diff --git a/.gitignore b/.gitignore index a029fef..8d62638 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,7 @@ node_modules *~ .DS_Store build +_build dist env.sh # ignore config file at the top-level of the repo diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..787897d --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,177 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/everware.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/everware.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/everware" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/everware" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +xml: + $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml + @echo + @echo "Build finished. The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/being_everware_compatible.md b/docs/being_everware_compatible.md new file mode 100644 index 0000000..0488da4 --- /dev/null +++ b/docs/being_everware_compatible.md @@ -0,0 +1,48 @@ +Being everware compatible +================ + +To make your existing repository work with `everware` it needs to contain a `Dockerfile` that describes how to create the image your code will run in. + +You can think of [`docker`](https://www.docker.com/) images as extremely lightweight virtual machines. [Find out more about docker](https://www.docker.com/whatisdocker). + +For most users the simplest way to make their repository `everware`-ready is to create a `Dockerfile` in their repositories top level directory which simply inherits `FROM` an existing `docker` image that works with `everware`. You can make small modifications to existing images to install extra libraries or pieces of software. If this is you, read about how to [use an existing docker image](). + +If you are an experienced `docker` user or have really specific needs you can also start from scratch. However this means you need to take care of making the image you create compatible with `everware`. If this is you, read about how to [start from scratch](https://github.com/everware/everware/wiki/Being-everware-compatible#building-your-own-image-from-scratch). + + +## Using an existing docker image + +A lot of different `docker` containers already exist, so your chances are good that you do not have to create one from scratch for your repository. + +The most basic `Dockerfile` to get your repository to work with `everware` is: + +``` +FROM everware/base +``` + +This is extremely barebones but brings with it all the infrastructure that is needed. Probably you want to extend your image with a few useful bits of software. Check out our [`everware/container-tools`](https://github.com/everware/basic-container) repository and the [`README.md`](https://github.com/everware/container-tools/blob/master/README.md) therein for ideas on how to do that. + +You can also use an image which has more software pre-installed. The [`everware-dimuon-example`](https://github.com/everware/everware-dimuon-example) repository uses a [`Dockerfile`](https://github.com/everware/everware-dimuon-example/blob/master/Dockerfile) which takes a base image (`anaderi/rep-jupyterhub`) and extends it by installing two additional python libraries. This is convenient as that docker image already contains a large number of libraries and all the `everware` specific setup steps. + +Check out the `anaderi/jupyterhub` [`Dockerfile`](https://hub.docker.com/r/anaderi/rep-jupyterhub/~/dockerfile/) to see the long list of software installed by default. + +If you do not need extra setup steps for your code to run you can use `anaderi/rep-jupyterhub` as the basis for your repository by creating a `Dockerfile` in the top level directory of your repository with the following contents: + +``` +FROM anaderi/rep-jupyterhub +MAINTAINER John Doe +``` + +This is enough to make your repository `everware`-ready. + + +## Building your own image from scratch + +If you are more experienced with `docker` or have special requirements then you can start from scratch. However this means you need to make sure your `docker` image contains a few extra things to make it work with `everware`. When the container is started it needs to launch a custom `singleuser.py` script which comes from `jupyterhub` (this takes care of setting up routing, etc) as well as cloning the `git` repository. + +For details of how to setup a container from the Ubuntu base image check out the [`everware/container-tools`](https://github.com/everware/basic-container) repository and the [`README.md`](https://github.com/everware/container-tools/blob/master/README.md). The repository contains two images: `everware/base` and `everware/science-python`. These are not meant for production use but to document the process of creating your own containers from scratch and then building on top of them. + +> The [`everware/container-tools`](https://github.com/everware/container-tools) repository +> contains examples, documentation, and tools for constructing and populating your containers. + +The `everware/base` container does just the bare minimum to be compatible with `everware`. As a result it does not contain any special libraries. It does install python 2 and 3. Python 3 is required for `jupyterhub` which is what `everware` uses as the web-interface. \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..52e8146 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,261 @@ +# -*- coding: utf-8 -*- +# +# everware documentation build configuration file, created by +# sphinx-quickstart on Thu Jun 2 16:48:13 2016. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import os +from recommonmark.parser import CommonMarkParser + +# 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. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# 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'] + +source_parsers = {'.md' : CommonMarkParser} + +# The suffix of source filenames. +source_suffix = ['.rst', '.md'] + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'everware' +copyright = u'2016, The Everware Contributers' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = 'none' +# The full version, including alpha/beta/rc tags. +release = 'none' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +#keep_warnings = False + + +# -- 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 = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +#html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'everwaredoc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ('index', 'everware.tex', u'everware Documentation', + u'The Everware Contributers', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'everware', u'everware Documentation', + [u'The Everware Contributers'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'everware', u'everware Documentation', + u'The Everware Contributers', 'everware', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +#texinfo_no_detailmenu = False diff --git a/docs/everware_compliant_notebooks_gallery.md b/docs/everware_compliant_notebooks_gallery.md new file mode 100644 index 0000000..802d66b --- /dev/null +++ b/docs/everware_compliant_notebooks_gallery.md @@ -0,0 +1,11 @@ +Everware compliant notebooks gallery +==================================== +## Examples of runnable notebooks & environments we are aware of + +This is placeholder repo with single file to list examples you can explore: + + * https://github.com/everware/everware-dimuon-example -- Measuring the J/psi mass on CERN opendata + * https://github.com/betatim/everware-demo -- Showing off integration with the CERN IT infrastructure (xrootd, kerberos, ROOT6, CERNBox) + * https://github.com/yandexdataschool/flavours-of-physics-start -- ['Flavours of Physics'](https://www.kaggle.com/c/flavours-of-physics) @ Kaggle starter kit + * https://github.com/everware/everware-cpp-example -- Sample Macros from the ROOT Tutorials + * https://github.com/arogozhnikov/hep_ml -- High Energy Physics Machine Learning library (see `notebooks` folder) diff --git a/docs/faq.md b/docs/faq.md new file mode 100644 index 0000000..c683267 --- /dev/null +++ b/docs/faq.md @@ -0,0 +1,22 @@ +FAQ +==== +## Launching is so sloooooww! + +Be patient when you click launch. Depending on how complicated the docker image is to build or how large it is to download it might take a while before your container will launch. Be patient, don't click back, the webpage will auto refresh and redirect you once your container is ready. The next time you launch the same container it should be much quicker. + +If you created your own docker image, check out our [[advice for building docker containers|https://github.com/everware/everware/wiki/Being-everware-compatible]]. + + +## How can I ask a question or contact you? + +We have a [[chat room on gitter|https://gitter.im/everware/everware]] join us there with all your questions and comments. + + +## The control panel doesn't do anything + +When you click the "Control panel" button next to the "Logout" button it currently takes you to a page that let's you paste a github URL. Clicking launch there just takes me back to my original repository. We are working on fixing that in [[issue #27|https://github.com/everware/everware/issues/27]] + + +## Logging out and back in gives errors + +If you logout and directly log back in `everware` can get confused about what stage your docker container is in. So when you logout, spend 10s checking the news (or telling someone how amazing `everware` is) and then log back in. This is being addressed in [[issue #28|https://github.com/everware/everware/issues/28]] \ No newline at end of file diff --git a/docs/hosting_everware.md b/docs/hosting_everware.md new file mode 100644 index 0000000..bc3b925 --- /dev/null +++ b/docs/hosting_everware.md @@ -0,0 +1,3 @@ +Hosting Everware +================= +To host an everware instance follow the setup instructions in the [README.md](https://github.com/everware/everware/blob/master/README.md). \ No newline at end of file diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..2bf863b --- /dev/null +++ b/docs/index.md @@ -0,0 +1,31 @@ + +Welcome to everware's documentation! +==================================== + +There are three different kinds of `everware` users: + +1. I want to use code in a repository that is `everware`-ready +1. I want to make my own code `everware`-ready +1. I want to host my own `everware` instance + +The rest of this document deals with using a repository that is already `everware`-ready. Read [being everware compatible](being_everware_compatible.html) to learn how to make your code compatible with `everware`. To host your own instance of `everware` read: [hosting an everware instance](hosting_everware.html). + + +## Using an `everware` compatible repository + +You need two ingredients for this. + +The first ingredient you will need is a link to a `git` repository that is compatible with `everware`. If you do not have one, take a look at the [everware gallery](everware_compliant_notebooks_gallery.html). In this example we will use [everware-dimuon-example](https://github.com/everware/everware-dimuon-example). + +The second ingredient you will need is access to a running `everware` instance. There are a few public ones: + +* [https://everware.rep.school.yandex.net](https://everware.rep.school.yandex.net) (used in this example) + +Open [https://everware.rep.school.yandex.net](https://everware.rep.school.yandex.net) in a new browser window. Paste the URL of the `git` repository you want to try out ([everware-dimuon-example](https://github.com/everware/everware-dimuon-example)) on the webpage and click "Launch". This should clone the repository, build the environment, and connect you to it after a few seconds. You are now ready to explore the code and what it does. + +.. toctree:: + :maxdepth: 2 + + + +