Python packaging and distribution (#26)

* first pass at python packaging and distribution

* fix formatting

* fix email addresses for commit

* don't worry about it

* add index.rst files

* add max depth

* appropriate spacing

* 3 spaces is the right amount of space

* pull out the terminology section to its own document

* fixing headings

* Updated formatting and organization

* update formatting and logical progression

* make it make sense

* Fix headings

* Update based on reviewer comments and add clarity

docs/source/index.rst

@@ -7,5 +7,6 @@ Welcome to the LASP Developer's Guide!
    :maxdepth: 1
 
    licensing
+   programming_languages/index
    data_management/index
    workflows/index

docs/source/programming_languages/index.rst

@@ -0,0 +1,7 @@
+Programming Languages
+=====================
+
+.. toctree::
+   :maxdepth: 1
+
+   python/index

docs/source/programming_languages/python/index.rst

@@ -0,0 +1,8 @@
+Python
+=====================
+
+.. toctree::
+   :maxdepth: 1
+
+   terminology
+   packaging_and_distribution

docs/source/programming_languages/python/packaging_and_distribution.md

@@ -0,0 +1,185 @@
+> **Warning:** More information is needed to complete this guideline.
+
+# Python Packaging and Distribution
+Examples of Python packaging and distribution options and how to use them.
+
+## Purpose
+> **Warning** Need to add an explanation of how this guideline supports DS workflows, meets internal and external
+> policies, and aids in collaboration and our overall success
+
+## Options
+The options for Python packaging and distribution that we often see used at LASP are:
+- [PyPI](#packaging-for-pypi--pip-install-)
+- [Conda](#packaging-for-conda--conda-install-)
+
+## Packaging for PyPI (`pip install`)
+
+### PyPI resources:
+
+- [PyPI Help Page](https://pypi.org/help/)
+
+- [Setting up a PyPI account](https://pypi.org/account/register/)
+
+- [Getting a PyPI access token](https://pypi.org/help/#apitoken)
+
+
+### Built-In (`build` + `twine`)
+
+> **Warning**: Need to add introductory paragraph that summarizes Built-In
+
+#### How to use Built-In
+Python Packaging User Guide: https://packaging.python.org/en/latest/
+The link below is a fairly complete tutorial. There are also instructions there for using various other build tools:
+https://packaging.python.org/en/latest/tutorials/packaging-projects/
+
+#### Built-In resources
+
+- [Python Packaging User Guide](https://packaging.python.org/en/latest/)
+
+#### Setuptools Example – Library Package
+<details>
+  <summary>setup.py</summary>
+
+```
+"""
+Setup file for the science data processing pipeline.
+
+The only required fields for setup are name, version, and packages. Other fields to consider (from looking at other
+projects): keywords, include_package_data, requires, tests_require, package_data
+"""
+from setuptools import setup, find_packages
+
+# Reads the requirements file
+with open('requirements.txt') as f:
+    requirements = f.read().splitlines()
+
+setup(
+    name='my_py_library',
+    version='0.1.0',
+    author='Jane Doe, John Doe, This is just a str',
+    author_email='jane.doe@lasp.colorado.edu',
+    description='Science data processing pipeline for the instrument',
+    long_description=open('README.md', 'r').read(),  # Reads the readme file
+    python_requires='>=3.8, <4',
+    url='https://some-git.url',
+    classifiers=[
+        "Natural Language :: English",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: Astronomy",
+        "Programming Language :: Python :: 3.8",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: POSIX :: Linux",
+    ],
+    packages=find_packages(exclude=('tests', 'tests.*')),
+    package_data={
+        "my_py_library": [
+            "some_necessary_config_data.json",
+            "calibration_data/*"
+        ]
+    },
+    py_modules=['root_level_module_name',],
+    install_requires=requirements,
+    entry_points={
+        'console_scripts': [
+            'run-processing=my_py_library.cli:main',  # package.module:function
+        ]
+    }
+)
+```
+</details>
+
+### Poetry
+
+> **Warning**: Need to add introductory paragraph that summarizes Poetry
+
+[Poetry Build and Publish Docs](https://python-poetry.org/docs/cli/#build)
+
+How to Publish to PyPI from Poetry
+```
+poetry lock
+poetry install
+poetry version
+poetry build
+PYPI_USERNAME=__token__
+PYPI_TOKEN=<token-copied-from-pypi-account>
+poetry publish  # You will be prompted for your PyPI credentials if you don't provide the environment variables
+```
+
+#### Poetry Project Configuration Example – Library Package
+
+<details>
+  <summary>pyproject.toml</summary>
+
+  ```
+    # pyproject.toml
+    # See: https://python-poetry.org/docs/pyproject/
+
+    [tool.poetry]
+    name = "my_python_package"
+    version = "0.1.0"
+    description = "Science data processing library and applications for some instrument."
+    authors = [  # Alphabetical
+        "Jane Doe <jane.doe@lasp.colorado.edu>",
+        "John Doe <john.doe@lasp.colorado.edu>"
+    ]
+
+    # Configure private PyPI repo to download packages
+    [[tool.poetry.source]]
+    name = "lasp-pypi"  # This name will be used in the configuration to retrieve the proper credentials
+    url = "https://artifacts.pdmz.lasp.colorado.edu/repository/lasp-pypi/simple"  # URL used to download your private packages
+
+    # Dependency specification for core package
+    [tool.poetry.dependencies]
+    python = "^3.9"
+    astropy = "^4.2.1"
+    h5py = "^3.3.0"
+    numpy = "^1.21.0"
+    spiceypy = "^4.0.1"
+    lasp-packets = "1.2"
+    requests = "^2.26.0"
+    SQLAlchemy = "^1.4.27"
+    psycopg2 = "^2.9.2"
+    cloudpathlib = {extras = ["s3"], version = "^0.6.2"}
+
+    # Development dependencies
+    [tool.poetry.dev-dependencies]
+    pytest-cov = "^2.12.1"
+    pylint = "^2.9.3"
+    responses = "^0.14.0"
+    pytest-randomly = "^3.10.2"
+    moto = {extras = ["s3"], version = "^2.2.16"}
+
+    # Script entrypoints to put in installed bin directory
+    [tool.poetry.scripts]
+    sdp = 'my_python_package.cli:main'
+
+    # Poetry boilerplate
+    [build-system]
+    requires = ["poetry-core>=1.0.0"]
+    build-backend = "poetry.core.masonry.api"
+  ```
+</details>
+
+## Packaging for Conda (`conda install`)
+> **Warning**: Need a volunteer to expand on Conda
+
+### How to install and use Conda
+https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html
+
+> Conda Develop:
+> There is a conda subcommand called `conda develop`, but it is not actively maintained. The maintainers of
+conda recommend using `pip install` to install an editable package in development mode.
+> See: https://github.com/conda/conda-build/issues/1992
+
+## Useful Links
+Here are some helpful resources:
+
+- [Python Packaging User's Guide](https://packaging.python.org/en/latest/)
+- [The Hitchhiker's Guide to Python - Packaging your Code](https://docs.python-guide.org/shipping/packaging/)
+- [The Sheer Joy of Packaging](https://python-packaging-tutorial.readthedocs.io/en/latest/index.html)
+- [Package Python Projects the Proper Way with Poetry](https://hackersandslackers.com/python-poetry-package-manager/)
+- [Poetry Documentation](https://python-poetry.org/docs/)
+- [Setuptools Documentation](https://setuptools.pypa.io/en/latest/)
+- [Building conda packages from scratch](https://conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html)
+
+Credit: Content taken from a Confluence guide written by Gavin Medley

