Merge pull request #4 from arcann-chem/develop

Refactor and rename
arcann-chem · May 15, 2024 · 5ffa35f · 5ffa35f
2 parents 980b7d4 + fd22139
commit 5ffa35f
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diff --git a/.github/workflows/unittests_matrix.yml b/.github/workflows/unittests_matrix.yml
@@ -63,4 +63,4 @@ jobs:
         
     - name: Run unit tests
       run: |
-        python -m unittest discover deepmd_iterative/unittests
+        python -m unittest discover arcann_training/unittests
diff --git a/.github/workflows/unittests_requirements.yml b/.github/workflows/unittests_requirements.yml
@@ -20,4 +20,4 @@ jobs:
         
     - name: Run unit tests
       run: |
-        python -m unittest discover deepmd_iterative/unittests
+        python -m unittest discover arcann_training/unittests
diff --git a/README.md b/README.md
@@ -3,6 +3,8 @@
 <!-- PROJECT SHIELDS -->
 
 [![GNU AGPL v3.0 License][license-shield]][license-url]
+[![Unit Tests Requirements](https://github.com/arcann-chem/arcann/actions/workflows/unittests_requirements.yml/badge.svg)](https://github.com/arcann-chem/arcann/actions/workflows/unittests_requirements.yml)
+[![Unit Tests Matrix](https://github.com/arcann-chem/arcann/actions/workflows/unittests_matrix.yml/badge.svg?branch=main)](https://github.com/arcann-chem/arcann/actions/workflows/unittests_matrix.yml)
 
 <!-- TABLE OF CONTENTS -->
 

diff --git a/deepmd_iterative/__init__.py → arcann_training/__init__.py b/deepmd_iterative/__init__.py → arcann_training/__init__.py
diff --git a/deepmd_iterative/__main__.py → arcann_training/__main__.py b/deepmd_iterative/__main__.py → arcann_training/__main__.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 """
 
 # Standard library modules
@@ -17,7 +17,7 @@
 from pathlib import Path
 
 # Local imports
-from deepmd_iterative.common.logging import setup_logging
+from arcann_training.common.logging import setup_logging
 
 # Parsing
 parser = argparse.ArgumentParser(description="Deepmd iterative program suite")
@@ -41,7 +41,7 @@
     # Step/Phase name
     step_name: str = args.step_name
     phase_name: str = args.phase_name
-    submodule_name: str = f"deepmd_iterative.{step_name}.{phase_name}"
+    submodule_name: str = f"arcann_training.{step_name}.{phase_name}"
 
     # Input
     input_fn: str = args.input
@@ -57,7 +57,7 @@
     # Start
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)
-    arcann_logger.info(f"DEEPMD ITERATIVE PROGRAM SUITE")
+    arcann_logger.info(f"ARCANN TRAINING PROGRAM SUITE")
     arcann_logger.info(f"Launching: {step_name.capitalize()} - {phase_name.capitalize()}")
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)

diff --git a/deepmd_iterative/assets/__init__.py → arcann_training/assets/__init__.py b/deepmd_iterative/assets/__init__.py → arcann_training/assets/__init__.py
diff --git a/deepmd_iterative/assets/default_config.json → arcann_training/assets/default_config.json b/deepmd_iterative/assets/default_config.json → arcann_training/assets/default_config.json
diff --git a/deepmd_iterative/assets/elements.json → arcann_training/assets/elements.json b/deepmd_iterative/assets/elements.json → arcann_training/assets/elements.json
diff --git a/deepmd_iterative/assets/others/__init__.py → arcann_training/assets/others/__init__.py b/deepmd_iterative/assets/others/__init__.py → arcann_training/assets/others/__init__.py
diff --git a/...d_iterative/assets/others/lammps_rerun.in → ...nn_training/assets/others/lammps_rerun.in b/...d_iterative/assets/others/lammps_rerun.in → ...nn_training/assets/others/lammps_rerun.in
diff --git a/...assets/others/vmd_dcd_selection_index.tcl → ...assets/others/vmd_dcd_selection_index.tcl b/...assets/others/vmd_dcd_selection_index.tcl → ...assets/others/vmd_dcd_selection_index.tcl
@@ -1,11 +1,11 @@
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 # Created: 2022/01/01
-# Last modified: 2023/08/16
+# Last modified: 2024/05/15
 
 # Load PDB file and clear all existing animations
 mol new _R_PDB_FILE_

diff --git a/...assets/others/vmd_xyz_selection_index.tcl → ...assets/others/vmd_xyz_selection_index.tcl b/...assets/others/vmd_xyz_selection_index.tcl → ...assets/others/vmd_xyz_selection_index.tcl
@@ -1,11 +1,11 @@
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 # Created: 2022/01/01
-# Last modified: 2023/08/16
+# Last modified: 2024/05/15
 
 # Load PDB file and clear all existing animations
 mol new _R_PDB_FILE_

diff --git a/deepmd_iterative/common/__init__.py → arcann_training/common/__init__.py b/deepmd_iterative/common/__init__.py → arcann_training/common/__init__.py
diff --git a/deepmd_iterative/common/check.py → arcann_training/common/check.py b/deepmd_iterative/common/check.py → arcann_training/common/check.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 This module contains functions for checking the availability of certain commands on the system, as well as a function for validating the current working directory during the execution of a specific step.
 
