Fix/rename project

Makefile

@@ -1,7 +1,7 @@
 .PHONY: Makefile setup-docs preview docs clear-docs watch
 
 test:
-	pytest tests --cov=gmx_top4py --cov-report=term-missing
+	pytest tests --cov=gmxtop --cov-report=term-missing
 
 format:
 	black src tests
@@ -11,6 +11,19 @@ venv:
 	uv sync
 	source .venv/bin/activate
 
+failing:
+	echo None
+
+package:
+	rm -r dist
+	python -m build 
+
+testpypi:
+	python -m twine upload --repository testpypi dist/*
+
+pypi:
+	python -m twine upload dist/*
+
 # Write explicitly all dependencies to a requirements_explicit.txt file
 # requirements:
 # 	source .venv/bin/activate

README.md

@@ -1,41 +1,36 @@
-# gmx-top4py 
+# gmxtop 
 
 <p align="left">
 <a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
 </p>
 
 GROMACS topology files for python
 
-**!!!!!!!!!!!!!!!!!!!!!! DEPRECATED !!!!!!!!!!!!!!!!!!!!!!!! <br>
-This projected has been renamed to gmxtop.<br>
-Please use `pip install gmxtop` instead.<br>
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!** <br> 
-
 ## Description
-The `gmx-top4py` project provides a python interface to
+The `gmxtop` project provides a python interface to
 * read and write toplogy and force field information from GROMACS-type top-files
 * alter force field parameters 
 
-The `gmx-top4py` project derives this functionality from the [kimmdy](https://github.com/graeter-group/kimmdy) project, originally developed by the graeter-group, and includes only minor modifications to parts of the original code to operate independently.
-The `kimmdy` project is licensed under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.html) and, as a derivative work, the `gmx-top4py` project is distributed under the same license. See [LICENSE](./LICENSE) for details.
+The `gmxtop` project derives this functionality from the [kimmdy](https://github.com/graeter-group/kimmdy) project, originally developed by the graeter-group, and includes only minor modifications to parts of the original code to operate independently.
+The `kimmdy` project is licensed under the [GNU General Public License v3.0](https://www.gnu.org/licenses/gpl-3.0.html) and, as a derivative work, the `gmxtop` project is distributed under the same license. See [LICENSE](./LICENSE) for details.
 
 ## Tutorials
 The following tutorials are avaiable as Google Colab notebooks and hence do not require a local installation:
-* [Basic tutorial](https://colab.research.google.com/drive/19zjIw2H5O6InLDQWLXEvrwrZ5w0AL7i1?usp=sharing) - Basic accessing of topology information with gmx-top4py
-* [Advanced tutorial](https://colab.research.google.com/drive/1uWgji2O1N4PnxnYpGc1yV68Qzm-PfVX1?usp=sharing) - Advanded accessing of topology information with gmx-top4py
-* [Force field parameter tutorial](https://colab.research.google.com/drive/1YOPPkCDudqSwd2QV0P7qEcd-1bogrvtY?usp=sharing) - Adapting force field parameters with gmx-top4py
+* [Basic tutorial](https://colab.research.google.com/drive/19zjIw2H5O6InLDQWLXEvrwrZ5w0AL7i1?usp=sharing) - Basic accessing of topology information with gmxtop
+* [Advanced tutorial](https://colab.research.google.com/drive/1uWgji2O1N4PnxnYpGc1yV68Qzm-PfVX1?usp=sharing) - Advanded accessing of topology information with gmxtop
+* [Force field parameter tutorial](https://colab.research.google.com/drive/1YOPPkCDudqSwd2QV0P7qEcd-1bogrvtY?usp=sharing) - Adapting force field parameters with gmxtop
 
