From 75a3731eae5ffb8e7b0c606dc5b1fe183b0a4880 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Thu, 4 Jan 2024 15:06:02 +0100 Subject: [PATCH 01/13] test numpy upper version --- requirements-minimal.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-minimal.txt b/requirements-minimal.txt index 33db468e2..60e8a30e5 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -1,4 +1,4 @@ -numpy>=1.22.0 +numpy>=1.26.0 jsonschema>=3.2.0 PyYAML>=5.4 scipy>=1.4.1 From ae7492fafffc0052492e7cd9ee8e870b1be41805 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Thu, 4 Jan 2024 15:19:23 +0100 Subject: [PATCH 02/13] numpy again --- requirements-minimal.txt | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/requirements-minimal.txt b/requirements-minimal.txt index 60e8a30e5..dbc28fbcd 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -1,11 +1,12 @@ -numpy>=1.26.0 +numpy>=1.22.0; python_version<'3.12' +numpy>=1.26.0; python_version>='3.12' jsonschema>=3.2.0 PyYAML>=5.4 scipy>=1.4.1 h5py>=3.9.0 hdmf>=3.11.0 hdmf_zarr>=0.4.0 -pynwb>=2.3.2;python_version>='3.8' +pynwb>=2.3.2 pydantic>=1.10.13,<2.0.0 psutil>=5.8.0 tqdm>=4.60.0 From 85164a732ae326dfa257c109ee5c3d6c2d2de6e8 Mon Sep 17 00:00:00 2001 From: Heberto Mayorquin Date: Thu, 4 Jan 2024 15:30:29 +0100 Subject: [PATCH 03/13] revert numpy --- requirements-minimal.txt | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/requirements-minimal.txt b/requirements-minimal.txt index dbc28fbcd..60e8a30e5 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -1,12 +1,11 @@ -numpy>=1.22.0; python_version<'3.12' -numpy>=1.26.0; python_version>='3.12' +numpy>=1.26.0 jsonschema>=3.2.0 PyYAML>=5.4 scipy>=1.4.1 h5py>=3.9.0 hdmf>=3.11.0 hdmf_zarr>=0.4.0 -pynwb>=2.3.2 +pynwb>=2.3.2;python_version>='3.8' pydantic>=1.10.13,<2.0.0 psutil>=5.8.0 tqdm>=4.60.0 From 9879f5c55aa404a0b4352193877320e56d7f82c9 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Tue, 23 Jan 2024 15:40:12 -0500 Subject: [PATCH 04/13] Update requirements-minimal.txt --- requirements-minimal.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-minimal.txt b/requirements-minimal.txt index d473ff536..f9f21439a 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -1,4 +1,4 @@ -numpy>=1.26.0 +numpy>=1.22.0 jsonschema>=3.2.0 PyYAML>=5.4 scipy>=1.4.1 From e212fb827deea7b4e2354c989a64f650d6287daa Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 23 Jan 2024 15:50:58 -0500 Subject: [PATCH 05/13] deprecate remaining se interfaces --- .../spikeinterface/sipickledatainterfaces.py | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 src/neuroconv/datainterfaces/ecephys/spikeinterface/sipickledatainterfaces.py diff --git a/src/neuroconv/datainterfaces/ecephys/spikeinterface/sipickledatainterfaces.py b/src/neuroconv/datainterfaces/ecephys/spikeinterface/sipickledatainterfaces.py deleted file mode 100644 index b5e245ef0..000000000 --- a/src/neuroconv/datainterfaces/ecephys/spikeinterface/sipickledatainterfaces.py +++ /dev/null @@ -1,55 +0,0 @@ -from warnings import warn - -from ..baserecordingextractorinterface import BaseRecordingExtractorInterface -from ..basesortingextractorinterface import BaseSortingExtractorInterface -from ....utils import FilePathType - - -class SIPickleRecordingInterface(BaseRecordingExtractorInterface): - """Primary interface for reading and converting SpikeInterface Recording objects through .pkl files.""" - - ExtractorModuleName = "spikeextractors" - ExtractorName = "load_extractor_from_pickle" - - def __init__(self, file_path: FilePathType, verbose: bool = True, es_key: str = "ElectricalSeries"): - """ - Initialize reading of SpikeInterface Pickle files. - - Parameters - ---------- - file_path : FilePathType - Path to .pkl file. - verbose : bool, optional, default=True - es_key: str, default: "ElectricalSeries" - """ - # TODO: Remove entire interfaces - warn( - message=( - "Interfaces using a spikeextractors backend will soon be deprecated! " - "Please use the SpikeInterface backend instead." - ), - category=DeprecationWarning, - stacklevel=2, - ) - - from spikeextractors import load_extractor_from_pickle - - self.recording_extractor = load_extractor_from_pickle(pkl_file=file_path) - self.subset_channels = None - self.source_data = dict(file_path=file_path) - self.verbose = verbose - self.es_key = es_key - - -class SIPickleSortingInterface(BaseSortingExtractorInterface): - """Primary interface for reading and converting SpikeInterface Sorting objects through .pkl files.""" - - ExtractorModuleName = "spikeextractors" - ExtractorName = "load_extractor_from_pickle" - - def __init__(self, file_path: FilePathType, verbose: bool = True): - from spikeextractors import load_extractor_from_pickle - - self.sorting_extractor = load_extractor_from_pickle(pkl_file=file_path) - self.source_data = dict(file_path=file_path) - self.verbose = verbose From afd36192028d01197b6c130c7eed45d9c82af514 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 23 Jan 2024 15:51:10 -0500 Subject: [PATCH 06/13] deprecate --- .../datainterfaces/ecephys/spikeinterface/requirements.