Decouple heavy plugins from core to optimize for serverless deployment

pyproject.toml

@@ -43,9 +43,6 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-torch = [
-  "torch>=2.0"
-]
 gui = [
   "pyqtgraph>=0.13.7",
   "PySide6>=6.6",
@@ -66,7 +63,6 @@ docs = [
   "sphinxcontrib-spelling>=7.1.0"
 ]
 all = [
-  "eegprep[torch]",
   "eegprep[gui]",
   "eegprep[console]",
   "eegprep[docs]",

src/eegprep/__init__.py

@@ -47,7 +47,6 @@
     "ExtensionStatus": ("eegprep.extensions", "ExtensionStatus"),
     "ExtensionTestHarness": ("eegprep.extension_testing", "ExtensionTestHarness"),
     "ExtensionValidationResult": ("eegprep.extensions", "ExtensionValidationResult"),
-    "ICL_feature_extractor": ("eegprep.plugins.ICLabel.ICL_feature_extractor", "ICL_feature_extractor"),
     "LazyImport": ("eegprep.extensions", "LazyImport"),
     "assert_extension_entry_point_loads": ("eegprep.extension_testing", "assert_extension_entry_point_loads"),
     "bids_list_eeg_files": ("eegprep.plugins.EEG_BIDS.bids_list_eeg_files", "bids_list_eeg_files"),
@@ -59,16 +58,7 @@
     "chancenter": ("eegprep.functions.sigprocfunc.chancenter", "chancenter"),
     "check_extension_compatibility": ("eegprep.extensions", "check_extension_compatibility"),
     "checkset": ("eegprep.functions.redefine_functions", "checkset"),
-    "clean_artifacts": ("eegprep.plugins.clean_rawdata.clean_artifacts", "clean_artifacts"),
-    "clean_asr": ("eegprep.plugins.clean_rawdata.clean_asr", "clean_asr"),
-    "clean_channels": ("eegprep.plugins.clean_rawdata.clean_channels", "clean_channels"),
-    "clean_channels_nolocs": ("eegprep.plugins.clean_rawdata.clean_channels_nolocs", "clean_channels_nolocs"),
-    "clean_drifts": ("eegprep.plugins.clean_rawdata.clean_drifts", "clean_drifts"),
-    "clean_flatlines": ("eegprep.plugins.clean_rawdata.clean_flatlines", "clean_flatlines"),
-    "clean_windows": ("eegprep.plugins.clean_rawdata.clean_windows", "clean_windows"),
-    "clean_rawdata_vis_artifacts": ("eegprep.plugins.clean_rawdata.vis_artifacts", "vis_artifacts"),
     "clean_rawdata_vis_artifacts_diagnostics": (
-        "eegprep.plugins.clean_rawdata.vis_artifacts",
         "vis_artifacts_diagnostics",
     ),
     "compare": ("eegprep.functions.redefine_functions", "compare"),
@@ -79,16 +69,12 @@
     "discover_extensions": ("eegprep.extensions", "discover_extensions"),
     "eeg2mne": ("eegprep.functions.redefine_functions", "eeg2mne"),
     "eeg_amica": ("eegprep.functions.popfunc.eeg_amica", "eeg_amica"),
-    "eeg_autocorr": ("eegprep.plugins.ICLabel.eeg_autocorr", "eeg_autocorr"),
-    "eeg_autocorr_fftw": ("eegprep.plugins.ICLabel.eeg_autocorr_fftw", "eeg_autocorr_fftw"),
-    "eeg_autocorr_welch": ("eegprep.plugins.ICLabel.eeg_autocorr_welch", "eeg_autocorr_welch"),
     "eeg_checkset": ("eegprep.functions.adminfunc.eeg_checkset", "eeg_checkset"),
     "eeg_checkset_strict_mode": ("eegprep.functions.adminfunc.eeg_checkset", "strict_mode"),
     "eeg_compare": ("eegprep.functions.popfunc.eeg_compare", "eeg_compare"),
     "eeg_decodechan": ("eegprep.functions.popfunc.eeg_decodechan", "eeg_decodechan"),
     "eeg_eeg2mne": ("eegprep.functions.miscfunc.eeg_eeg2mne", "eeg_eeg2mne"),
     "eeg_eegrej": ("eegprep.functions.popfunc.eeg_eegrej", "eeg_eegrej"),
-    "eeg_icalabelstat": ("eegprep.plugins.ICLabel.eeg_icalabelstat", "eeg_icalabelstat"),
     "eeg_emptyset": ("eegprep.functions.popfunc.eeg_emptyset", "eeg_emptyset"),
     "eeg_multieegplot": ("eegprep.functions.popfunc.eeg_multieegplot", "eeg_multieegplot"),
     "eegplot": ("eegprep.functions.sigprocfunc.eegplot", "eegplot"),
@@ -104,7 +90,6 @@
     "eeg_pvaf": ("eegprep.functions.sigprocfunc.ica_helpers", "eeg_pvaf"),
     "eeg_rejsuperpose": ("eegprep.functions.popfunc.eeg_rejsuperpose", "eeg_rejsuperpose"),
     "eeg_retrieve": ("eegprep.functions.adminfunc.eeg_retrieve", "eeg_retrieve"),
-    "eeg_rpsd": ("eegprep.plugins.ICLabel.eeg_rpsd", "eeg_rpsd"),
