Adding set-up files to repo

.github/workflows/deploy.yaml

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+name: Deploy to GitHub Pages
+
+permissions:
+  contents: write
+  pages: write
+
+on:
+  push:
+    branches: [ "main", "master" ]
+  workflow_dispatch:
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps: [uses: fastai/workflows/quarto-ghp@master]

.github/workflows/test.yaml

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+name: CI
+on:  [workflow_dispatch, pull_request, push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps: [uses: fastai/workflows/nbdev-ci@master]

.gitignore

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+#dev
+# NOTE: For .gitignore, order matters. The last match wins. meaning if you want to ignore a folder but keep something in the folder, first ignore the folder, then unignore the file.
+.venv
+
+token
+# input/output is designed as a generic folder for input files if the config isn't adjusted. Because of this we want to ensure it's documented out. As it'll be an empty folder a .gitkeep file is used for git to maintain the structure.
+input/*
+!input/.gitkeep
+output/*
+!output/.gitkeep
+# The config folder is intended to keep multiple program configs, these are sensitive to the system, a default is included for people to work off of while the others are hidden
+config/*
+# If you are using pypi integration
+.pypirc
+
+_proc/
+# The following files ignored are part of a standard python project with minor additions
+_docs/
+
+*.bak
+.gitattributes
+.last_checked
+.gitconfig
+*.bak
+*.log
+*~
+~*
+_tmp*
+tmp*
+tags
+*.pkg
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+*.swp
+
+# osx generated files
+.DS_Store
+.DS_Store?
+.Trashes
+ehthumbs.db
+Thumbs.db
+.idea
+
+# pytest
+.pytest_cache
+
+# tools/trust-doc-nbs
+docs_src/.last_checked
+
+# symlinks to fastai
+docs_src/fastai
+tools/fastai
+
+# link checker
+checklink/cookies.txt
+
+# .gitconfig is now autogenerated
+.gitconfig
+
+# Quarto installer
+.deb
+.pkg
+
+# Quarto
+.quarto

LICENSE

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+The MIT License (MIT)
+Copyright © 2023 Statens Serum Institut
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

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+include settings.ini
+include LICENSE
+include CONTRIBUTING.md
+include README.md
+recursive-exclude * __pycache__
+include bifrost_bridge/config/config.default.env
+include bifrost_bridge/config/config.default.yaml

README.md

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+# bifrost_bridge
+
+
+<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
+
+This file will become your README and also the index of your
+documentation.
+
+## Developer Guide
+
+If you are new to using `nbdev` here are some useful pointers to get you
+started.
+
+### Install bifrost_bridge in Development mode
+
+``` sh
+# make sure bifrost_bridge package is installed in development mode
+$ pip install -e .
+
+# make changes under nbs/ directory
+# ...
+
+# compile to have changes apply to bifrost_bridge
+$ nbdev_prepare
+```
+
+## Usage
+
+### Installation
+
+Install latest from the GitHub
+[repository](https://github.com/$GIT_USER_NAME/bifrost_bridge):
+
+``` sh
+$ pip install git+https://github.com/$GIT_USER_NAME/bifrost_bridge.git
+```
+
+or from [conda](https://anaconda.org/$GIT_USER_NAME/bifrost_bridge)
+
+``` sh
+$ conda install -c $GIT_USER_NAME bifrost_bridge
+```
+
+or from [pypi](https://pypi.org/project/bifrost_bridge/)
+
+``` sh
+$ pip install bifrost_bridge
+```
+
+### Documentation
+
+Documentation can be found hosted on this GitHub
+[repository](https://github.com/$GIT_USER_NAME/bifrost_bridge)’s
+[pages](https://$GIT_USER_NAME.github.io/bifrost_bridge/). Additionally
+you can find package manager specific guidelines on
+[conda](https://anaconda.org/$GIT_USER_NAME/bifrost_bridge) and
+[pypi](https://pypi.org/project/bifrost_bridge/) respectively.
+
+## How to use
+
+Fill me in please! Don’t forget code examples:
+
+``` python
+1+1
+```
+
+    2

bifrost_bridge/__init__.py

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+__version__ = "0.0.1"

bifrost_bridge/_modidx.py

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+# Autogenerated by nbdev
+
+d = { 'settings': { 'branch': 'main',
+                'doc_baseurl': '/bifrost_bridge',
+                'doc_host': 'https://$GIT_USER_NAME.github.io',
+                'git_url': 'https://github.com/$GIT_USER_NAME/bifrost_bridge',
+                'lib_path': 'bifrost_bridge'},
+  'syms': { 'bifrost_bridge.core': { 'bifrost_bridge.core.cli': ('core.html#cli', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.get_config': ('core.html#get_config', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.get_samplesheet': ('core.html#get_samplesheet', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.hello_world': ('core.html#hello_world', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.set_env_variables': ('core.html#set_env_variables', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.show_project_env_vars': ( 'core.html#show_project_env_vars',
+                                                                                    'bifrost_bridge/core.py')},
+            'bifrost_bridge.hello_world': { 'bifrost_bridge.hello_world.cli': ('hello_world.html#cli', 'bifrost_bridge/hello_world.py'),
+                                            'bifrost_bridge.hello_world.hello_two_world': ( 'hello_world.html#hello_two_world',
+                                                                                            'bifrost_bridge/hello_world.py')}}}

bifrost_bridge/config/config.default.env

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+# environmental (ENV) variables. These are written as BIFROST_BRIDGE_VARIABLENAME=VALUE to avoid conflicts with other ENV variables. 
+# Using the standard template these values can be overwritten by:
+# - defining BIFROST_BRIDGE_CONFIG_FILE pointing to a similar file with a subset of values
+# - setting the values as environmental variables.
+# The priority goes env variables > config file > default file.
+# The all configs other than config.default.env are in .gitignore
+# All .env config files should have an associated .yaml config file with it which the program interacts with.
+
+# NOTE: remember if referencing another ENV var as a variable it needs to be defined first
+
+# If more structured variables are needed use config.default.yaml or another of your own creation
+# This file path is stored as CORE_CONFIG_FILE when overriding
+# It is commented out because of the default use case, but should be included for all non default cases.
+# CORE_YAML_CONFIG_FILE=
+CORE_PROJECT_VARIABLE_PREFIX=BIFROST_BRIDGE_
+# For testing purposes
+CORE_TEST_VAR="Test"
+
+# Example variable please exchange with relevant variables
+BIFROST_BRIDGE_INPUT_DIR=./input
+BIFROST_BRIDGE_OUTPUT_DIR=./output
+BIFROST_BRIDGE_OUTPUT_FILE=${BIFROST_BRIDGE_OUTPUT_DIR}/output.txt
+BIFROST_BRIDGE_USER_INPUT_NAME=Kim
+

bifrost_bridge/config/config.default.yaml

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+# When accessing this in the code you'll work with it as a dict.
+# ENV variables will be replaced with their values. This is done with the envyaml package that is in the code template `load_config`.
+# By convention all variables for the project should have the BIFROST_BRIDGE_* prefix.
+# e.g
+# name: ${BIFROST_BRIDGE_NAME}
+example:
+    input:
+        name: ${BIFROST_BRIDGE_USER_INPUT_NAME}
+        alternative_name: Lee