Skip to content

Commit

Permalink
Merge branch 'master' into enh/trials_unitary_event_analysis
Browse files Browse the repository at this point in the history
  • Loading branch information
@Moritz-Alexander-Kern
Moritz-Alexander-Kern authored Nov 14, 2024
2 parents 167361d + 123ca04 commit 594e002
Show file tree
Hide file tree
Showing 14 changed files with 373 additions and 178 deletions.
161 changes: 109 additions & 52 deletions .github/workflows/CI.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,34 +70,32 @@ jobs:
fail-fast: false

steps:
# used to reset cache every month
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

- name: Get pip cache dir
id: pip-cache
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- uses: actions/checkout@v3
- uses: actions/[email protected]

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5.1.0
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: '**/requirements.txt'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Cache test_env
uses: actions/cache@v3
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(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: ${{ steps.pip-cache.outputs.dir }}
# 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') }}
-${{ steps.date.outputs.date }}
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true

- name: Install dependencies
run: |
Expand All @@ -112,6 +110,11 @@ jobs:
- 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:
Expand Down Expand Up @@ -146,6 +149,19 @@ jobs:
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
Expand Down Expand Up @@ -173,6 +189,10 @@ jobs:
- 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
# __ ___ _
Expand All @@ -192,24 +212,32 @@ jobs:
os: [windows-latest]

steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

- uses: actions/checkout@v3
- uses: actions/[email protected]

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5.1.0
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Cache pip
uses: actions/cache@v3
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dataset_hash=$(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: ~\AppData\Local\pip\Cache
# Look to see if there is a cache hit for the corresponding requirements files
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
-${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true

- name: Install dependencies
run: |
Expand All @@ -224,6 +252,10 @@ jobs:
- 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
# __ __ ____ ___
Expand All @@ -246,29 +278,32 @@ jobs:
fail-fast: false

steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/checkout@v3
- uses: actions/[email protected]

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5.1.0
with:
python-version: ${{ matrix.python-version }}
check-latest: true
cache: 'pip'
cache-dependency-path: |
**/requirements.txt
**/requirements-extras.txt
**/requirements-tests.txt
- name: Get pip cache dir
id: pip-cache
- name: Get current hash (SHA) of the elephant_data repo
id: elephant-data
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/elephant-data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT
- name: Cache test_env
uses: actions/cache@v3
- uses: actions/cache/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ${{ steps.pip-cache.outputs.dir }}
# 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') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}
restore-keys: datasets-
enableCrossOsArchive: true

- name: Setup environment
run: |
Expand All @@ -287,6 +322,10 @@ jobs:
- name: Test with pytest
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest
coveralls --service=github || echo "Coveralls submission failed"
env:
Expand Down Expand Up @@ -316,7 +355,7 @@ jobs:
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

- uses: actions/checkout@v3
- uses: actions/checkout@v4.1.6

- name: Get pip cache dir
id: pip-cache
Expand All @@ -330,6 +369,20 @@ jobs:

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
Expand Down Expand Up @@ -358,6 +411,10 @@ jobs:
- name: Test with pytest
shell: bash -el {0}
run: |
if [ -d ~/elephant-data ]; then
export ELEPHANT_DATA_LOCATION=~/elephant-data
echo $ELEPHANT_DATA_LOCATION
fi
pytest --cov=elephant
# ____
Expand All @@ -383,7 +440,7 @@ jobs:
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

- uses: actions/checkout@v3
- uses: actions/checkout@v4.1.6

- name: Get pip cache dir
id: pip-cache
Expand Down Expand Up @@ -448,10 +505,10 @@ jobs:
- name: Get current year-month
id: date
run: echo "::set-output name=date::$(date +'%Y-%m')"
- uses: actions/checkout@v3
- uses: actions/checkout@v4.1.6

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5.1.0
with:
python-version: ${{ matrix.python-version }}

Expand Down
65 changes: 65 additions & 0 deletions .github/workflows/cache_elephant_data.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
name: Create caches for elephant_data

on:
workflow_dispatch: # Workflow can be triggered manually via GH actions webinterface
push: # When something is pushed into master this checks if caches need to re-created
branches:
- master
schedule:
- cron: "11 23 * * *" # Daily at 23:11 UTC


jobs:
create-data-cache-if-missing:
name: Caching data env
runs-on: ubuntu-latest
strategy:
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false

steps:
- 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)" >> $GITHUB_OUTPUT
- uses: actions/[email protected]
# Loading cache of elephant-data
id: cache-datasets
with:
path: ~/elephant-data
key: datasets-${{ steps.elephant-data.outputs.dataset_hash }}

- name: Cache found?
run: echo "Cache-hit == ${{steps.cache-datasets.outputs.cache-hit == 'true'}}"

- name: Configuring git
if: steps.cache-datasets.outputs.cache-hit != 'true'
run: |
git config --global user.email "elephant_ci@fake_mail.com"
git config --global user.name "elephant CI"
git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency
- name: Install Datalad Linux
if: steps.cache-datasets.outputs.cache-hit != 'true'
run: |
python -m pip install -U pip # Official recommended way
pip install datalad-installer
datalad-installer --sudo ok git-annex --method datalad/packages
pip install datalad
- name: Download dataset
id: download-dataset
if: steps.cache-datasets.outputs.cache-hit != 'true'
# Download repository and also fetch data
run: |
cd ~
datalad --version
datalad install --recursive --get-data https://gin.g-node.org/NeuralEnsemble/elephant-data
- name: Show size of the cache to assert data is downloaded
run: |
cd ~
du -hs ~/elephant-data
ls -lh ~/elephant-data
2 changes: 1 addition & 1 deletion elephant/conversion.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -854,7 +854,7 @@ def to_spike_trains(self, spikes="random", as_array=False,
array_ants = dict(bins=bin_indices)
spiketrain = neo.SpikeTrain(spiketrain, t_start=self._t_start,
t_stop=self._t_stop,
units=self.units, copy=False,
units=self.units,
description=description,
array_annotations=array_ants,
bin_size=self.bin_size)
Expand Down
Loading

0 comments on commit 594e002

Please sign in to comment.