breaking: move deepmd_utils to deepmd (#3178)

Signed-off-by: Jinzhe Zeng <[email protected]>

.github/labeler.yml

@@ -2,7 +2,6 @@ Python:
 - changed-files:
   - any-glob-to-any-file:
     - deepmd/**/*
-    - deepmd_utils/**/*
     - source/tests/**/*
 Docs:
 - changed-files:

.github/workflows/test_cuda.yml

@@ -43,7 +43,7 @@ jobs:
         DP_VARIANT: cuda
         CUDA_PATH: /usr/local/cuda-12.2
     - run: dp --version
-    - run: python -m pytest -s --cov=deepmd --cov=deepmd_utils source/tests --durations=0
+    - run: python -m pytest -s --cov=deepmd source/tests --durations=0
     - run: source/install/test_cc_local.sh
       env:
         OMP_NUM_THREADS: 1

.github/workflows/test_python.yml

@@ -38,7 +38,7 @@ jobs:
         HOROVOD_WITH_TENSORFLOW: 1
         HOROVOD_WITHOUT_GLOO: 1
     - run: dp --version
-    - run: pytest --cov=deepmd --cov=deepmd_utils source/tests --durations=0
+    - run: pytest --cov=deepmd source/tests --durations=0
     - uses: codecov/codecov-action@v3
       with:
         gcov: true

backend/dynamic_metadata.py

@@ -27,7 +27,7 @@ def dynamic_metadata(
     _, _, find_libpython_requires, extra_scripts, tf_version = get_argument_from_env()
     if field == "scripts":
         return {
-            "dp": "deepmd_utils.main:main",
+            "dp": "deepmd.main:main",
             **extra_scripts,
         }
     elif field == "optional-dependencies":

codecov.yml

@@ -20,7 +20,6 @@ component_management:
       name: Python
       paths:
         - deepmd/**
-        - deepmd_utils/**
     - component_id: module_op
       name: OP
       paths:

deepmd/__init__.py

@@ -1,6 +1,14 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
+"""DeePMD-kit is a package written in Python/C++, designed to
+minimize the effort required to build deep learning-based model
+of interatomic potential energy and force field and to perform
+molecular dynamics (MD).
+
+The top module (deepmd.__init__) should not import any third-party
+modules for performance.
+"""
 try:
-    from deepmd_utils._version import version as __version__
+    from deepmd._version import version as __version__
 except ImportError:
     from .__about__ import (
         __version__,

deepmd/__main__.py

@@ -0,0 +1,9 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+"""Package dp entry point."""
+
+from deepmd.main import (
+    main,
+)
+
+if __name__ == "__main__":
+    main()

deepmd_utils/calculator.py → deepmd/calculator.py

@@ -19,7 +19,7 @@
     all_changes,
 )
 
-from deepmd_utils.infer import (
+from deepmd.infer import (
     DeepPot,
 )
 

deepmd_utils/common.py → deepmd/common.py

@@ -22,10 +22,10 @@
 import numpy as np
 import yaml
 
-from deepmd_utils.env import (
+from deepmd.env import (
     GLOBAL_NP_FLOAT_PRECISION,
 )
-from deepmd_utils.utils.path import (
+from deepmd.utils.path import (
     DPPath,
 )
 

deepmd_utils/driver.py → deepmd/driver.py

@@ -29,7 +29,7 @@ class DPDriver(dpdata.driver.Driver):
     """
 
     def __init__(self, dp: str) -> None:
-        from deepmd_utils.infer.deep_pot import (
+        from deepmd.infer.deep_pot import (
             DeepPot,
         )
 

deepmd_utils/entrypoints/doc.py → deepmd/entrypoints/doc.py

@@ -1,7 +1,7 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Module that prints train input arguments docstrings."""
 
