diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3b16a4cc67..041d47f0da 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -30,7 +30,7 @@ repos: exclude: ^source/3rdparty - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.2.1 + rev: v0.2.2 hooks: - id: ruff args: ["--fix"] @@ -75,7 +75,7 @@ repos: #- id: cmake-lint # license header - repo: https://github.com/Lucas-C/pre-commit-hooks - rev: v1.5.4 + rev: v1.5.5 hooks: # C++, js - id: insert-license diff --git a/source/tests/common/dpmodel/test_neighbor_stat.py b/source/tests/common/dpmodel/test_neighbor_stat.py index 90764a049c..2a9296057b 100644 --- a/source/tests/common/dpmodel/test_neighbor_stat.py +++ b/source/tests/common/dpmodel/test_neighbor_stat.py @@ -16,11 +16,11 @@ def gen_sys(nframes): X, Y, Z = np.mgrid[0:2:3j, 0:2:3j, 0:2:3j] positions = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T # + 0.1 data["coords"] = np.repeat(positions[np.newaxis, :, :], nframes, axis=0) - data["forces"] = np.random.random([nframes, natoms, 3]) + data["forces"] = np.random.default_rng().random([nframes, natoms, 3]) data["cells"] = np.array([3.0, 0.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 3.0]).reshape( 1, 3, 3 ) - data["energies"] = np.random.random([nframes, 1]) + data["energies"] = np.random.default_rng().random([nframes, 1]) data["atom_names"] = ["TYPE"] data["atom_numbs"] = [27] data["atom_types"] = np.repeat(0, 27) diff --git a/source/tests/pt/model/test_force_grad.py b/source/tests/pt/model/test_force_grad.py index 0a4dc32d9f..d695c821e5 100644 --- a/source/tests/pt/model/test_force_grad.py +++ b/source/tests/pt/model/test_force_grad.py @@ -89,7 +89,7 @@ def test_force_grad(self, threshold=1e-2, delta0=1e-6, seed=20): errors = np.zeros((self.dpdatasystem._natoms, 3)) for atom_index in range(self.dpdatasystem._natoms): for axis_index in range(3): - delta = np.random.random() * delta0 + delta = np.random.default_rng().random() * delta0 disturb_batch = self.dpdatasystem.get_disturb( self.batch_index, atom_index, axis_index, delta ) diff --git a/source/tests/pt/test_neighbor_stat.py b/source/tests/pt/test_neighbor_stat.py index 63ec684792..4cbb46f66b 100644 --- a/source/tests/pt/test_neighbor_stat.py +++ b/source/tests/pt/test_neighbor_stat.py @@ -16,11 +16,11 @@ def gen_sys(nframes): X, Y, Z = np.mgrid[0:2:3j, 0:2:3j, 0:2:3j] positions = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T # + 0.1 data["coords"] = np.repeat(positions[np.newaxis, :, :], nframes, axis=0) - data["forces"] = np.random.random([nframes, natoms, 3]) + data["forces"] = np.random.default_rng().random([nframes, natoms, 3]) data["cells"] = np.array([3.0, 0.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 3.0]).reshape( 1, 3, 3 ) - data["energies"] = np.random.random([nframes, 1]) + data["energies"] = np.random.default_rng().random([nframes, 1]) data["atom_names"] = ["TYPE"] data["atom_numbs"] = [27] data["atom_types"] = np.repeat(0, 27) diff --git a/source/tests/tf/test_data_modifier_shuffle.py b/source/tests/tf/test_data_modifier_shuffle.py index e6985b9e0f..fb9da948f1 100644 --- a/source/tests/tf/test_data_modifier_shuffle.py +++ b/source/tests/tf/test_data_modifier_shuffle.py @@ -105,8 +105,10 @@ def _setUp_data(self): self.nsel = 0 for ii in self.sel_type: self.nsel += np.sum(self.atom_types0 == ii) - self.coords0 = np.random.random([self.nframes, self.natoms * 3]) * scale - self.dipoles0 = np.random.random([self.nframes, self.nsel * 3]) + self.coords0 = ( + np.random.default_rng().random([self.nframes, self.natoms * 3]) * scale + ) + self.dipoles0 = np.random.default_rng().random([self.nframes, self.nsel * 3]) self.box0 = np.reshape(np.eye(3) * scale, [-1, 9]) self.box0 = np.tile(self.box0, [self.nframes, 1]) self._write_sys_data( diff --git a/source/tests/tf/test_deepmd_data.py b/source/tests/tf/test_deepmd_data.py index b1a0147771..3998e0f3e3 100644 --- a/source/tests/tf/test_deepmd_data.py +++ b/source/tests/tf/test_deepmd_data.py @@ -37,13 +37,13 @@ def setUp(self): self.natoms = 6 # coord path = os.path.join(self.data_name, "set.foo", "coord.npy") - self.coord = np.random.random([self.nframes, self.natoms, 3]) + self.coord = np.random.default_rng().random([self.nframes, self.natoms, 3]) np.save(path, np.reshape(self.coord, [self.nframes, -1])) self.coord = self.coord[:, [0, 3, 1, 2, 4, 5], :] self.coord = self.coord.reshape([self.nframes, -1]) # box path = os.path.join(self.data_name, "set.foo", "box.npy") - self.box = np.random.random([self.nframes, 9]) + self.box = np.random.default_rng().random([self.nframes, 9]) np.save(path, self.box) # value path = os.path.join(self.data_name, "set.foo", "value_1.npy") @@ -93,49 +93,51 @@ def setUp(self): self.natoms = 2 # coord path = os.path.join(self.data_name, "set.foo", "coord.npy") - self.coord = np.random.random([self.nframes, self.natoms, 3]) + self.coord = np.random.default_rng().random([self.nframes, self.natoms, 3]) np.save(path, np.reshape(self.coord, [self.nframes, -1])) self.coord = self.coord[:, [1, 0], :] self.coord = self.coord.reshape([self.nframes, -1]) # coord bar path = os.path.join(self.data_name, "set.bar", "coord.npy") - self.coord_bar = np.random.random([self.nframes, 3 * self.natoms]) + self.coord_bar = np.random.default_rng().random([self.nframes, 3 * self.natoms]) np.save(path, self.coord_bar) self.coord_bar = self.coord_bar.reshape([self.nframes, self.natoms, 3]) self.coord_bar = self.coord_bar[:, [1, 0], :] self.coord_bar = self.coord_bar.reshape([self.nframes, -1]) # coord tar path = os.path.join(self.data_name, "set.tar", "coord.npy") - self.coord_tar = np.random.random([2, 3 * self.natoms]) + self.coord_tar = np.random.default_rng().random([2, 3 * self.natoms]) np.save(path, self.coord_tar) self.coord_tar = self.coord_tar.reshape([2, self.natoms, 3]) self.coord_tar = self.coord_tar[:, [1, 0], :] self.coord_tar = self.coord_tar.reshape([2, -1]) # box path = os.path.join(self.data_name, "set.foo", "box.npy") - self.box = np.random.random([self.nframes, 9]) + self.box = np.random.default_rng().random([self.nframes, 9]) np.save(path, self.box) # box bar path = os.path.join(self.data_name, "set.bar", "box.npy") - self.box_bar = np.random.random([self.nframes, 9]) + self.box_bar = np.random.default_rng().random([self.nframes, 9]) np.save(path, self.box_bar) # box tar path = os.path.join(self.data_name, "set.tar", "box.npy") - self.box_tar = np.random.random([2, 9]) + self.box_tar = np.random.default_rng().random([2, 9]) np.save(path, self.box_tar) # t a path = os.path.join(self.data_name, "set.foo", "test_atomic.npy") - self.test_atomic = np.random.random([self.nframes, self.natoms, 7]) + self.test_atomic = np.random.default_rng().random( + [self.nframes, self.natoms, 7] + ) self.redu_atomic = np.sum(self.test_atomic, axis=1) np.save(path, np.reshape(self.test_atomic, [self.nframes, -1])) self.test_atomic = self.test_atomic[:, [1, 0], :] self.test_atomic = self.test_atomic.reshape([self.nframes, -1]) # t f path = os.path.join(self.data_name, "set.foo", "test_frame.npy") - self.test_frame = np.random.random([self.nframes, 5]) + self.test_frame = np.random.default_rng().random([self.nframes, 5]) np.save(path, self.test_frame) path = os.path.join(self.data_name, "set.bar", "test_frame.npy") - self.test_frame_bar = np.random.random([self.nframes, 5]) + self.test_frame_bar = np.random.default_rng().random([self.nframes, 5]) np.save(path, self.test_frame_bar) # t n self.test_null = np.zeros([self.nframes, 2 * self.natoms]) diff --git a/source/tests/tf/test_deepmd_data_sys.py b/source/tests/tf/test_deepmd_data_sys.py index 49ad8f501c..84b5d39a05 100644 --- a/source/tests/tf/test_deepmd_data_sys.py +++ b/source/tests/tf/test_deepmd_data_sys.py @@ -40,13 +40,15 @@ def setUp(self): set_name = os.path.join(sys_name, "set.