Add basic sphinx API documentation

.gitlab-ci.yml

@@ -10,3 +10,21 @@ unittest:
   script:
     - pip install -r requirements.txt
     - python setup.py test
+
+doc:
+  image: python:3.7
+  script:
+    - pip install -r requirements.txt
+    - pip install sphinx
+    - cd doc
+    - sphinx-apidoc -o . ../nnfwtbn
+    - make html
+    - cp -a _build/html ../_public
+  artifacts:
+    paths:
+      - _public
+    expire_in: 1 mos
+
+  
+ 
+

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = nnfwtbn
+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

doc/api_reference.rst

+*************
+API reference
+*************
+
+.. autoclass:: nnfwtbn.Cut
+   :members:
+   :special-members:
+
+.. autoclass:: nnfwtbn.Process
+   :members:
+   :special-members:
+
+
+.. autoclass:: nnfwtbn.Variable
+   :members:
+   :special-members:
+
+.. autoclass:: nnfwtbn.variable.BlindingStrategy
+   :members:
+   :special-members:
+
+.. autoclass:: nnfwtbn.RangeBlindingStrategy
+   :members:
+   :special-members:
+
+.. automodule:: nnfwtbn.plot
+	:members:
+

doc/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
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'nnfwtbn'
+copyright = '2019, Frank Sauerburger'
+author = 'Frank Sauerburger'
+
+# 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.doctest',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# 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'
+
+autodoc_default_options = {
+    'members': None,
+    'special-members': None,
+    'exclude-members': '__weakref__'
+}
+
+# -- 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'
+
+# 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 = 'nnfwtbndoc'
+
+
+# -- 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, 'nnfwtbn.tex', 'nnfwtbn Documentation',
+     'Frank Sauerburger', '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, 'nnfwtbn', 'nnfwtbn 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, 'nnfwtbn', 'nnfwtbn Documentation',
+     author, 'nnfwtbn', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

doc/index.rst

+.. nnfwtbn documentation master file, created by
+   sphinx-quickstart on Tue Jun 25 19:59:43 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to nnfwtbn's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Advanced topics
+
+   api_reference
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

nnfwtbn/cut.py

@@ -10,6 +10,7 @@ class Cut:
     Cuts store the condition to be applied to a dataframe. New cut objects
     accept all event by default. The selection can be limited by passing a
     lambda to the constructor. 
+
     >>> sel_all = Cut()
     >>> sel_pos = Cut(lambda df: df.value > 0)
 
@@ -34,6 +35,7 @@ class Cut:
 
     Cuts can be used to build logical expression using the bitwise and (&), or
     (|), xor (^) and not (~).
+
     >>> sel_even = Cut(lambda df: df.value % 2 == 0)
     >>> sel_pos_even = sel_pos & sel_even
     >>> sel_pos_even(df)
@@ -45,6 +47,7 @@ class Cut:
     Name: value, dtype: bool
 
     Equivalently, cuts support logical operations directly using lambdas.
+
     >>> sel_pos_even_lambda = sel_pos & (lambda df: df.value % 2 == 0)
     >>> sel_pos_even_lambda(df)
     0    False

nnfwtbn/plot.py

@@ -34,7 +34,7 @@ class HistogramFactory:
         """
 
 
-def type_to_histtype(type):
+def _type_to_histtype(type):
     """
     Returns the matplotlib histogram type for a given process plotting type.
 
@@ -133,7 +133,7 @@ def hist(dataframe, variable, bins, *stacks, data=None, selection=None,
                                 bins=bins, range=range,
                                 bottom=bottom,
                                 label=process.label,
-                                histtype=type_to_histtype(process.type),
+                                histtype=_type_to_histtype(process.type),
                                 weights=weight(dataframe[sel(dataframe)]))
             bottom += n 
 
@@ -142,14 +142,16 @@ def hist(dataframe, variable, bins, *stacks, data=None, selection=None,
     axes.legend(frameon=False)
 
     if variable.unit is not None:
-        axes.set_xlabel("%s in %s" % (variable.name, variable.unit))
+        axes.set_xlabel("%s in %s" % (variable.name, variable.unit),
+                        horizontalalignment='right', x=0.95)
     else:
-        axes.set_xlabel(variable.name)
+        axes.set_xlabel(variable.name, horizontalalignment='right', x=0.95)
 
     if equidistant_bins:
-        axes.set_ylabel("Events / %g %s" % (bins[1] - bins[0], variable.unit))
+        axes.set_ylabel("Events / %g %s" % (bins[1] - bins[0], variable.unit),
+                        horizontalalignment='right', y=0.95)
     else:
-        axes.set_ylabel("Events / bin")
+        axes.set_ylabel("Events / bin", horizontalalignment='right', y=0.95)
     
 
 

nnfwtbn/process.py

@@ -40,6 +40,7 @@ class Process:
 
         Any other Keyword argument is passed directly to the matplotlib upon
         plotting.
+
         >>> Process("VBF", lambda d: d.is_VBFH, linestyle="--")
         <Process 'VBF': (func)>
         """