that starts with the restore-key
68-
restore-keys: |
69-
${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
70-
${{ runner.os }}-conda-env-
70+
# restore-keys: |
71+
# ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-
72+
# ${{ runner.os }}-conda-env-
7173

7274
- name: Install testing dependencies
7375
# testing environment is only created from yml if no cache was found
7476
# restore-key hits should result in `cache-hit` == 'false'
75-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
77+
#if: steps.cache-conda-env.outputs.cache-hit != 'true'
7678
run: |
77-
conda env update --name neo-test-env --file environment_testing.yml --prune
79+
conda install datalad pip numpy=${{ matrix.numpy-version }} -c conda-forge
80+
# this command is for updating cache. We are resting removal.
81+
# conda env update --name neo-test-env-${{ matrix.python-version }} --file environment_testing.yml --prune
7882

7983
- name: Configure git
8084
run: |
@@ -89,16 +93,17 @@ jobs:
8993
- name: Install neo including dependencies
9094
# installation with dependencies is only required if no cache was found
9195
# restore-key hits should result in `cache-hit` == 'false'
92-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
96+
# if: steps.cache-conda-env.outputs.cache-hit != 'true'
9397
run: |
9498
pip install --upgrade -e .
9599
pip install .[test]
96100
97-
- name: Install neo without dependencies
101+
# TEST NOT USING CACHE
102+
#- name: Install neo without dependencies
98103
# only installing neo version to test as dependencies should be in cached conda env already
99-
if: steps.cache-conda-env.outputs.cache-hit == 'true'
100-
run: |
101-
pip install --no-dependencies -e .
104+
# if: steps.cache-conda-env.outputs.cache-hit == 'true'
105+
# run: |
106+
# pip install --no-dependencies -e .
102107

103108
- name: Install wine
104109
run: |
@@ -107,6 +112,14 @@ jobs:
107112
sudo apt-get update -qq
108113
sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
109114
115+
- name: Pip list
116+
run: |
117+
pip list
118+
119+
- name: Conda list
120+
run: |
121+
conda list
122+
110123
- name: Test with pytest
111124
env:
112125
HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path

‎.gitignore‎

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Original file line numberDiff line numberDiff line change
@@ -76,4 +76,8 @@ doc/*.plx
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doc/*.nev
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doc/*.ns5
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doc/*.nix
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doc/*.nwb
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doc/*.nwb
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*.plx
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*.smr
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B95.zip
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grouped_ephys

‎LICENSE.txt‎

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@@ -1,4 +1,4 @@
1-
Copyright (c) 2010-2024, Neo authors and contributors
1+
Copyright (c) 2010-2025, Neo authors and contributors
22
All rights reserved.
33

44
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

‎README.rst‎

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@@ -31,10 +31,13 @@ A project with similar aims but for neuroimaging file formats is `NiBabel`_.
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Code status
3232
-----------
3333

34+
.. image:: https://img.shields.io/pypi/v/neo.svg
35+
:target: https://pypi.python.org/pypi/neo
36+
:alt: PyPI Release Version
3437
.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/core-test.yml/badge.svg?event=push&branch=master
3538
:target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
3639
:alt: Core Test Status (Github Actions)
37-
.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/io-test.yml/badge.svg?event=push&branch=master
40+
.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/io-test_trigger.yml/badge.svg?event=push&branch=master
3841
:target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
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:alt: IO Test Status (Github Actions)
4043
.. image:: https://coveralls.io/repos/NeuralEnsemble/python-neo/badge.png
@@ -53,7 +56,7 @@ For installation instructions, see doc/source/install.rst
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5457
To cite Neo in publications, see CITATION.txt
5558

56-
:copyright: Copyright 2010-2024 by the Neo team, see doc/source/authors.rst.
59+
:copyright: Copyright 2010-2025 by the Neo team, see doc/source/authors.rst.
5760
:license: 3-Clause Revised BSD License, see LICENSE.txt for details.
5861

5962
Funding
@@ -64,7 +67,8 @@ grant agreement FETPI-015879 (FACETS), by the European Union Seventh Framework P
6467
under grant agreements no. 269921 (BrainScaleS) and no. 604102 (HBP),
6568
and by the European Union’s Horizon 2020 Framework Programme for
6669
Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1),
67-
No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3).
70+
No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3),
71+
and by the European Union's Research and Innovation Program Horizon Europe Grant Agreement No. 101147319 (EBRAINS 2.0).
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.. _OpenElectrophy: https://github.com/OpenElectrophy/OpenElectrophy
7074
.. _Elephant: http://neuralensemble.org/elephant

