Named the package in the template.

.github/workflows/tests.yaml

@@ -38,7 +38,7 @@ jobs:
           uv pip install --system .[dev]
 
       - name: Run tests with pytest
-        run: pytest --cov=template --cov-report=xml
+        run: pytest --cov=MolecularDockingKit --cov-report=xml
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

MANIFEST.in

@@ -1 +1 @@
-graft src/template
+graft src/MolecularDockingKit

README.md

@@ -1,3 +1,3 @@
-# template
+# MolecularDockingKit
 
-A simple-to-use resource for creating open-source Python packages.
+A simple python tool to perform molecular docking computations.

docs/example_docs/code/hints.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-In the sample functions provided with the template repository, you will see something like:
+In the sample functions provided with the MolecularDockingKit repository, you will see something like:
 
 ```
 def make_array(val: float, length: int = 3) -> NDArray:
@@ -12,7 +12,7 @@ If you aren't familiar with [type-hinting](https://docs.python.org/3/library/typ
 
 !!! Tip
 
-    If you have to import a given function solely for type-hinting purposes, you should put it within an [`if TYPE_CHECKING` block](https://docs.python.org/3/library/typing.html#typing.TYPE_CHECKING) (as demonstrated in `/src/template/examples/sample.py`). It will then only be imported when using a type-checking utility, reducing the overall import time of your module.
+    If you have to import a given function solely for type-hinting purposes, you should put it within an [`if TYPE_CHECKING` block](https://docs.python.org/3/library/typing.html#typing.TYPE_CHECKING) (as demonstrated in `/src/MolecularDockingKit/examples/sample.py`). It will then only be imported when using a type-checking utility, reducing the overall import time of your module.
 
 !!! Note
 

docs/example_docs/code/source.md

@@ -8,7 +8,7 @@ All the code in the `src` directory can be imported now that you have installed
 
 !!! Tip
 
-    As an example, you can import and use the demonstration [template.examples.sample][] functions as follows:
+    As an example, you can import and use the demonstration [MolecularDockingKit.examples.sample][] functions as follows:
 
     ```python
     from MyPackageName.examples.sample import add, make_array

docs/example_docs/installation/install.md

@@ -14,4 +14,4 @@ Here, the `-e` means editable mode, the `.` means the current directory, and the
 
     You should generally start from a clean Python environment, such as a new Conda environment if you are using Anaconda or one of its variants.
 
-To make sure you installed your package successfully, open a Python console and run `import <MyPackageName>`. It should return without any errors. If there are errors, it's likely because you forgot to replace a "template" placeholder with the name of your package.
+To make sure you installed your package successfully, open a Python console and run `import <MyPackageName>`. It should return without any errors. If there are errors, it's likely because you forgot to replace a "MolecularDockingKit" placeholder with the name of your package.

docs/example_docs/installation/pyproject.md

@@ -4,7 +4,7 @@ The `pyproject.toml` file contains all of the necessary information on how Pytho
 
 ## Metadata
 
-There are several metadata-related fields that you will likely want to update. You should have already updated the `name` of the package in a prior step when you replaced "template" everywhere, but you will also want to change the following:
+There are several metadata-related fields that you will likely want to update. You should have already updated the `name` of the package in a prior step when you replaced "MolecularDockingKit" everywhere, but you will also want to change the following:
 
 - `description`
 - `license` (if you changed the default `LICENSE.md` file)
@@ -17,7 +17,7 @@ Aside from the `name`, none of the above are strictly necessary and can be left
 
 The most important fields to update are related to the dependencies: the Python packages that your own code relies on. This will ensure that they are automatically installed when installing your Python package.
 
-The required dependencies are listed under the `[project]` header in the `dependencies` field. By default, the template repository lists `["numpy"]`. Include any dependencies you want in this list, separated by commas. This should be all the packages you import in your code that are not standard Python libraries.
+The required dependencies are listed under the `[project]` header in the `dependencies` field. By default, the MolecularDockingKit repository lists `["numpy"]`. Include any dependencies you want in this list, separated by commas. This should be all the packages you import in your code that are not standard Python libraries.
 
