Relax pandas<3 pin

.github/workflows/caches_cron_job.yml

@@ -2,11 +2,11 @@ name: Create caches for gin ecephys data and virtual env
 
 on:
   workflow_dispatch:
-  push:  # When something is pushed into main this checks if caches need to be re-created
+  push: # When something is pushed into main this checks if caches need to be re-created
     branches:
       - main
   schedule:
-    - cron: "0 12 * * *"  # Daily at noon UTC
+    - cron: "0 12 * * *" # Daily at noon UTC
 
 jobs:
   create-gin-data-cache-if-missing:
@@ -19,10 +19,10 @@ jobs:
     steps:
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.11'
+          python-version: "3.10"
           enable-cache: true
           ignore-nothing-to-cache: true # some runs do not require building a cache (ie macOS) this says this is okay
       - name: Create the directory to store the data
@@ -41,7 +41,7 @@ jobs:
         with:
           path: ~/spikeinterface_datasets
           key: ${{ runner.os }}-datasets-${{ steps.repo_hash.outputs.dataset_hash }}
-          lookup-only: 'true'   # Avoids downloading the data, saving behavior is not affected.
+          lookup-only: "true" # Avoids downloading the data, saving behavior is not affected.
       - name: Cache found?
         run: echo "Cache-hit == ${{steps.cache-datasets.outputs.cache-hit == 'true'}}"
         shell: bash

.github/workflows/core-test.yml

@@ -6,7 +6,7 @@ on:
     branches:
       - main
 
-concurrency:  # Cancel previous workflows on the same pull request
+concurrency: # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
@@ -22,10 +22,10 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.11'
+          python-version: "3.10"
           enable-cache: true
       - name: Install dependencies
         run: |
@@ -35,7 +35,7 @@ jobs:
       - name: Test core with pytest
         run: |
           pytest -m "core" -vv -ra --durations=0 --durations-min=0.001 | tee report.txt; test $? -eq 0 || exit 1
-        shell: bash  # Necessary for pipeline to work on windows
+        shell: bash # Necessary for pipeline to work on windows
       - name: Build test summary
         run: |
           uv pip install --system pandas
@@ -45,4 +45,4 @@ jobs:
           python ./.github/scripts/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
           cat $GITHUB_STEP_SUMMARY
           rm report.txt
-        shell: bash  # Necessary for pipeline to work on windows
+        shell: bash # Necessary for pipeline to work on windows

.github/workflows/cross_version_serialization.yml

@@ -20,11 +20,11 @@ on:
     # watches core only; a break introduced in generation/ or preprocessing/ would not
     # trigger it.
     paths:
-      - 'src/spikeinterface/core/**'
-      - '.github/scripts/serialization/**'
-      - '.github/workflows/cross_version_serialization.yml'
+      - "src/spikeinterface/core/**"
+      - ".github/scripts/serialization/**"
+      - ".github/workflows/cross_version_serialization.yml"
   schedule:
-    - cron: '0 4 * * 0'  # weekly, Sunday 04:00 UTC
+    - cron: "0 4 * * 0" # weekly, Sunday 04:00 UTC
   workflow_dispatch:
 
 concurrency:
@@ -43,13 +43,13 @@ jobs:
     steps:
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.10"
       - id: set
         env:
           GITHUB_EVENT_NAME: ${{ github.event_name }}
           # Support floor: oldest minor to test. Below this, installs fail on the CI
           # Python (numcodecs dependency rot in 0.100/0.101). Raise when 0.102 rots.
-          MIN_VERSION_TO_TEST: "0.102"  # We will change this when making breaking changes (hopefully not too often)
+          MIN_VERSION_TO_TEST: "0.102" # We will change this when making breaking changes (hopefully not too often)
         run: |
           python -m pip install -q packaging
           available_versions=$(python -m pip index versions spikeinterface | sed -n 's/.*Available versions: //p')
@@ -93,17 +93,17 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.11'
+          python-version: "3.10"
 
       - name: Set up uv
         uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.11'
+          python-version: "3.10"
           enable-cache: false
 
