Refactor V2 tests to tests_version2 and add V2/V3 documentation READMEs

.github/PULL_REQUEST_TEMPLATE.md

@@ -45,7 +45,7 @@ See CONTRIBUTING.md for guidelines.
 ## Testing
 
 **How has this been tested?**
-<!-- Describe the tests you ran to verify your changes -->
+<!-- Describe the tests_version2 you ran to verify your changes -->
 
 ```python
 # Example test code or commands used

.github/labeler.yml

@@ -19,7 +19,7 @@ dependencies:
 # Tests
 tests:
   - changed-files:
-    - any-glob-to-any-file: ['tests/**/*', '**/*test*.py']
+    - any-glob-to-any-file: ['tests_version2/**/*', '**/*test*.py']
 
 # Examples
 examples:

.github/workflows/CI-models.yml

@@ -37,7 +37,7 @@ jobs:
           pip install -e .
       - name: Test with pytest
         run: |
-          pytest tests/
+          pytest tests_version2/
 
   test_macos:
     runs-on: macos-latest
@@ -59,7 +59,7 @@ jobs:
           pip install -e .
       - name: Test with pytest
         run: |
-          pytest tests/
+          pytest tests_version2/
 
   test_windows:
     runs-on: windows-latest
@@ -81,4 +81,4 @@ jobs:
           pip install -e .
       - name: Test with pytest
         run: |
-          pytest tests/
+          pytest tests_version2/

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies, run tests_version2 and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: Continuous Integration
@@ -76,8 +76,6 @@ jobs:
           python -m pip install --upgrade pip
           if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
           pip install -e .
-#          pip install jax==0.4.30
-#          pip install jaxlib==0.4.30
       - name: Test with pytest
         run: |
           pytest brainpy/

CONTRIBUTING.md

@@ -114,12 +114,12 @@ Branch naming conventions:
 
 Run the test suite:
 ```bash
-pytest tests/
+pytest tests_version2/
 ```
 
 Run specific tests:
 ```bash
-pytest tests/test_specific.py -v
+pytest tests_version2/test_specific.py -v
 ```
 
 ### 4. Commit Your Changes
@@ -203,7 +203,7 @@ def simulate_network(network, duration, dt=0.1):
 
 Aim for high test coverage on new code:
 ```bash
-pytest --cov=brainpy tests/
+pytest --cov=brainpy tests_version2/
 ```
 
 ## Documentation

brainpy/_base_test.py

@@ -13,20 +13,6 @@
 # limitations under the License.
 # ==============================================================================
 
-"""
-Comprehensive tests for the Neuron and Synapse base classes in _base.py.
-
-This module tests:
-- Neuron base class functionality and abstract interface
-- Synapse base class functionality and abstract interface
-- Proper initialization and parameter handling
-- State management (init_state, reset_state)
-- Surrogate gradient function integration
-- Reset mechanisms (soft/hard)
-- Custom implementations
-- Edge cases and error handling
-"""
-
 import unittest
 
 import braintools

brainpy/version2/math/einops_parsing.py

@@ -51,7 +51,7 @@ def __init__(self, expression: str, *, allow_underscore: bool = False,
         self.identifiers: Set[str] = set()
         # that's axes like 2, 3, 4 or 5. Axes with size 1 are exceptional and replaced with empty composition
         self.has_non_unitary_anonymous_axes: bool = False
-        # composition keeps structure of composite axes, see how different corner cases are handled in tests
+        # composition keeps structure of composite axes, see how different corner cases are handled in tests_version2
         self.composition: List[Union[List[str], str]] = []
         if '.' in expression:
             if '...' not in expression:

brainpy/version2/math/tests/test_einops.py

@@ -118,7 +118,7 @@ def test_rearrange_consistency_numpy():
 
 
 def test_rearrange_permutations_numpy():
-    # tests random permutation of axes against two independent numpy ways
+    # tests_version2 random permutation of axes against two independent numpy ways
     for n_axes in range(1, 10):
         input = numpy.arange(2 ** n_axes).reshape([2] * n_axes)
         permutation = numpy.random.permutation(n_axes)

brainpy/version2/math/tests/test_environment.py

@@ -21,7 +21,7 @@
 
 class TestEnvironment(unittest.TestCase):
     def test_numpy_func_return(self):
-        # Reset random state to ensure clean state between tests
+        # Reset random state to ensure clean state between tests_version2
         bm.random.seed()
 
         with bm.environment(numpy_func_return='jax_array'):

brainpy/version2/math/tests/test_numpy_einsum.py

@@ -236,7 +236,7 @@ def test_tf_unsupported_3(self):
         s = 'ij,ij,jk->ik'
         self._check(s, x, y, z)
 
-    # these tests are based on https://github.com/dask/dask/pull/3412/files
+    # these tests_version2 are based on https://github.com/dask/dask/pull/3412/files
     @parameterized.named_parameters(
         {"testcase_name": "_{}_dtype={}".format(einstr, dtype.__name__), "einstr": einstr,
          "dtype": dtype}

brainpy/version2/math/tests/test_numpy_ops.py

@@ -337,7 +337,7 @@ def op_record(name, nargs, dtypes, shapes, rng_factory, diff_modes,
     # TODO(phawkins): np.unwrap does not correctly promote its default period
     # argument under NumPy 1.21 for bfloat16 inputs. It works fine if we
     # explicitly pass a bfloat16 value that does not need promition. We should
-    # probably add a custom test harness for unwrap that tests the period
+    # probably add a custom test harness for unwrap that tests_version2 the period
