Initial commit

.gitignore

+*.so
+MANIFEST
+*.py[cod]
+*.egg-info
+.DS_Store
+_build
+_generate
+build

README.rst

+The jppy Python package
+=======================
+
+.. image:: https://git.km3net.de/km3py/jppy/badges/master/pipeline.svg
+    :target: https://git.km3net.de/km3py/jppy/pipelines
+
+.. image:: https://git.km3net.de/km3py/jppy/badges/master/coverage.svg
+    :target: https://km3py.pages.km3net.de/jppy/coverage
+
+.. image:: https://examples.pages.km3net.de/km3badges/docs-latest-brightgreen.svg
+    :target: https://km3py.pages.km3net.de/jppy
+
+This software provides access to the PDF functionalities in Jpp. It depends on
+some Jpp headers (no Jpp compilation needed) and on the ROOT ``TMath`` (a
+compiled ROOT installation is needed).
+
+**Note:** Beware that this package is in the development phase, so the API will
+change until version ``1.0.0`` is released!
+
+Installation
+============
+
+Run ``make`` to compile the Python modules::
+
+  make
+
+Example
+=======
+
+Here is an example how to play around with muon PDFs using the ``jppy`` module::
+
+    In [1]: import jppy
+
+    In [2]: jppy.pdf.JMuonPDF?
+    Docstring:      <no docstring>
+    Init docstring: __init__(self: jppy.pdf.JMuonPDF, file_descriptor: str, TTS: float, number_of_points: int = 25, epsilon: float = 1e-10) -> None
+    File:           ~/dev/pybind/jppy.pdf.cpython-37m-x86_64-linux-gnu.so
+    Type:           pybind11_type
+    Subclasses:
+
+    In [3]:
+    Do you really want to exit ([y]/n)? n
+
+    In [3]: muon_pdf = jppy.pdf.JMuonPDF("/pbs/throng/km3net/src/Jpp/master/data/J%p.dat", 0)
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J1p.dat... OK
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J2p.dat... OK
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J3p.dat... OK
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J4p.dat... OK
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J5p.dat... OK
+    loading input from file /pbs/throng/km3net/src/Jpp/master/data/J6p.dat... OK
+    adding PDFs... OK
+
+    In [4]: muon_pdf.calculate?
+    Docstring: calculate(self: jppy.pdf.JMuonPDF, E: float, R: float, theta: float, phi: float, t1: float) -> JTOOLS::JResultPDF<double>
+    Type:      method
+
+    In [5]: result = muon_pdf.calculate(10, 5, 0, 0, 23)
+
+    In [6]: result.f
+    Out[6]: 0.0015357848280127355
+
+    In [7]: result.fp
+    Out[7]: -2.228096911939611e-05
+
+    In [8]: result.v
+    Out[8]: 0.02490276362751662
+
+    In [9]: result.V
+    Out[9]: 0.1164929687159807
+
+    In [10]: %timeit muon_pdf.calculate(10, 5, 0, 0, 23)
+    2.13 µs ± 242 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)

docs/Makefile

+# 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
+help:
+	@echo "Please use \`make <target>' where <target> 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 "  applehelp  to make an Apple Help Book"
+	@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)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+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."
+
+.PHONY: qthelp
+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/jppy.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/jppy.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/jppy"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/jppy"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: latex
+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)."
+
+.PHONY: latexpdf
+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."
+
+.PHONY: latexpdfja
+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."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+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)."
+
+.PHONY: info
+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."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+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."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/conf.py

