rename project to 'mindlessgen'

Signed-off-by: Marcel Müller <[email protected]>

.gitignore

@@ -2,7 +2,7 @@
 .vscode/
 
 # Version file generated by setuptools_scm
-src/mlmgen/__version__.py
+src/mindlessgen/__version__.py
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

environment.yml

@@ -1,5 +1,5 @@
 # conda env create -f environment.yaml
-name: mlmgen
+name: mindlessgen
 channels:
   - conda-forge
 dependencies:

mlmgen.toml → mindlessgen.toml

@@ -1,4 +1,4 @@
-# Default configuration for the 'MindLess Molecule GENerator' (MLMGen)
+# Default configuration for the 'Mindless Molecule GENerator' (MindlessGen) package
 # Following file locations are searched for in the following order:
 # 1. Location specified by the `--config < str | Path >` command-line argument
 # 2. Current working directory (`Path.cwd()`)

pyproject.toml

@@ -3,11 +3,11 @@ requires = ["wheel", "setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "mlmgen"
+name = "mindlessgen"
 authors = [
     { name = "Marcel Müller", email = "[email protected]" },
 ]
-description = "MindLess Molecule GENerator"
+description = "Mindless Molecule GENerator"
 readme = "README.md"
 requires-python = ">=3.10"
 license = { file = "LICENSE.md" }
@@ -37,10 +37,10 @@ dev = [
 ]
 
 [project.scripts]
-mlmgen = "mlmgen:console_entry_point"
+mindlessgen = "mindlessgen:console_entry_point"
 
 [tool.setuptools_scm]
-version_file = "src/mlmgen/__version__.py"
+version_file = "src/mindlessgen/__version__.py"
 
 [tool.pytest.ini_options]
 testpaths = ["test"]

src/mlmgen/cli/entrypoint.py → src/mindlessgen/cli/entrypoint.py

@@ -65,8 +65,8 @@ def find_config_file(cli_config_path: str | Path | None = None) -> Path | None:
 
     # Search paths
     search_paths = [
-        Path.home() / "mlmgen.toml",  # $USER/mlmgen.toml
-        Path.cwd() / "mlmgen.toml",  # Current directory
+        Path.home() / "mindlessgen.toml",  # $USER/mindlessgen.toml
+        Path.cwd() / "mindlessgen.toml",  # Current directory
     ]
 
     # Find the config file

src/mlmgen/molecules/molecule.py → src/mindlessgen/molecules/molecule.py

@@ -347,7 +347,7 @@ def write_xyz_to_file(self, filename: str | Path | None = None):
         The layout of the file is as follows:
         ```
         num_atoms
-        'Generated by mlmgen-v{__version__}'
+        'Generated by mindlessgen-v{__version__}'
         <symbol 1> <x1> <y1> <z1>
         <symbol 2> <x2> <y2> <z2>
         ...
@@ -371,7 +371,7 @@ def write_xyz_to_file(self, filename: str | Path | None = None):
 
         with open(filename, "w", encoding="utf8") as f:
             f.write(f"{self.num_atoms}\n")
-            f.write(f"Generated by mlmgen-v{__version__}\n")
+            f.write(f"Generated by mindlessgen-v{__version__}\n")
             for i in range(self.num_atoms):
                 f.write(
                     f"{PSE[self.ati[i]+1]:<5} "
@@ -392,7 +392,7 @@ def read_xyz_from_file(self, filename: str | Path):
         The layout of the file is as follows:
         ```
         num_atoms
-        'Generated by mlmgen-v{__version__}'
+        'Generated by mindlessgen-v{__version__}'
         <symbol 1> <x1> <y1> <z1>
         <symbol 2> <x2> <y2> <z2>
         ...

test/test_config/test_config_set_attributes.py

@@ -1,5 +1,5 @@
 import pytest
-from mlmgen.prog import GeneralConfig  # type: ignore
+from mindlessgen.prog import GeneralConfig  # type: ignore
 
 
 @pytest.mark.parametrize(

test/test_generator/test_generate.py

@@ -1,8 +1,8 @@
 import pytest
 
-from mlmgen.generator import generator  # type: ignore
-from mlmgen.prog import ConfigManager  # type: ignore
-from mlmgen.molecules import Molecule  # type: ignore
+from mindlessgen.generator import generator  # type: ignore
+from mindlessgen.prog import ConfigManager  # type: ignore
+from mindlessgen.molecules import Molecule  # type: ignore
 
 
 @pytest.mark.optional

test/test_molecules/test_generate_molecules.py

@@ -5,7 +5,7 @@
 from __future__ import annotations
 import pytest
 import numpy as np
-from mlmgen.molecules import (  # type: ignore
+from mindlessgen.molecules import (  # type: ignore
     generate_random_molecule,
     generate_coordinates,
     generate_atom_list,
@@ -17,8 +17,8 @@
     get_alkali_metals,
     get_alkaline_earth_metals,
 )
-from mlmgen.molecules.molecule import Molecule  # type: ignore
-from mlmgen.prog import ConfigManager  # type: ignore
+from mindlessgen.molecules.molecule import Molecule  # type: ignore
+from mindlessgen.prog import ConfigManager  # type: ignore
 
 
 def test_generate_molecule() -> None:

test/test_molecules/test_miscellaneous.py

@@ -4,7 +4,7 @@
 
 import pytest
 import numpy as np
-from mlmgen.molecules.miscellaneous import set_random_charge  # type: ignore
+from mindlessgen.molecules.miscellaneous import set_random_charge  # type: ignore
 
 
 # CAUTION: We use 0-based indexing for atoms and molecules!

test/test_molecules/test_molecule.py

@@ -5,7 +5,7 @@
 from __future__ import annotations
 import numpy as np
 import pytest
-from mlmgen.molecules.molecule import Molecule  # type: ignore
+from mindlessgen.molecules.molecule import Molecule  # type: ignore
 
 
 @pytest.mark.parametrize(

test/test_molecules/test_postprocessing.py

@@ -7,8 +7,8 @@
 from pathlib import Path
 import numpy as np
 import pytest
-from mlmgen.molecules import detect_fragments  # type: ignore
-from mlmgen.molecules.molecule import Molecule  # type: ignore
+from mindlessgen.molecules import detect_fragments  # type: ignore
+from mindlessgen.molecules.molecule import Molecule  # type: ignore
 
 
 @pytest.fixture

test/test_qm/test_xtb.py

@@ -6,8 +6,8 @@
 from pathlib import Path
 import pytest
 import numpy as np
-from mlmgen.qm import XTB, get_xtb_path  # type: ignore
-from mlmgen.molecules import Molecule  # type: ignore
+from mindlessgen.qm import XTB, get_xtb_path  # type: ignore
+from mindlessgen.molecules import Molecule  # type: ignore
 
 
 # mark all tests as optional as they depend on the availability of xtb