Start docs

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     = 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

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+@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/source/changelog.rst

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+Changelog
+---------
+
+Release 0.3
+~~~~~~~~~~~
+
+`3rd June, 2022`
+
+* Allow module-level run methods for directly running pipelines.
+* Allow for running pipelines with different Nextflow versions.
+* Imroved datetime parsing.
+* Simplified process execution parsing.
+* Fixed concatenation of process executions with no parentheses.
+* Tests now check compatability with different Nextflow versions.
+
+Release 0.2.2
+~~~~~~~~~~~~~
+
+`21st March, 2022`
+
+* Log outputs now have ANSI codes removed.
+
+Release 0.2.1
+~~~~~~~~~~~~~
+
+`19th February, 2022`
+
+* Execution polling now handles unready execution directory.
+* Better detection of failed process executions mid execution.
+
+
+Release 0.2
+~~~~~~~~~~~
+
+`14th February, 2022`
+
+* Added method for running while continuously polling pipeline execution.
+* Optimised process execution object creation from file state.
+
+Release 0.1.4
+~~~~~~~~~~~~~
+
+`12th January, 2022`
+
+* Pipeline command generation no longer applies quotes if there are already quotes.
+
+
+Release 0.1.3
+~~~~~~~~~~~~~
+
+`24th November, 2021`
+
+* Fixed Windows file separator issues.
+* Renamed NextflowProcess -> ProcessExecution.
+
+Release 0.1.2
+~~~~~~~~~~~~~
+
+`3rd November, 2021`
+
+* Better handling of missing Nextflow executable.
+
+Release 0.1.1
+~~~~~~~~~~~~~
+
+`29th October, 2021`
+
+* Renamed `nextflow_processes` to `process_executions`.
+* Added quotes around paths to handle spaces in paths.
+
+Release 0.1
+~~~~~~~~~~~~~
+
+`18th October, 2021`
+
+* Basic Pipeline object.
+* Basic Execution object.
+* Basic ProcessExecution object.

docs/source/conf.py

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+# 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
+# sys.path.insert(0, os.path.abspath("."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "nextflow.py"
+copyright = "2022, Sam Ireland"
+author = "Sam Ireland"
+
+# The full version, including alpha/beta/rc tags
+release = "0.3"
+
+
+# -- 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 = [
+]
+
+# 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 = "sphinx_rtd_theme"
+
+# 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/index.rst

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+nextflow.py
+===========
+
+nextflow.py is a Python wrapper around the Nextflow pipeline framework. It lets
+you run Nextflow pipelines from Python code.
+
+Example
+-------
+
+   >>> import nextflow
+   >>> pipeline = nextflow.Pipeline("main.nf")
+   >>> execution = pipeline.run(params={"param1": "123"})
+   >>> print(execution.status)
+
+Table of Contents
+-----------------
+
+.. toctree ::
+  changelog