 !!! Tip
 

docs/example_docs/intro/why.md

@@ -2,7 +2,7 @@
 
 ## Purpose
 
-The first question to address is: why? Why use a template repository like this? Why make a Python package at all, as opposed to writing custom scripts or Jupyter Notebooks?
+The first question to address is: why? Why use a MolecularDockingKit repository like this? Why make a Python package at all, as opposed to writing custom scripts or Jupyter Notebooks?
 
 The answer, in short, is _sustainable and reproducible_ software development. Here are some of the benefits:
 
@@ -15,12 +15,12 @@ Of course, there are many more reasons, but hopefully that's convincing enough!
 
 ## Alternatives
 
-This is by no means the only template of its kind. Some alternatives include:
+This is by no means the only MolecularDockingKit of its kind. Some alternatives include:
 
 - [cookiecutter](https://github.com/cookiecutter/cookiecutter)
 - [pyscaffold](https://github.com/pyscaffold/pyscaffold)
-- [python-package-template](https://github.com/microsoft/python-package-template)
+- [python-package-MolecularDockingKit](https://github.com/microsoft/python-package-MolecularDockingKit)
 
 ... and many more.
 
-Feel free to use them if you wish! This template repository exists because we are all opinionated people, and this template focuses on things that I value most. But the point is to just use something that works well for you.
+Feel free to use them if you wish! This MolecularDockingKit repository exists because we are all opinionated people, and this MolecularDockingKit focuses on things that I value most. But the point is to just use something that works well for you.

docs/example_docs/mkdocs/docs.md

@@ -8,7 +8,7 @@ Now it's time to write some documentation! This isn't very difficult, and of cou
 
     Check out the [Markdown Guide](https://www.markdownguide.org/basic-syntax/) for an overview of the basic syntax.
 
-This template repository uses a documentation format called mkdocs, specifically a useful theme called [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/). This enables many wonderful goodies like the "tip" callout you see above and much more.
+This MolecularDockingKit repository uses a documentation format called mkdocs, specifically a useful theme called [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/). This enables many wonderful goodies like the "tip" callout you see above and much more.
 
 ## Adding Markdown Files
 

docs/example_docs/setup/basics.md

@@ -1,19 +1,19 @@
 # Initial Changes
 
-At this point, you now have your template repository on GitHub and locally on your machine. Now it's time to start making some modifications.
+At this point, you now have your MolecularDockingKit repository on GitHub and locally on your machine. Now it's time to start making some modifications.
 
 ### README
 
 The first thing to do is update the README (`/README.md`), which should contain a user-friendly summary of what your package is all about. This can be whatever you want. Feel free to be creative!
 
 ### License
 
-The template repository comes premade with a sample license (`/LICENSE.md`), in this case the very popular and permissive [BSD 3-Clause license](https://opensource.org/license/bsd-3-clause/). Feel free to change this for your own project or keep it as-is if you don't quite know yet.
+The MolecularDockingKit repository comes premade with a sample license (`/LICENSE.md`), in this case the very popular and permissive [BSD 3-Clause license](https://opensource.org/license/bsd-3-clause/). Feel free to change this for your own project or keep it as-is if you don't quite know yet.
 
 !!! Tip
 
     There are *many* licenses that one can consider. A comprehensive list can be found on the [Open Source Initiative](https://opensource.org/licenses/?categories=popular-strong-community) website, but a less overwhelming route is to use [choosealicense.com](https://choosealicense.com/).
 
 ### Code of Conduct
 
-The template repository ships with a premade Code of Conduct (`/CODE_OF_CONDUCT.md`) that is obtained from the [Contributor Covenant](https://www.contributor-covenant.org/). Of course, you can feel free to keep or change this as you see fit, but it is often a good idea to have a code of conduct for public repositories.
+The MolecularDockingKit repository ships with a premade Code of Conduct (`/CODE_OF_CONDUCT.md`) that is obtained from the [Contributor Covenant](https://www.contributor-covenant.org/). Of course, you can feel free to keep or change this as you see fit, but it is often a good idea to have a code of conduct for public repositories.