     "eeg_runica": ("eegprep.functions.popfunc.eeg_runica", "eeg_runica"),
     "eeg_store": ("eegprep.functions.adminfunc.eeg_store", "eeg_store"),
     "eegh": ("eegprep.functions.adminfunc.eegh", "eegh"),
@@ -131,8 +116,6 @@
     "icaact": ("eegprep.functions.sigprocfunc.ica_helpers", "icaact"),
     "icaproj": ("eegprep.functions.sigprocfunc.ica_helpers", "icaproj"),
     "icavar": ("eegprep.functions.sigprocfunc.ica_helpers", "icavar"),
-    "iclabel": ("eegprep.plugins.ICLabel.iclabel", "iclabel"),
-    "eeg_icflag": ("eegprep.plugins.ICLabel.eeg_icflag", "eeg_icflag"),
     "inputgui": ("eegprep.functions.guifunc.inputgui", "inputgui"),
     "interp": ("eegprep.functions.redefine_functions", "interp"),
     "jointprob": ("eegprep.functions.sigprocfunc.jointprob", "jointprob"),
@@ -168,8 +151,6 @@
     "rspdfsolv": ("eegprep.functions.timefreqfunc.rspdfsolv", "rspdfsolv"),
     "rspfunc": ("eegprep.functions.timefreqfunc.rspfunc", "rspfunc"),
     "tf_cycle_calc": ("eegprep.functions.timefreqfunc.tf_cycle_calc", "tf_cycle_calc"),
-    "vis_artifacts": ("eegprep.plugins.clean_rawdata.vis_artifacts", "vis_artifacts"),
-    "vis_artifacts_diagnostics": ("eegprep.plugins.clean_rawdata.vis_artifacts", "vis_artifacts_diagnostics"),
     "options": ("eegprep.functions.redefine_functions", "options"),
     "picard": ("eegprep.functions.redefine_functions", "picard"),
     "plugin_menu": ("eegprep.functions.adminfunc.plugin_menu", "plugin_menu"),
@@ -186,7 +167,6 @@
     "pop_chanplot": ("eegprep.functions.studyfunc.pop_chanplot", "pop_chanplot"),
     "pop_chancoresp": ("eegprep.functions.popfunc.pop_chancoresp", "pop_chancoresp"),
     "pop_chansel": ("eegprep.functions.popfunc.pop_chansel", "pop_chansel"),
-    "pop_clean_rawdata": ("eegprep.plugins.clean_rawdata.pop_clean_rawdata", "pop_clean_rawdata"),
     "pop_chanedit": ("eegprep.functions.popfunc.pop_chanedit", "pop_chanedit"),
     "pop_comments": ("eegprep.functions.popfunc.pop_comments", "pop_comments"),
     "pop_clust": ("eegprep.functions.studyfunc.pop_clust", "pop_clust"),
@@ -234,8 +214,6 @@
     "pop_firwsord": ("eegprep.plugins.firfilt.pop_firwsord", "pop_firwsord"),
     "pop_fusechanrej": ("eegprep.functions.popfunc.pop_fusechanrej", "pop_fusechanrej"),
     "pop_headplot": ("eegprep.functions.popfunc.pop_headplot", "pop_headplot"),
-    "pop_icflag": ("eegprep.plugins.ICLabel.pop_icflag", "pop_icflag"),
-    "pop_iclabel": ("eegprep.plugins.ICLabel.pop_iclabel", "pop_iclabel"),
     "pop_icathresh": ("eegprep.functions.popfunc.pop_icathresh", "pop_icathresh"),
     "pop_jointprob": ("eegprep.functions.popfunc.pop_jointprob", "pop_jointprob"),
     "pop_kaiserbeta": ("eegprep.plugins.firfilt.pop_kaiserbeta", "pop_kaiserbeta"),
@@ -266,7 +244,6 @@
     "pop_preclust": ("eegprep.functions.studyfunc.pop_preclust", "pop_preclust"),
     "pop_precomp": ("eegprep.functions.studyfunc.pop_precomp", "pop_precomp"),
     "pop_prop": ("eegprep.functions.popfunc.pop_prop", "pop_prop"),
-    "pop_prop_extended": ("eegprep.plugins.ICLabel.pop_prop_extended", "pop_prop_extended"),
     "pop_rejchan": ("eegprep.functions.popfunc.pop_rejchan", "pop_rejchan"),
     "pop_rejcont": ("eegprep.functions.popfunc.pop_rejcont", "pop_rejcont"),
     "pop_rejepoch": ("eegprep.functions.popfunc.pop_rejepoch", "pop_rejepoch"),
@@ -300,7 +277,6 @@
     "pop_timef": ("eegprep.functions.popfunc.pop_timef", "pop_timef"),
     "pop_topochansel": ("eegprep.functions.popfunc.pop_topochansel", "pop_topochansel"),
     "pop_topoplot": ("eegprep.functions.popfunc.pop_topoplot", "pop_topoplot"),
-    "pop_viewprops": ("eegprep.plugins.ICLabel.pop_viewprops", "pop_viewprops"),
     "pop_writeeeg": ("eegprep.functions.popfunc.pop_writeeeg", "pop_writeeeg"),
     "pop_writelocs": ("eegprep.functions.popfunc.pop_writelocs", "pop_writelocs"),
     "pop_xfirws": ("eegprep.plugins.firfilt.pop_xfirws", "pop_xfirws"),
@@ -400,8 +376,35 @@
 __all__ = ["__version__", *_LAZY_EXPORTS]
 