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 src/neuroconv/datainterfaces/ecephys/spikeinterface/requirements.txt diff --git a/src/neuroconv/datainterfaces/ecephys/spikeinterface/requirements.txt b/src/neuroconv/datainterfaces/ecephys/spikeinterface/requirements.txt deleted file mode 100644 index 31453f660..000000000 --- a/src/neuroconv/datainterfaces/ecephys/spikeinterface/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -spikeextractors From 443866aa53210519284620bb097e63ded16d3adb Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Tue, 23 Jan 2024 16:23:18 -0500 Subject: [PATCH 07/13] bump numpy in 3.12; numba will still be a problem --- requirements-minimal.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements-minimal.txt b/requirements-minimal.txt index f9f21439a..52b09211c 100644 --- a/requirements-minimal.txt +++ b/requirements-minimal.txt @@ -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 From 6654a0eda980199763a0ecd5111fe63ce5fd42ce Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:01:48 -0500 Subject: [PATCH 08/13] try relative paths in reused workflows --- .github/workflows/deploy-tests.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/deploy-tests.yml b/.github/workflows/deploy-tests.yml index fdec8a63c..72227839e 100644 --- a/.github/workflows/deploy-tests.yml +++ b/.github/workflows/deploy-tests.yml @@ -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@add_support_to_python_312 + uses: ./.github/workflows/assess-file-changes.yml detect-changelog-updates: needs: assess-file-changes @@ -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@add_support_to_python_312 + uses: ./.github/workflows/testing.yml secrets: AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} @@ -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@add_support_to_python_312 + uses: ./.github/workflows/live-service-testing.yml 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@add_support_to_python_312 + uses: ./.github/workflows/dev-testing.yml secrets: DANDI_API_KEY: ${{ secrets.DANDI_API_KEY }} AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} @@ -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@add_support_to_python_312 + uses: ./.github/workflows/doctests.yml check-final-status: name: All tests passing From bfe3127c84459cef6e761c84167311cf26d9a671 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:14:36 -0500 Subject: [PATCH 09/13] simple fix --- .../test_models/test_dataset_io_configuration_model.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_models/test_dataset_io_configuration_model.py b/tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_models/test_dataset_io_configuration_model.py index b2587bd5a..b5fffa134 100644 --- a/tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_models/test_dataset_io_configuration_model.py +++ b/tests/test_minimal/test_tools/test_backend_and_dataset_configuration/test_models/test_dataset_io_configuration_model.py @@ -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(): From 45c76b7223e5bfcf15b75d48b7cec67cbed16583 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:26:35 -0500 Subject: [PATCH 10/13] try relaxing edf --- src/neuroconv/datainterfaces/ecephys/edf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt b/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt index 6f166a274..b493c6fcf 100644 --- a/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt +++ b/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt @@ -1,2 +1,2 @@ pyedflib>=0.1.30 -numpy<1.25.0;python_version>="3.11" +#numpy<1.25.0;python_version>="3.11" # Trying to relax EDF to see what the problem is From 8720689d3b3f9f0d1133afe3fbe99a947a40aa81 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:46:32 -0500 Subject: [PATCH 11/13] try relaxing maxwell h5py --- src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt b/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt index d7b53e65f..19279247a 100644 --- a/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt +++ b/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt @@ -1 +1 @@ -h5py<=3.9.0 +#h5py<=3.9.0 # Trying to relax to see what happens From 74ac3b220d66d38b341eb0651e60250be8ca9d10 Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 15:28:29 -0500 Subject: [PATCH 12/13] bump pyedf to minimal numpy compatability --- src/neuroconv/datainterfaces/ecephys/edf/requirements.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt b/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt index b493c6fcf..2ca43feaa 100644 --- a/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt +++ b/src/neuroconv/datainterfaces/ecephys/edf/requirements.txt @@ -1,2 +1 @@ -pyedflib>=0.1.30 -#numpy<1.25.0;python_version>="3.11" # Trying to relax EDF to see what the problem is +pyedflib>=0.1.36 From 833a1752a1ad7eeaf0a8af94ebe47d4a466ba0dd Mon Sep 17 00:00:00 2001 From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com> Date: Wed, 21 Feb 2024 15:29:40 -0500 Subject: [PATCH 13/13] just remove reqs for maxwell --- src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt diff --git a/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt b/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt deleted file mode 100644 index 19279247a..000000000 --- a/src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -#h5py<=3.9.0 # Trying to relax to see what happens