fix(inputs,algorithms,connect): deprecation aliases, regression fits, CSR guard, dtype (#853)

fix(inputs,algorithms,connect): deprecation aliases, regression fits, CSR guard, dtype/off-by-one

- spike_current/ramp_current deprecation aliases forwarded to constant_input
  with wrong kwargs (crash); forward to spike_input/ramp_input (Critical)
- LogisticRegression.call crashed (flattened targets then read .shape[1]);
  init a 1-D parameter vector (Critical)
- ElasticNetRegression trained with default add_bias=True while predict used
  self.add_bias -> feature mismatch crash; pass add_bias=self.add_bias (High)
- CSRConn.build_csr guard "pre_num != pre_num" was a tautology; compare against
  inptr.size-1 and raise on inconsistent pre_size (High)
- connect.coo2csr scattered int counts into a uint32 buffer (int32->uint32
  warning, future JAX error); use get_idx_type() (Medium)
- polynomial_features allocated one extra always-zero column (off-by-one) (Medium)

Findings recorded in docs/issues-found-20260619-small-modules.md

Author: chaoming0625

brainpy/algorithms/offline.py

@@ -385,8 +385,11 @@ def call(self, targets, inputs, outputs=None) -> ArrayType:
             raise ValueError(f'Target must be a scalar, but got multiple variables: {targets.shape}. ')
         targets = targets.flatten()
 
-        # initialize parameters
-        param = self.init_weights(inputs.shape[1], targets.shape[1])
+        # Initialize a 1-D parameter vector to match the flattened 1-D
+        # ``targets`` used below. (``init_weights`` returns a 2-D ``(n_features,
+        # n_out)`` array; reading ``targets.shape[1]`` after the flatten raised
+        # IndexError, so request a single output and squeeze to 1-D.)
+        param = self.init_weights(inputs.shape[1], 1).flatten()
 
         def cond_fun(a):
             i, par_old, par_new = a
@@ -538,8 +541,9 @@ def call(self, targets, inputs, outputs=None):
         # checking
         inputs = _check_data_2d_atls(bm.as_jax(inputs))
         targets = _check_data_2d_atls(bm.as_jax(targets))
-        # solving
-        inputs = normalize(polynomial_features(inputs, degree=self.degree))
+        # solving. ``add_bias`` must match ``predict`` so the fitted weight
+        # length equals the feature width seen at prediction time.
+        inputs = normalize(polynomial_features(inputs, degree=self.degree, add_bias=self.add_bias))
         return super(ElasticNetRegression, self).gradient_descent_solve(targets, inputs)
 
     def predict(self, W, X):

brainpy/algorithms/offline_test.py

@@ -154,18 +154,24 @@ def test_fit_and_predict(self):
 
 
 class TestLogisticRegression:
-    def test_call_is_currently_broken(self):
-        # NOTE (defect): LogisticRegression.call flattens ``targets`` to 1-D
-        # (offline.py line ~386) and then immediately reads ``targets.shape[1]``
-        # at line ~389, which raises IndexError. The closed-form (non gradient
-        # descent) branch is also unreachable because of this. The fit path is
-        # therefore broken for both gradient_descent=True and =False.
+    def test_call_runs_and_separates(self):
+        # P16-C2 (was test_call_is_currently_broken): ``LogisticRegression.call``
+        # used to crash with IndexError because it flattened ``targets`` to 1-D
+        # and then read ``targets.shape[1]``. After the fix it must run and learn
+        # a usable separator on a trivially separable problem.
         rng = np.random.RandomState(1)
         x = rng.uniform(-1, 1, size=(30, 2)).astype(np.float32)
         y = (x[:, :1] > 0).astype(np.float32)
-        algo = offline.LogisticRegression(max_iter=50, learning_rate=0.1)
-        with pytest.raises(IndexError):
-            algo(bm.asarray(y), bm.asarray(x))
+        algo = offline.LogisticRegression(max_iter=200, learning_rate=0.5)
+        w = algo(bm.asarray(y), bm.asarray(x))
+        w = np.asarray(bm.as_jax(w))
+        # one weight per input feature (1-D parameter vector)
+        assert w.reshape(-1).shape == (2,)
+        assert np.all(np.isfinite(w))
+        # predictions should mostly agree with the (separable) labels
+        pred = np.asarray(bm.as_jax(algo.predict(bm.asarray(w), bm.asarray(x))))
+        acc = np.mean((pred.reshape(-1) > 0.5) == y.reshape(-1))
+        assert acc >= 0.8
 
     def test_predict_applies_sigmoid(self):
         # ``predict`` itself works in isolation (it does not hit the broken call).
@@ -209,19 +215,29 @@ def test_elastic_net_regression_fit(self):
         w = np.asarray(bm.as_jax(algo(y, x)))
         assert np.all(np.isfinite(w))
 