‎codemeta.json‎

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Original file line numberDiff line numberDiff line change
@@ -4,15 +4,15 @@
44
"license": "https://spdx.org/licenses/BSD-3-Clause",
55
"codeRepository": "https://github.com/NeuralEnsemble/python-neo",
66
"contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions",
7-
"dateModified": "2024-02-02",
8-
"downloadUrl": "https://files.pythonhosted.org/packages/b2/07/b8653dd235919dc13671fc31bd8bcbb57571e72d75e4cb04dc1347416357/neo-0.13.0.tar.gz",
7+
"dateModified": "2025-01-20",
8+
"downloadUrl": "https://files.pythonhosted.org/packages/3b/91/c3630d766b3b959f8e604d8d41580c78973ece5f1e070b13bd9755dba60b/neo-0.14.0.tar.gz",
99
"issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
1010
"name": "Neo",
11-
"version": "0.13.0",
11+
"version": "0.14.0",
1212
"identifier": "RRID:SCR_000634",
1313
"description": "Neo is a Python package for working with electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5.\n\nThe goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization.\n\nNeo is used by a number of other software tools, including SpykeViewer (data analysis and visualization), Elephant (data analysis), the G-node suite (databasing), PyNN (simulations), tridesclous_ (spike sorting) and ephyviewer (data visualization).\n\nNeo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.",
1414
"applicationCategory": "neuroscience",
15-
"releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.13.0.html",
15+
"releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.14.0.html",
1616
"funding": "https://cordis.europa.eu/project/id/945539",
1717
"developmentStatus": "active",
1818
"referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -23,7 +23,7 @@
2323
"programmingLanguage": ["Python"],
2424
"operatingSystem": ["Linux", "Windows", "macOS"],
2525
"softwareRequirements": [
26-
"Python (version 3.8+)",
26+
"Python (version 3.9+)",
2727
"see https://github.com/NeuralEnsemble/python-neo/blob/master/pyproject.toml"
2828
],
2929
"relatedLink": ["https://neo.readthedocs.io", "https://neuralensemble.org/community"],
@@ -54,6 +54,7 @@
5454
{ "@type": "Person", "givenName": "Kyler", "familyName": "Brown" },
5555
{ "@type": "Person", "givenName": "Mikkel Elle", "familyName": "Lepperød" },
5656
{ "@type": "Person", "givenName": "C Daniel", "familyName": "Meliza" },
57+
{ "@type": "Person", "givenName": "Michael", "familyName": "Denker" },
5758
{ "@type": "Person", "givenName": "Julia", "familyName": "Sprenger" },
5859
{ "@type": "Person", "givenName": "Maximilian", "familyName": "Schmidt" },
5960
{ "@type": "Person", "givenName": "Johanna", "familyName": "Senk" },
@@ -103,6 +104,16 @@
103104
{ "@type": "Person", "givenName": "Cody", "familyName": "Baker" },
104105
{ "@type": "Person", "givenName": "Fernando J.", "familyName": "Chaure" },
105106
{ "@type": "Person", "alternateName": "Filipe@github" },
106-
{ "@type": "Person", "givenName": "Matthias Klumpp" }
107+
{ "@type": "Person", "givenName": "Matthias", "familyName": "Klumpp" },
108+
{ "@type": "Person", "givenName": "Greg", "familyName": "Knoll" },
109+
{ "@type": "Person", "givenName": "Chris", "familyName": "Halcrow" },
110+
{ "@type": "Person", "givenName": "Szonja", "familyName": "Weigl" },
111+
{ "@type": "Person", "givenName": "Teo", "familyName": "Lohrer"},
112+
{ "@type": "Person", "givenName": "Kyu Hun", "familyName": "Lee"},
113+
{ "@type": "Person", "givenName": "Xin", "familyName": "Niu"},
114+
{ "@type": "Person", "givenName": "Anthony", "familyName": "Pinto"},
115+
{ "@type": "Person", "givenName": "Chris", "familyName": "Heydrick"},
116+
{"@type": "Person", "givenName": "Nikhil", "familyName": "Chandra"},
117+
{"@type": "Person", "givenName": "Luigi", "familyName": "Petrucco"}
107118
]
108119
}

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