MDANSE 2.0.0a1__tar.gz

MDANSE-2.0.0a1/AUTHORS

@@ -0,0 +1,18 @@
+MDANSE project has been created by:
+
+* Eric Pellegrini
+
+MDANSE source code is currently developed by
+
+* Eric Pellegrini
+* Maciej Bartkowiak
+* Chi Cheng
+* Sanghamitra Mukhopadhyay
+
+MDANSE former contributors:
+
+* Bachir Aoun
+* Gael Goret
+* Remi Perenon
+* Rastislav Turanyi
+

MDANSE-2.0.0a1/Doc/_static/custom.css

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+.math {
+    text-align: left;
+}
+.eqno {
+    float: right;
+}

MDANSE-2.0.0a1/Doc/conf_api.py

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+# MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+# ------------------------------------------------------------------------------------------
+# Copyright (C)
+# 2015- Eric C. Pellegrini Institut Laue-Langevin
+# BP 156
+# 6, rue Jules Horowitz
+# 38042 Grenoble Cedex 9
+# France
+# pellegrini[at]ill.fr
+# goret[at]ill.fr
+# aoun[at]ill.fr
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+""" 
+Created on Mar 30, 2015
+
+@author: Gael Goret and Eric C. Pellegrini
+"""
+
+# -- 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.viewcode",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.inheritance_diagram",
+    "sphinx.ext.pngmath",
+]  # ,'rst2pdf.pdfbuilder']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix of source filenames.
+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 = "MDANSE"
+copyright = "2015, Gael Goret, Bachir Aoun and Eric C. Pellegrini"
+
+# 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 = "1.0"
+# The full version, including alpha/beta/rc tags.
+release = "1.0"
+
+html_logo = "_static/mdanse_logo.png"
+
+inheritance_graph_attrs = dict(size='""')
+
+inheritance_graph_attrs = dict(rankdir="TB", size='""')
+
+inheritance_node_attrs = dict(color="lightblue", style="filled")
+
+# The following is uncommented only in Windows CI/CD
+# graphviz_dot = r'C:\Miniconda\envs\mdanse\Library\bin\graphviz\dot.exe'
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# -- Options for HTML output ---------------------------------------------------
+
+html_sidebars = {"**": ["localtoc.html", "sourcelink.html", "searchbox.html"]}
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = "nature"
+html_theme_options = {"sidebarwidth": 250}  # , 'nosidebar':True}
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "MDANSE_doc"
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+    (
+        "index",
+        "MDANSE.tex",
+        "MDANSE Documentation",
+        "Gael Goret \\& Eric C. Pellegrini",
+        "manual",
+    ),
+]
+
+pdf_documents = [
+    ("index", "MDANSE", "MDANSE Documentation", "Gael Goret & Eric C. Pellegrini"),
+]
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ("index", "MDANSE", "MDANSE Documentation", "Gael Goret & Eric C. Pellegrini"),
+]
+
+# 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",
+        "MDANSE",
+        "MDANSE Documentation",
+        "Gael Goret & Eric C. Pellegrini",
+        "MDANSE",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
+]
+
+# List of directories, relative to source directory, that shouldn't be searched for source files.
+exclude_patterns = ["Externals"]
+
+members_to_watch = ["class"]
+
+from MDANSE.Framework.Jobs.IJob import IJob
+
+klsNames = [kls.__name__ for kls in IJob.indirect_subclasses()]
+
+
+def flag_onthefly(app, what, name, obj, options, lines):
+    if getattr(obj, "__name__", None) in klsNames:
+        lines.extend(obj.build_doc().splitlines())
+
+    if what in members_to_watch:
+        # modify the docstring so the rendered output is highlights the omission
+        if lines:
+            lines.insert(0, "")
+            lines.insert(0, ":Description:")
+            lines.insert(0, "")
+            lines.insert(0, ".. inheritance-diagram:: %s" % name.split(".")[-1])
+            lines.insert(0, "")
+            lines.insert(0, "**Inheritance-diagram:**")
+            lines.insert(0, "")
+
+
+def setup(app):
+    app.connect("autodoc-process-docstring", flag_onthefly)

MDANSE-2.0.0a1/Doc/conf_help.py

@@ -0,0 +1,155 @@
+# MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+# ------------------------------------------------------------------------------------------
+# Copyright (C)
+# 2015- Eric C. Pellegrini Institut Laue-Langevin
+# BP 156
+# 6, rue Jules Horowitz
+# 38042 Grenoble Cedex 9
+# France
+# pellegrini[at]ill.fr
+# goret[at]ill.fr
+# aoun[at]ill.fr
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 2.1 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+""" 
+Created on Mar 30, 2015
+
+@author: Gael Goret and Eric C. Pellegrini
+"""
+
+# 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.graphviz",
+    "sphinx.ext.pngmath",
+]  # ,'rst2pdf.pdfbuilder']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix of source filenames.
+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 = "MDANSE"
+copyright = "2015, Gael Goret & Eric C. Pellegrini"
+
+# 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 = "1.0"
+# The full version, including alpha/beta/rc tags.
+release = "1.0"
+
+html_logo = "_static/mdanse_logo.png"
+
+inheritance_graph_attrs = dict(size='""')
+
+inheritance_graph_attrs = dict(rankdir="TB", size='""')
+
+inheritance_node_attrs = dict(color="lightblue", style="filled")
+
+# 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 = "default"
+html_theme_options = {"sidebarwidth": 250}
+
+html_show_copyright = False
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "MDANSE_doc"
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+    (
+        "index",
+        "MDANSE.tex",
+        "MDANSE Documentation",
+        "Gael Goret & Eric C. Pellegrini",
+        "manual",
+    ),
+]
+
+pdf_documents = [
+    ("index", "MDANSE", "MDANSE Documentation", "Gael Goret & Eric C. Pellegrini"),
+]
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_patterns = ["Externals"]
+
+members_to_watch = ["class"]
+
+from MDANSE.Framework.Jobs.IJob import IJob
+
+klsNames = [kls.__name__ for kls in IJob.indirect_subclasses()]
+
+
+def flag_onthefly(app, what, name, obj, options, lines):
+    if getattr(obj, "__name__", None) in klsNames:
+        lines.extend(obj.build_doc().splitlines())
+
+    if what in members_to_watch:
+        # modify the docstring so the rendered output is highlights the omission
+        if lines:
+            lines.insert(0, "")
+            lines.insert(0, ":Description:")
+            lines.insert(0, "")
+
+
+exclusions = (
+    "__weakref__",
+    "__doc__",
+    "__module__",
+    "__dict__",
+)
+
+
+def autodoc_skip_member(app, what, name, obj, skip, options):
+    if what in ["method", "attribut", "function", "exception"]:
+        return True
+
+    if name in exclusions:
+        return True
+
+    if what in ["class"]:
+        if name is not "__doc__":
+            return True
+
+    return skip
+
+
+def setup(app):
+    app.connect("autodoc-skip-member", autodoc_skip_member)
+    app.connect("autodoc-process-docstring", flag_onthefly)