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Add support for python 3.12 #626

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merged 29 commits into from
Feb 22, 2024
Merged

Add support for python 3.12 #626

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b01d9fe
Merge branch 'main' into add_support_to_python_312
CodyCBakerPhD Nov 25, 2023
7450dc1
Merge branch 'main' into add_support_to_python_312
h-mayorquin Dec 1, 2023
f9d0fc5
Merge branch 'main' into add_support_to_python_312
h-mayorquin Dec 4, 2023
c3fdfa9
Merge branch 'main' into add_support_to_python_312
h-mayorquin Dec 19, 2023
c524aee
Merge branch 'main' into add_support_to_python_312
h-mayorquin Dec 19, 2023
8c01c3d
Merge branch 'main' into add_support_to_python_312
h-mayorquin Jan 4, 2024
75a3731
test numpy upper version
h-mayorquin Jan 4, 2024
ae7492f
numpy again
h-mayorquin Jan 4, 2024
85164a7
revert numpy
h-mayorquin Jan 4, 2024
58ec74a
Merge branch 'main' into add_support_to_python_312
bendichter Jan 23, 2024
9879f5c
Update requirements-minimal.txt
bendichter Jan 23, 2024
e212fb8
deprecate remaining se interfaces
CodyCBakerPhD Jan 23, 2024
afd3619
deprecate
CodyCBakerPhD Jan 23, 2024
443866a
bump numpy in 3.12; numba will still be a problem
CodyCBakerPhD Jan 23, 2024
1a924b7
Merge branch 'main' into add_support_to_python_312
h-mayorquin Jan 31, 2024
5fe1501
Merge branch 'main' into add_support_to_python_312
CodyCBakerPhD Feb 11, 2024
72f7aa7
Merge branch 'main' into add_support_to_python_312
h-mayorquin Feb 13, 2024
b9fc3a1
Merge branch 'main' into add_support_to_python_312
h-mayorquin Feb 13, 2024
0e55c17
Merge branch 'main' into add_support_to_python_312
bendichter Feb 21, 2024
6654a0e
try relative paths in reused workflows
CodyCBakerPhD Feb 21, 2024
bfe3127
simple fix
CodyCBakerPhD Feb 21, 2024
45c76b7
try relaxing edf
CodyCBakerPhD Feb 21, 2024
8720689
try relaxing maxwell h5py
CodyCBakerPhD Feb 21, 2024
3f86d1d
Merge branch 'main' into add_support_to_python_312
CodyCBakerPhD Feb 21, 2024
74ac3b2
bump pyedf to minimal numpy compatability
CodyCBakerPhD Feb 21, 2024
833a175
just remove reqs for maxwell
CodyCBakerPhD Feb 21, 2024
a4c76cc
Merge branch 'main' into add_support_to_python_312
h-mayorquin Feb 21, 2024
0f9b63e
Merge branch 'main' into add_support_to_python_312
bendichter Feb 21, 2024
8e60912
Merge branch 'main' into add_support_to_python_312
CodyCBakerPhD Feb 21, 2024
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10 changes: 5 additions & 5 deletions .github/workflows/deploy-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ concurrency: # Cancel previous workflows on the same pull request
jobs:

assess-file-changes:
uses: catalystneuro/neuroconv/.github/workflows/assess-file-changes.yml@main
uses: catalystneuro/neuroconv/.github/workflows/assess-file-changes.yml@add_support_to_python_312
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detect-changelog-updates:
needs: assess-file-changes
Expand All @@ -30,7 +30,7 @@ jobs:
run-tests:
needs: assess-file-changes
if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
uses: catalystneuro/neuroconv/.github/workflows/testing.yml@main
uses: catalystneuro/neuroconv/.github/workflows/testing.yml@add_support_to_python_312
secrets:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
Expand All @@ -40,14 +40,14 @@ jobs:
run-live-service-tests:
needs: assess-file-changes
if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
uses: catalystneuro/neuroconv/.github/workflows/live-service-testing.yml@main
uses: catalystneuro/neuroconv/.github/workflows/live-service-testing.yml@add_support_to_python_312
secrets:
DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}

run-dev-tests:
needs: assess-file-changes
if: ${{ needs.assess-file-changes.outputs.SOURCE_CHANGED == 'true' }}
uses: catalystneuro/neuroconv/.github/workflows/dev-testing.yml@main
uses: catalystneuro/neuroconv/.github/workflows/dev-testing.yml@add_support_to_python_312
secrets:
DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }}
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
Expand All @@ -57,7 +57,7 @@ jobs:
run-doctests-only:
needs: assess-file-changes
if: ${{ needs.assess-file-changes.outputs.CONVERSION_GALLERY_CHANGED == 'true' || needs.assess-file-changes.outputs.SOURCE_CHANGED != 'true' }}
uses: catalystneuro/neuroconv/.github/workflows/doctests.yml@main
uses: catalystneuro/neuroconv/.github/workflows/doctests.yml@add_support_to_python_312

check-final-status:
name: All tests passing
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2 changes: 1 addition & 1 deletion .github/workflows/dev-testing.yml
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Expand Up @@ -23,7 +23,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
steps:
- uses: s-weigand/setup-conda@v1
- uses: actions/checkout@v3
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2 changes: 1 addition & 1 deletion .github/workflows/doctests.yml
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Expand Up @@ -9,7 +9,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
os: [ubuntu-latest, macos-latest, windows-latest]
steps:
- uses: s-weigand/setup-conda@v1
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2 changes: 1 addition & 1 deletion .github/workflows/live-service-testing.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
os: [ubuntu-latest, macos-latest, windows-latest]
steps:
- uses: s-weigand/setup-conda@v1
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/testing.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10", "3.11"]
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
os: [ubuntu-latest, macos-latest, windows-latest]
steps:
- uses: s-weigand/setup-conda@v1
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -49,6 +49,7 @@
* The `CEDRecordingInterface` has now been removed; use the `Spike2RecordingInterface` instead. [PR #602](https://github.com/catalystneuro/neuroconv/pull/602)

### Features
* Added support for python 3.12 [PR #626](https://github.com/catalystneuro/neuroconv/pull/626)
* Added `session_start_time` extraction to `FicTracDataInterface`. [PR #598](https://github.com/catalystneuro/neuroconv/pull/598)
* Added `imaging_plane_name` keyword argument to `add_imaging_plane` function to determine which imaging plane to add from the metadata by name instead of `imaging_plane_index`.
* Added reference for `imaging_plane` to default plane segmentation metadata. [PR #594](https://github.com/catalystneuro/neuroconv/pull/594)
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2 changes: 1 addition & 1 deletion requirements-minimal.txt
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@@ -1,4 +1,4 @@
numpy>=1.22.0
numpy>=1.26.0
jsonschema>=3.2.0
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PyYAML>=5.4
scipy>=1.4.1
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2 changes: 1 addition & 1 deletion src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py
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Expand Up @@ -10,7 +10,7 @@ def _test_sonpy_installation() -> None:
get_package(
package_name="sonpy",
excluded_python_versions=["3.10", "3.11"],
excluded_platforms_and_python_versions=dict(darwin=dict(arm=["3.8", "3.9", "3.10", "3.11"])),
excluded_platforms_and_python_versions=dict(darwin=dict(arm=["3.8", "3.9", "3.10", "3.11", "3.12"])),
)


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