     # argument anyway.
     op_record("unwrap", 1, [t for t in float_dtypes if t != dtypes.bfloat16],
               nonempty_nonscalar_array_shapes,
@@ -539,7 +539,7 @@ def _promote_like_jnp(fun, inexact=False):
     """Decorator that promotes the arguments of `fun` to `jnp.result_type(*args)`.
 
   jnp and np have different type promotion semantics; this decorator allows
-  tests make an np reference implementation act more like an jnp
+  tests_version2 make an np reference implementation act more like an jnp
   implementation.
   """
     _promote = _promote_dtypes_inexact if inexact else _promote_dtypes
@@ -3056,7 +3056,7 @@ def testIdentity(self, n, dtype):
         for left in [None, 0]
         for right in [None, 1]
         for dtype in default_dtypes
-        # following types lack precision for meaningful tests
+        # following types lack precision for meaningful tests_version2
         if dtype not in [np.int8, np.int16, np.float16, jnp.bfloat16]
     ))
     def testInterp(self, shape, dtype, period, left, right):
@@ -3562,7 +3562,7 @@ def testHistogramBinEdges(self, shape, dtype, bins, range, weights):
         for shape in [(5,), (5, 5)]
         for dtype in default_dtypes
         # We only test explicit integer-valued bin edges because in other cases
-        # rounding errors lead to flaky tests.
+        # rounding errors lead to flaky tests_version2.
         for bins in [np.arange(-5, 6), np.array([-5, 0, 3])]
         for density in [True, False]
         for weights in [True, False]
@@ -5108,7 +5108,7 @@ def testLongLong(self):
     @jtu.ignore_warning(category=UserWarning,
                         message="Explicitly requested dtype.*")
     def testArange(self):
-        # test cases inspired by dask tests at
+        # test cases inspired by dask tests_version2 at
         # https://github.com/dask/dask/blob/main/dask/array/tests/test_creation.py#L92
         np_arange = jtu.with_jax_dtype_defaults(np.arange)
         self.assertAllClose(bm.arange(77).value,
@@ -5777,7 +5777,7 @@ def testDisableNumpyRankPromotionBroadcasting(self):
             FLAGS.jax_numpy_rank_promotion = prev_flag
 
     def testStackArrayArgument(self):
-        # tests https://github.com/google/jax/issues/1271
+        # tests_version2 https://github.com/google/jax/issues/1271
         @jax.jit
         def foo(x):
             return bm.stack(x)
@@ -6050,7 +6050,7 @@ def testFromString(self):
         self.assertArraysEqual(expected, actual)
 
 
-# Most grad tests are at the lax level (see lax_test.py), but we add some here
+# Most grad tests_version2 are at the lax level (see lax_test.py), but we add some here
 # as needed for e.g. particular compound ops of interest.
 
 GradTestSpec = collections.namedtuple(
@@ -6126,7 +6126,7 @@ def testOpGradSpecialValue(self, op, special_value, order):
                     atol={np.float32: 3e-3})
 
     def testSincGradArrayInput(self):
-        # tests for a bug almost introduced in #5077
+        # tests_version2 for a bug almost introduced in #5077
         jax.grad(lambda x: bm.sinc(x).sum())(jnp.arange(10.))  # doesn't crash
 
     def testTakeAlongAxisIssue1521(self):

brainpy/version2/running/tests/test_pathos_multiprocessing.py

@@ -24,7 +24,7 @@
 if sys.platform == 'win32' and sys.version_info.minor >= 11:
     pytest.skip('python 3.11 does not support.', allow_module_level=True)
 else:
-    pytest.skip('Cannot pass tests.', allow_module_level=True)
+    pytest.skip('Cannot pass tests_version2.', allow_module_level=True)
 
 
 class TestParallel(parameterized.TestCase):

docs_version2/README.md

@@ -0,0 +1,64 @@
+# BrainPy Version 2 Documentation
+
+This directory contains documentation for BrainPy 2.x, the previous major version of BrainPy.
+
+## Overview
+
+BrainPy 2.x is a highly flexible and extensible framework targeting general-purpose Brain Dynamics Programming (BDP). This documentation is maintained for users who are still using BrainPy 2.x.
+
+## Important Note
+
+**As of September 2025, BrainPy has been upgraded to version 3.x.** If you are using BrainPy 3.x, please refer to the main documentation.
+
+To use BrainPy 2.x APIs within version 3.x installations, update your imports:
+
+```python
+# Old version (v2.x standalone)
+import brainpy as bp
+import brainpy.math as bm
+
+# Using v2.x API in BrainPy 3.x
+import brainpy.version2 as bp
+import brainpy.version2.math as bm
+```
+
+## Documentation Contents
+
+- **index.rst** - Main documentation entry point
+- **core_concepts.rst** - Fundamental concepts of Brain Dynamics Programming
+- **tutorials.rst** - Step-by-step tutorials
+- **advanced_tutorials.rst** - Advanced usage patterns
+- **toolboxes.rst** - Specialized toolboxes for different applications
+- **api.rst** - Complete API reference
+- **FAQ.rst** - Frequently asked questions
+- **brainpy-changelog.md** - Version history and changes
+- **brainpylib-changelog.md** - BrainPyLib backend changes
+
+## Building Documentation
+
+This documentation is written in reStructuredText (RST) format and can be built using Sphinx:
+
+```bash
+cd docs_version2
+make html  # or use the appropriate build script
+```
+
+## Installation
+
+For BrainPy 2.x compatibility:
+
+```bash
+pip install -U brainpy[cpu]
+```
+
+## Learn More
+
+- [Core Concepts](core_concepts.rst) - Understand the fundamentals
+- [Tutorials](tutorials.rst) - Learn through examples
+- [API Documentation](api.rst) - Complete reference
+- [BrainPy Examples](https://brainpy-v2.readthedocs.io/projects/examples/) - Code examples
+- [BrainPy Ecosystem](https://brainmodeling.readthedocs.io) - Related projects
+
+## Support
+
+For questions and support, please visit the [BrainPy GitHub repository](https://github.com/brainpy/BrainPy).

docs_version2/quickstart/simulation.ipynb

@@ -1337,7 +1337,7 @@
      "start_time": "2025-10-06T03:15:11.632401Z"
     }
    },
-   "source": "PATH = '../../tests/simulation/data/hcp.npz'",
+   "source": "PATH = '../../tests_version2/simulation/data/hcp.npz'",
    "outputs": [],
    "execution_count": 26
   },

docs_version2/tutorial_advanced/contributing.md

@@ -71,21 +71,21 @@ Follow these steps to contribute code:
    the repository:
 
    ```bash
-   pytest -n auto tests/
+   pytest -n auto tests_version2/
    ```
 
    BrainPy's test suite is quite large, so if you know the specific test file that covers your
    changes, you can limit the tests to that; for example:
 
    ```bash
-   pytest -n auto brainpy/_src/tests/test_mixin.py
+   pytest -n auto brainpy/_src/tests_version2/test_mixin.py
    ```
 
    You can narrow the tests further by using the `pytest -k` flag to match particular test
    names:
 
    ```bash
-   pytest -n auto brainpy/_src/tests/test_mixin.py -k testLogSumExp
+   pytest -n auto brainpy/_src/tests_version2/test_mixin.py -k testLogSumExp
    ```
 
    BrainPy also offers more fine-grained control over which particular tests are run;