docs/example_docs/setup/name.md

@@ -1,13 +1,13 @@
 # Updating the Name
 
-Now for your first major task: **replace all instances of the word "template" with your desired package name**.
+Now for your first major task: **replace all instances of the word "MolecularDockingKit" with your desired package name**.
 
 !!! Note
 
-    Don't forget to update the name of the `/src/template` folder, e.g. so that it is of the form `src/<MyPackageName>`.
+    Don't forget to update the name of the `/src/MolecularDockingKit` folder, e.g. so that it is of the form `src/<MyPackageName>`.
 
 !!! Tip
 
-    If you're using [Visual Studio Code](https://code.visualstudio.com/) as your editor, you can do `ctrl+shift+H` to find-and-replace all instances of "template" with your own package name.
+    If you're using [Visual Studio Code](https://code.visualstudio.com/) as your editor, you can do `ctrl+shift+H` to find-and-replace all instances of "MolecularDockingKit" with your own package name.
 
     ![](../media/find_replace.png)

docs/example_docs/setup/prep.md

@@ -10,7 +10,7 @@ So, you have an idea for your own Python package. The first thing you'll need to
 
 ## Making a Repository
 
-With a nice name in mind, [create a new repository](https://github.com/new?template_name=template&template_owner=Quantum-Accelerators) using this template. Give it a name, a description, and decide if you want it to be public or private.
+With a nice name in mind, [create a new repository](https://github.com/new?MolecularDockingKit_name=MolecularDockingKit&MolecularDockingKit_owner=Quantum-Accelerators) using this MolecularDockingKit. Give it a name, a description, and decide if you want it to be public or private.
 
 ![](../media/create_a_repo.png)
 

docs/index.md

@@ -1,5 +1,5 @@
-# template
+# MolecularDockingKit
 
-Welcome to the documentation for the `template` code! Here you will find everything you need to get started with your own Python package.
+Welcome to the documentation for the `MolecularDockingKit` code! Here you will find everything you need to get started with your own Python package.
 
 **Check out the corresponding ⭐[YouTube tutorial](https://www.youtube.com/watch?v=th2CqJ6oBuM)⭐ for a video overview!**

mkdocs.yml

@@ -1,7 +1,7 @@
-site_name: template
+site_name: MolecularDockingKit
 site_author: YourName
 site_description: >-
-  This is the template package!
+  This is the MolecularDockingKit package!
 nav:
   - Home: index.md
   - Overview:
@@ -33,7 +33,7 @@ nav:
       - example_docs/about/conduct.md
       - example_docs/about/license.md
 
-repo_url: https://github.com/Quantum-Accelerators/template/
+repo_url: https://github.com/Quantum-Accelerators/MolecularDockingKit/
 edit_uri: blob/main/docs/
 
 theme:

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "template"
+name = "MolecularDockingKit"
 description="A Python package description goes here."
 version = "0.0.1"
 readme = "README.md"
@@ -39,15 +39,15 @@ docs = [
 ]
 
 [project.urls]
-repository = "https://github.com/Quantum-Accelerators/template"
-documentation = "https://quantum-accelerators.github.io/template/"
-changelog = "https://github.com/Quantum-Accelerators/template/blob/main/CHANGELOG.md"
+repository = "https://github.com/Quantum-Accelerators/MolecularDockingKit"
+documentation = "https://quantum-accelerators.github.io/MolecularDockingKit/"
+changelog = "https://github.com/Quantum-Accelerators/MolecularDockingKit/blob/main/CHANGELOG.md"
 
 [tool.setuptools.package-data]
-template = ["py.typed"]
+MolecularDockingKit = ["py.typed"]
 
 [tool.pyright]
-include = ["template"]
+include = ["MolecularDockingKit"]
 exclude = ["**/__pycache__"]
 
 [tool.pytest.ini_options]
@@ -137,7 +137,7 @@ lint.unfixable = [
   "F841", # Removes unused variables
 ]
 lint.pydocstyle.convention = "numpy"
-lint.isort.known-first-party = ["template"]
+lint.isort.known-first-party = ["MolecularDockingKit"]
 lint.isort.required-imports = ["from __future__ import annotations"]
 extend-include = ["*.ipynb"]
 

src/template/__init__.py → src/MolecularDockingKit/__init__.py

@@ -1,8 +1,8 @@
-"""Init data"""
-
-from __future__ import annotations
-
-from importlib.metadata import version
-
-# Load the version
-__version__ = version("template")
+"""Init data"""
+
+from __future__ import annotations
+
+from importlib.metadata import version
+
+# Load the version
+__version__ = version("MolecularDockingKit")

tests/examples/test_sample.py

@@ -4,7 +4,7 @@
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
 
-from template.examples.sample import add, divide, make_array
+from MolecularDockingKit.examples.sample import add, divide, make_array
 
 
 def test_add():