Merge pull request #79 from ethanwhite/add-docs

Add package documentation

.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+import os
+import sys
+
+# -- Add current path to PATH for autodoc
+
+curr_path = os.path.dirname(os.path.abspath(os.path.expanduser(__file__)))
+sys.path.insert(0, os.path.join(curr_path, '..'))
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'offlinedatasci'
+copyright = '2023, Virnaliz Cruz, Abhishek Dasgupta, Colin Sauze, Jannetta Steyn, Ethan P. White'
+author = 'Virnaliz Cruz, Abhishek Dasgupta, Colin Sauze, Jannetta Steyn, Ethan P. White'
+release = 'v0.2.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['myst_parser',
+              'sphinx.ext.autodoc']
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'furo'
+html_static_path = []

docs/getting-started.md

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+# Getting started
+
+## Command line interface
+
+### Installing everything
+
+If you want to download and configure everything use `install all` and pass it the location store files:
+
+```sh
+offlinedatasci install all \<path\>
+```
+
+### Installing individual components
+
+You can download and configure the different components separately:
+
+* Python: `offlinedatasci install python \<path\>`
+* Python packages: `offlinedatasci install python_libraries \<path\>`
+* R: `offlinedatasci install r \<path\>`
+* RStudio: `offlinedatasci install rstudio \<path\>`
+* R packages: `offlinedatasci install minicran \<path\>`
+* Lessons: `offlinedatasci install lessons \<path\>`
+
+### Managing R and Python packages
+
+By default offlinedatasci creates local package mirrors of the most common data science packages.
+You can add additional packages yourself using `add-packages`, then language `r` or `python`, and the name of the packages to install:
+
+```sh
+offlinedatasci add-packages r package1 package2 ... \<path\>`
+```
+
+```sh
+offlinedatasci add-packages python package1 package2 ... \<path\>`
+```
+
+## Python interface
+
+Coming soon!

docs/index.rst

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+.. offlinedatasci documentation master file, created by
+   sphinx-quickstart on Sat Nov 18 22:08:21 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to offlinedatasci's documentation!
+==========================================
+
+offlinedatsci is a tool for supporting teaching and doing data science in internet-limited environments.
+It helps you download and configure common tools for teaching and doing data science without an internet connection.
+This includes:
+
+* Installers for data science languages: Currently R and Python
+* Installers for common data science IDEs: Currently RStudio
+* Partial, data science focused, local mirrors of package repositories: Currently CRAN (for R) and PyPI (for Python)
+* Locally browseable clones of data science teaching websites: Currently Data Carpentry, Software Carpentry, and Library Carpentry
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+   getting-started
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.md

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+# Installation
+
+## Basic installation
+
+offlinedatasci is available for Python >=3.6 and can be installed using `pip`:
+
+```
+pip install DeepForest
+```
+
+## External dependencies
+
+offlinedatasci relies on two external dependencies:
+
+1. R - for for creating the partial CRAN mirror to deliver R packages
+2. wget - for downloading lesson material
+
+### wget
+
+#### Linux
+
+wget is available by default on almost all Linux distributions.
+
+#### macOS
+
+The easiest to install wget on macOS is using homebrew:
+
+```
+brew install wget
+```
+
+If you are using conda for Python environment management you can also install it using `conda`/`mamba`:
+
+```
+conda install wget
+```
+
+or
+
+```
+mamba install wget
+```
+
+#### Windows
+
+Download the appropriate wget executable from https://eternallybored.org/misc/wget/ and place it on your PATH.

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

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+sphinx==7.2.6
+furo==2023.09.10
+myst_parser==2.0.0

docs/source/modules.rst

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+offlinedatasci
+==============
+
+.. toctree::
+   :maxdepth: 4
+
+   offlinedatasci

docs/source/offlinedatasci.rst

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+offlinedatasci package
+======================
+
+Submodules
+----------
+
+offlinedatasci.cli module
+-------------------------
+
+.. automodule:: offlinedatasci.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+offlinedatasci.main module
+--------------------------
+
+.. automodule:: offlinedatasci.main
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: offlinedatasci
+   :members:
+   :undoc-members:
+   :show-inheritance: