Merge pull request #79 from TheoChem-VU/76-restructuring-package-into…

…-src-structure

45 restructuring package into src structure

.github/workflows/build_python_versions.yml

@@ -23,16 +23,15 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ruff==0.0.177 pytest pytest-cov
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install ruff==0.0.250 pytest pytest-cov
           pip install -e .
       - name: Lint with ruff
         run: |
           # stop the build if there are Python syntax errors or undefined names
           # Note, line length is put on a very high margin (200). PEP8 prefers a value of 79
-          ruff --format=github --select=E9,F63,F7,F82 --target-version=py37 --line-length=250 .
+          ruff --format=github --select=E9,F63,F7,F82 --target-version=py38 --line-length=250 .
           # default set of ruff rules with GitHub Annotations
-          ruff --format=github --target-version=py37 --line-length=250 .
+          ruff --format=github --target-version=py38 --line-length=250 .
       - name: Test with pytest
         run: |
           pytest --cov

MANIFEST.in

@@ -1,2 +1,2 @@
-include TCutility/results/input_blocks
-include TCutility/atom_data/*
+include src/tcutility/results/input_blocks
+include src/tcutility/atom_data/*

README.md

@@ -1,34 +1,35 @@
-[![Documentation](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml) [![Testing](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml) [![Publishing to PyPI](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml/badge.svg?branch=main)](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml)
+# TCutility
 
+[![Documentation](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_docs.yml) [![Testing](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml/badge.svg)](https://github.com/TheoChem-VU/TCutility/actions/workflows/build_python_versions.yml) [![Publishing to PyPI](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml/badge.svg?branch=main)](https://github.com/TheoChem-VU/TCutility/actions/workflows/pypi_publish.yml)
 
 [![TCutility version](https://badge.fury.io/py/TCutility.svg)](https://pypi.org/project/TCutility/)
 
-# TCutility
 Utility functions/classes for the TheoCheM programs
 
-# Installation
+## Installation
+
 The easiest and recommended installation method is via pip:
 
-``` python -m pip install TCutility```
+```python -m pip install tcutility```
 
 To update the package, please run:
 
-``` python -m pip install --upgrade TCutility```
+```python -m pip install --upgrade tcutility```
 
 <details>
 <summary><h4>Manual Installation</h4></summary>
 The following is for people who would like to install the repository themselves. For example, to edit and/or contribute code to the project.
-  
-First clone this repository: 
+
+First clone this repository:
 
 ``` git clone https://github.com/TheoChem-VU/TCutility.git ```
 
 Then move into the new directory and install the package:
 
-```
+```python
 cd TCutility
-python -m pip install --upgrade build 
-python -m build 
+python -m pip install --upgrade build
+python -m build
 python -m pip install -e .
 ```
 
@@ -38,12 +39,14 @@ To get new updates, simply run:
 
 </details>
 
-# Documentation
-Documentation of TCutility is hosted at https://theochem-vu.github.io/TCutility/ (work in progress)
+## Documentation
+
+Documentation of TCutility is hosted at <https://theochem-vu.github.io/TCutility/> (work in progress)
+
+## Usage
 
-# Usage
 List of available utilities and their usage:
-- TCutility.results | Read information from AMS calculations such as timings, settings, results, etc. from files in the calculation directory. Currently supports the ADF and DFTB engines.
-- TCutility.molecule | Read and write rich xyz files. These are used to conveniently supply extra information with your xyz files, for example to let a program know what calculations to perform, or to include properties such as charge and spin-polarization.
-- TCutility.analysis | Useful functions that are used for further analysis of calculation results. Currently includes vibrational mode checking to obtain or verify the reaction coordinate of an imaginary mode.
 
+- tcutility.results | Read information from AMS calculations such as timings, settings, results, etc. from files in the calculation directory. Currently supports the ADF and DFTB engines.
+- tcutility.molecule | Read and write rich xyz files. These are used to conveniently supply extra information with your xyz files, for example to let a program know what calculations to perform, or to include properties such as charge and spin-polarization.
+- tcutility.analysis | Useful functions that are used for further analysis of calculation results. Currently includes vibrational mode checking to obtain or verify the reaction coordinate of an imaginary mode.

docs/_build/html/_sources/modules.rst.txt → docs/__modules.rst

@@ -4,4 +4,4 @@ TCutility
 .. toctree::
    :maxdepth: 4
 
-   TCutility
+   tcutility