-    def test_elastic_net_predict_bias_mismatch_is_broken(self):
-        # NOTE (defect): ElasticNetRegression.call builds features with
-        # ``polynomial_features(inputs, degree=self.degree)`` which defaults to
-        # add_bias=True, while ``predict`` calls it with add_bias=self.add_bias
-        # (default False). The resulting feature width differs from the fitted
-        # weight length, so predicting on freshly-built features raises a
-        # shape-mismatch TypeError from jnp.dot.
+    def test_elastic_net_train_predict_consistent(self):
+        # P16-H1 (was test_elastic_net_predict_bias_mismatch_is_broken):
+        # ``call`` used to build features with the default add_bias=True while
+        # ``predict`` used add_bias=self.add_bias (default False), giving a
+        # train/predict feature-count mismatch that crashed jnp.dot. After the
+        # fix, training and prediction must use identical feature construction.
         x, y = _xy(slope=2.0)
         algo = offline.ElasticNetRegression(alpha=0.01, degree=2, l1_ratio=0.5,
                                             max_iter=50, learning_rate=0.001)
         w = bm.asarray(np.asarray(bm.as_jax(algo(y, x))))
-        with pytest.raises(TypeError):
-            algo.predict(w, x)
+        pred = np.asarray(bm.as_jax(algo.predict(w, x)))
+        assert pred.shape[0] == np.asarray(bm.as_jax(x)).shape[0]
+        assert np.all(np.isfinite(pred))
+
+    def test_elastic_net_add_bias_true_consistent(self):
+        # The fix must also hold when add_bias=True is requested explicitly.
+        x, y = _xy(slope=2.0)
+        algo = offline.ElasticNetRegression(alpha=0.01, degree=2, l1_ratio=0.5,
+                                            add_bias=True, max_iter=50,
+                                            learning_rate=0.001)
+        w = bm.asarray(np.asarray(bm.as_jax(algo(y, x))))
+        pred = np.asarray(bm.as_jax(algo.predict(w, x)))
+        assert np.all(np.isfinite(pred))
 
 
 class TestRegistry:

brainpy/algorithms/utils.py

@@ -106,7 +106,11 @@ def polynomial_features(X, degree: int, add_bias: bool = True):
         return bm.insert(X, 0, 1, axis=1) if add_bias else X
     if add_bias:
         n_features += 1
-    X_new = bm.zeros((n_samples, 1 + n_features + len(combinations)))
+    # ``n_features`` already accounts for the bias slot (when ``add_bias``); the
+    # design matrix is exactly the (bias +) original features plus the degree>=2
+    # interaction terms. The previous extra leading ``1 +`` left a dead all-zero
+    # trailing column and over-counted the feature dimension by one.
+    X_new = bm.zeros((n_samples, n_features + len(combinations)))
     if add_bias:
         X_new[:, 0] = 1
         X_new[:, 1:n_features] = X

brainpy/algorithms/utils_test.py

@@ -97,25 +97,25 @@ def test_degree1_shortcircuit_without_bias(self):
     def test_degree2_with_bias(self):
         X = bm.asarray([[2.0, 3.0]])
         out = np.asarray(bm.as_jax(utils.polynomial_features(X, degree=2, add_bias=True)))
-        # X_new has shape (n_samples, 1 + n_features + len(combinations)).
-        # With add_bias, n_features is bumped to 3 (2 + 1), combos == 3, so the
-        # allocated width is 1 + 3 + 3 == 7. NOTE: the leading "1 +" plus the
-        # bumped n_features leaves one all-zero trailing column unused, i.e. the
-        # output is wider than the mathematically expected 6 columns.
-        assert out.shape == (1, 7)
+        # P16-M2: width is exactly 1 bias + 2 linear + 3 interaction == 6
+        # (previously a dead all-zero trailing column made it 7).
+        assert out.shape == (1, 6)
         assert out[0, 0] == 1.0
         # the linear features should appear
         assert 2.0 in out[0] and 3.0 in out[0]
         # interactions: 4 (=2^2), 6 (=2*3), 9 (=3^2)
         for v in (4.0, 6.0, 9.0):
             assert np.any(np.isclose(out[0], v))
+        # no dead all-zero column anymore
+        assert not np.any(np.all(out == 0, axis=0))
 
     def test_degree2_without_bias(self):
         X = bm.asarray([[2.0, 3.0]])
         out = np.asarray(bm.as_jax(utils.polynomial_features(X, degree=2, add_bias=False)))
-        # 1 + 2 linear + 3 interaction -> 6 cols (again one extra leading column;
-        # see NOTE in test_degree2_with_bias).
-        assert out.shape == (1, 6)
+        # P16-M2: 2 linear + 3 interaction -> 5 cols (previously 6 with a dead
+        # leading allocation slot).
+        assert out.shape == (1, 5)
+        assert not np.any(np.all(out == 0, axis=0))
 
 
 class TestNormalize:

brainpy/connect/base.py

@@ -689,15 +689,20 @@ def coo2csr(coo, num_pre):
         post_ids = post_ids[sort_ids]
         indices = post_ids
         unique_pre_ids, pre_count = onp.unique(pre_ids, return_counts=True)
-        final_pre_count = onp.zeros(num_pre, dtype=jnp.uint32)
+        # Use the connection index dtype (not uint32) so the assignment below does
+        # not trigger an int->uint scatter dtype mismatch.
+        final_pre_count = onp.zeros(num_pre, dtype=get_idx_type())
         final_pre_count[unique_pre_ids] = pre_count
     else:
         sort_ids = onp.argsort(bm.as_jax(pre_ids))
         post_ids = bm.as_jax(post_ids)
         post_ids = post_ids[sort_ids]
         indices = post_ids
         unique_pre_ids, pre_count = jnp.unique(pre_ids, return_counts=True)
-        final_pre_count = bm.zeros(num_pre, dtype=jnp.uint32)
+        # Use the connection index dtype (not uint32) so the in-place update below
+        # does not trigger an int->uint scatter dtype mismatch (FutureWarning that
+        # becomes an error in future JAX releases).
+        final_pre_count = bm.zeros(num_pre, dtype=get_idx_type())
         final_pre_count[unique_pre_ids] = pre_count
         final_pre_count = bm.as_jax(final_pre_count)
     indptr = final_pre_count.cumsum()

brainpy/connect/custom_conn.py

@@ -100,7 +100,7 @@ def __init__(self, indices, inptr, **kwargs):
         self.max_post = self.indices.max()
 
     def build_csr(self):
-        if self.pre_num != self.pre_num:
+        if self.pre_num != self.inptr.size - 1:
             raise ConnectorError(f'(pre_size, post_size) is inconsistent with '
                                  f'the shape of the sparse matrix.')
         if self.post_num <= self.max_post:

brainpy/connect/custom_conn_test.py

@@ -61,6 +61,45 @@ def test_MatConn2(self):
             conn(pre_size=5, post_size=1)
 
 
+class TestCSRConn(TestCase):
+    def _csr(self):
+        # 3 pre-synaptic neurons (indptr has 4 entries), max post id == 2
+        indices = np.array([0, 1, 2, 0, 1], dtype=np.int32)
+        indptr = np.array([0, 2, 3, 5], dtype=np.int32)
+        return indices, indptr
+
+    def test_csrconn_consistent_ok(self):
+        # P16-H2: a CSRConn whose declared pre_size matches the indptr length
+        # must build without error.
+        indices, indptr = self._csr()
+        conn = bp.conn.CSRConn(indices, indptr)
+        ind, ip = conn.require(3, 3, 'csr')
+        assert np.array_equal(np.asarray(ind), indices)
+        assert np.array_equal(np.asarray(ip), indptr)
+
+    def test_csrconn_inconsistent_pre_num_raises(self):
+        # P16-H2: previously the guard ``self.pre_num != self.pre_num`` was a
+        # tautology (always False), so an inconsistent pre_size silently produced
+        # a malformed CSR. It must now raise.
+        indices, indptr = self._csr()  # indptr implies 3 pre
+        conn = bp.conn.CSRConn(indices, indptr)
+        with pytest.raises(bp.errors.ConnectorError):
+            conn.require(5, 3, 'csr')  # pre=5 inconsistent with indptr (3)
+
+    def test_coo2csr_no_dtype_warning(self):
+        # P16-M1: coo2csr must not emit the int32->uint32 scatter FutureWarning
+        # (which is slated to become an error in future JAX).
+        import warnings
+        import jax.numpy as jnp
+        from brainpy.connect.base import coo2csr
+        pre = jnp.array([0, 0, 1, 2, 2, 2])
+        post = jnp.array([1, 2, 0, 0, 1, 2])
+        with warnings.catch_warnings():
+            warnings.simplefilter('error', FutureWarning)
+            ind, indptr = coo2csr((pre, post), 3)
+        assert np.array_equal(np.asarray(indptr), np.array([0, 2, 3, 6]))
+
+
 class TestSparseMatConn(TestCase):
     def test_sparseMatConn(self):
         conn_mat = np.random.randint(2, size=(5, 3), dtype=bp.math.bool_)