 ## Installation
 ### From PyPI
 ```bash
-pip install gmx-top4py
+pip install gmxtop
 ```
 
 ### From source via uv
 Clone repository and move into
 ```bash
-git clone git@github.com:graeter-group/gmx-top4py.git
-cd gmx-top4py
+git clone git@github.com:graeter-group/gmxtop.git
+cd gmxtop
 ```
 Install repository
 ```bash
@@ -53,13 +48,13 @@ pytest tests
 ### From source via conda and pip
 Clone repository and move into
 ```bash
-git clone git@github.com:graeter-group/gmx-top4py.git
-cd gmx-top4py
+git clone git@github.com:graeter-group/gmxtop.git
+cd gmxtop
 ```
 Install repository into conda environment
 ```bash
-conda create -n gmx-top4py python -y
-conda activate gmx-top4py
+conda create -n gmxtop python -y
+conda activate gmxtop
 pip install -e '.[dev]' # install with dev dependencies
 ```
 Verify install by running the tests

examples/advanced/advanced.py

@@ -1,7 +1,7 @@
 # %%
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -25,9 +25,9 @@
 from pathlib import Path
 from copy import deepcopy
 
-from gmx_top4py.topology.topology import Topology
-from gmx_top4py.parsing import read_top, write_top
-from gmx_top4py.topology.utils import get_is_selected_moleculetype_f
+from gmxtop.topology.topology import Topology
+from gmxtop.parsing import read_top, write_top
+from gmxtop.topology.utils import get_is_selected_moleculetype_f
 # %% [markdown]
 # # 1. Reading a topology file
 # Internally, the `Topology.from_path` class method uses the `read_top` function to parse the topology file into a dictionary, and then creates an instance of the `Topology` object from that dictionary. <br>

examples/basic/basic.py

@@ -1,7 +1,7 @@
 # %%
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -24,7 +24,7 @@
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 from pathlib import Path
 
-from gmx_top4py.topology.topology import Topology
+from gmxtop.topology.topology import Topology
 # %% [markdown]
 # # 1. Reading a topology file
 # Let's read the GROMACS topology file 'urea.top' into a `Topology` object.

examples/ff_params/ff_params.py

@@ -1,7 +1,7 @@
 # %%
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -25,13 +25,13 @@
 from pathlib import Path
 from copy import deepcopy
 
-from gmx_top4py.topology.topology import Topology
-from gmx_top4py.parsing import read_top
-from gmx_top4py.parameterizing import Parameterizer
-from gmx_top4py.topology.atomic import Dihedral
+from gmxtop.topology.topology import Topology
+from gmxtop.parsing import read_top
+from gmxtop.parameterizing import Parameterizer
+from gmxtop.topology.atomic import Dihedral
 # %% [markdown]
 # # Manipulation of force field parameters
-# In this example, we demonstrate how to manipulate force field parameters in a topology file using gmx-top4py.
+# In this example, we demonstrate how to manipulate force field parameters in a topology file using gmxtop.
 # We will use a topology file for a hexamer of alanine ('hexala.top') parameterized with the 'amber99sb-star-ildnp.ff' force field.
 
 # %% [markdown]

pyproject.toml

@@ -3,9 +3,9 @@ requires = ["setuptools>=61.2"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "gmx-top4py"
-version = "0.1.5"
-description = "A Python library to parse GROMACS topology files and alter associated force fields parameters."
+name = "gmxtop"
+version = "0.0.1"
+description = "Read and write GROMACS topology files and alter associated force fields parameters."
 license-files = ["LICEN[CS]E*"]
 authors = [{ name = "graeter-group"}]
 classifiers = [
@@ -25,14 +25,14 @@ package-dir = { "" = "src" }
 include-package-data = true
 
 [tool.setuptools.package-data]
-"gmx_top4py" = [ "py.typed" ]
+"gmxtop" = [ "py.typed" ]
 
 [tool.setuptools.packages.find]
 where=["src"]
 namespaces = false
 
 [tool.uv.sources]
-"gmx_top4py" = { workspace = true }
+"gmxtop" = { workspace = true }
 
 [project.optional-dependencies]
 dev = [

src/gmxtop/__init__.py

@@ -0,0 +1,29 @@
+# This file is part of the gmxtop project.
+#
+# The gmxtop project is based on or includes code from:
+#    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
+#    Copyright (C) graeter-group
+#    Licensed under the GNU General Public License v3.0 (GPLv3).
+#
+# Modifications and additional code:
+#    Copyright (C) 2025 graeter-group
+#    Licensed under the GNU General Public License v3.0 (GPLv3).
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Welcome to gmxtop!
+"""
+
+from __future__ import annotations

src/gmx_top4py/constants.py → src/gmxtop/constants.py

@@ -1,6 +1,6 @@
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -23,7 +23,7 @@
 # along with this program. If not, see <https://www.gnu.org/licenses/>.
 
 """
-Constants used throughout gmx-top4py.
+Constants used throughout gmxtop.
 """
 
 ATOM_ID_FIELDS = {

src/gmx_top4py/parameterizing.py → src/gmxtop/parameterizing.py

@@ -1,6 +1,6 @@
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -30,7 +30,7 @@
 from typing import TYPE_CHECKING, Optional
 
 if TYPE_CHECKING:
-    from gmx_top4py.topology.topology import Topology
+    from gmxtop.topology.topology import Topology
 
 
 class Parameterizer(ABC):

src/gmx_top4py/parsing.py → src/gmxtop/parsing.py

@@ -1,6 +1,6 @@
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -36,11 +36,11 @@
 from typing import Optional, TypeAlias, TypedDict, Union
 import numpy as np
 
-from gmx_top4py.utils import get_gmx_dir
+from gmxtop.utils import get_gmx_dir
 
 logger = logging.getLogger(__name__)
 TopologyDict = dict
-"""A raw representation of a topology file returned by [](`~gmx-top4py.parsing.read_top`).
+"""A raw representation of a topology file returned by [](`~gmxtop.parsing.read_top`).
 """
 
 

src/gmx_top4py/topology/atomic.py → src/gmxtop/topology/atomic.py

@@ -1,6 +1,6 @@
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -32,8 +32,8 @@
 from dataclasses import dataclass, field
 from typing import Optional, Union
 
-from gmx_top4py.constants import FFFUNC
-from gmx_top4py.utils import field_or_none
+from gmxtop.constants import FFFUNC
+from gmxtop.utils import field_or_none
 
 logger = logging.getLogger(__name__)
 

src/gmx_top4py/topology/ff.py → src/gmxtop/topology/ff.py

@@ -1,6 +1,6 @@
-# This file is part of the gmx-top4py project.
+# This file is part of the gmxtop project.
 #
-# The gmx-top4py project is based on or includes code from:
+# The gmxtop project is based on or includes code from:
 #    kimmdy (https://github.com/graeter-group/kimmdy/tree/main)
 #    Copyright (C) graeter-group
 #    Licensed under the GNU General Public License v3.0 (GPLv3).
@@ -29,9 +29,9 @@
 from pathlib import Path
 from typing import Optional
 
-from gmx_top4py.constants import FFFUNC
-from gmx_top4py.parsing import read_top
-from gmx_top4py.topology.atomic import (
+from gmxtop.constants import FFFUNC
+from gmxtop.parsing import read_top
+from gmxtop.topology.atomic import (
     AngleId,
     AngleType,
     AtomId,
@@ -44,8 +44,8 @@
     ProperDihedralId,
     ResidueType,
 )
-from gmx_top4py.topology.utils import get_top_section
-from gmx_top4py.utils import get_gmx_dir
+from gmxtop.topology.utils import get_top_section
+from gmxtop.utils import get_gmx_dir
 
 logger = logging.getLogger(__name__)