+# -*- coding: utf-8 -*-
+#
+# jppy documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb 26 00:29:33 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
+
+# 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 = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+]
+
+autosummary_generate = True
+
+# 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 encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'jppy'
+copyright = u'2020, Tamas Gal'
+author = u'Tamas Gal'
+
+# 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 = u'3.0.0'
+# The full version, including alpha/beta/rc tags.
+release = u'3.0.0'
+
+# 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
+
+# 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
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = 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 = '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 themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> 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 <link> 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
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
+#html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# Now only 'ja' uses this config value
+#html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'jppydoc'
+
+# -- 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, 'jppy.tex', u'jppy Documentation',
+     u'Tamas Gal', '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 = [
+    (master_doc, 'jppy', u'jppy Documentation',
+     [author], 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 = [
+    (master_doc, 'jppy', u'jppy Documentation',
+     author, 'jppy', 'Jpp Python Package',
+     'Science'),
+]
+
+# 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
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}

docs/index.rst

+jppy Documentation
+============================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   jppy
+

docs/jppy.rst

+.. automodule:: jppy

pyproject.toml

+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]

setup.py

+import os
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
+import sys
+import setuptools
+import subprocess as sp
+
+__version__ = '3.0.0'
+
+
+class get_pybind_include(object):
+    """Helper class to determine the pybind11 include path
+
+    The purpose of this class is to postpone importing pybind11
+    until it is actually installed, so that the ``get_include()``
+    method can be invoked. """
+    def __init__(self, user=False):
+        self.user = user
+
+    def __str__(self):
+        import pybind11
+        return pybind11.get_include(self.user)
+
+
+def get_root_flags(kind):
+    """Retrieve the root flags for kind='inc' or kind'='lib'"""
+    return sp.Popen(["root-config", "--{}dir".format(kind)],
+                    stdout=sp.PIPE).communicate()[0].strip().decode()
+
+
+def get_jpp_include():
+    return os.path.join(os.getenv("JPP_DIR"), "software")
+
+
+ext_modules = [
+    Extension(
+        'jppy.pdf',
+        ['src/pdf.cc'],
+        include_dirs=[
+            get_pybind_include(),
+            get_pybind_include(user=True),
+            get_root_flags("inc"),
+            get_jpp_include()
+        ],
+        library_dirs=[get_root_flags("lib")],
+        libraries=["MathCore"],
+        language='c++')
+]
+
+# Populating the __init__.py with submodule imports, so that one can import
+# the package and use the submodules directly with the dot-sytax.
+with open("jppy/__init__.py", "w") as fobj:
+    for module in ext_modules:
+        fobj.write("from . import {}\n".format(module.name.split('.')[1]))
+
+
+try:
+    with open("README.rst") as fh:
+        long_description = fh.read()
+except UnicodeDecodeError:
+    long_description = "jppy - Jpp Python Package"
+
+
+# As of Python 3.6, CCompiler has a `has_flag` method.
+# cf http://bugs.python.org/issue26689
+def has_flag(compiler, flagname):
+    """Return a boolean indicating whether a flag name is supported on
+    the specified compiler.
+    """
+    import tempfile
+    with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
+        f.write('int main (int argc, char **argv) { return 0; }')
+        try:
+            compiler.compile([f.name], extra_postargs=[flagname])
+        except setuptools.distutils.errors.CompileError:
+            return False
+    return True
+
+
+def cpp_flag(compiler):
+    """Return the -std=c++[11/14/17] compiler flag.
+
+    The newer version is prefered over c++11 (when it is available).
+    """
+    flags = ['-std=c++17', '-std=c++14', '-std=c++11']
+
+    for flag in flags:
+        if has_flag(compiler, flag): return flag
+
+    raise RuntimeError('Unsupported compiler -- at least C++11 support '
+                       'is needed!')
+
+
+class BuildExt(build_ext):
+    """A custom build extension for adding compiler-specific options."""
+    c_opts = {
+        'msvc': ['/EHsc'],
+        'unix': [],
+    }
+    l_opts = {
+        'msvc': [],
+        'unix': [],
+    }
+
+    if sys.platform == 'darwin':
+        darwin_opts = ['-stdlib=libc++', '-mmacosx-version-min=10.7']
+        c_opts['unix'] += darwin_opts
+        l_opts['unix'] += darwin_opts
+
+    def build_extensions(self):
+        ct = self.compiler.compiler_type
+        opts = self.c_opts.get(ct, [])
+        link_opts = self.l_opts.get(ct, [])
+        if ct == 'unix':
+            opts.append('-DVERSION_INFO="%s"' %
+                        self.distribution.get_version())
+            opts.append(cpp_flag(self.compiler))
+            if has_flag(self.compiler, '-fvisibility=hidden'):
+                opts.append('-fvisibility=hidden')
+        elif ct == 'msvc':
+            opts.append('/DVERSION_INFO=\\"%s\\"' %
+                        self.distribution.get_version())
+        for ext in self.extensions:
+            ext.extra_compile_args = opts
+            ext.extra_link_args = link_opts
+        build_ext.build_extensions(self)
+
+
+setup(
+    name='jppy',
+    version=__version__,
+    author='Tamas Gal',
+    author_email='tgal@km3net.de',
+    url='https://git.km3net.de/km3py/jppy',
+    description='Jpp Python Package',
+    packages=["jppy"],
+    long_description=long_description,
+    ext_modules=ext_modules,
+    install_requires=['pybind11>=2.4'],
+    setup_requires=['pybind11>=2.4'],
+    cmdclass={'build_ext': BuildExt},
+    zip_safe=False,
+)

