Added a documentation system.

README.md

 This project tries and test approaches that might lead to an improved architecture for NOMAD (XT).
 
-## Getting started
+## Generate the docs (and continue there)
 
-### Install the legacy NOMAD submoduels.
-This has to be done differently in the future. For no init the submodules and checkout
-working branches/tags:
-- submodules/parsers/parser-vasp master
-- submodules/python-common master
-- submodules/nomad-meta-info 1.6.0
-
-To checkout a tag use:
-```
-git fetch --all --tags --prune
-git checkout tags/1.6.0 -b 1.6.0
-```
-
-`pip install -r requirements` in `python-common`, and `pip install -e .` in `python-common` and
-`parsers/parser-vasp`. Futhermore, there are some dependency issues in `python-commons` requirments.
-
-### Install the python in your own virtual environment.
-
-```
-pip install -r requirements.txt
-pip install -e .
-```
-
-### Run dev infrastructure with docker.
-You can do it with or without the ELK stack.
-
-To run is without (default):
-```
-cd ./infrastructure
-docker-compose build
-sh up-wo-elk.sh
-```
-
-To run with ELK, enable `logstash` in nomad.config:logstash, and start the docker compose with
+First, clone this repo:
 ```
-docker-compose up
+git clone git@gitlab.mpcdf.mpg.de:mscheidg/nomad-xt.git
+cd nomad-xt
 ```
-You can reach the Kibana with [localhost:5601](http://localhost:5601).
-The index prefix for logs is `logstash-`.
 
-Optionally register the infrastructue minio host to the minio client (mc).
+Second, create and source your own virtual python environment:
 ```
-mc config host add minio http://localhost:9007 AKIAIOSFODNN7EXAMPLE wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY
+pip install virtualenv
+virtualenv -p `which phyton3` .pyenv
+source .pyenv/bin/activate
 ```
 
-### Run the celery worker (should be moved to docker TODO)
-
+Third, install the documentation system [sphinx](http://www.sphinx-doc.org/en/master/index.html):
 ```
-celery -A nomad.processing worker -l info
+pip install sphinx
+pip install recommonmark
 ```
-You can use different debug level (e.g. switch `info` to `debug`)
 
-Use watchdog during development. Install (i.e. [fixed](https://github.com/gorakhargosh/watchdog/issues/330) version fo MacOS)
+Forth, generate the documentation:
 ```
-pip install git+https://github.com/gorakhargosh/watchdog.git
+cd docs
+make html
 ```
 
-Now use this to auto relead worker:
+Conintue with reading the documentation for further setup and contribution guidelines:
 ```
-watchmedo auto-restart -d ./nomad -p '*.py' -- celery worker -l info -A nomad.processing
-```
-
-### Run tests.
+cd .build/html
+python -m SimpleHTTPServer .build -p 8888
 ```
-python tests/test_files.py
-```
-
-### Generate the documentation
-
-Install [pdoc](https://pypi.org/project/pdoc/) if necessary, and run this from the project root:
-```
-pdoc --html --html-dir=./build/docs --overwrite nomad
-```
-
-Do serve the current docs via HTTP during development, run
-```
-pdoc --http --http-port 8080
-```
-and open [http://localhost:8080/nomad](http://localhost:8080/nomad).
-
-We will probably move to Sphynx at an apropriate moment.
-
-## Contributing
-
-### Code quality
-
-- Use an IDE (e.g. [vscode](https://code.visualstudio.com/)) to enforce code [formatting and linting](https://code.visualstudio.com/docs/python/linting).
-- There is a style guide to python. Write [pep-8](https://www.python.org/dev/peps/pep-0008/) compliant python code. An exception is the line cap at 79, which can be broken but keep it 90-ish.
-- Use docstrings and document any *public* API of each submodule (e.g. python file). Public meaning API that is exposed to other submodules (i.e. other python files). Keep docstrings compliant to [pep-257](https://www.python.org/dev/peps/pep-0257/). Use sphynx references a lot!
-- Be [pythonic](https://docs.python-guide.org/writing/style/) and watch [this](https://www.youtube.com/watch?v=wf-BqAjZb8M).
-- The project structure is according to [this](https://docs.python-guide.org/writing/structure/) guide. Keep it!
-- Test the public API of each submodule (i.e. python file)
-
-
-
+Open [http://localhost:8888/html/setup.html](http://localhost:8888/html/setup.html) in
+your browser.

