Adding project scaffolding

.coveragerc

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+[run]
+source=deeprootgen
+omit=tests/*
+
+[report]
+skip_empty = true
+fail_under = 0

.dockerignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+*.db
+*.pkl
+*.cache
+.hydra
+mlruns
+*.xml
+slurm-*.out
+.python-version

.env

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+# Project 
+COMPOSE_PROJECT_NAME=deep-root-gen
+APP_VERSION=0.1.0
+GITHUB_CONTAINER_REPO=ghcr.io/jbris/${COMPOSE_PROJECT_NAME}
+
+# Postgres
+DB_NAME=deeprootgen
+DB_USER=user
+DB_PASSWORD=password
+
+# MLFlow
+MLFLOW_BACKEND_STORE_URI=postgresql://${DB_USER}:${DB_PASSWORD}@postgres:5432/${DB_NAME}
+MLFLOW_TRACKING_URI=http://mlflow:5000
+
+# Prefect
+PREFECT_API_DATABASE_CONNECTION_URL=postgresql+asyncpg://${DB_USER}:${DB_PASSWORD}@postgres:5432/prefect
+
+# Minio
+MINIO_ROOT_USER=$DB_USER
+MINIO_ROOT_PASSWORD=$DB_PASSWORD
+MINIO_ACCESS_KEY=$DB_USER
+MINIO_SECRET_KEY=$DB_PASSWORD
+AWS_ACCESS_KEY_ID=$DB_USER
+AWS_SECRET_ACCESS_KEY=$DB_PASSWORD

.flake8

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+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
+exclude = .venv

.gitattributes

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+# Common settings that generally should always be used with your language specific settings
+
+# Auto detect text files and perform LF normalization
+*          text=auto
+
+#
+# The above will handle all files NOT found below
+#
+
+# Documents
+*.bibtex   text diff=bibtex
+*.doc      diff=astextplain
+*.DOC      diff=astextplain
+*.docx     diff=astextplain
+*.DOCX     diff=astextplain
+*.dot      diff=astextplain
+*.DOT      diff=astextplain
+*.pdf      diff=astextplain
+*.PDF      diff=astextplain
+*.rtf      diff=astextplain
+*.RTF      diff=astextplain
+*.md       text diff=markdown
+*.mdx      text diff=markdown
+*.tex      text diff=tex
+*.adoc     text
+*.textile  text
+*.mustache text
+*.csv      text eol=crlf
+*.tab      text
+*.tsv      text
+*.txt      text eol=lf
+*.sql      text eol=lf
+*.epub     diff=astextplain
+
+# Graphics
+*.png      binary
+*.jpg      binary
+*.jpeg     binary
+*.gif      binary
+*.tif      binary
+*.tiff     binary
+*.ico      binary
+# SVG treated as text by default.
+*.svg      text
+# If you want to treat it as binary,
+# use the following line instead.
+# *.svg    binary
+*.eps      binary
+
+# Scripts
+*.env.*    text eol=lf
+*.dockerignore  text eol=lf
+*.bash     text eol=lf
+*.fish     text eol=lf
+*.sh       text eol=lf
+*.zsh      text eol=lf
+# These are explicitly windows files and should use crlf
+*.bat      text eol=crlf
+*.cmd      text eol=crlf
+*.ps1      text eol=crlf
+
+# Serialisation
+*.json     text
+*.toml     text
+*.xml      text
+*.yaml     text eol=lf
+*.yml      text eol=lf
+
+# Archives
+*.7z       binary
+*.gz       binary
+*.tar      binary
+*.tgz      binary
+*.zip      binary
+
+# Text files where line endings should be preserved
+*.patch    -text
+
+#
+# Exclude files from exporting
+#
+
+.gitattributes export-ignore
+.gitignore     export-ignore
+.gitkeep       export-ignore
+
+# Basic .gitattributes for a python repo.
+
+# Source files
+# ============
+*.pxd    text diff=python
+*.py     text diff=python
+*.py3    text diff=python
+*.pyw    text diff=python
+*.pyx    text diff=python
+*.pyz    text diff=python
+*.pyi    text diff=python
+
+# Binary files
+# ============
+*.db     binary
+*.p      binary
+*.pkl    binary
+*.pickle binary
+*.pyc    binary export-ignore
+*.pyo    binary export-ignore
+*.pyd    binary
+
+# Jupyter notebook
+*.ipynb  text eol=lf
+
+# Note: .db, .p, and .pkl files are associated
+# with the python modules ``pickle``, ``dbm.*``,
+# ``shelve``, ``marshal``, ``anydbm``, & ``bsddb``
+# (among others).

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.