 
+_DECOUPLED_PLUGINS = {
+    "pop_iclabel": "eegprep-iclabel",
+    "iclabel": "eegprep-iclabel",
+    "pop_icflag": "eegprep-iclabel",
+    "eeg_icalabelstat": "eegprep-iclabel",
+    "eeg_icflag": "eegprep-iclabel",
+    "ICL_feature_extractor": "eegprep-iclabel",
+    "pop_viewprops": "eegprep-iclabel",
+    "pop_prop_extended": "eegprep-iclabel",
+    "pop_clean_rawdata": "eegprep-clean-rawdata",
+    "clean_artifacts": "eegprep-clean-rawdata",
+    "clean_asr": "eegprep-clean-rawdata",
+    "clean_channels": "eegprep-clean-rawdata",
+    "clean_channels_nolocs": "eegprep-clean-rawdata",
+    "clean_drifts": "eegprep-clean-rawdata",
+    "clean_flatlines": "eegprep-clean-rawdata",
+    "clean_windows": "eegprep-clean-rawdata",
+    "vis_artifacts": "eegprep-clean-rawdata",
+}
+
 def __getattr__(name: str) -> Any:
     """Load public EEGPrep exports on first access."""
+    if name in _DECOUPLED_PLUGINS:
+        pkg = _DECOUPLED_PLUGINS[name]
+        raise RuntimeError(
+            f"The feature {name!r} requires an uninstalled plugin package. "
+            f"Please install it using: pip install {pkg}"
+        )
+
     try:
         module_name, attr_name = _LAZY_EXPORTS[name]
     except KeyError as exc:

src/eegprep/cli/commands/transforms.py

@@ -31,7 +31,6 @@
 from eegprep.functions.popfunc.pop_resample import pop_resample
 from eegprep.functions.popfunc.pop_runica import pop_runica
 from eegprep.functions.popfunc.pop_saveset import pop_saveset
-from eegprep.plugins.clean_rawdata.pop_clean_rawdata import pop_clean_rawdata
 from eegprep.plugins.firfilt.pop_eegfiltnew import pop_eegfiltnew
 