docs/.gitignore

+.build/
+.static/
\ No newline at end of file

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = NOMAD
+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)
\ No newline at end of file

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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 recommonmark.transform import AutoStructify
+
+sys.path.insert(0, os.path.abspath('../nomad'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'NOMAD-XT'
+copyright = '2018, the NOMAD developers'
+author = 'the NOMAD developers'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- 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 = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.napoleon'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['.templates']
+
+source_parsers = {
+   '.md': 'recommonmark.parser.CommonMarkParser',
+}
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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 = ['.build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- 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 = 'alabaster'
+
+# 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 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'NOMADdoc'
+
+
+# -- 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': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (master_doc, 'NOMAD-XT.tex', 'NOMAD-XT Documentation',
+     'the NOMAD developers', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'nomad', 'NOMAD-XT Documentation',
+     [author], 1)
+]
+
+
+# -- 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 = [
+    (master_doc, 'NOMAD-XT', 'NOMAD-XT Documentation',
+     author, 'NOMAD-XT', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# Enably sphinx specifc markdown features
+def setup(app):
+    app.add_config_value('recommonmark_config', {
+        'enable_auto_doc_ref': True,
+        'enable_eval_rst': True
+    }, True)
+    app.add_transform(AutoStructify)

docs/contributing.md

+# Contributing
+
+The are some *rules* or better strong *guidelines*
+
+- Use an IDE (e.g. [vscode](https://code.visualstudio.com/)) or otherwise automatically
+enforce code [formatting and linting](https://code.visualstudio.com/docs/python/linting).
+
+- There is a style guide to python. Write [pep-8](https://www.python.org/dev/peps/pep-0008/)
+compliant python code. An exception is the line cap at 79, which can be broken but keep it 90-ish.
+
+- Test the public API of each submodule (i.e. python file)
+
+- Be [pythonic](https://docs.python-guide.org/writing/style/) and watch
+[this](https://www.youtube.com/watch?v=wf-BqAjZb8M).
+
+- Document any *public* API of each submodule (e.g. python file). Public meaning API that
+is exposed to other submodules (i.e. other python files).
+
+- Use google [docstrings](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
+
+- Add your docstrings to the sphinx documentation in `docs`. Use .md, follow the example.
+Markdown in sphix is supported via [recommonmark](https://recommonmark.readthedocs.io/en/latest/index.html#autostructify)
+and [AutoStructify](http://recommonmark.readthedocs.io/en/latest/auto_structify.html)
+
+- The project structure is according to [this](https://docs.python-guide.org/writing/structure/)
+guide. Keep it!

docs/index.rst

+Welcome to NOMAD's documentation!
+=================================
+
+This project tries and test approaches that might lead to an improved architecture for NOMAD (XT).
+
+.. toctree::
+   :maxdepth: 2
+
+   setup
+   contributing
+   modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=.build
+set SPHINXPROJ=NOMAD
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/modules.md

+# Modules
+
+## Files
+```eval_rst
+.. automodule:: nomad.files
+```

docs/setup.md

+# Setup
+
+### Install the legacy NOMAD submoduels.
+This has to be done differently in the future. For no init the submodules and checkout
+working branches/tags:
+- submodules/parsers/parser-vasp master
+- submodules/python-common master
+- submodules/nomad-meta-info 1.6.0
+
+To checkout a tag use:
+```
+git fetch --all --tags --prune
+git checkout tags/1.6.0 -b 1.6.0
+```
+
+`pip install -r requirements` in `python-common`, and `pip install -e .` in `python-common` and
+`parsers/parser-vasp`. Futhermore, there are some dependency issues in `python-commons` requirments.
+
+### Install the python in your own virtual environment.
+
+```
+pip install -r requirements.txt
+pip install -e .
+```
+
+### Run dev infrastructure with docker.
+You can do it with or without the ELK stack.
+
+To run is without (default):
+```
+cd ./infrastructure
+docker-compose build
+sh up-wo-elk.sh
+```
+
+To run with ELK, enable `logstash` in nomad.config:logstash, and start the docker compose with
+```
+docker-compose up
+```
+You can reach the Kibana with [localhost:5601](http://localhost:5601).
+The index prefix for logs is `logstash-`.
+
+Optionally register the infrastructue minio host to the minio client (mc).
+```
+mc config host add minio http://localhost:9007 AKIAIOSFODNN7EXAMPLE wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY
+```
+
+### Run the celery worker (should be moved to docker TODO)
+
+```
+celery -A nomad.processing worker -l info
+```
+You can use different debug level (e.g. switch `info` to `debug`)
+
+Use watchdog during development. Install (i.e. [fixed](https://github.com/gorakhargosh/watchdog/issues/330) version fo MacOS)
+```
+pip install git+https://github.com/gorakhargosh/watchdog.git
+```
+
+Now use this to auto relead worker:
+```
+watchmedo auto-restart -d ./nomad -p '*.py' -- celery worker -l info -A nomad.processing
+```
+
+### Run tests.
+```
+python tests/test_files.py
+```

