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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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2 changes: 1 addition & 1 deletion .github/workflows/dev-testing.yml
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Original file line number Diff line number Diff line change
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@v4
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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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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
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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 @@ -66,6 +66,7 @@
* 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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3 changes: 2 additions & 1 deletion requirements-minimal.txt
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@@ -1,4 +1,5 @@
numpy>=1.22.0
numpy>=1.22.0; python_version<='3.11'
numpy>=1.26.0; python_version>='3.12'
jsonschema>=3.2.0
PyYAML>=5.4
scipy>=1.4.1
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3 changes: 1 addition & 2 deletions src/neuroconv/datainterfaces/ecephys/edf/requirements.txt
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@@ -1,2 +1 @@
pyedflib>=0.1.30
numpy<1.25.0;python_version>="3.11"
pyedflib>=0.1.36
1 change: 0 additions & 1 deletion src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt
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Heh, well this is an interesting one

I'm not quite sure what to do with the MaxOne interface or MaxTwo #221 because various platforms on the CI have always had trouble getting the custom HDF5 plugin to work properly to decompress data contained in the files

I had gotten the tests and functionality to work on local devices, so it is/was somewhat functional in practice

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What do you mean, what are the options here?

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(a) Keep Maxwell interfaces around despite no CI tests

(b) Deprecate and remove

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Can we add?
h5py<=3.9.0; python_version<='3.12'

Aren't they still tested on ubuntu for python <3.12?

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Aren't they still tested on ubuntu for python <3.12?

I even had to exclude ubuntu a while back

https://github.com/catalystneuro/neuroconv/blob/main/tests/test_on_data/test_recording_interfaces.py#L187

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I see.

My vote: I say let's keep it and we pin down the correct CI testing when and if we get a job / contract related to it.

Meanwhile, probably not worth figuring it out at this very moment.

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2 changes: 1 addition & 1 deletion src/neuroconv/datainterfaces/ecephys/spike2/spike2datainterface.py
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Expand Up @@ -9,7 +9,7 @@ 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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2 changes: 1 addition & 1 deletion ...test_backend_and_dataset_configuration/test_models/test_dataset_io_configuration_model.py
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Expand Up @@ -9,7 +9,7 @@
def test_get_data_io_kwargs_abstract_error():
with pytest.raises(TypeError) as error_info:
DatasetIOConfiguration(dataset_info=mock_DatasetInfo(), chunk_shape=(78_125, 64), buffer_shape=(1_250_000, 384))
assert "Can't instantiate abstract class DatasetIOConfiguration with abstract" in str(error_info.value)
assert "Can't instantiate abstract class DatasetIOConfiguration" in str(error_info.value)


def test_get_data_io_kwargs_not_implemented():
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