Merge pull request #346 from NeuroML/feat/warn-optional-deps

feat(optional-deps): add warnings to inform users of optional packages

.pre-commit-config.yaml

@@ -11,4 +11,5 @@ repos:
   rev: v0.4.1
   hooks:
     - id: ruff
+      args: [ --exit-zero ]
     - id: ruff-format

pyneuroml/analysis/__init__.py

@@ -10,12 +10,19 @@
 from pyneuroml.utils.plot import get_next_hex_color
 from pyneuroml.plot import generate_plot
 import neuroml as nml
-from pyelectro.analysis import max_min
-from pyelectro.analysis import mean_spike_frequency
+
 from typing import Optional
 
 
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    from pyelectro.analysis import max_min
+    from pyelectro.analysis import mean_spike_frequency
+except ImportError:
+    logger.warning("Please install optional dependencies to use analysis features:")
+    logger.warning("pip install pyneuroml[analysis]")
 
 
 def generate_current_vs_frequency_curve(
@@ -202,9 +209,7 @@ def generate_current_vs_frequency_curve(
     stims = []
     if len(custom_amps_nA) > 0:
         stims = [float(a) for a in custom_amps_nA]
-        stim_info = [
-            "%snA" % float(a) for a in custom_amps_nA
-        ]  # type: typing.Union[str, typing.List[str]]
+        stim_info = ["%snA" % float(a) for a in custom_amps_nA]  # type: typing.Union[str, typing.List[str]]
     else:
         # else generate a list using the provided arguments
         amp = start_amp_nA

pyneuroml/annotations.py

@@ -7,20 +7,23 @@
 Copyright 2024 NeuroML contributors
 """
 
-
 import logging
 import pprint
 import typing
 
 from lxml import etree
-from rdflib import RDF, BNode, Graph, Literal, Namespace, URIRef
-from rdflib.namespace import DC, DCTERMS, FOAF, RDF, RDFS
-
 from pyneuroml.utils.xml import _find_elements, _get_attr_in_element
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
+try:
+    from rdflib import BNode, Graph, Literal, Namespace, URIRef
+    from rdflib.namespace import DC, DCTERMS, FOAF, RDFS
+except ImportError:
+    logger.warning("Please install optional dependencies to use annotation features:")
+    logger.warning("pip install pyneuroml[annotations]")
+
 
 # From https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/
 PREDICATES_MAP = {

pyneuroml/biosimulations.py

@@ -7,14 +7,11 @@
 Copyright 2024 NeuroML contributors
 """
 
-
 import logging
 import typing
 from datetime import datetime
 
 import requests
-from pydantic import BaseModel
-from requests_toolbelt.multipart.encoder import MultipartEncoder
 
 from pyneuroml import __version__
 from pyneuroml.annotations import create_annotation
@@ -24,6 +21,16 @@
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
+try:
+    from pydantic import BaseModel
+    from requests_toolbelt.multipart.encoder import MultipartEncoder
+except ImportError:
+    logger.warning(
+        "Please install optional dependencies to use Biosimulation.org features:"
+    )
+    logger.warning("pip install pyneuroml[combine]")
+
+
 biosimulators_api_url = "https://api.biosimulators.org"
 biosimulations_api_url = "https://api.biosimulations.org"
 
@@ -59,7 +66,7 @@ def get_simulator_versions(
         "xpp",
         "brian2",
         "copasi",
-    ]
+    ],
 ) -> typing.Dict[str, typing.List[str]]:
     """Get simulator list from biosimulators.
 

pyneuroml/neuron/__init__.py

@@ -25,14 +25,17 @@
 from pyneuroml.pynml import validate_neuroml1
 from pyneuroml.pynml import validate_neuroml2
 
-from pyneuroml.neuron.nrn_export_utils import set_erev_for_mechanism
-from neuron import h
-
-
 pp = pprint.PrettyPrinter(depth=4)
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
+try:
+    from neuron import h
+    from pyneuroml.neuron.nrn_export_utils import set_erev_for_mechanism
+except ImportError:
+    logger.warning("Please install optional dependencies to use NEURON features:")
+    logger.warning("pip install pyneuroml[neuron]")
+
 
 def get_utils_hoc() -> pathlib.Path:
     """Get full path of utils.hoc file

pyneuroml/neuron/nrn_export_utils.py

@@ -6,9 +6,17 @@
 
 """
 
+import logging
 
-from neuron import h
-from nrn import *
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    from neuron import h
+    from nrn import *
+except ImportError:
+    logger.warning("Please install optional dependencies to use NEURON features:")
+    logger.warning("pip install pyneuroml[neuron]")
 
 
 def clear_neuron() -> None:

pyneuroml/nsgr.py

@@ -7,19 +7,23 @@
 Copyright 2024 NeuroML contributors
 """
 