nomad/files.py

@@ -13,11 +13,30 @@
 # limitations under the License.
 
 """
-This module (and its main class :class:`Files`) represents an abstraction for NOMAD
-file storage system.
+NOMAD's file storage implementation
+===================================
 
-Responsibilities: create, access files; create, receive, notify on, and access uploads.
+This file storage abstraction currently uses the object storage API
+http://minio.io to manage and organize files. Object storage
+organizes files in *buckets/ids*, with small amounts of *buckets* and virtually
+unlimited numbers of *ids*. *Ids* can contain delimiters like `/` to mimic
+filesystem structure. There is a 1024 utf-8 character limit on *id* length.
+
+The file storage is organized in multiple buckets:
+
+* *uploads*: used for uploaded user code input/output archives. Currently only .zip files \
+are suported
+
+Presigned URLs
+--------------
+Users (or GUI clients) can upload files directly to the object storage system. To avoid
+authentication hassly, presigned URLs can be created that can be used directly to safely
+*PUT* files.
+
+.. autofunction:: nomad.files.get_presigned_upload_url
+.. autofunction:: nomad.files.create_curl_upload_cmd
 """
+import sys
 import os
 from os.path import join
 from zipfile import ZipFile, BadZipFile
@@ -31,24 +50,52 @@ import nomad.config as config
 
 logger = logging.getLogger(__name__)
 
-_client = Minio('%s:%s' % (config.minio.host, config.minio.port),
-                access_key=config.minio.accesskey,
-                secret_key=config.minio.secret,
-                secure=False)
+_client = None
+
+if _client is None and 'sphinx' not in sys.modules:
+    _client = Minio('%s:%s' % (config.minio.host, config.minio.port),
+                    access_key=config.minio.accesskey,
+                    secret_key=config.minio.secret,
+                    secure=False)
+
+    # ensure all neccessary buckets exist
+    try:
+        _client.make_bucket(bucket_name=config.s3.uploads_bucket)
+        logger.info("Created uploads bucket with name %s." % config.s3.uploads_bucket)
+    except minio.error.BucketAlreadyOwnedByYou:
+        logger.debug(
+            "Uploads bucket with name %s already existed." % config.s3.uploads_bucket)
 
-# ensure all neccessary buckets exist
-try:
-    _client.make_bucket(bucket_name=config.s3.uploads_bucket)
-    logger.info("Created uploads bucket with name %s." % config.s3.uploads_bucket)
-except minio.error.BucketAlreadyOwnedByYou:
-    logger.debug("Uploads bucket with name %s already existed." % config.s3.uploads_bucket)
 
+def get_presigned_upload_url(upload_id: str) -> str:
+    """Generates a presigned upload URL.
 
-def get_presigned_upload_url(upload_id):
+    Presigned URL allows users (and their client programs) to safely *PUT*
+    a single file without further authorization or API to the *uploads* bucket
+    using the given ``upload_id``. Example usages for presigned URLs include
+    browser based uploads or simple *curl* commands (see also :func:`create_curl_upload_cmd`).
+
+    Args:
+        upload_id: The upload id for the uploaded file.
+
+    Returns:
+        The presigned URL string.
+    """
     return _client.presigned_put_object(config.s3.uploads_bucket, upload_id)
 
 
 def create_curl_upload_cmd(presigned_url, file_dummy='<ZIPFILE>'):
+    """Creates a readymade curl command for uploading.
+
+    Args:
+        presigned_url: The presigned URL to base the command on.
+
+    Kwargs:
+        file_dummy: A placeholder for the file that the user/client has to replace.
+
+    Returns:
+        The curl shell command with correct method, url, headers, etc.
+    """
     headers = 'Content-Type: application/octet-steam'
     return 'curl -X PUT "%s" -H "%s" -F file=@%s' % (presigned_url, headers, file_dummy)