src/pdf.cc

+#include <pybind11/pybind11.h>
+
+#include "JLang/JException.hh"
+#include "JTools/JCollection.hh"
+#include "JTools/JMap.hh"
+#include "JTools/JGridMap.hh"
+#include "JTools/JMapList.hh"
+#include "JTools/JSpline.hh"
+#include "JTools/JPolint.hh"
+#include "JTools/JElement.hh"
+#include "JTools/JResult.hh"
+#include "JPhysics/JPDFTable.hh"
+#include "JPhysics/JPDFTypes.hh"
+#include "JMath/JZero.hh"
+
+
+/**
+ * Auxiliary data structure for muon PDF.
+ */
+struct JMuonPDF_t {
+
+  typedef JPP::JSplineFunction1D<JPP::JSplineElement2S<double, double>, 
+				 JPP::JCollection, 
+				 JPP::JResultPDF<double> >         JFunction1D_t;
+
+  typedef JPP::JMAPLIST<JPP::JPolint1FunctionalMap,
+			JPP::JPolint0FunctionalGridMap,
+			JPP::JPolint0FunctionalGridMap>::maplist   JPDFMaplist_t;
+  typedef JPP::JPDFTable<JFunction1D_t, JPDFMaplist_t>             JPDF_t;
+  typedef JFunction1D_t::result_type                               result_type;
+
+
+  /**
+   * Constructor.
+   *
+   * The PDF file descriptor should contain the wild card character JPHYSICS::WILD_CARD.\n
+   * The <tt>TTS</tt> corresponds to the additional time smearing applied to the PDFs.
+   *
+   * \param  fileDescriptor     PDF file descriptor
+   * \param  TTS                TTS [ns]
+   * \param  numberOfPoints     number of points for Gauss-Hermite integration of TTS
+   * \param  epsilon            precision        for Gauss-Hermite integration of TTS
+   */
+  JMuonPDF_t(const std::string& fileDescriptor,
+	     const double       TTS,
+	     const int          numberOfPoints = 25,
+	     const double       epsilon        = 1.0e-10)
+  {
+    using namespace std;
+    using namespace JPP;
+
+    const JPDFType_t pdf_t[] = { DIRECT_LIGHT_FROM_MUON,
+				 SCATTERED_LIGHT_FROM_MUON,
+				 DIRECT_LIGHT_FROM_EMSHOWERS,
+				 SCATTERED_LIGHT_FROM_EMSHOWERS,
+				 DIRECT_LIGHT_FROM_DELTARAYS,
+				 SCATTERED_LIGHT_FROM_DELTARAYS };
+
+    const  int N = sizeof(pdf_t) / sizeof(pdf_t[0]);
+    
+    JPDF_t pdf[N];
+
+    const JPDF_t::JSupervisor supervisor(new JPDF_t::JDefaultResult(zero));
+
+    for (int i = 0; i != N; ++i) {
+
+      const string file_name = getFilename(fileDescriptor, pdf_t[i]);
+
+      cout << "loading input from file " << file_name << "... " << flush;
+
+      pdf[i].load(file_name.c_str());
+
+      pdf[i].setExceptionHandler(supervisor);
+
+      cout << "OK" << endl;
+    }
+
+    // Add PDFs
+
+    cout << "adding PDFs... " << flush;
+
+    pdfA = pdf[1];  pdfA.add(pdf[0]);
+    pdfB = pdf[3];  pdfB.add(pdf[2]);
+    pdfC = pdf[5];  pdfC.add(pdf[4]);
+
+    cout << "OK" << endl;
+
+    if        (TTS > 0.0) {
+
+      cout << "bluring PDFs... " << flush;
+
+      pdfA.blur(TTS, numberOfPoints, epsilon);
