Rename project from BrainScale to BrainTrace

.github/ISSUE_TEMPLATE/bug_report.md

@@ -10,7 +10,7 @@ Please:
 - [ ] Provide a complete example of how to reproduce the bug, wrapped in triple backticks like this:
 
 ```python
-import brainscale
+import braintrace
 ```
 
 - [ ] If applicable, include full error messages/tracebacks.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,6 +1,6 @@
 ---
 name: 'Feature Request'
-about: 'Suggest a new idea or improvement for BrainScale'
+about: 'Suggest a new idea or improvement for BrainTrace'
 labels: 'enhancement'
 ---
 

.github/workflows/CI-daily.yml

@@ -69,5 +69,5 @@ jobs:
           python -m pip install . || exit 1
       - name: Test with pytest
         run: |
-          pytest brainscale/
+          pytest braintrace/
 

.github/workflows/CI.yml

@@ -50,7 +50,7 @@ jobs:
           pip install .
       - name: Test with pytest
         run: |
-          pytest brainscale/
+          pytest braintrace/
 
 
   test_macos:
@@ -80,7 +80,7 @@ jobs:
           pip install .
       - name: Test with pytest
         run: |
-          pytest brainscale/
+          pytest braintrace/
 
 
   test_windows:
@@ -110,5 +110,5 @@ jobs:
           pip install .
       - name: Test with pytest
         run: |
-          pytest brainscale/ -p no:faulthandler
+          pytest braintrace/ -p no:faulthandler
 

.github/workflows/Publish.yml

@@ -39,15 +39,15 @@ jobs:
           echo "Release tag: $TAG"
           PKG_VERSION=$(python - <<'PY'
           import re, pathlib
-          init = pathlib.Path('brainscale/__init__.py').read_text(encoding='utf-8')
+          init = pathlib.Path('braintrace/__init__.py').read_text(encoding='utf-8')
           m = re.search(r"__version__\s*=\s*\"([^\"]+)\"", init)
           print(m.group(1) if m else '')
           PY
           )
           echo "Package version: ${PKG_VERSION}"
           TAG_STRIPPED=${TAG#v}
           if [[ -z "$PKG_VERSION" ]]; then
-            echo "Could not determine package version from brainscale/__init__.py" >&2
+            echo "Could not determine package version from braintrace/__init__.py" >&2
             exit 1
           fi
           if [[ "$TAG_STRIPPED" != "$PKG_VERSION" ]]; then

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# Contributing to BrainScale
+# Contributing to BrainTrace
 
-We welcome contributions to BrainScale! 
+We welcome contributions to BrainTrace! 
 Please fork this repository and submit a pull request with your changes. 
 We will review your changes and merge them if they are appropriate.
 

README.md

@@ -1,57 +1,71 @@
-<h1 align="center">BrainScale</h1>
-<h2 align="center">Scalable Online Learning for Brain Dynamics</h2>
+<h1 align="center">BrainTrace</h1>
+<h2 align="center">SEligibility Trace-based Online Learning for Brain Dynamics</h2>
 
 <p align="center">
-  	<img alt="Header image of brainscale." src="https://raw.githubusercontent.com/chaobrain/brainscale/main/docs/_static/brainscale.png" width=40%>
+  	<img alt="Header image of braintrace." src="https://raw.githubusercontent.com/chaobrain/braintrace/main/docs/_static/braintrace.png" width=40%>
 </p>
 
 <p align="center">
-	<a href="https://pypi.org/project/brainscale/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/brainscale"></a>
-	<a href="https://github.com/chaobrain/brainscale/blob/main/LICENSE"><img alt="LICENSE" src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"></a>
-  	<a href="https://brainscale.readthedocs.io/?badge=latest"><img alt="Documentation" src="https://readthedocs.org/projects/brainscale/badge/?version=latest"></a>
-  	<a href="https://badge.fury.io/py/brainscale"><img alt="PyPI version" src="https://badge.fury.io/py/brainscale.svg"></a>
-    <a href="https://github.com/chaobrain/brainscale/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/chaobrain/brainscale/actions/workflows/CI.yml/badge.svg"></a>
+	<a href="https://pypi.org/project/braintrace/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/braintrace"></a>
+	<a href="https://github.com/chaobrain/braintrace/blob/main/LICENSE"><img alt="LICENSE" src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"></a>
+  	<a href="https://braintrace.readthedocs.io/?badge=latest"><img alt="Documentation" src="https://readthedocs.org/projects/braintrace/badge/?version=latest"></a>
+  	<a href="https://badge.fury.io/py/braintrace"><img alt="PyPI version" src="https://badge.fury.io/py/braintrace.svg"></a>
+    <a href="https://github.com/chaobrain/braintrace/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/chaobrain/braintrace/actions/workflows/CI.yml/badge.svg"></a>
 </p>
 
-[``brainscale``](https://github.com/chaobrain/brainscale) provides online learning algorithms for biological neural networks.
+[``braintrace``](https://github.com/chaobrain/braintrace) provides online learning algorithms for biological neural networks.
 It has been integrated into our establishing [brain modeling ecosystem](https://brainmodeling.readthedocs.io/).
 
