From 711562e83fa3e0b5abe4765754855d648a114ccf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marcel=20M=C3=BCller?= Date: Thu, 15 Aug 2024 18:31:38 +0200 Subject: [PATCH] rename project to 'mindlessgen' MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Marcel Müller --- .gitignore | 2 +- environment.yml | 2 +- mlmgen.toml => mindlessgen.toml | 2 +- pyproject.toml | 8 ++++---- src/{mlmgen => mindlessgen}/__init__.py | 0 src/{mlmgen => mindlessgen}/__main__.py | 0 src/{mlmgen => mindlessgen}/cli/__init__.py | 0 src/{mlmgen => mindlessgen}/cli/cli_parser.py | 0 src/{mlmgen => mindlessgen}/cli/entrypoint.py | 4 ++-- src/{mlmgen => mindlessgen}/generator/__init__.py | 0 src/{mlmgen => mindlessgen}/generator/main.py | 0 src/{mlmgen => mindlessgen}/molecules/__init__.py | 0 .../molecules/generate_molecule.py | 0 src/{mlmgen => mindlessgen}/molecules/miscellaneous.py | 0 src/{mlmgen => mindlessgen}/molecules/molecule.py | 6 +++--- src/{mlmgen => mindlessgen}/molecules/postprocess.py | 0 src/{mlmgen => mindlessgen}/prog/__init__.py | 0 src/{mlmgen => mindlessgen}/prog/config.py | 0 src/{mlmgen => mindlessgen}/qm/__init__.py | 0 src/{mlmgen => mindlessgen}/qm/base.py | 0 src/{mlmgen => mindlessgen}/qm/xtb.py | 0 test/test_config/test_config_set_attributes.py | 2 +- test/test_generator/test_generate.py | 6 +++--- test/test_molecules/test_generate_molecules.py | 6 +++--- test/test_molecules/test_miscellaneous.py | 2 +- test/test_molecules/test_molecule.py | 2 +- test/test_molecules/test_postprocessing.py | 4 ++-- test/test_qm/test_xtb.py | 4 ++-- 28 files changed, 25 insertions(+), 25 deletions(-) rename mlmgen.toml => mindlessgen.toml (92%) rename src/{mlmgen => mindlessgen}/__init__.py (100%) rename src/{mlmgen => mindlessgen}/__main__.py (100%) rename src/{mlmgen => mindlessgen}/cli/__init__.py (100%) rename src/{mlmgen => mindlessgen}/cli/cli_parser.py (100%) rename src/{mlmgen => mindlessgen}/cli/entrypoint.py (94%) rename src/{mlmgen => mindlessgen}/generator/__init__.py (100%) rename src/{mlmgen => mindlessgen}/generator/main.py (100%) rename src/{mlmgen => mindlessgen}/molecules/__init__.py (100%) rename src/{mlmgen => mindlessgen}/molecules/generate_molecule.py (100%) rename src/{mlmgen => mindlessgen}/molecules/miscellaneous.py (100%) rename src/{mlmgen => mindlessgen}/molecules/molecule.py (98%) rename src/{mlmgen => mindlessgen}/molecules/postprocess.py (100%) rename src/{mlmgen => mindlessgen}/prog/__init__.py (100%) rename src/{mlmgen => mindlessgen}/prog/config.py (100%) rename src/{mlmgen => mindlessgen}/qm/__init__.py (100%) rename src/{mlmgen => mindlessgen}/qm/base.py (100%) rename src/{mlmgen => mindlessgen}/qm/xtb.py (100%) diff --git a/.gitignore b/.gitignore index 4049b98..28e3b31 100644 --- a/.gitignore +++ b/.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__/ diff --git a/environment.yml b/environment.yml index 4e1db69..be9d9ec 100644 --- a/environment.yml +++ b/environment.yml @@ -1,5 +1,5 @@ # conda env create -f environment.yaml -name: mlmgen +name: mindlessgen channels: - conda-forge dependencies: diff --git a/mlmgen.toml b/mindlessgen.toml similarity index 92% rename from mlmgen.toml rename to mindlessgen.toml index 7b302fc..31f966e 100644 --- a/mlmgen.toml +++ b/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()`) diff --git a/pyproject.toml b/pyproject.toml index b9e3790..dfa8fa7 100644 --- a/pyproject.toml +++ b/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 = "marcel.mueller@thch.uni-bonn.de" }, ] -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"] diff --git a/src/mlmgen/__init__.py b/src/mindlessgen/__init__.py similarity index 100% rename from src/mlmgen/__init__.py rename to src/mindlessgen/__init__.py diff --git a/src/mlmgen/__main__.py b/src/mindlessgen/__main__.py similarity index 100% rename from src/mlmgen/__main__.py rename to src/mindlessgen/__main__.py diff --git a/src/mlmgen/cli/__init__.py b/src/mindlessgen/cli/__init__.py similarity index 100% rename from src/mlmgen/cli/__init__.py rename to src/mindlessgen/cli/__init__.py diff --git a/src/mlmgen/cli/cli_parser.py b/src/mindlessgen/cli/cli_parser.py similarity index 100% rename from src/mlmgen/cli/cli_parser.py rename to src/mindlessgen/cli/cli_parser.py diff --git a/src/mlmgen/cli/entrypoint.py b/src/mindlessgen/cli/entrypoint.py similarity