-
 import logging
 import os
 import pathlib
 import typing
 from zipfile import ZipFile
 
 from pyneuroml.runners import generate_sim_scripts_in_folder
-from pynsgr.commands.nsgr_submit import nsgr_submit
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
+try:
+    from pynsgr.commands.nsgr_submit import nsgr_submit
+except ImportError:
+    logger.warning("Please install optional dependencies to use NSG features:")
+    logger.warning("pip install pyneuroml[nsgr]")
+
 
 def run_on_nsg(
     engine: str,

pyneuroml/plot/PlotMorphologyPlotly.py

@@ -12,13 +12,18 @@
 import os
 import typing
 import logging
-import plotly.graph_objects as go
 from neuroml import Cell, NeuroMLDocument
 from pyneuroml.pynml import read_neuroml2_file
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
+try:
+    import plotly.graph_objects as go
+except ImportError:
+    logger.warning("Please install optional dependencies to use plotly features:")
+    logger.warning("pip install pyneuroml[plotly]")
+
 
 def plot_3D_cell_morphology_plotly(
     nml_file: typing.Union[str, Cell, NeuroMLDocument],

pyneuroml/plot/PlotMorphologyVispy.py

@@ -9,7 +9,6 @@
 Copyright 2023 NeuroML contributors
 """
 
-
 import logging
 import math
 import random
@@ -28,16 +27,22 @@
     load_minimal_morphplottable__model,
 )
 from scipy.spatial.transform import Rotation
-from vispy import app, scene, use
-from vispy.geometry.generation import create_sphere
-from vispy.geometry.meshdata import MeshData
-from vispy.scene.visuals import InstancedMesh
-from vispy.util.transforms import rotate
 from typing import Optional
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
+try:
+    from vispy import app, scene, use
+    from vispy.geometry.generation import create_sphere
+    from vispy.geometry.meshdata import MeshData
+    from vispy.scene.visuals import InstancedMesh
+    from vispy.util.transforms import rotate
+except ImportError:
+    logger.warning("Please install optional dependencies to use vispy features:")
+    logger.warning("pip install pyneuroml[vispy]")
+    logger.warning("or (for Qt5):")
+    logger.warning("pip install pyneuroml[vispy-qt5]")
 
 VISPY_THEME = {
     "light": {"bg": "white", "fg": "black"},

pyneuroml/plot/PlotSpikes.py

@@ -6,6 +6,7 @@
 
 Copyright 2023 NeuroML contributors
 """
+
 import argparse
 import logging
 import os
@@ -18,6 +19,13 @@
 from pyneuroml.utils.cli import build_namespace
 
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    import tables  # pytables for HDF5 support
+except ImportError:
+    logger.warning("Please install optional dependencies to use hdf5 features:")
+    logger.warning("pip install pyneuroml[hdf5]")
 
 FORMAT_ID_T = "id_t"
 FORMAT_ID_TIME_NEST_DAT = "id_t_nest_dat"
@@ -121,8 +129,6 @@ def read_sonata_spikes_hdf5_file(file_name: str):
     full_path = os.path.abspath(file_name)
     logger.info("Loading SONATA spike times from: %s (%s)" % (file_name, full_path))
 
-    import tables  # pytables for HDF5 support
-
     h5file = tables.open_file(file_name, mode="r")
 
     sorting = (

pyneuroml/povray/MakeMovie.py

@@ -1,11 +1,9 @@
-import cv2
 import colorsys
 import argparse
 import sys
 import os.path
 import logging
 
-
 """
 
             STILL IN DEVELOPMENT
@@ -18,6 +16,15 @@
 
 
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    import cv2
+except ImportError:
+    logger.warning("Please install optional dependencies to use povray features:")
+    logger.warning("pip install pyneuroml[povray]")
+
+
 scale_font = 1
 
 font = cv2.FONT_HERSHEY_COMPLEX_SMALL

pyneuroml/sbml/__init__.py

@@ -5,11 +5,22 @@
 
 import os
 import errno
-import libsbml
-from libsbml import SBMLReader
 from typing import List
 
 
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    import libsbml
+    from libsbml import SBMLReader
+except ImportError:
+    logger.warning("Please install optional dependencies to use SBML features:")
+    logger.warning("pip install pyneuroml[combine]")
+
+
 def validate_sbml_files(input_files: List[str], strict_units: bool = False) -> bool:
     """Validate input files using libsbml.SBMLDocument.checkConsistency
 

pyneuroml/tellurium/__init__.py

@@ -2,13 +2,28 @@
 run a model using the tellurium engine
 """
 
+import os
+import logging
 from pyneuroml.sedml import validate_sedml_files
-import tellurium as te
 
-te.setDefaultPlottingEngine("matplotlib")
 
-import os
-import libsedml
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+try:
+    import tellurium as te
+
+    te.setDefaultPlottingEngine("matplotlib")
+except ImportError:
+    logger.warning("Please install optional dependencies to use Tellurium features:")
+    logger.warning("pip install pyneuroml[tellurium]")
+
+try:
+    import libsedml
+except ImportError:
+    logger.warning("Please install optional dependencies to use SED-ML features:")
+    logger.warning("pip install pyneuroml[combine]")
+
 
 # # For technical reasons, any software which uses libSEDML
 # # must provide a custom build - Tellurium uses tesedml