change name

.github/workflows/main_documentation.yml

@@ -24,12 +24,12 @@ jobs:
           git submodule foreach --recursive pip install -e .
           pip install -e .
       - name: Generate documentation
-        run: pdoc --html --output-dir docs src/pyskel
+        run: pdoc --html --output-dir docs src/lung_utils
       - name: Upload documentation artifact
         uses: actions/upload-pages-artifact@v3
         with:
           name: documentation
-          path: docs/pyskel
+          path: docs/lung_utils
   deploy:
     name: Deploy documentation
     permissions:

.github/workflows/pull_request_pipeline.yml

@@ -78,7 +78,7 @@ jobs:
           git submodule foreach --recursive pip install -e .
           pip install -e .
       - name: Generate documentation
-        run: pdoc --html --output-dir docs src/pyskel
+        run: pdoc --html --output-dir docs src/lung_utils
       - name: Upload documentation artifact
         uses: actions/upload-pages-artifact@v3
         with:

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "src/pytoda"]
 	path = src/pytoda
-	url = git@github.com:davidrudlstorfer/pytoda.git
+	url = git@github.com:maxiludwig/pytoda.git

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
     rev: 1.7.9
     hooks:
       - id: bandit
-        args: ["-c", "pyproject.toml", "-r", "-ll", "src/pyskel/", "tests/"]
+        args: ["-c", "pyproject.toml", "-r", "-ll", "src/lung_utils/", "tests/"]
         additional_dependencies: ["bandit[toml]"]
   - repo: https://github.com/psf/black
     rev: 24.4.2
@@ -32,7 +32,7 @@ repos:
     rev: v1.7.5
     hooks:
       - id: docformatter
-        args: ["--in-place", "--config=./pyproject.toml", "-r", "src/pyskel/", "tests/"]
+        args: ["--in-place", "--config=./pyproject.toml", "-r", "src/lung_utils/", "tests/"]
   - repo: https://github.com/kplaube/pre-commit-dodgy
     rev: 0.0.2
     hooks:
@@ -45,12 +45,12 @@ repos:
     rev: 1.7.0
     hooks:
       - id: interrogate
-        args: [--fail-under=100, --ignore-init-module, --style=google, -vv, src/pyskel/, tests/]
+        args: [--fail-under=100, --ignore-init-module, --style=google, -vv, src/lung_utils/, tests/]
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
       - id: isort
-        args: ["--profile", "black", "--line-length", "79", "--filter-files", "--src", "[src/pyskel/, tests/]"]
+        args: ["--profile", "black", "--line-length", "79", "--filter-files", "--src", "[src/lung_utils/, tests/]"]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to PySkel
+# Contributing to LungUtils
 We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:
 
 - Reporting a bug
@@ -23,7 +23,7 @@ Pull requests are the best way to propose changes to the codebase (we use [Githu
 ## Any contributions you make will be under the MIT Software License
 In short, when you submit code changes, your submissions are understood to be under the same [MIT License](http://choosealicense.com/licenses/mit/) that covers the project. Feel free to contact the maintainers if that's a concern.
 
-## Report bugs using Github's [issues](https://github.com/davidrudlstorfer/pyskel/issues)
+## Report bugs using Github's [issues](https://github.com/maxiludwig/lung_utils/issues)
 We use GitHub issues to track public bugs. Report a bug by opening a new issue - it's that easy!
 
 ## Write bug reports with detail, background, and sample code

LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 David Rudlstorfer
+Copyright (c) 2024 Maxi Ludwig
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,29 +1,29 @@
 <h1 align="center">
-  PySkel 🐍🩻
+  LungUtils 🐍🩻
 </h1>
 
 <div align="center">
 
-[![Pipeline](https://github.com/davidrudlstorfer/pyskel/actions/workflows/main_pipeline.yml/badge.svg)](https://github.com/davidrudlstorfer/pyskel/actions/workflows/main_pipeline.yml)
-[![Documentation](https://github.com/davidrudlstorfer/pyskel/actions/workflows/main_documentation.yml/badge.svg)](https://davidrudlstorfer.github.io/pyskel/)
-[![Coverage badge](https://github.com/davidrudlstorfer/pyskel/raw/python-coverage-comment-action-data/badge.svg)](https://github.com/davidrudlstorfer/pyskel/tree/python-coverage-comment-action-data)
+[![Pipeline](https://github.com/maxiludwig/lung_utils/actions/workflows/main_pipeline.yml/badge.svg)](https://github.com/maxiludwig/lung_utils/actions/workflows/main_pipeline.yml)
+[![Documentation](https://github.com/maxiludwig/lung_utils/actions/workflows/main_documentation.yml/badge.svg)](https://maxiludwig.github.io/lung_utils/)
+[![Coverage badge](https://github.com/maxiludwig/lung_utils/raw/python-coverage-comment-action-data/badge.svg)](https://github.com/maxiludwig/lung_utils/tree/python-coverage-comment-action-data)
 
