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samuelgarciasamuelgarcia
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fix with main
2 parents f7487a4 + 132c84e commit e072d18

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‎.github/workflows/caches_cron_job.yml‎

Lines changed: 51 additions & 51 deletions
Original file line numberDiff line numberDiff line change
@@ -10,57 +10,57 @@ on:
1010

1111
jobs:
1212

13-
create-conda-env-cache-if-missing:
14-
name: Caching conda env
15-
runs-on: "ubuntu-latest"
16-
strategy:
17-
fail-fast: true
18-
defaults:
19-
# by default run in bash mode (required for conda usage)
20-
run:
21-
shell: bash -l {0}
22-
steps:
23-
- uses: actions/checkout@v3
24-
25-
- name: Get current year-month
26-
id: date
27-
run: |
28-
echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
29-
30-
- name: Get current dependencies hash
31-
id: dependencies
32-
run: |
33-
echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
34-
35-
- uses: actions/cache@v3
36-
# the cache for python package is reset:
37-
# * every month
38-
# * when package dependencies change
39-
id: cache-conda-env
40-
with:
41-
path: /usr/share/miniconda/envs/neo-test-env
42-
key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
43-
44-
- name: Cache found?
45-
run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
46-
47-
# activate environment if not restored from cache
48-
- uses: conda-incubator/[email protected]
49-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
50-
with:
51-
activate-environment: neo-test-env
52-
environment-file: environment_testing.yml
53-
python-version: 3.9
54-
55-
- name: Create the conda environment to be cached
56-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
57-
# create conda env, configure git and install pip, neo and test dependencies from master
58-
# for PRs that change dependencies, this environment will be updated in the test workflow
59-
run: |
60-
git config --global user.email "neo_ci@fake_mail.com"
61-
git config --global user.name "neo CI"
62-
python -m pip install -U pip # Official recommended way
63-
pip install --upgrade -e .[test]
13+
# create-conda-env-cache-if-missing:
14+
# name: Caching conda env
15+
# runs-on: "ubuntu-latest"
16+
# strategy:
17+
# fail-fast: true
18+
# defaults:
19+
# # by default run in bash mode (required for conda usage)
20+
# run:
21+
# shell: bash -l {0}
22+
# steps:
23+
# - uses: actions/checkout@v3
24+
25+
# - name: Get current year-month
26+
# id: date
27+
# run: |
28+
# echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
29+
30+
# - name: Get current dependencies hash
31+
# id: dependencies
32+
# run: |
33+
# echo "hash=${{hashFiles('**/pyproject.toml', '**/environment_testing.yml')}}" >> $GITHUB_OUTPUT
34+
35+
# - uses: actions/cache@v3
36+
# # the cache for python package is reset:
37+
# # * every month
38+
# # * when package dependencies change
39+
# id: cache-conda-env
40+
# with:
41+
# path: /usr/share/miniconda/envs/neo-test-env
42+
# key: ${{ runner.os }}-conda-env-${{ steps.dependencies.outputs.hash }}-${{ steps.date.outputs.date }}
43+
44+
# - name: Cache found?
45+
# run: echo "Cache-hit == ${{steps.cache-conda-env.outputs.cache-hit == 'true'}}"
46+
47+
# # activate environment if not restored from cache
48+
# - uses: conda-incubator/[email protected]
49+
# if: steps.cache-conda-env.outputs.cache-hit != 'true'
50+
# with:
51+
# activate-environment: neo-test-env
52+
# environment-file: environment_testing.yml
53+
# python-version: 3.9
54+
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]
6464