+      pdfB.blur(TTS, numberOfPoints, epsilon);
+      pdfC.blur(TTS, numberOfPoints, epsilon);
+
+      cout << "OK" << endl;
+
+    } else if (TTS < 0.0) {
+
+      THROW(JValueOutOfRange, "Illegal value of TTS [ns]: " << TTS); 
+    }
+  }
+
+
+  /**
+   * Get PDF.
+   *
+   * The orientation of the PMT should be defined according this <a href="https://common.pages.km3net.de/jpp/JPDF.PDF">documentation</a>.\n
+   * In this, the zenith and azimuth angles are limited to \f[\left[0, \pi\right]\f].
+   *
+   * \param  E                  muon energy at minimum distance of approach [GeV]
+   * \param  R                  minimum distance of approach [m]
+   * \param  theta              PMT zenith  angle [rad]
+   * \param  phi                PMT azimuth angle [rad]
+   * \param  t1                 arrival time relative to Cherenkov hypothesis [ns]
+   * \return                    hypothesis value
+   */
+  result_type calculate(const double E,
+			 const double R,
+			 const double theta,
+			 const double phi,
+			 const double t1) const
+  {
+    using namespace JPP;
+
+    result_type h1 = (pdfA(R, theta, phi, t1)                               +
+		      pdfB(R, theta, phi, t1) * E                           +
+		      pdfC(R, theta, phi, t1) * getDeltaRaysFromMuon(E));
+
+    // safety measures
+
+    if (h1.f <= 0.0) {
+      h1.f  = 0.0;
+      h1.fp = 0.0;
+    }
+          
+    if (h1.v <= 0.0) {
+      h1.v  = 0.0;
+    }
+          
+    return h1;
+  }
+
+  JPDF_t pdfA;   //!< PDF for minimum ionisong particle
+  JPDF_t pdfB;   //!< PDF for average energy losses
+  JPDF_t pdfC;   //!< PDF for delta-rays
+};
+
+
+/**
+   Python bindings.
+ */
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(pdf, m) {
+    m.doc() = "PDF utilities";
+    py::class_<JMuonPDF_t>(m, "JMuonPDF")
+        .def(py::init<const std::string &, double, int, double>(),
+             py::arg("file_descriptor"),
+             py::arg("TTS"),
+             py::arg("number_of_points") = 25,
+             py::arg("epsilon") = 1e-10)
+        .def("calculate", &JMuonPDF_t::calculate,
+             py::arg("E"),
+             py::arg("R"),
+             py::arg("theta"),
+             py::arg("phi"),
+             py::arg("t1")
+            ),
+    py::class_<JTOOLS::JResultPDF<double>>(m, "JResultPDF")
+        .def(py::init<double, double, double, double>(),
+             py::arg("f"),
+             py::arg("fp"),
+             py::arg("v"),
+             py::arg("V"))
+        .def_readonly("f", &JTOOLS::JResultPDF<double>::f)
+        .def_readonly("fp", &JTOOLS::JResultPDF<double>::fp)
+        .def_readonly("v", &JTOOLS::JResultPDF<double>::v)
+        .def_readonly("V", &JTOOLS::JResultPDF<double>::V);
+}