       - name: Generate fixtures with spikeinterface ${{ matrix.si-version }}
         run: |
-          uv run --isolated --no-project --python 3.11 \
+          uv run --isolated --no-project --python 3.10 \
             --with "spikeinterface[core]==${{ matrix.si-version }}" \
             python .github/scripts/serialization/serialize_objects.py "$SI_SERIALIZATION_FIXTURES_DIR"
 

.github/workflows/deepinterpolation.yml

@@ -6,7 +6,7 @@ on:
     branches:
       - main
 
-concurrency:  # Cancel previous workflows on the same pull request
+concurrency: # Cancel previous workflows on the same pull request
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
@@ -22,10 +22,10 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
+          python-version: "3.10"
           enable-cache: false
       - name: Get changed files
         id: changed-files
@@ -55,4 +55,4 @@ jobs:
         if: ${{ steps.modules-changed.outputs.DEEPINTERPOLATION_CHANGED == 'true' }}
         run: |
           pytest -v src/spikeinterface/preprocessing/deepinterpolation
-        shell: bash  # Necessary for pipeline to work on windows
+        shell: bash # Necessary for pipeline to work on windows

.github/workflows/test_containers_docker.yml

@@ -2,7 +2,6 @@ name: Test sorter images in Docker
 
 on: workflow_dispatch
 
-
 jobs:
   test-images:
     name: Test on (${{ matrix.os }})
@@ -15,17 +14,15 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
+          python-version: "3.10"
           enable-cache: true
       - name: Python version
-        run:
-          python --version
+        run: python --version
       - name: Docker version
-        run:
-          docker --version
+        run: docker --version
       - name: Install dependencies
         run: |
           uv pip install --system pytest

.github/workflows/test_containers_singularity.yml

@@ -2,7 +2,6 @@ name: Test sorter images in singularity
 
 on: workflow_dispatch
 
-
 jobs:
   test-images:
     name: Test on (${{ matrix.os }})
@@ -11,25 +10,23 @@ jobs:
       fail-fast: false
       matrix:
         # "macos-latest", "windows-latest"
-        os: ["ubuntu-latest", ]
+        os: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
+          python-version: "3.10"
           enable-cache: true
       - uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.8.7
       - name: Python version
-        run:
-          python --version
+        run: python --version
       - name: Singularity version
-        run:
-          singularity --version
+        run: singularity --version
       - name: Install dependencies
         run: |
           uv pip install --system pytest

.github/workflows/test_imports.yml

@@ -22,10 +22,10 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: "3.11"
+          python-version: "3.10"
       - uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.11"
+          python-version: "3.10"
           enable-cache: true
       - name: Install Spikeinterface with only core dependencies
         run: |

pyproject.toml

@@ -68,16 +68,15 @@ extractors = [
     "pynwb>=2.6.0",
     "hdmf-zarr>=0.11.0",
     "pyedflib>=0.1.30",
-    "sonpy;python_version<'3.10'",
     "lxml", # lxml for neuroscope
     "scipy",
-    "ibllib>=3.4.1;python_version>='3.10'", # streaming IBL
+    "ibllib>=3.4.1", # streaming IBL
     "pymatreader>=0.0.32", # For cell explorer matlab files
     "zugbruecke>=0.2; sys_platform!='win32'", # For plexon2
 ]
 
 streaming_extractors = [
-    "ibllib>=3.4.1;python_version>='3.10'", # streaming IBL
+    "ibllib>=3.4.1", # streaming IBL
     # Following dependencies are for streaming with nwb files
     "pynwb>=2.6.0",
     "fsspec",
@@ -104,19 +103,19 @@ postprocessing = [
 metrics = [
     "scikit-learn<1.8",
     "scipy",
-    "pandas<3",
+    "pandas",
     "numba>=0.59",
 ]
 
 comparison = [
     "scipy",
-    "pandas<3",
+    "pandas",
     "networkx",
 ]
 
 generation = [
     "scipy",
-    "pandas<3",
+    "pandas",
 ]
 
 sorters = [
@@ -149,7 +148,7 @@ curation = [
     "spikeinterface[metrics]",
     "spikeinterface[postprocessing]",
     "spikeinterface[comparison]",
-    "pandas<3",
+    "pandas",
     "scikit-learn<1.8",
     "skops",
     "huggingface_hub",
@@ -160,7 +159,7 @@ curation = [
 exporters = [
     "spikeinterface[postprocessing]",
     "spikeinterface[widgets]",
-    "pandas<3",
+    "pandas",
     "pynapple",
 ]
 