brainpy/inputs/currents.py

@@ -150,7 +150,7 @@ def spike_current(*args, **kwargs):
     warnings.warn('Please use "brainpy.inputs.spike_input()" instead. '
                   '"brainpy.inputs.spike_current()" is deprecated since version 2.1.13.',
                   DeprecationWarning)
-    return constant_input(*args, **kwargs)
+    return spike_input(*args, **kwargs)
 
 
 def ramp_input(c_start, c_end, duration, t_start=0, t_end=None, dt=None):
@@ -189,7 +189,7 @@ def ramp_current(*args, **kwargs):
     warnings.warn('Please use "brainpy.inputs.ramp_input()" instead. '
                   '"brainpy.inputs.ramp_current()" is deprecated since version 2.1.13.',
                   DeprecationWarning)
-    return constant_input(*args, **kwargs)
+    return ramp_input(*args, **kwargs)
 
 
 def wiener_process(duration, dt=None, n=1, t_start=0., t_end=None, seed=None):

brainpy/inputs/currents_coverage_test.py

@@ -43,25 +43,27 @@ def test_constant_current_warns_and_delegates(self):
         self.assertEqual(duration, 200)
 
     def test_spike_current_warns(self):
-        # NOTE: ``spike_current`` is documented as a spike-input shim but its
-        # body actually delegates to ``constant_input`` (copy/paste defect in
-        # the deprecation wrapper), so it must be fed constant_input-style
-        # ``[(value, duration), ...]`` pairs rather than spike arguments.
+        # P16-C1: ``spike_current`` now correctly delegates to ``spike_input``
+        # (it previously delegated to ``constant_input`` and crashed on spike
+        # arguments). It must warn AND accept spike-style arguments.
+        kwargs = dict(sp_times=[10, 20, 30], sp_lens=1., sp_sizes=0.5, duration=40.)
         with warnings.catch_warnings(record=True) as w:
             warnings.simplefilter('always')
-            out = bp.inputs.spike_current([(0, 50), (1, 50)])
+            out = bp.inputs.spike_current(**kwargs)
         self.assertTrue(any(issubclass(x.category, DeprecationWarning) for x in w))
         self.assertIsNotNone(out)
+        self.assertTrue(np.array_equal(np.asarray(out), np.asarray(bp.inputs.spike_input(**kwargs))))
 
     def test_ramp_current_warns(self):
-        # NOTE: like ``spike_current``, ``ramp_current`` also delegates to
-        # ``constant_input`` rather than ``ramp_input`` (same wrapper defect),
-        # so it expects ``[(value, duration), ...]`` pairs.
+        # P16-C1: ``ramp_current`` now correctly delegates to ``ramp_input``
+        # (it previously delegated to ``constant_input``). It must warn AND
+        # accept ramp-style arguments.
         with warnings.catch_warnings(record=True) as w:
             warnings.simplefilter('always')
-            out = bp.inputs.ramp_current([(0, 50), (1, 50)])
+            out = bp.inputs.ramp_current(0., 1., 100.)
         self.assertTrue(any(issubclass(x.category, DeprecationWarning) for x in w))
         self.assertIsNotNone(out)
+        self.assertTrue(np.array_equal(np.asarray(out), np.asarray(bp.inputs.ramp_input(0., 1., 100.))))
 
 
 @unittest.skipUnless(HAS_BRAINUNIT, 'brainunit required for unit-aware inputs')

brainpy/inputs/currents_test.py

@@ -105,3 +105,24 @@ def test_general2(self):
                                                   bp.math.random.random((3, 10))],
                                           durations=[100, 300, 100])
         self.assertTrue(current.shape == (5000, 3, 10))
+
+    def test_spike_current_alias(self):
+        # P16-C1: the deprecated ``spike_current`` alias must forward to
+        # ``spike_input`` (it used to forward to ``constant_input`` and crash).
+        import warnings
+        kwargs = dict(sp_times=[10, 20, 30], sp_lens=1., sp_sizes=0.5, duration=40.)
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', DeprecationWarning)
+            aliased = bp.inputs.spike_current(**kwargs)
+        direct = bp.inputs.spike_input(**kwargs)
+        self.assertTrue(np.array_equal(np.asarray(aliased), np.asarray(direct)))
+
+    def test_ramp_current_alias(self):
+        # P16-C1: the deprecated ``ramp_current`` alias must forward to
+        # ``ramp_input`` (it used to forward to ``constant_input`` and crash).
+        import warnings
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore', DeprecationWarning)
+            aliased = bp.inputs.ramp_current(0., 1., 100.)
+        direct = bp.inputs.ramp_input(0., 1., 100.)
+        self.assertTrue(np.array_equal(np.asarray(aliased), np.asarray(direct)))