Merge pull request SpikeInterface#3129 from h-mayorquin/remove_stream…

…ing_extractors

Add streaming extractor tests to main  test script

.github/determine_testing_environment.py

@@ -30,19 +30,25 @@
 exporters_changed = False
 sortingcomponents_changed = False
 generation_changed = False
+stream_extractors_changed = False
 
 
 for changed_file in changed_files_in_the_pull_request_paths:
 
     file_is_in_src = changed_file.parts[0] == "src"
 
-
     if changed_file.name == "pyproject.toml":
         pyproject_toml_changed = True
     elif changed_file.name == "neobaseextractor.py":
         neobaseextractor_changed = True
+        extractors_changed = True
     elif changed_file.name == "plexon2.py":
         plexon2_changed = True
+    elif changed_file.name == "nwbextractors.py":
+        extractors_changed = True  # There are NWB tests that are not streaming
+        stream_extractors_changed = True
+    elif changed_file.name == "iblextractors.py":
+        stream_extractors_changed = True
     elif "core" in changed_file.parts:
         core_changed = True
     elif "extractors" in changed_file.parts:
@@ -90,8 +96,11 @@
 run_sorters_test = run_everything or sorters_changed
 run_internal_sorters_test = run_everything or run_sortingcomponents_tests or sorters_internal_changed
 
+run_streaming_extractors_test = stream_extractors_changed
+
 install_plexon_dependencies = plexon2_changed
 
+
 environment_varaiables_to_add = {
     "RUN_EXTRACTORS_TESTS": run_extractor_tests,
     "RUN_PREPROCESSING_TESTS": run_preprocessing_tests,
@@ -106,6 +115,7 @@
     "RUN_SORTERS_TESTS": run_sorters_test,
     "RUN_INTERNAL_SORTERS_TESTS": run_internal_sorters_test,
     "INSTALL_PLEXON_DEPENDENCIES": install_plexon_dependencies,
+    "RUN_STREAMING_EXTRACTORS_TESTS": run_streaming_extractors_test,
 }
 
 # Write the conditions to the GITHUB_ENV file

.github/workflows/all-tests.yml

@@ -68,6 +68,7 @@ jobs:
           echo "RUN_SORTERS_TESTS=${RUN_SORTERS_TESTS}"
           echo "RUN_INTERNAL_SORTERS_TESTS=${RUN_INTERNAL_SORTERS_TESTS}"
           echo "INSTALL_PLEXON_DEPENDENCIES=${INSTALL_PLEXON_DEPENDENCIES}"
+          echo "RUN_STREAMING_EXTRACTORS_TESTS=${RUN_STREAMING_EXTRACTORS_TESTS}"
 
       - name: Install packages
         run: |
@@ -136,6 +137,13 @@ jobs:
           pip install -e .[extractors,streaming_extractors,test_extractors]
           ./.github/run_tests.sh "extractors and not streaming_extractors" --no-virtual-env
 
+      - name: Test streaming extracotors
+        shell: bash
+        if: env.RUN_STREAMING_EXTRACTORS_TESTS
+        run: |
+          pip install -e .[streaming_extractors,test_extractors]
+          ./.github/run_tests.sh "streaming_extractors" --no-virtual-env
+
       - name: Test preprocessing
         shell: bash
         if: env.RUN_PREPROCESSING_TESTS == 'true'

conftest.py

@@ -1,19 +1,7 @@
 import pytest
-import shutil
-import os
 from pathlib import Path
 
 
-ON_GITHUB = bool(os.getenv('GITHUB_ACTIONS'))
-
-
-# define marks
-mark_names = ["core", "extractors", "preprocessing", "postprocessing",
-              "sorters_external", "sorters_internal", "sorters",
-              "qualitymetrics", "comparison", "curation",
-              "widgets", "exporters", "sortingcomponents", "generation"]
-
-
 @pytest.fixture(scope="module")
 def create_cache_folder(tmp_path_factory):
     cache_folder = tmp_path_factory.mktemp("cache_folder")

src/spikeinterface/extractors/iblextractors.py

@@ -307,7 +307,7 @@ class IblSortingExtractor(BaseSorting):
     name = "ibl"
     installation_mesg = "IBL extractors require ibllib as a dependency." " To install, run: \n\n pip install ibllib\n\n"
 
-    def __init__(self, pid, good_clusters_only=False, load_unit_properties=True, one=None):
+    def __init__(self, pid: str, good_clusters_only: bool = False, load_unit_properties: bool = True, one=None):
         try:
             from one.api import ONE
             from brainbox.io.one import SpikeSortingLoader