6565
create-data-cache-if-missing:
6666
name: Caching data env

‎.github/workflows/core-test.yml‎

Lines changed: 22 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -24,42 +24,40 @@ jobs:
2424
strategy:
2525
fail-fast: true
2626
matrix:
27-
os: ["ubuntu-latest", "windows-latest"]
28-
# "macos-latest",
29-
python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
30-
numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
27+
os: ["ubuntu-latest", "windows-latest", "macos-latest"]
28+
python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
29+
numpy-version: ['1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1.3', '2.2.4']
30+
# 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
3131
exclude:
32-
- python-version: '3.8'
33-
numpy-version: '1.25.1'
34-
- python-version: '3.8'
35-
numpy-version: '1.26.4'
36-
- python-version: '3.10'
37-
numpy-version: '1.20.3'
38-
- python-version: '3.11'
39-
numpy-version: '1.20.3'
40-
- python-version: '3.11'
41-
numpy-version: '1.21.6'
42-
- python-version: '3.12'
43-
numpy-version: '1.20.3'
44-
# python 3.12 only works on latest numpy
32+
- python-version: '3.9'
33+
numpy-version: '2.1.3'
34+
- python-version: '3.9'
35+
numpy-version: '2.2.4'
4536
- python-version: '3.12'
46-
numpy-version: '1.21.6'
37+
numpy-version: '1.24.4'
4738
- python-version: '3.12'
39+
numpy-version: '1.25.1'
40+
- python-version: '3.13'
4841
numpy-version: '1.22.4'
49-
- python-version: '3.12'
42+
- python-version: '3.13'
5043
numpy-version: '1.23.5'
51-
- python-version: '3.12'
52-
numpy-version: '1.24.1'
53-
- python-version: '3.12'
44+
- python-version: '3.13'
45+
numpy-version: '1.24.4'
46+
- python-version: '3.13'
5447
numpy-version: '1.25.1'
48+
- python-version: '3.13'
49+
numpy-version: '1.26.4'
50+
- python-version: '3.13'
51+
numpy-version: '2.0.2'
52+
5553
steps:
5654
- name: Set up Python ${{ matrix.python-version }}
57-
uses: actions/setup-python@v4
55+
uses: actions/setup-python@v5
5856
with:
5957
python-version: ${{ matrix.python-version }}
6058

6159
- name: Checkout repository
62-
uses: actions/checkout@v3
60+
uses: actions/checkout@v4
6361

6462
- name: Install numpy ${{ matrix.numpy-version }}
6563
run: |

‎.github/workflows/io-test.yml‎

Lines changed: 40 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -13,20 +13,21 @@ concurrency: # Cancel previous workflows on the same pull request
1313

1414
jobs:
1515
build-and-test:
16-
name: Test on (${{ inputs.os }}) (${{ matrix.python-version}})
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', '3.11']
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:
2728

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:
@@ -48,34 +49,45 @@ jobs:
4849

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
78-
conda install python=${{ matrix.python-version }}
79+
conda install pip numpy=${{ 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
82+
83+
- name: Install git-annex
84+
# this is the trick from the spikeinterface repo for getting git-annex to work with datalad
85+
# see https://github.com/SpikeInterface/spikeinterface/pull/3877 for more info
86+
shell: bash
87+
run: |
88+
pip install datalad-installer
89+
datalad-installer --sudo ok git-annex --method datalad/packages
90+
git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency
7991
8092
- name: Configure git
8193
run: |
@@ -90,23 +102,17 @@ jobs:
90102
- name: Install neo including dependencies
91103
# installation with dependencies is only required if no cache was found
92104
# restore-key hits should result in `cache-hit` == 'false'
93-
if: steps.cache-conda-env.outputs.cache-hit != 'true'
105+
# if: steps.cache-conda-env.outputs.cache-hit != 'true'
94106
run: |
95107
pip install --upgrade -e .
96108
pip install .[test]
97109
98-
- name: Install neo without dependencies
110+
# TEST NOT USING CACHE
111+
#- name: Install neo without dependencies
99112
# only installing neo version to test as dependencies should be in cached conda env already
100-
if: steps.cache-conda-env.outputs.cache-hit == 'true'
101-
run: |
102-
pip install --no-dependencies -e .
103-
104-
- name: Install wine
105-
run: |
106-
sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
107-
sudo dpkg --add-architecture i386
108-
sudo apt-get update -qq
109-
sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
113+
# if: steps.cache-conda-env.outputs.cache-hit == 'true'
114+
# run: |
115+
# pip install --no-dependencies -e .
110116

111117
- name: Pip list
112118
run: |

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