docs/source/programming_languages/python/terminology.md

@@ -0,0 +1,40 @@
+# Python Terminology
+
+Some Python terminology that a user might encounter, particularly when working through this Python guide.
+
+## Purpose
+Like all programming languages, Python has some terminology that is unique to it and it is helpful to have that language
+explained. This page may be updated over time so that it holds the most useful terminology to those that use this
+developer's guide.
+
+### Library Packages vs Applications vs Scripts
+
+Python is a highly flexible interpreted language. This means it's easy to get started, quick to write, and easy to run.
+Unfortunately, this also means it's very easy to write code that works in one context but not in others or code that is
+robust but isn't designed to be inherited.
+
+**Package**: A `python` package, intended for redistribution, containing objects that serve as building blocks for
+other developers to use. Examples are `numpy`, `pytest`, and `sqlalchemy`.
+
+> **Note** While most people think of a Python package as the above definition, a Python "package" is technically
+> any directory containing an `__init__.py` file.
+
+**Application**: A python project (which may or may not be a packaged distribution) that provides specific and possibly
+configurable functionality. Examples are Poetry, the AWS CLI, the Conda CLI, the Green Unicorn WSGI HTTP server, any
+Django "app".
+
+**Script**: Pretty much anything else written in Python. One could arguably say that a Script is just a trivial Application
+with little configuration or portability. Scripts are usually run with `python my_script.py argv`. They tend to be
+difficult to maintain, update, or distribute.
+
+**Packaging Tooling**: Not only managing a local environment, but also providing tooling for developing, building, and
+distributing python packages for other users. While Conda does support this use case (it's how one creates and
+distributes conda packages to `conda-forge`), Poetry and `setuptools` are much easier to develop with (for PyPI) and Poetry
+boasts a similar dependency resolver to Conda. One major drawback to Conda in packaging is that there is no notion of an
+"editable install" so the developer is forced to build and test end user functionality (e.g. script entrypoints) over
+and over instead of simply making code changes in place.
+
+## Useful Links
+Helpful links to additional resources on the topic
+
+Credit: Content taken from a Confluence guide written by Gavin Medley

guideline_template.md

@@ -13,4 +13,6 @@ An explanation of the options available for this guideline (could be one or more
 Detailed instructions or general guidance for implementation of the guideline
 
 ## Useful Links
-Helpful links to additional resources on the topic
+Helpful links to additional resources on the topic
+
+Credit: Content taken from a Confluence guide written by <add_name>