-from deepmd_utils.utils.argcheck import (
+from deepmd.utils.argcheck import (
     gen_doc,
     gen_json,
 )

deepmd_utils/infer/deep_pot.py → deepmd/infer/deep_pot.py

@@ -12,7 +12,7 @@
 
 import numpy as np
 
-from deepmd_utils.utils.batch_size import (
+from deepmd.utils.batch_size import (
     AutoBatchSize,
 )
 

deepmd_utils/infer/model_devi.py → deepmd/infer/model_devi.py

@@ -7,13 +7,13 @@
 
 import numpy as np
 
-from deepmd_utils.common import (
+from deepmd.common import (
     expand_sys_str,
 )
-from deepmd_utils.infer.deep_pot import (
+from deepmd.infer.deep_pot import (
     DeepPot,
 )
-from deepmd_utils.utils.data import (
+from deepmd.utils.data import (
     DeepmdData,
 )
 

deepmd_utils/main.py → deepmd/main.py

@@ -13,7 +13,7 @@
 )
 
 try:
-    from deepmd_utils._version import version as __version__
+    from deepmd._version import version as __version__
 except ImportError:
     __version__ = "unknown"
 

deepmd_utils/model_format/network.py → deepmd/model_format/network.py

@@ -18,7 +18,7 @@
 import numpy as np
 
 try:
-    from deepmd_utils._version import version as __version__
+    from deepmd._version import version as __version__
 except ImportError:
     __version__ = "unknown"
 

deepmd_utils/model_format/se_e2_a.py → deepmd/model_format/se_e2_a.py

@@ -2,7 +2,7 @@
 import numpy as np
 
 try:
-    from deepmd_utils._version import version as __version__
+    from deepmd._version import version as __version__
 except ImportError:
     __version__ = "unknown"
 

deepmd/tf/__init__.py

@@ -32,7 +32,7 @@
 set_mkl()
 
 try:
-    from deepmd_utils._version import version as __version__
+    from deepmd._version import version as __version__
 except ImportError:
     from .__about__ import (
         __version__,

deepmd/tf/calculator.py

@@ -1,5 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-from deepmd_utils.calculator import (
+from deepmd.calculator import (
     DP,
 )
 

deepmd/tf/common.py

@@ -17,12 +17,7 @@
     tensor_util,
 )
 
-from deepmd.tf.env import (
-    GLOBAL_TF_FLOAT_PRECISION,
-    op_module,
-    tf,
-)
-from deepmd_utils.common import (
+from deepmd.common import (
     add_data_requirement,
     data_requirement,
     expand_sys_str,
@@ -32,15 +27,20 @@
     make_default_mesh,
     select_idx_map,
 )
+from deepmd.tf.env import (
+    GLOBAL_TF_FLOAT_PRECISION,
+    op_module,
+    tf,
+)
 
 if TYPE_CHECKING:
-    from deepmd_utils.common import (
+    from deepmd.common import (
         _ACTIVATION,
         _PRECISION,
     )
 
 __all__ = [
-    # from deepmd_utils.common
+    # from deepmd.common
     "data_requirement",
     "add_data_requirement",
     "select_idx_map",

deepmd/tf/entrypoints/doc.py

@@ -1,5 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-from deepmd_utils.entrypoints.doc import (
+from deepmd.entrypoints.doc import (
     doc_train_input,
 )
 

deepmd/tf/entrypoints/gui.py

@@ -1,5 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-from deepmd_utils.entrypoints.gui import (
+from deepmd.entrypoints.gui import (
     start_dpgui,
 )
 

deepmd/tf/entrypoints/main.py

@@ -11,6 +11,11 @@
     Union,
 )
 
+from deepmd.main import (
+    get_ll,
+    main_parser,
+    parse_args,
+)
 from deepmd.tf.common import (
     clear_session,
 )
@@ -32,11 +37,6 @@
 from deepmd.tf.nvnmd.entrypoints.train import (
     train_nvnmd,
 )
-from deepmd_utils.main import (
-    get_ll,
-    main_parser,
-    parse_args,
-)
 
