chaobrain · chaoming0625 · Jan 19, 2026 · Jan 14, 2026 · Jan 14, 2026 · Jan 19, 2026
diff --git a/.gitignore b/.gitignore
@@ -231,3 +231,4 @@ cython_debug/
 /examples/MC13_golgi_model/x86_64/
 /.claude/
 /dev/replace_init.py
+/dev/replace_all.py
diff --git a/README.md b/README.md
@@ -117,7 +117,7 @@ The official documentation is hosted on Read the Docs: [https://braincell.readth
 
 
 
-## See also the brain modeling ecosystem
+## See also the ecosystem
 
-We are building the brain modeling ecosystem: https://brainmodeling.readthedocs.io/
+BrainCell is one part of our brain modeling ecosystem: https://brainmodeling.readthedocs.io/
 
diff --git a/braincell/__init__.py b/braincell/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -14,12 +14,14 @@
 # ==============================================================================
 
 
-__version__ = "0.0.6"
-__version_info__ = (0, 0, 6)
+__version__ = "0.0.7"
+__version_info__ = tuple(map(int, __version__.split(".")))
 
 from . import channel
 from . import ion
+from . import morph
 from . import neuron
+from . import quad
 from ._base import (
     HHTypedNeuron,
     IonChannel,
@@ -29,27 +31,10 @@
     mix_ions,
     IonInfo,
 )
-from ._integrator import *
-from ._integrator_protocol import (
-    DiffEqState,
-    DiffEqModule,
-    IndependentIntegration,
-)
-from ._morphology import (
-    Segment,
-    Section,
-    CylinderSection,
-    PointSection,
-    Morphology,
-)
-from ._morphology_from_asc import from_asc
-from ._morphology_from_swc import from_swc
-from ._multi_compartment import (
-    MultiCompartment,
-)
-from ._single_compartment import (
-    SingleCompartment,
-)
+from ._multi_compartment import MultiCompartment
+from ._single_compartment import SingleCompartment
+from .morph import *
+from .quad import *
 
 _deprecations = {
     'SingleCompartment': (
@@ -65,5 +50,6 @@
 }
 
 from braincell._misc import deprecation_getattr
+
 neuron.__getattr__ = deprecation_getattr(__name__, _deprecations)
 del deprecation_getattr
diff --git a/braincell/_base.py b/braincell/_base.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -88,7 +88,7 @@
 import numpy as np
 from brainstate.mixin import _JointGenericAlias
 
-from ._integrator_protocol import DiffEqModule, IndependentIntegration
+from .quad import DiffEqModule, IndependentIntegration
 from ._misc import set_module_as, Container, TreeNode
 
 __all__ = [

diff --git a/braincell/_base_test.py b/braincell/_base_test.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/_misc.py b/braincell/_misc.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/_multi_compartment.py b/braincell/_multi_compartment.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -19,9 +19,8 @@
 import brainunit as u
 
 from ._base import HHTypedNeuron, IonChannel
-from ._integrator import get_integrator
-from ._integrator_protocol import DiffEqState, IndependentIntegration
-from ._morphology import Morphology
+from .quad import get_integrator, DiffEqState, IndependentIntegration
+from .morph import Morphology
 from ._typing import Initializer
 
 __all__ = [

diff --git a/braincell/_single_compartment.py b/braincell/_single_compartment.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,8 +20,7 @@
 import braintools
 
 from ._base import HHTypedNeuron, IonChannel
-from ._integrator import get_integrator
-from ._integrator_protocol import DiffEqState, IndependentIntegration
+from .quad import get_integrator, DiffEqState, IndependentIntegration
 from ._typing import Initializer
 
 __all__ = [

diff --git a/braincell/_typing.py b/braincell/_typing.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/channel/calcium.py b/braincell/channel/calcium.py
@@ -12,7 +12,7 @@
 import brainunit as u
 
 from braincell._base import Channel, IonInfo
-from braincell._integrator_protocol import DiffEqState
+from braincell.quad import DiffEqState
 from braincell.ion import Calcium
 
 __all__ = [

diff --git a/braincell/channel/hyperpolarization_activated.py b/braincell/channel/hyperpolarization_activated.py
@@ -11,7 +11,7 @@
 import brainunit as u
 
 from braincell._base import Channel, HHTypedNeuron
-from braincell._integrator_protocol import DiffEqState
+from braincell.quad import DiffEqState
 
 __all__ = [
     'Ih_HM1992',

diff --git a/braincell/channel/potassium.py b/braincell/channel/potassium.py
@@ -12,7 +12,7 @@
 import brainunit as u
 
 from braincell._base import Channel, IonInfo
-from braincell._integrator_protocol import DiffEqState
+from braincell.quad import DiffEqState
 from braincell.ion import Potassium
 
 __all__ = [

diff --git a/braincell/channel/potassium_calcium.py b/braincell/channel/potassium_calcium.py
@@ -13,7 +13,7 @@
 import jax
 
 from braincell._base import IonInfo, Channel
-from braincell._integrator_protocol import DiffEqState
+from braincell.quad import DiffEqState
 from braincell.ion import Calcium, Potassium
 
 __all__ = [

diff --git a/braincell/channel/sodium.py b/braincell/channel/sodium.py
@@ -13,7 +13,7 @@
 import jax.tree
 
 from braincell._base import Channel, IonInfo
-from braincell._integrator_protocol import DiffEqState, IndependentIntegration
+from braincell.quad import DiffEqState, IndependentIntegration
 from braincell.ion import Sodium
 
 __all__ = [

diff --git a/braincell/ion/__init__.py b/braincell/ion/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/ion/calcium.py b/braincell/ion/calcium.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -22,7 +22,7 @@
 import brainunit as u
 
 from braincell._base import Ion, Channel, HHTypedNeuron
-from braincell._integrator_protocol import DiffEqState
+from braincell.quad import DiffEqState
 