@@ -221,9 +220,9 @@ docs = [
 
     # for notebooks in the gallery
     "MEArec", # Use as an example
-    "pandas<3", # in the modules gallery comparison tutorial
+    "pandas", # in the modules gallery comparison tutorial
     "hdbscan>=0.8.33",   # For sorters spykingcircus2 + tridesclous
-    "numba", # For many postprocessing functions
+    "numba>=0.59", # For many postprocessing functions
     "networkx",
     "seaborn",
     "skops", # For automated curation
@@ -248,7 +247,7 @@ test-common = [
 
 test-core = [
     {include-group = "test-common"},
-    "pandas<3",
+    "pandas",
 ]
 
 test-extractors = [
@@ -270,15 +269,15 @@ test-streaming-extractors = [
 
 test-preprocessing = [
     {include-group = "test-common"},
-    "ibllib>=3.4.1;python_version>='3.10'",
+    "ibllib>=3.4.1",
     "pooch",
     "datalad",
     "torch",  # preprocessing tests exercise sortingcomponents.motion.dredge
 ]
 
 test-postprocessing = [
     {include-group = "test-common"},
-    "pandas<3",
+    "pandas",
     ]
 test-metrics = [{include-group = "test-common"}]
 
@@ -305,6 +304,7 @@ test-widgets = [
     "scikit-learn",
     "pyvips",
     "networkx",
+    "upsetplot-bombcell",  # pandas>=3 compatible fork used by BombcellUpsetPlotWidget
 ]
 
 test-exporters = [{include-group = "test-common"}]

readthedocs.yml

@@ -4,7 +4,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "3.10"
+    python: "3.13"
   commands:
     - asdf plugin add uv
     - asdf install uv latest

src/spikeinterface/extractors/tests/test_iblextractors.py

@@ -11,9 +11,6 @@
 EID = "e2b845a1-e313-4a08-bc61-a5f662ed295e"
 PID = "80f6ffdd-f692-450f-ab19-cd6d45bfd73e"
 
-if sys.version_info < (3, 10):
-    pytest.skip("IBL support requires Python 3.10 or higher", allow_module_level=True)
-
 
 @pytest.mark.streaming_extractors
 class TestDefaultIblRecordingExtractorApBand(TestCase):

src/spikeinterface/extractors/tests/test_neoextractors.py

@@ -392,20 +392,20 @@ class Spike2RecordingTest(RecordingCommonTestSuite, unittest.TestCase):
     ]
 
 
-@pytest.mark.skipif(
-    version.parse(platform.python_version()) >= version.parse("3.10") or platform.system() == "Darwin",
-    reason="Sonpy only testing with Python < 3.10 and not supported on macOS!",
-)
-class CedRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
-    ExtractorClass = CedRecordingExtractor
-    downloads = [
-        "spike2/130322-1LY.smr",
-        "spike2/m365_1sec.smrx",
-    ]
-    entities = [
-        ("spike2/130322-1LY.smr", {"stream_id": "1"}),
-        "spike2/m365_1sec.smrx",
-    ]
+# @pytest.mark.skipif(
+#     version.parse(platform.python_version()) >= version.parse("3.10") or platform.system() == "Darwin",
+#     reason="Sonpy only testing with Python < 3.10 and not supported on macOS!",
+# )
+# class CedRecordingTest(RecordingCommonTestSuite, unittest.TestCase):
+#     ExtractorClass = CedRecordingExtractor
+#     downloads = [
+#         "spike2/130322-1LY.smr",
+#         "spike2/m365_1sec.smrx",
+#     ]
+#     entities = [
+#         ("spike2/130322-1LY.smr", {"stream_id": "1"}),
+#         "spike2/m365_1sec.smrx",
+#     ]
 
 
 @pytest.mark.skipif(platform.system() == "Darwin", reason="Maxwell plugin not supported on macOS")