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[Fix] neo v0.13.4 deprecated copy (#646) #97

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[Fix] neo v0.13.4 deprecated copy (#646)

[Fix] neo v0.13.4 deprecated copy (#646) #97

Workflow file for this run

.github/workflows/CI.yml at 123ca04
# This workflow will set up GitHub-hosted runners and install the required dependencies for elephant tests.
# On a pull requests and on pushes to master it will run different tests for elephant.
name: tests
# define events that trigger workflow 'tests'
on:
workflow_dispatch: # enables manual triggering of workflow
inputs:
logLevel:
description: 'Log level'
required: true
default: 'warning'
type: choice
options:
- info
- warning
- debug
pull_request:
branches:
- master
types:
#- assigned
#- unassigned
#- labeled
#- unlabeled
- opened
#- edited
#- closed
- reopened
- synchronize
#- converted_to_draft
#- ready_for_review
#- locked
#- unlocked
#- review_requested
#- review_request_removed
#- auto_merge_enabled
#- auto_merge_disabled
push:
branches:
- master
# Cancel previous workflows on the same pull request
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
# jobs define the steps that will be executed on the runner
jobs:
# _
# _ __ (_)_ __
# | '_ \| | '_ \
# | |_) | | |_) |
# | .__/|_| .__/
# |_| |_|
# install dependencies and elephant with pip and run tests with pytest
build-and-test-pip:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, "3.10", 3.11, 3.12]
python-version: [3.9, "3.10", 3.11, 3.12]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/[email protected]
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install coveralls
pip install -e .[extras,tests]
- name: List packages
run: |
pip list
python --version
- name: Test with pytest
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
coverage run --source=elephant -m pytest
coveralls --service=github || echo "Coveralls submission failed"
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# ___ ____
# _ __ ___ __ _ ___ / _ \/ ___|
# | '_ ` _ \ / _` |/ __| | | \___ \
# | | | | | | (_| | (__| |_| |___) |
# |_| |_| |_|\__,_|\___|\___/|____/
test-macOS:
name: conda (${{ matrix.python-version }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
matrix:
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [macos-12,macos-13]
python-version: [3.11]
steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/[email protected]
- name: Cache conda
uses: actions/cache@v3
with:
path: ~/conda_pkgs_dir
key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # corresponds to v3.0.4
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
mamba-version: "*"
channels: conda-forge,defaults
channel-priority: true
activate-environment: elephant
environment-file: requirements/environment-tests.yml
- name: Install dependencies
shell: bash -l {0}
run: |
python --version
mamba install pytest pytest-cov coveralls
pip install -e .[extras]
- name: List packages
shell: bash -l {0}
run: |
pip list
mamba list
python --version
- name: Test with pytest
shell: bash -l {0}
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
pytest --cov=elephant
# __ ___ _
# \ \ / (_)_ __ __| | _____ _____
# \ \ /\ / /| | '_ \ / _` |/ _ \ \ /\ / / __|
# \ V V / | | | | | (_| | (_) \ V V /\__ \
# \_/\_/ |_|_| |_|\__,_|\___/ \_/\_/ |___/
# install dependencies with pip and run tests with pytest
test-pip:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
python-version: [3.11,]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [windows-latest]
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/[email protected]
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pytest-cov coveralls
pip install -e .[extras,tests]
- name: List packages
run: |
pip list
python --version
- name: Test with pytest
run: |
if (Test-Path "$env:USERPROFILE\elephant-data") {
$env:ELEPHANT_DATA_LOCATION = "$env:USERPROFILE\elephant-data"
Write-Output $env:ELEPHANT_DATA_LOCATION
}
pytest --cov=elephant
# __ __ ____ ___
# | \/ | _ \_ _|
# | |\/| | |_) | |
# | | | | __/| |
# |_| |_|_| |___|
# install dependencies and elephant with pip and run MPI
test-pip-MPI:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
python-version: [3.9]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/[email protected]
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true
- name: Setup environment
run: |
sudo apt-get update
sudo apt install -y libopenmpi-dev openmpi-bin
python -m pip install --upgrade pip
pip install mpi4py
pip install pytest-cov coveralls
pip install -e .[extras,tests]
- name: List packages
run: |
pip list
python --version
- name: Test with pytest
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest
coveralls --service=github || echo "Coveralls submission failed"
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# ____ _
# / ___|___ _ __ __| | __ _
# | | / _ \| '_ \ / _` |/ _` |
# | |__| (_) | | | | (_| | (_| |
# \____\___/|_| |_|\__,_|\__,_|
# install dependencies with conda and run tests with pytest
test-conda:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
python-version: [3.11]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/[email protected]
- name: Get pip cache dir
id: pip-cache
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- name: Cache pip
uses: actions/cache@v3
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-${{hashFiles('requirements/environment-tests.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true
- uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
mamba-version: "*"
channels: conda-forge,defaults
channel-priority: true
activate-environment: elephant
environment-file: requirements/environment-tests.yml
- name: Install dependencies
shell: bash -el {0}
run: |
python --version
conda install mpi4py openmpi
mamba install pytest pytest-cov coveralls
pip install -e .
- name: List packages
shell: bash -el {0}
run: |
pip list
mamba list
python --version
- name: Test with pytest
shell: bash -el {0}
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
pytest --cov=elephant
# ____
# | _ \ ___ ___ ___
# | | | |/ _ \ / __/ __|
# | |_| | (_) | (__\__ \
# |____/ \___/ \___|___/
# install dependencies for the documentation and build .html
docs:
name: docs (${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, 3.10, 3.11, 3.12]
python-version: [3.12]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/[email protected]
- name: Get pip cache dir
id: pip-cache
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- name: Cache pip
uses: actions/cache@v3
with:
path: ${{ steps.pip-cache.outputs.dir }}
# Look to see if there is a cache hit for the corresponding requirements files
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-docs.txt') }}-${{ hashFiles('**/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
- uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
mamba-version: "*"
activate-environment: elephant
environment-file: requirements/environment.yml
- name: Install dependencies
shell: bash -el {0} # enables conda incubator to activate environment
run: |
sudo apt-get update
sudo apt install -y libopenmpi-dev openmpi-bin
conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
mamba env update --file requirements/environment-docs.yml --name elephant
python -m pip install --upgrade pip
pip install -e .[extras,tutorials,docs]
# run notebooks
sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py
- name: List packages
shell: bash -el {0}
run: |
pip list
mamba list
python --version
- name: make html
shell: bash -el {0}
run: |
cd doc
make html
# install dependencies and elephant with pip and run tests with pytest
doctests:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
python-version: ["3.10"]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
steps:
# used to reset cache every month
- name: Get current year-month
id: date
run: echo "::set-output name=date::$(date +'%Y-%m')"
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/[email protected]
with:
python-version: ${{ matrix.python-version }}
- name: Cache test_env
uses: actions/cache@v3
with:
path: ~/test_env
# Look to see if there is a cache hit for the corresponding requirements files
# cache will be reset on changes to any requirements or every month
key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
-${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('**/CI.yml') }}-${{ hashFiles('setup.py') }}
-${{ steps.date.outputs.date }}
- name: Install dependencies
run: |
# create an environment and install everything
python -m venv ~/test_env
source ~/test_env/bin/activate
sudo apt install -y libopenmpi-dev openmpi-bin
python -m pip install --upgrade pip
pip install mpi4py
pip install pytest-cov coveralls
pip install -e .[extras,tests]
- name: List packages
run: |
source ~/test_env/bin/activate
pip list
python --version
- name: Run doctests
run: |
source ~/test_env/bin/activate
pytest elephant --doctest-modules --ignore=elephant/test/