Adds sphinx docs

docs/Makefile

+# 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   ?= poetry run sphinx-build
+SOURCEDIR     = source
+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/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+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

+sphinx
+myst_parser

docs/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).parent / ".." / ".."))
+import bitia
+
+print(bitia.__file__)
+
+# -- Project information -----------------------------------------------------
+
+project = "BiTIA"
+copyright = "2022, Subconscious Compute"
+author = "Subconscious Compute"
+
+# The full version, including alpha/beta/rc tags
+release = "0.0.1"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["myst_parser", "sphinx.ext.autodoc"]
+
+napoleon_google_docstring = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+# html_theme = "furo"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]

docs/source/developer.md

+## Developer guide
+
+
+
+### Testing
+
+
+#### Testing bitia inside official image
+
+```bash
+python tests/bitia_in_docker.py
+```

docs/source/examples.md

+# Example
+
+
+**Example 1**
+```bash
+bitia trim_galore --gzip --fastqc --max_n 2 --paired --length 50 SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz
+```
+This does the following :
+
+- Installs trim_galore on top of biarchlinux image in a docker container
+- mounts the current working directory to the container  so that all necessory files needed and input files `SRR11862696_1.fastq.gz` and `SRR11862696_2.fastq.gz` for the command to work is available inside the container.
+- Runs the command and returns the output to stdout
+
+**Example 2**
+ ```bash
+bitia pipeline.sh
+```
+for pipeline.sh:
+```
+#!/usr/bin/env bash
+
+fastqc *.gz
+
+for file in *_1.fastq.gz
+do
+   trim_galore --cores 8 --gzip --fastqc --max_n 2 --output_dir Trimmed_Data/ --paired $file ${file%_1.fastq.gz}_2.fastq.gz
+done
+
+hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa index
+```
+
+This does the following:
+- Extract all exeutables in the file - `fastqc`, `trim_galore`,`hisat2`
+- Extract all comments given in the file - `#!/usr/bin/env bash`
+- Extract all files that are given as input for commands and download them if not available by the given url.
+- Installs given executables in the docker container.
+- mounts the current working directory to the containern so that all necessory files needed and input files for the command to work is available inside the container.
+- Runs the command and returns the output to stdout.
\ No newline at end of file

docs/source/getting_started.md

+# Getting Started
+
+
+## Installation
+To get started with using BiTIA, you should [install Python] and make sure [python-pip] is installed with it on your system.
+
+[install Python]: https://realpython.com/installing-python/
+[python-pip]: https://pypi.org/project/pip/ 
+### Ensure you have a working pip
+
+As a first step, you should check that you have a working Python with pip
+installed. This can be done by running the following commands and making
+sure that the output looks similar.
+
+``` bash
+$ python --version
+Python 3.N.N
+$ pip --version
+pip X.Y.Z from ... (python 3.N.N)
+```
+If that worked, congratulations! You have a working pip in your environment.
+
+
+
+To Install **BiTIA** using pip:
+
+```bash
+$ python3 -m pip install bitia
+```
+

docs/source/index.md

+# Welcome to BiTIA's documentation!
+
+## BioInformatics Tool for Infrastructure Automation (BiTIA)
+
+BiTIA makes it easy to orchestrate the infrastructure required to run 
+complex bioinformatics pipelines. BiTIA plays well with existing pipeline
+solution such as snakement. [See some examples]
+
+[see some examples]: examples
+
+```{toctree}
+:hidden:
+getting_started
+developer
+```
+
+
+If you want to learn how to use BiTIA, check out the following resources:
+
+- [Getting Started](getting_started) 
+- [Features](features)
+
+
+```{eval-rst}
+.. automodule:: bitia
+
+
+