From 3b49cd37c71f252ba2f8ccc3b67eb0e8482fd4c8 Mon Sep 17 00:00:00 2001 From: Sam Ireland Date: Fri, 3 Jun 2022 02:22:12 +0100 Subject: [PATCH] Start docs --- docs/Makefile | 20 ++++++++++ docs/make.bat | 35 ++++++++++++++++++ docs/source/changelog.rst | 78 +++++++++++++++++++++++++++++++++++++++ docs/source/conf.py | 55 +++++++++++++++++++++++++++ docs/source/index.rst | 19 ++++++++++ 5 files changed, 207 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/changelog.rst create mode 100644 docs/source/conf.py create mode 100644 docs/source/index.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# 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) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@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 diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst new file mode 100644 index 0000000..62017b7 --- /dev/null +++ b/docs/source/changelog.rst @@ -0,0 +1,78 @@ +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. \ No newline at end of file diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..ff7d53a --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,55 @@ +# 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"] \ No newline at end of file diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..a775682 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,19 @@ +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