 __all__ = ["main", "parse_args", "get_ll", "main_parser"]
 

deepmd/tf/env.py

@@ -28,7 +28,7 @@
 )
 
 import deepmd.lib
-from deepmd_utils.env import (
+from deepmd.env import (
     GLOBAL_ENER_FLOAT_PRECISION,
     GLOBAL_NP_FLOAT_PRECISION,
     global_float_prec,

deepmd/tf/infer/deep_pot.py

@@ -11,6 +11,7 @@
 
 import numpy as np
 
+from deepmd.infer.deep_pot import DeepPot as DeepPotBase
 from deepmd.tf.common import (
     make_default_mesh,
 )
@@ -26,7 +27,6 @@
 from deepmd.tf.utils.sess import (
     run_sess,
 )
-from deepmd_utils.infer.deep_pot import DeepPot as DeepPotBase
 
 if TYPE_CHECKING:
     from pathlib import (

deepmd/tf/infer/model_devi.py

@@ -1,5 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-from deepmd_utils.infer.model_devi import (
+from deepmd.infer.model_devi import (
     calc_model_devi,
     calc_model_devi_e,
     calc_model_devi_f,

deepmd/tf/loggers/__init__.py

@@ -1,7 +1,7 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-"""Alias of deepmd_utils.loggers for backward compatibility."""
+"""Alias of deepmd.loggers for backward compatibility."""
 
-from deepmd_utils.loggers.loggers import (
+from deepmd.loggers.loggers import (
     set_log_handles,
 )
 

deepmd/tf/loggers/loggers.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-"""Alias of deepmd_utils.loggers.loggers for backward compatibility."""
-from deepmd_utils.loggers.loggers import (
+"""Alias of deepmd.loggers.loggers for backward compatibility."""
+from deepmd.loggers.loggers import (
     set_log_handles,
 )
 

deepmd/tf/model/model_stat.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.model_stat import (
+from deepmd.utils.model_stat import (
     _make_all_stat_ref,
     make_stat_input,
     merge_sys_stat,

deepmd/tf/nvnmd/utils/argcheck.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.argcheck_nvnmd import (
+from deepmd.utils.argcheck_nvnmd import (
     nvnmd_args,
 )
 

deepmd/tf/utils/argcheck.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.argcheck import (
+from deepmd.utils.argcheck import (
     gen_args,
     gen_doc,
     gen_json,

deepmd/tf/utils/batch_size.py

@@ -10,7 +10,7 @@
 from deepmd.tf.utils.errors import (
     OutOfMemoryError,
 )
-from deepmd_utils.utils.batch_size import AutoBatchSize as AutoBatchSizeBase
+from deepmd.utils.batch_size import AutoBatchSize as AutoBatchSizeBase
 
 
 class AutoBatchSize(AutoBatchSizeBase):

deepmd/tf/utils/compat.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.compat import (
+from deepmd.utils.compat import (
     convert_input_v0_v1,
     convert_input_v1_v2,
     deprecate_numb_test,

deepmd/tf/utils/data.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.data import (
+from deepmd.utils.data import (
     DeepmdData,
 )
 

deepmd/tf/utils/data_system.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.data_system import (
+from deepmd.utils.data_system import (
     DeepmdDataSystem,
     prob_sys_size_ext,
     process_sys_probs,

deepmd/tf/utils/errors.py

@@ -1,5 +1,5 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
-from deepmd_utils.utils.errors import (
+from deepmd.utils.errors import (
     OutOfMemoryError,
 )
 

deepmd/tf/utils/pair_tab.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.pair_tab import (
+from deepmd.utils.pair_tab import (
     PairTab,
 )
 

deepmd/tf/utils/path.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.path import (
+from deepmd.utils.path import (
     DPH5Path,
     DPOSPath,
     DPPath,

deepmd/tf/utils/plugin.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.plugin import (
+from deepmd.utils.plugin import (
     Plugin,
     PluginVariant,
     VariantABCMeta,

deepmd/tf/utils/random.py

@@ -1,6 +1,6 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 """Alias for backward compatibility."""
-from deepmd_utils.utils.random import (
+from deepmd.utils.random import (
     choice,
     random,
     seed,