 ## Installation
 
-``brainscale`` can run on Python 3.10+ installed on Linux, MacOS, and Windows. You can install ``brainscale`` via pip:
+``braintrace`` can run on Python 3.10+ installed on Linux, MacOS, and Windows. You can install ``braintrace`` via pip:
 
 ```bash
-pip install brainscale --upgrade
+pip install braintrace --upgrade
 ```
 
-Alternatively, you can install `BrainX`, which bundles `brainscale` with other compatible packages for a comprehensive brain modeling ecosystem:
+Alternatively, you can install `BrainX`, which bundles `braintrace` with other compatible packages for a comprehensive brain modeling ecosystem:
 
 ```bash
 pip install BrainX -U
 ```
 
 ## Documentation
 
-The official documentation is hosted on Read the Docs: [https://brainscale.readthedocs.io](https://brainscale.readthedocs.io)
+The official documentation is hosted on Read the Docs: [https://braintrace.readthedocs.io](https://braintrace.readthedocs.io)
 
-## Citation
+[//]: # (## Citation)
 
-If you use this package in your research, please cite:
+[//]: # ()
+[//]: # (If you use this package in your research, please cite:)
 
-```bibtex
-@article {Wang2024.09.24.614728,
-	author = {Wang, Chaoming and Dong, Xingsi and Ji, Zilong and Jiang, Jiedong and Liu, Xiao and Wu, Si},
-	title = {BrainScale: Enabling Scalable Online Learning in Spiking Neural Networks},
-	elocation-id = {2024.09.24.614728},
-	year = {2025},
-	doi = {10.1101/2024.09.24.614728},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2025/07/27/2024.09.24.614728},
-	eprint = {https://www.biorxiv.org/content/early/2025/07/27/2024.09.24.614728.full.pdf},
-	journal = {bioRxiv}
-}
-```
+[//]: # ()
+[//]: # (```bibtex)
+
+[//]: # (@article {Wang2024.09.24.614728,)
+
+[//]: # (	author = {Wang, Chaoming and Dong, Xingsi and Ji, Zilong and Jiang, Jiedong and Liu, Xiao and Wu, Si},)
+
+[//]: # (	title = {Enabling Scalable Online Learning in Spiking Neural Networks},)
+
+[//]: # (	elocation-id = {2024.09.24.614728},)
+
+[//]: # (	year = {2025},)
+
+[//]: # (	doi = {10.1101/2024.09.24.614728},)
+
+[//]: # (	publisher = {Cold Spring Harbor Laboratory},)
+
+[//]: # (	URL = {https://www.biorxiv.org/content/early/2025/07/27/2024.09.24.614728},)
+
+[//]: # (	eprint = {https://www.biorxiv.org/content/early/2025/07/27/2024.09.24.614728.full.pdf},)
+
+[//]: # (	journal = {bioRxiv})
+
+[//]: # (})
+
+[//]: # (```)
 
 ## See also the ecosystem
 
-``brainscale`` is one part of our brain simulation ecosystem: https://brainmodeling.readthedocs.io/
+``braintrace`` is one part of our brain simulation ecosystem: https://brainmodeling.readthedocs.io/

brainscale/__init__.py → braintrace/__init__.py

@@ -19,32 +19,32 @@
 __version__ = "0.1.0"
 __version_info__ = (0, 1, 0)
 