@@ -31,7 +31,7 @@
 from pathlib import Path
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # Unittested

diff --git a/deepmd_iterative/common/filesystem.py → arcann_training/common/filesystem.py b/deepmd_iterative/common/filesystem.py → arcann_training/common/filesystem.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 The filesystem module provides functions to handle file and directory management
 
@@ -42,7 +42,7 @@
 from pathlib import Path
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # Unittested

diff --git a/deepmd_iterative/common/ipi.py → arcann_training/common/ipi.py b/deepmd_iterative/common/ipi.py → arcann_training/common/ipi.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/03/31
+Last modified: 2024/05/15
 
 The ipi module provides functions to manipulate i-PI data (as XML tree).
 
@@ -22,7 +22,7 @@
 import xml.etree.ElementTree as ET
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # Unittested

diff --git a/deepmd_iterative/common/json.py → arcann_training/common/json.py b/deepmd_iterative/common/json.py → arcann_training/common/json.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 The json module provides functions to manipulate JSON data (as dict).
 
@@ -45,7 +45,7 @@
 
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # Unittested

diff --git a/deepmd_iterative/common/lammps.py → arcann_training/common/lammps.py b/deepmd_iterative/common/lammps.py → arcann_training/common/lammps.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/04/01
+Last modified: 2024/05/15
 
 The lammps module provides functions to manipulate LAMMPS data (as list of strings).
 
@@ -26,8 +26,8 @@
 import numpy as np
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
-from deepmd_iterative.common.list import textfile_to_string_list
+from arcann_training.common.utils import catch_errors_decorator
+from arcann_training.common.list import textfile_to_string_list
 
 
 # Unittested

diff --git a/deepmd_iterative/common/list.py → arcann_training/common/list.py b/deepmd_iterative/common/list.py → arcann_training/common/list.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/03/31
+Last modified: 2024/05/15
 
 The utils module provides functions to manipulate lists.
 
@@ -32,7 +32,7 @@
 from typing import List
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # Unittested

diff --git a/deepmd_iterative/common/logging.py → arcann_training/common/logging.py b/deepmd_iterative/common/logging.py → arcann_training/common/logging.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2024/05/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 """
 from typing import Dict
 
@@ -49,7 +49,7 @@ def setup_logging(verbose: int = 0) -> Dict:
                     'class': 'logging.FileHandler',
                     'level': 'INFO',
                     'formatter': 'simple_file',
-                    'filename': 'arcann.log',
+                    'filename': 'arcann_training.log',
                     'mode': 'a',  # Append mode
                 },
             },

diff --git a/deepmd_iterative/common/machine.py → arcann_training/common/machine.py b/deepmd_iterative/common/machine.py → arcann_training/common/machine.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 The machine module provides functions for machine operations.
 
@@ -39,8 +39,8 @@
 from typing import Any, Dict, List, Tuple, Union
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
-from deepmd_iterative.common.json import load_json_file
+from arcann_training.common.utils import catch_errors_decorator
+from arcann_training.common.json import load_json_file
 
 
 # Unittested

diff --git a/deepmd_iterative/common/parsing_labeling.py → arcann_training/common/parsing_labeling.py b/deepmd_iterative/common/parsing_labeling.py → arcann_training/common/parsing_labeling.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2024/03/01
-Last modified: 2024/05/14
+Last modified: 2024/05/15
 """
 
 # TODO: Homogenize the docstrings for this module
@@ -19,7 +19,7 @@
 import numpy as np
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # TODO: Add tests for this function

diff --git a/deepmd_iterative/common/plumed.py → arcann_training/common/plumed.py b/deepmd_iterative/common/plumed.py → arcann_training/common/plumed.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/03/31
+Last modified: 2024/05/15
 
 The plumed module provides functions to manipulate PLUMED data (as list of strings).
 
@@ -23,7 +23,7 @@
 from typing import List, Tuple, Union
 
 # Local imports
-from deepmd_iterative.common.utils import catch_errors_decorator
+from arcann_training.common.utils import catch_errors_decorator
 
 
 # TODO: Add tests for this function

diff --git a/deepmd_iterative/common/slurm.py → arcann_training/common/slurm.py b/deepmd_iterative/common/slurm.py → arcann_training/common/slurm.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 The slurm module provides functions to manipulate SLURM data (as list of strings).
 
@@ -24,11 +24,11 @@
 from typing import Dict, List
 
 # Local imports
-from deepmd_iterative.common.utils import (
+from arcann_training.common.utils import (
     catch_errors_decorator,
     convert_seconds_to_hh_mm_ss,
 )
-from deepmd_iterative.common.list import (
+from arcann_training.common.list import (
     exclude_substring_from_string_list,
     replace_substring_in_string_list,
 )

diff --git a/deepmd_iterative/common/utils.py → arcann_training/common/utils.py b/deepmd_iterative/common/utils.py → arcann_training/common/utils.py
@@ -1,12 +1,12 @@
 """
 #----------------------------------------------------------------------------------------------------#
 #   ArcaNN: Automatic training of Reactive Chemical Architecture with Neural Networks                #
-#   Copyright 2023 ArcaNN developers group <https://github.com/arcann-chem>                          #
+#   Copyright 2022-2024 ArcaNN developers group <https://github.com/arcann-chem>                     #
 #                                                                                                    #
 #   SPDX-License-Identifier: AGPL-3.0-only                                                           #
 #----------------------------------------------------------------------------------------------------#
 Created: 2022/01/01
-Last modified: 2024/05/01
+Last modified: 2024/05/15
 
 Utility module providing helper functions.