 __all__ = [
     'Calcium',

diff --git a/braincell/ion/potassium.py b/braincell/ion/potassium.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/ion/sodium.py b/braincell/ion/sodium.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/morph/__init__.py b/braincell/morph/__init__.py
@@ -0,0 +1,18 @@
+# Copyright 2026 BrainX Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+from ._from_asc import from_asc
+from ._from_swc import from_swc
+from ._morphology import Morphology, Segment, Section, CylinderSection, PointSection
diff --git a/braincell/_morphology_branch_tree.py → braincell/morph/_branch_tree.py b/braincell/_morphology_branch_tree.py → braincell/morph/_branch_tree.py
@@ -1,4 +1,4 @@
-# Copyright 2025 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

diff --git a/braincell/_morphology_from_asc.py → braincell/morph/_from_asc.py b/braincell/_morphology_from_asc.py → braincell/morph/_from_asc.py
@@ -1,4 +1,4 @@
-# Copyright 2025 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -22,7 +22,7 @@
 from scipy.interpolate import interp1d
 
 from ._morphology import Morphology
-from ._morphology_utils import get_type_name
+from ._utils import get_type_name
 
 
 class Token:

diff --git a/braincell/_morphology_from_swc.py → braincell/morph/_from_swc.py b/braincell/_morphology_from_swc.py → braincell/morph/_from_swc.py
@@ -1,4 +1,4 @@
-# Copyright 2025 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -21,7 +21,7 @@
 import numpy as np
 
 from ._morphology import Morphology
-from ._morphology_utils import get_type_name
+from ._utils import get_type_name
 
 
 class Import3dSection:

diff --git a/braincell/_morphology.py → braincell/morph/_morphology.py b/braincell/_morphology.py → braincell/morph/_morphology.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -21,15 +21,15 @@
 import brainunit as u
 import numpy as np
 
-from ._morphology_branch_tree import BranchingTree
-from ._morphology_utils import (
+from ._branch_tree import BranchingTree
+from ._utils import (
     calculate_total_resistance_and_area,
     generate_interpolated_nodes,
     compute_connection_seg,
     compute_line_ratios,
     init_coupling_weight_nodes,
 )
-from ._typing import SectionName
+from braincell._typing import SectionName
 
 __all__ = [
     'Segment',
@@ -925,7 +925,7 @@ def from_swc(cls, filename: str | Path):
         Morphology
             A Morphology object created from the SWC file
         """
-        from ._morphology_from_swc import from_swc
+        from ._from_swc import from_swc
         return from_swc(filename)
 
     @classmethod
@@ -943,7 +943,7 @@ def from_asc(cls, filename: str | Path):
         Morphology
             A Morphology object created from the ASC file
         """
-        from ._morphology_from_asc import from_asc
+        from ._from_asc import from_asc
         return from_asc(filename)
 
     def visualize(self):

diff --git a/braincell/_morphology_test.py → braincell/morph/_morphology_test.py b/braincell/_morphology_test.py → braincell/morph/_morphology_test.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -22,7 +22,7 @@
 class TestMorphologyConstruction:
     def test_single(self):
         # Instantiate a Morphology object
-        morphology = braincell.Morphology()
+        morphology = braincell.morph.Morphology()
         # Create individual sections using the creation methods
         morphology.add_cylinder_section(
             'soma', length=20 * u.um, diam=10 * u.um, nseg=1
@@ -53,7 +53,7 @@ def test_single(self):
 
     def test_multiple(self):
         # Instantiate a Morphology object
-        morphology = braincell.Morphology()
+        morphology = braincell.morph.Morphology()
 
         # Define sections using a property dictionary
         section_dicts = {
@@ -87,16 +87,16 @@ def test_multiple(self):
 
     def test_swc(self):
         # Load morphology from SWC file
-        swc_file = os.path.join(os.path.dirname(__file__), "../dev/swc_file/io.swc")
-        morphology = braincell.Morphology.from_swc(swc_file)
+        swc_file = os.path.join(os.path.dirname(__file__), "../../dev/swc_file/io.swc")
+        morphology = braincell.morph.from_swc(swc_file)
         print(morphology)
         # Initialize DHS
         morphology.to_branch_tree()
 
     def test_asc(self):
         # Load morphology from ASC file
-        asc_file = os.path.join(os.path.dirname(__file__), "../dev/asc_file/golgi.asc")
-        morphology = braincell.Morphology.from_asc(asc_file)
+        asc_file = os.path.join(os.path.dirname(__file__), "../../dev/asc_file/golgi.asc")
+        morphology = braincell.morph.from_asc(asc_file)
         print(morphology)
         # Initialize DHS
         morphology.to_branch_tree()
diff --git a/braincell/_morphology_utils.py → braincell/morph/_utils.py b/braincell/_morphology_utils.py → braincell/morph/_utils.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,6 +17,7 @@
 import brainunit as u
 import numpy as np
 
+
 def calculate_total_resistance_and_area(
     points: brainstate.typing.Array,
     resistivity: u.Quantity = 100.0

diff --git a/braincell/_morphology_utils_test.py → braincell/morph/_utils_test.py b/braincell/_morphology_utils_test.py → braincell/morph/_utils_test.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,7 +20,7 @@
 import numpy as np
 import pytest
 
-from braincell._morphology_utils import (
+from braincell.morph._utils import (
     compute_line_ratios,
     calculate_total_resistance_and_area,
     find_ratio_interval,

diff --git a/braincell/neuron/__init__.py b/braincell/neuron/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+# Copyright 2024 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.