-from brainscale._etrace_algorithms import *
-from brainscale._etrace_algorithms import __all__ as _alg_all
-from brainscale._etrace_compiler_graph import *
-from brainscale._etrace_compiler_graph import __all__ as _compiler_all
-from brainscale._etrace_compiler_hid_param_op import *
-from brainscale._etrace_compiler_hid_param_op import __all__ as _hid_param_all
-from brainscale._etrace_compiler_hidden_group import *
-from brainscale._etrace_compiler_hidden_group import __all__ as _hid_group_all
-from brainscale._etrace_compiler_hidden_pertubation import *
-from brainscale._etrace_compiler_hidden_pertubation import __all__ as _hid_pertub_all
-from brainscale._etrace_compiler_module_info import *
-from brainscale._etrace_compiler_module_info import __all__ as _mod_info_all
-from brainscale._etrace_concepts import *
-from brainscale._etrace_concepts import __all__ as _con_all
-from brainscale._etrace_graph_executor import *
-from brainscale._etrace_graph_executor import __all__ as _exec_all
-from brainscale._etrace_input_data import *
-from brainscale._etrace_input_data import __all__ as _data_all
-from brainscale._etrace_operators import *
-from brainscale._etrace_operators import __all__ as _op_all
-from brainscale._etrace_vjp import *
-from brainscale._etrace_vjp import __all__ as _vjp_all
-from brainscale._grad_exponential import *
-from brainscale._grad_exponential import __all__ as _grad_exp_all
-from brainscale._misc import *
-from brainscale._misc import __all__ as _misc_all
+from braintrace._etrace_algorithms import *
+from braintrace._etrace_algorithms import __all__ as _alg_all
+from braintrace._etrace_compiler_graph import *
+from braintrace._etrace_compiler_graph import __all__ as _compiler_all
+from braintrace._etrace_compiler_hid_param_op import *
+from braintrace._etrace_compiler_hid_param_op import __all__ as _hid_param_all
+from braintrace._etrace_compiler_hidden_group import *
+from braintrace._etrace_compiler_hidden_group import __all__ as _hid_group_all
+from braintrace._etrace_compiler_hidden_pertubation import *
+from braintrace._etrace_compiler_hidden_pertubation import __all__ as _hid_pertub_all
+from braintrace._etrace_compiler_module_info import *
+from braintrace._etrace_compiler_module_info import __all__ as _mod_info_all
+from braintrace._etrace_concepts import *
+from braintrace._etrace_concepts import __all__ as _con_all
+from braintrace._etrace_graph_executor import *
+from braintrace._etrace_graph_executor import __all__ as _exec_all
+from braintrace._etrace_input_data import *
+from braintrace._etrace_input_data import __all__ as _data_all
+from braintrace._etrace_operators import *
+from braintrace._etrace_operators import __all__ as _op_all
+from braintrace._etrace_vjp import *
+from braintrace._etrace_vjp import __all__ as _vjp_all
+from braintrace._grad_exponential import *
+from braintrace._grad_exponential import __all__ as _grad_exp_all
+from braintrace._misc import *
+from braintrace._misc import __all__ as _misc_all
 from . import nn
 
 __all__ = ['nn'] + _alg_all + _compiler_all + _hid_param_all + _hid_group_all + _hid_pertub_all
@@ -69,7 +69,7 @@ def __getattr__(name):
         import brainstate
 
         warnings.warn(
-            f"brainscale.{name} is deprecated and will be removed in a future release. "
+            f"braintrace.{name} is deprecated and will be removed in a future release. "
             f"Please use brainstate.{mapping[name]} instead.",
             DeprecationWarning,
             stacklevel=2,

brainscale/_compatible_imports_test.py → braintrace/_compatible_imports_test.py

@@ -16,7 +16,7 @@
 import jax.numpy as jnp
 from jax import jit, make_jaxpr, lax
 
-from brainscale._compatible_imports import (
+from braintrace._compatible_imports import (
     is_jit_primitive, is_scan_primitive, is_while_primitive,
     is_cond_primitive
 )

brainscale/_etrace_algorithms.py → braintrace/_etrace_algorithms.py

@@ -40,15 +40,15 @@ class EligibilityTrace(brainstate.ShortTermState):
 
     Examples
     --------
-    When you are using :class:`brainscale.IODimVjpAlgorithm`, you can get
+    When you are using :class:`braintrace.IODimVjpAlgorithm`, you can get
     the eligibility trace of the weight by calling:
 
     .. code-block:: python
 
         >>> etrace = etrace_algorithm.etrace_of(weight)
 
     """
-    __module__ = 'brainscale'
+    __module__ = 'braintrace'
 
 
 class ETraceAlgorithm(brainstate.nn.Module):
@@ -77,7 +77,7 @@ class ETraceAlgorithm(brainstate.nn.Module):
     running_index : brainstate.ParamState[int]
         The running index.
     """
-    __module__ = 'brainscale'
+    __module__ = 'braintrace'
 
     def __init__(
         self,

brainscale/_etrace_compiler_base.py → braintrace/_etrace_compiler_base.py

@@ -168,7 +168,7 @@ class JaxprEvaluation(object):
     outvar_to_hidden_path : Dict[Var, Path]
         Stored mapping from output variables to hidden paths.
     """
-    __module__ = 'brainscale'
+    __module__ = 'braintrace'
 
     def __init__(
         self,

brainscale/_etrace_compiler_graph.py → braintrace/_etrace_compiler_graph.py

@@ -86,12 +86,12 @@ class ETraceGraph(NamedTuple):
 
     Example::
 
-        >>> import brainscale
+        >>> import braintrace
         >>> import brainstate
-        >>> gru = brainscale.nn.GRUCell(10, 20)
+        >>> gru = braintrace.nn.GRUCell(10, 20)
         >>> gru.init_state()
         >>> inputs = brainstate.random.randn(10)
-        >>> compiled_graph = brainscale.compile_etrace_graph(gru, inputs)
+        >>> compiled_graph = braintrace.compile_etrace_graph(gru, inputs)
         >>> compiled_graph.dict().keys()
 
     """
@@ -127,7 +127,7 @@ def __repr__(self) -> str:
         return repr(brainstate.util.PrettyMapping(self._asdict(), type_name=self.__class__.__name__))
 
 
-ETraceGraph.__module__ = 'brainscale'
+ETraceGraph.__module__ = 'braintrace'
 
 
 class CONTEXT(threading.local):