%03d" % jj) os.makedirs(set_name, exist_ok=True) path = os.path.join(set_name, "coord.npy") - val = np.random.random([self.nframes[ii] + jj, self.natoms[ii] * 3]) + val = np.random.default_rng().random( + [self.nframes[ii] + jj, self.natoms[ii] * 3] + ) np.save(path, val) path = os.path.join(set_name, "box.npy") - val = np.random.random([self.nframes[ii] + jj, 9]) * 10 + val = np.random.default_rng().random([self.nframes[ii] + jj, 9]) * 10 np.save(path, val) path = os.path.join(set_name, "test.npy") - val = np.random.random( + val = np.random.default_rng().random( [self.nframes[ii] + jj, self.natoms[ii] * self.test_ndof] ) np.save(path, val) diff --git a/source/tests/tf/test_descrpt_sea_ef_rot.py b/source/tests/tf/test_descrpt_sea_ef_rot.py index 8cdbc19ca2..6ebc067211 100644 --- a/source/tests/tf/test_descrpt_sea_ef_rot.py +++ b/source/tests/tf/test_descrpt_sea_ef_rot.py @@ -97,7 +97,7 @@ def build_efv(self, dcoord, dbox, dtype, tnatoms, name, op, reuse=None): return energy, force, virial, atom_ener, atom_vir def make_test_data(self, nframes): - dcoord = np.random.random([nframes, self.natoms[0], 3]) + dcoord = np.random.default_rng().random([nframes, self.natoms[0], 3]) for ii in range(nframes): dcoord[ii, :, :] = dcoord[ii, :, :] - np.tile( dcoord[ii, 0, :], [self.natoms[0], 1] @@ -111,7 +111,7 @@ def make_test_data(self, nframes): np.random.shuffle(one_type) # noqa: NPY002 one_type = np.array(one_type, dtype=int).reshape([1, -1]) dtype = np.tile(one_type, [nframes, 1]) - defield = np.random.random(dcoord.shape) + defield = np.random.default_rng().random(dcoord.shape) return dcoord, dbox, dtype, defield def rotate_mat(self, axis_, theta): diff --git a/source/tests/tf/test_ewald.py b/source/tests/tf/test_ewald.py index 74b65e9be3..c68a0c84ee 100644 --- a/source/tests/tf/test_ewald.py +++ b/source/tests/tf/test_ewald.py @@ -38,16 +38,16 @@ def setUp(self): box = np.eye(3) * boxl box[1][1] += 1 box[2][2] += 2 - box += np.random.random([3, 3]) * box_pert + box += np.random.default_rng().random([3, 3]) * box_pert box = 0.5 * (box + box.T) self.dbox.append(box) # scaled - coord = np.random.random([self.natoms, 3]) + coord = np.random.default_rng().random([self.natoms, 3]) self.rcoord.append(coord) # real coords self.dcoord.append(np.matmul(coord, box)) # charge - dcharge = np.random.random([self.natoms]) + dcharge = np.random.default_rng().random([self.natoms]) dcharge -= np.average(dcharge) assert np.abs(np.sum(self.dcharge) - 0) < 1e-12 self.dcharge.append(dcharge) diff --git a/source/tests/tf/test_gen_stat_data.py b/source/tests/tf/test_gen_stat_data.py index fe4ec36b24..5442fded75 100644 --- a/source/tests/tf/test_gen_stat_data.py +++ b/source/tests/tf/test_gen_stat_data.py @@ -25,10 +25,10 @@ def gen_sys(nframes, atom_types): natoms = len(atom_types) data = {} - data["coords"] = np.random.random([nframes, natoms, 3]) - data["forces"] = np.random.random([nframes, natoms, 3]) - data["cells"] = np.random.random([nframes, 9]) - data["energies"] = np.random.random([nframes, 1]) + data["coords"] = np.random.default_rng().random([nframes, natoms, 3]) + data["forces"] = np.random.default_rng().random([nframes, natoms, 3]) + data["cells"] = np.random.default_rng().random([nframes, 9]) + data["energies"] = np.random.default_rng().random([nframes, 1]) types = list(set(atom_types)) types.sort() data["atom_names"] = [] diff --git a/source/tests/tf/test_neighbor_stat.py b/source/tests/tf/test_neighbor_stat.py index 6fcba36914..653634d674 100644 --- a/source/tests/tf/test_neighbor_stat.py +++ b/source/tests/tf/test_neighbor_stat.py @@ -16,11 +16,11 @@ def gen_sys(nframes): X, Y, Z = np.mgrid[0:2:3j, 0:2:3j, 0:2:3j] positions = np.vstack([X.ravel(), Y.ravel(), Z.ravel()]).T # + 0.1 data["coords"] = np.repeat(positions[np.newaxis, :, :], nframes, axis=0) - data["forces"] = np.random.random([nframes, natoms, 3]) + data["forces"] = np.random.default_rng().random([nframes, natoms, 3]) data["cells"] = np.array([3.0, 0.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 3.0]).reshape( 1, 3, 3 ) - data["energies"] = np.random.random([nframes, 1]) + data["energies"] = np.random.default_rng().random([nframes, 1]) data["atom_names"] = ["TYPE"] data["atom_numbs"] = [27] data["atom_types"] = np.repeat(0, 27)