index 94% rename from src/mlmgen/cli/entrypoint.py rename to src/mindlessgen/cli/entrypoint.py index a8054d6..2e4d9f0 100644 --- a/src/mlmgen/cli/entrypoint.py +++ b/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 diff --git a/src/mlmgen/generator/__init__.py b/src/mindlessgen/generator/__init__.py similarity index 100% rename from src/mlmgen/generator/__init__.py rename to src/mindlessgen/generator/__init__.py diff --git a/src/mlmgen/generator/main.py b/src/mindlessgen/generator/main.py similarity index 100% rename from src/mlmgen/generator/main.py rename to src/mindlessgen/generator/main.py diff --git a/src/mlmgen/molecules/__init__.py b/src/mindlessgen/molecules/__init__.py similarity index 100% rename from src/mlmgen/molecules/__init__.py rename to src/mindlessgen/molecules/__init__.py diff --git a/src/mlmgen/molecules/generate_molecule.py b/src/mindlessgen/molecules/generate_molecule.py similarity index 100% rename from src/mlmgen/molecules/generate_molecule.py rename to src/mindlessgen/molecules/generate_molecule.py diff --git a/src/mlmgen/molecules/miscellaneous.py b/src/mindlessgen/molecules/miscellaneous.py similarity index 100% rename from src/mlmgen/molecules/miscellaneous.py rename to src/mindlessgen/molecules/miscellaneous.py diff --git a/src/mlmgen/molecules/molecule.py b/src/mindlessgen/molecules/molecule.py similarity index 98% rename from src/mlmgen/molecules/molecule.py rename to src/mindlessgen/molecules/molecule.py index b58d986..a8ea158 100644 --- a/src/mlmgen/molecules/molecule.py +++ b/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__}' ... @@ -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__}' ... diff --git a/src/mlmgen/molecules/postprocess.py b/src/mindlessgen/molecules/postprocess.py similarity index 100% rename from src/mlmgen/molecules/postprocess.py rename to src/mindlessgen/molecules/postprocess.py diff --git a/src/mlmgen/prog/__init__.py b/src/mindlessgen/prog/__init__.py similarity index 100% rename from src/mlmgen/prog/__init__.py rename to src/mindlessgen/prog/__init__.py diff --git a/src/mlmgen/prog/config.py b/src/mindlessgen/prog/config.py similarity index 100% rename from src/mlmgen/prog/config.py rename to src/mindlessgen/prog/config.py diff --git a/src/mlmgen/qm/__init__.py b/src/mindlessgen/qm/__init__.py similarity index 100% rename from src/mlmgen/qm/__init__.py rename to src/mindlessgen/qm/__init__.py diff --git a/src/mlmgen/qm/base.py b/src/mindlessgen/qm/base.py similarity index 100% rename from src/mlmgen/qm/base.py rename to src/mindlessgen/qm/base.py diff --git a/src/mlmgen/qm/xtb.py b/src/mindlessgen/qm/xtb.py similarity index 100% rename from src/mlmgen/qm/xtb.py rename to src/mindlessgen/qm/xtb.py diff --git a/test/test_config/test_config_set_attributes.py b/test/test_config/test_config_set_attributes.py index 09c363f..6a7b8fe 100644 --- a/test/test_config/test_config_set_attributes.py +++ b/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( diff --git a/test/test_generator/test_generate.py b/test/test_generator/test_generate.py index e06ae60..de76823 100644 --- a/test/test_generator/test_generate.py +++ b/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 diff --git a/test/test_molecules/test_generate_molecules.py b/test/test_molecules/test_generate_molecules.py index 64b6732..e73f7fc 100644 --- a/test/test_molecules/test_generate_molecules.py +++ b/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: diff --git a/test/test_molecules/test_miscellaneous.py b/test/test_molecules/test_miscellaneous.py index bb7cff1..e2bdd94 100644 --- a/test/test_molecules/test_miscellaneous.py +++ b/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! diff --git a/test/test_molecules/test_molecule.py b/test/test_molecules/test_molecule.py index 1b25cef..7c5ea30 100644 --- a/test/test_molecules/test_molecule.py +++ b/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( diff --git a/test/test_molecules/test_postprocessing.py b/test/test_molecules/test_postprocessing.py index 6aa1064..23d5c3a 100644 --- a/test/test_molecules/test_postprocessing.py +++ b/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 diff --git a/test/test_qm/test_xtb.py b/test/test_qm/test_xtb.py index 27a41f9..bc64457 100644 --- a/test/test_qm/test_xtb.py +++ b/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