 </div>
 
-PySkel (**Py**thon **Skel**eton) is a quick-start Python repository to act as a skeleton for various projects around the multiphysics research code [4C](https://www.4c-multiphysics.org/) and leverages utilities from [PyToDa](https://github.com/davidrudlstorfer/pytoda). It includes the following basic amenities and tools:
+LungUtils (**Py**thon **Skel**eton) is a quick-start Python repository to act as a skeleton for various projects around the multiphysics research code [4C](https://www.4c-multiphysics.org/) and leverages utilities from [PyToDa](https://github.com/maxiludwig/pytoda). It includes the following basic amenities and tools:
 
 - [PyTest](https://docs.pytest.org/) testing framework including an enforced minimum coverage check
 - Automated [Github CI/CD](https://resources.github.com/devops/ci-cd/)
 - Exhaustive [Pre-Commit](https://pre-commit.com) framework to automatically check code formatting and code quality
 - Automatically generated [Documentation](https://pdoc.dev) based on the included Python docstrings
-- Pre-defined framework to gather global settings (see [`main_example_config.yaml`](./src/pyskel/main_example_config.yaml)) and execute a specific workflow
+- Pre-defined framework to gather global settings (see [`main_example_config.yaml`](./src/lung_utils/main_example_config.yaml)) and execute a specific workflow
 
 The remaining parts of the readme are structured as follows:
 
 - [Setup](#setup)
 - [Installation](#installation)
 - [Execution](#execution)
-  - [Execute PySkel](#execute-pyskel)
+  - [Execute LungUtils](#execute-lung_utils)
   - [Run testing framework and create coverage report](#run-testing-framework-and-create-coverage-report)
   - [Create documentation](#create-documentation)
 - [Dependency Management](#dependency-management)
@@ -33,18 +33,18 @@ The remaining parts of the readme are structured as follows:
 
 ## Setup
 
-To setup a project based on PySkel simply follow these steps:
+To setup a project based on LungUtils simply follow these steps:
 
 1. On Github create a new repository with `Use this template` and `Create a new repository`.
 2. Clone your new repository to your local machine and setup the project according to the installation procedure down below.
-3. Rename all occurrences of PySkel to your new code project's name.
+3. Rename all occurrences of LungUtils to your new code project's name.
 4. Within your GitHub project's settings, enable GitHub Pages for GitHub Actions (`Settings` -> `Pages` -> `Source` = `GitHub Actions`).
 5. Create a new branch protection rule for the main branch on GitHub (`Settings` -> `Branches` -> `Add rule` -> Set up your rules`).
 6. Activate to automatically delete branches after merging (`Settings` -> `General` -> `Automatically delete head branches`)
 
 ## Installation
 
-For a quick and easy start an Anaconda/Miniconda environment is highly recommended. Other ways to install PySkel are possible but here the installation procedure is explained based on a conda install. After installing Anaconda/Miniconda
+For a quick and easy start an Anaconda/Miniconda environment is highly recommended. Other ways to install LungUtils are possible but here the installation procedure is explained based on a conda install. After installing Anaconda/Miniconda
 execute the following steps:
 
 - Create a new Anaconda environment based on the [`environment.yml`](./environment.yml) file:
@@ -54,7 +54,7 @@ conda env create -f environment.yml
 
 - Activate your newly created environment:
 ```
-conda activate pyskel
+conda activate lung_utils
 ```
 
 - Initialize all submodules
@@ -67,7 +67,7 @@ git submodule update --init --recursive
 git submodule --quiet foreach --recursive pip install -e .
 ```
 
-- Install all PySkel requirements with:
+- Install all LungUtils requirements with:
 ```
 pip install -e .
 ```
@@ -81,18 +81,18 @@ Now you are up and running 🎉
 
 ## Execution
 
-### Execute PySkel
+### Execute LungUtils
 
-To execute PySkel either run
+To execute LungUtils either run
 
 ```
-pyskel
+lung_utils
 ````
 
-to execute PySkel with the provided exemplary config or use
+to execute LungUtils with the provided exemplary config or use
 
 ```
-pyskel --config_file_path ../path/to/config.yaml
+lung_utils --config_file_path ../path/to/config.yaml
 ````
 
 to utilize your own externally provided config file. Therein, all necessary configurations can be found.
@@ -110,7 +110,7 @@ pytest
 To locally create the documentation from the provided docstrings simply run
 