 

src/eegprep/extensions.py

@@ -19,8 +19,6 @@
     eeg_bids_import_items,
     eeg_bids_tools_menu,
 )
-from eegprep.plugins.ICLabel.menu import iclabel_menu, viewprops_plot_menus
-from eegprep.plugins.clean_rawdata.menu import clean_rawdata_menu
 from eegprep.plugins.dipfit.menu import dipfit_menu
 from eegprep.plugins.firfilt.menu import firfilt_filter_items
 
@@ -328,62 +326,6 @@ def get(self, name: str) -> ExtensionRecord | None:
 
     def _bundled_records(self) -> list[ExtensionRecord]:
         specs = (
-            ExtensionSpec(
-                name="clean_rawdata",
-                display_name="clean_rawdata",
-                version="bundled",
-                package_name="eegprep.plugins.clean_rawdata",
-                source_type=ExtensionSourceType.BUNDLED,
-                description="Artifact Subspace Reconstruction and related channel/window cleaning workflows.",
-                capabilities=("artifact", "preprocessing"),
-                menus=(
-                    _extension_menu_from_spec(
-                        clean_rawdata_menu(),
-                        path=("tools",),
-                        insert_after="pop_eegplot:data",
-                    ),
-                ),
-                pop_functions=(
-                    ExtensionPopFunction(
-                        name="pop_clean_rawdata",
-                        target=LazyImport(
-                            "eegprep.plugins.clean_rawdata.pop_clean_rawdata",
-                            "pop_clean_rawdata",
-                        ),
-                    ),
-                ),
-            ),
-            ExtensionSpec(
-                name="ICLabel",
-                display_name="ICLabel",
-                version="bundled",
-                package_name="eegprep.plugins.ICLabel",
-                source_type=ExtensionSourceType.BUNDLED,
-                description="Independent-component classification, flagging, and extended component properties.",
-                capabilities=("ica", "classification"),
-                menus=(
-                    _extension_menu_from_spec(
-                        iclabel_menu(),
-                        path=("tools",),
-                        insert_after="pop_selectcomps",
-                    ),
-                    *(_extension_menu_from_spec(item, path=("plot",)) for item in viewprops_plot_menus()),
-                ),
-                pop_functions=(
-                    ExtensionPopFunction(
-                        name="pop_iclabel",
-                        target=LazyImport("eegprep.plugins.ICLabel.pop_iclabel", "pop_iclabel"),
-                    ),
-                    ExtensionPopFunction(
-                        name="pop_icflag",
-                        target=LazyImport("eegprep.plugins.ICLabel.pop_icflag", "pop_icflag"),
-                    ),
-                    ExtensionPopFunction(
-                        name="pop_viewprops",
-                        target=LazyImport("eegprep.plugins.ICLabel.pop_viewprops", "pop_viewprops"),
-                    ),
-                ),
-            ),
             ExtensionSpec(
                 name="firfilt",
                 display_name="firfilt",

src/eegprep/functions/guifunc/menu_actions.py

@@ -40,7 +40,6 @@
     "pop_chanplot",
     "pop_clust",
     "pop_clustedit",
-    "pop_clean_rawdata",
     "pop_chanedit",
     "pop_comperp",
     "pop_delset",
@@ -78,8 +77,6 @@
     "pop_firpm",
     "pop_firws",
     "pop_headplot",
-    "pop_icflag",
-    "pop_iclabel",
     "pop_jointprob",
     "pop_leadfield",
     "pop_importbids",
@@ -125,7 +122,6 @@
     "pop_timtopo",
     "pop_taskinfo",
     "pop_topoplot",
-    "pop_viewprops",
     "pop_participantinfo",
     "pop_mergeset",
     "pop_multifit",
@@ -150,16 +146,13 @@
 EEGPREP_SOURCE_URL = f"{EEGPREP_REPO_URL}/blob/develop"
 
 _MULTIPLE_DATASET_ACTIONS = {
-    "pop_clean_rawdata",
     "pop_chanedit",
     "pop_eegfilt",
     "pop_eegfiltnew",
     "pop_epoch",
     "pop_firma",
     "pop_firpm",
     "pop_firws",
-    "pop_icflag",
-    "pop_iclabel",
     "pop_reref",
     "pop_rmdat",
     "pop_resample",
@@ -198,7 +191,6 @@
 }
 
 _NEWSET_COMMIT_ACTIONS = {
-    "pop_clean_rawdata",
     "pop_eegfilt",
     "pop_eegfiltnew",
     "pop_epoch",
@@ -225,7 +217,6 @@
     "pop_editeventfield",
     "pop_editeventvals",
     "pop_chanedit",
-    "pop_clean_rawdata",
     "pop_eegfilt",
     "pop_eegfiltnew",
     "pop_epoch",
@@ -240,8 +231,6 @@
     "pop_runica",
     "pop_select",
     "pop_selectevent",
-    "pop_iclabel",
-    "pop_icflag",
     "pop_subcomp",
 }
 
@@ -400,7 +389,6 @@ def dispatch(self, action: str, parent: Any | None = None) -> None:
             "pop_rejspec",
             "pop_rejtrend",
             "pop_selectcomps",
-            "pop_viewprops",
         }:
             self._run_pop_function(base, parent, variant=variant)
             return
@@ -1065,10 +1053,6 @@ def _run_pop_function(self, name: str, parent: Any | None, *, variant: str = "")
             from eegprep.functions.popfunc.pop_chanedit import pop_chanedit
 
             out = pop_chanedit(selection, return_com=True)
-        elif name == "pop_clean_rawdata":
-            from eegprep.plugins.clean_rawdata.pop_clean_rawdata import pop_clean_rawdata
-
-            out = pop_clean_rawdata(selection, return_com=True)
         elif name == "pop_eegfilt":
             from eegprep.functions.popfunc.pop_eegfilt import pop_eegfilt
 
@@ -1101,14 +1085,6 @@ def _run_pop_function(self, name: str, parent: Any | None, *, variant: str = "")
             from eegprep.functions.popfunc.pop_interp import pop_interp
 
             out = pop_interp(selection, alleeg=self.session.ALLEEG, return_com=True)
-        elif name == "pop_iclabel":
-            from eegprep.plugins.ICLabel.pop_iclabel import pop_iclabel
-
-            out = pop_iclabel(selection, return_com=True)
-        elif name == "pop_icflag":
-            from eegprep.plugins.ICLabel.pop_icflag import pop_icflag
-
-            out = pop_icflag(selection, return_com=True)
         elif name == "pop_resample":
             from eegprep.functions.popfunc.pop_resample import pop_resample
 
@@ -1238,33 +1214,14 @@ def accept_browser_result(eeg_out: Any, command: str) -> None:
             from eegprep.functions.popfunc.pop_selectcomps import pop_selectcomps
 
             out = pop_selectcomps(selection, return_com=True)
-        elif name == "pop_viewprops":
-            from eegprep.plugins.ICLabel.pop_viewprops import pop_viewprops
-
-            target_index = list(self.session.CURRENTSET)
-
-            def commit_component_rejection(eeg_out: Any, _states: dict[int, bool]) -> None:
-                with self.session.gui_action("pop_viewprops"):
-                    self._store_current_from_gui(eeg_out, command="", index=target_index)
-                    self._refresh()
 
-            out = pop_viewprops(
-                selection,
-                typecomp=0 if variant == "components" else 1,
-                reject_callback=commit_component_rejection,
-                return_com=True,
-            )
         else:
             self.show_coming_soon(name, parent)
             return
         if isinstance(out, tuple):
             eeg_out, command = out[0], out[1] if len(out) > 1 else ""
         else:
             eeg_out, command = out, ""
-        if name == "pop_viewprops":
-            self._add_history_from_gui(command)
-            self._refresh()
-            return
         if command:
             if name in _NEWSET_COMMIT_ACTIONS:
                 self._commit_processed_dataset_from_gui(eeg_out, command=command, parent=parent)

src/eegprep/functions/sigprocfunc/runica.py

@@ -24,11 +24,18 @@
 
 import numpy as np
 from scipy.linalg import sqrtm, pinv, eig
-from ...plugins.clean_rawdata.private.ransac import rand_permutation
-from ..miscfunc.misc import finite_pinv
+from ..miscfunc.misc import finite_pinv, round_mat
 
 logger = logging.getLogger(__name__)
 
+def rand_permutation(n: int, stream: np.random.RandomState) -> np.ndarray:
+    """Random permutation with MATLAB parity using Fisher-Yates shuffle."""
+    result = np.arange(n)
+    for k in range(n - 1, 0, -1):
+        j = int(round_mat(k * stream.rand()))
+        result[k], result[j] = result[j], result[k]
+    return result
+
 
 def _matmul(left, right):
     # MATLAB mtimes does not surface BLAS floating-point status warnings for