 ```
-pdoc --html --output-dir docs src/pyskel
+pdoc --html --output-dir docs src/lung_utils
 ```
 
 ## Dependency Management

environment.yml

@@ -1,4 +1,4 @@
-name: pyskel
+name: lung_utils
 channels:
   - conda-forge
   - nodefaults

pyproject.toml

@@ -5,10 +5,10 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "PySkel"
+name = "LungUtils"
 version = "1.0"
-authors = [{ name = "David Rudlstorfer" }]
-maintainers = [{ name = "David Rudlstorfer" }]
+authors = [{ name = "Maxi Ludwig" }]
+maintainers = [{ name = "Maxi Ludwig" }]
 description = "A quick start Python skeleton with many amenities"
 readme = "README.md"
 license = {file = "LICENSE.md"}
@@ -20,13 +20,13 @@ dynamic = ["dependencies"]
 
 [tool.setuptools.packages.find]
 where = ["src"]
-include = ["pyskel"]
+include = ["lung_utils"]
 
 [tool.setuptools.dynamic]
 dependencies = { file = ["requirements.txt"] }
 
 [project.scripts]
-pyskel = "pyskel.main:main"
+lung_utils = "lung_utils.main:main"
 
 ## Tools
 
@@ -46,8 +46,8 @@ relative_files = true
 profile = "black"
 line_length = 79
 filter_files = true
-src_paths = ["src/pyskel/", "tests/"]
+src_paths = ["src/lung_utils/", "tests/"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=90 --cov=src/pyskel/ --cov-append"
+addopts = "-p pytest_cov --cov-report=term --cov-report=html --cov-fail-under=90 --cov=src/lung_utils/ --cov-append"

requirements.in

@@ -1,4 +1,4 @@
-# This file contains all the requirements for PySkel
+# This file contains all the requirements for LungUtils
 
 # dependencies from conda environment.yml
 numba==0.59.1

src/pyskel/core/example.py

@@ -1,4 +1,4 @@
-"""Exemplary function to be executed within PySkel."""
+"""Exemplary function to be executed within LungUtils."""
 
 
 def exemplary_function(a: float, b: float) -> float:

src/pyskel/core/run.py

@@ -1,17 +1,17 @@
-"""Runner which executes the main routine of PySkel."""
+"""Runner which executes the main routine of LungUtils."""
 
 import logging
 import time
 from typing import Any
 
-from pyskel.core.example import exemplary_function
-from pyskel.core.utilities import RunManager
+from lung_utils.core.example import exemplary_function
+from lung_utils.core.utilities import RunManager
 
-log = logging.getLogger("pyskel")
+log = logging.getLogger("lung_utils")
 
 
-def run_pyskel(config: Any) -> None:
-    """General run procedure of PySkel.
+def run_lung_utils(config: Any) -> None:
+    """General run procedure of LungUtils.
 
     Args:
         config (Any): Munch type object containing all configs for current

src/pyskel/core/utilities.py

@@ -1,4 +1,4 @@
-"""Utilities for PySkel main routine."""
+"""Utilities for LungUtils main routine."""
 
 import logging
 import os
@@ -7,29 +7,29 @@
 import yaml
 from pytoda.logger import log_full_width, print_header, setup_logging
 
-log = logging.getLogger("pyskel")
+log = logging.getLogger("lung_utils")
 
 
 class RunManager:
-    """Helper functions to manage a PySkel run."""
+    """Helper functions to manage a LungUtils run."""
 
     def __init__(self, config):
 
         self.config = config
 
     def init_run(self) -> None:
-        """Set up PySkel run including logger."""
+        """Set up LungUtils run including logger."""
 
         setup_logging(
             self.config.general.log_to_console,
             self.config.general.log_file,
             self.config.general.output_directory,
             self.config.general.sim_name,
-            "pyskel",
+            "lung_utils",
         )
 
         print_header(
-            title="PySkel",
+            title="LungUtils",
             description="General Python Skeleton",
         )
 

src/pyskel/main.py

@@ -1,15 +1,15 @@
-"""Main routine of PySkel."""
+"""Main routine of LungUtils."""
 
 import argparse
 import os
 
 import yaml
 from munch import munchify
-from pyskel.core.run import run_pyskel
+from lung_utils.core.run import run_lung_utils
 
 
 def main() -> None:
-    """Call PySkel runner with config.
+    """Call LungUtils runner with config.
 
     Raises:
         RuntimeError: If provided config is not a valid file.
@@ -20,21 +20,21 @@ def main() -> None:
         "-cfp",
         help="Path to config file.",
         type=str,
-        default="src/pyskel/main_example_config.yaml",
+        default="src/lung_utils/main_example_config.yaml",
     )
     args = parser.parse_args()
 
     if not os.path.isfile(args.config_file_path):
         raise RuntimeError(
-            "Config file not found! PySkel can not be executed!"
+            "Config file not found! LungUtils can not be executed!"
         )
 
     # load config and convert to simple namespace for easier access
     with open(args.config_file_path, "r") as file:
         config = munchify(yaml.safe_load(file))
 
-    # execute pyskel
-    run_pyskel(config)
+    # execute lung_utils
+    run_lung_utils(config)
 
 
 if __name__ == "__main__":  # pragma: no cover

src/pyskel/main_example_config.yaml

@@ -1,5 +1,5 @@
 general:
   output_directory: output
   sim_name: test_sim
-  log_file: pyskel.log
+  log_file: lung_utils.log
   log_to_console: true

tests/pyskel/core/test_example.py

@@ -1,6 +1,6 @@
 """Test example."""
 
-from pyskel.core.example import exemplary_function
+from lung_utils.core.example import exemplary_function
 
 
 def test_exemplary_function() -> None: