xcoll 0.3.6__py3-none-any.whl → 0.5.0__py3-none-any.whl

xcoll/scattering_routines/geant4/collimasim/CMakeLists.txt

@@ -0,0 +1,26 @@
+cmake_minimum_required(VERSION 3.17)
+SET(CMAKE_BUILD_TYPE Debug)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -g -O0")
+
+project(g4interface)
+
+add_subdirectory(lib/pybind11)
+
+set(SOURCE_DIR "src/collimasim")
+
+# The headers are in the source directory
+include_directories(${SOURCE_DIR})
+
+set(SOURCES ${SOURCE_DIR}/BDSPyATInterface.cpp
+            ${SOURCE_DIR}/BDSXtrackInterface.cpp
+            ${SOURCE_DIR}/BDSPyATInterface.hh
+            ${SOURCE_DIR}/BDSXtrackInterface.hh
+            ${SOURCE_DIR}/bindings.cpp)
+
+find_package(BDSIM REQUIRED HINTS $ENV{BDSIM})
+
+pybind11_add_module(g4interface ${SOURCES} "${SOURCE_DIR}/bindings.cpp")
+
+
+target_link_libraries(g4interface PRIVATE ${BDSIM_LIBRARIES})
+target_include_directories(g4interface PUBLIC ${BDSIM_INCLUDE_DIR})

xcoll/scattering_routines/geant4/collimasim/README.md

@@ -0,0 +1,21 @@
+# Collimasim
+
+Collimasim provides Python bindings to BDSIM (Geant4) in order to enable collimation studies in pure tracking codes
+
+## Requiremends
+ - BDSIM installed on the system
+ - python3
+ - CMake >3.17
+
+## Installation
+
+To isntall use:
+
+```bash
+git clone --recurse-submodules https://gitlab.cern.ch/anabramo/collimasim.git
+python -m pip install --user --editable ./
+```
+
+## Usage
+
+See tests/test.py for an example of how to use

xcoll/scattering_routines/geant4/collimasim/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+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)

xcoll/scattering_routines/geant4/collimasim/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+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% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

xcoll/scattering_routines/geant4/collimasim/docs/source/collimasim.rst

@@ -0,0 +1,10 @@
+.. _collimasim:
+
+==============
+ Collimasim
+==============
+
+.. automodule:: pyflusix
+    :members:
+    :undoc-members:
+    :show-inheritance:

xcoll/scattering_routines/geant4/collimasim/docs/source/conf.py

@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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 = 'collimasim'
+copyright = '2021, Andrey Abramov, Laurie Nevay'
+author = 'Andrey Abramov, Laurie Nevay'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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.todo',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autodoc',
+    "sphinx_rtd_theme",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = []
+
+
+# -- 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'
+
+# 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']

xcoll/scattering_routines/geant4/collimasim/docs/source/index.rst

@@ -0,0 +1,26 @@
+.. collimasim documentation master file, created by
+   sphinx-quickstart on Fri Jul 23 14:56:04 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to collimasim's documentation!
+======================================
+
+Collimasim provides Python bindings to BDSIM (Geant4) in order to enable collimation studies in pure tracking codes.
+
+Several magical fairies have been contacted about writing the documentation. It is expected to appear here shortly.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   collimasim
+
+..
+  Indices and tables
+  ==================
+..  
+  * :ref:`genindex`
+  * :ref:`modindex`
+  * :ref:`search`
+  

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.appveyor.yml

@@ -0,0 +1,37 @@
+version: 1.0.{build}
+image:
+- Visual Studio 2015
+test: off
+skip_branch_with_pr: true
+build:
+  parallel: true
+platform:
+- x86
+environment:
+  matrix:
+  - PYTHON: 36
+    CONFIG: Debug
+  - PYTHON: 27
+    CONFIG: Debug
+install:
+- ps: |
+    $env:CMAKE_GENERATOR = "Visual Studio 14 2015"
+    if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" }
+    $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH"
+    python -W ignore -m pip install --upgrade pip wheel
+    python -W ignore -m pip install pytest numpy --no-warn-script-location pytest-timeout
+- ps: |
+    Start-FileDownload 'https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.zip'
+    7z x eigen-3.3.7.zip -y > $null
+    $env:CMAKE_INCLUDE_PATH = "eigen-3.3.7;$env:CMAKE_INCLUDE_PATH"
+build_script:
+- cmake -G "%CMAKE_GENERATOR%" -A "%CMAKE_ARCH%"
+    -DCMAKE_CXX_STANDARD=14
+    -DPYBIND11_WERROR=ON
+    -DDOWNLOAD_CATCH=ON
+    -DCMAKE_SUPPRESS_REGENERATION=1
+    .
+- set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
+- cmake --build . --config %CONFIG% --target pytest -- /m /v:m /logger:%MSBuildLogger%
+- cmake --build . --config %CONFIG% --target cpptest -- /m /v:m /logger:%MSBuildLogger%
+on_failure: if exist "tests\test_cmake_build" type tests\test_cmake_build\*.log*

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.clang-format

@@ -0,0 +1,19 @@
+---
+# See all possible options and defaults with:
+# clang-format --style=llvm --dump-config
+BasedOnStyle: LLVM
+AccessModifierOffset: -4
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBinaryOperators: All
+BreakConstructorInitializers: BeforeColon
+ColumnLimit: 99
+IndentCaseLabels: true
+IndentPPDirectives: AfterHash
+IndentWidth: 4
+Language: Cpp
+SpaceAfterCStyleCast: true
+Standard: Cpp11
+TabWidth: 4
+...

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.clang-tidy

@@ -0,0 +1,65 @@
+FormatStyle: file
+
+Checks: '
+*bugprone*,
+cppcoreguidelines-init-variables,
+cppcoreguidelines-slicing,
+clang-analyzer-optin.cplusplus.VirtualCall,
+google-explicit-constructor,
+llvm-namespace-comment,
+misc-misplaced-const,
+misc-non-copyable-objects,
+misc-static-assert,
+misc-throw-by-value-catch-by-reference,
+misc-uniqueptr-reset-release,
+misc-unused-parameters,
+modernize-avoid-bind,
+modernize-make-shared,
+modernize-redundant-void-arg,
+modernize-replace-auto-ptr,
+modernize-replace-disallow-copy-and-assign-macro,
+modernize-replace-random-shuffle,
+modernize-shrink-to-fit,
+modernize-use-auto,
+modernize-use-bool-literals,
+modernize-use-equals-default,
+modernize-use-equals-delete,
+modernize-use-default-member-init,
+modernize-use-noexcept,
+modernize-use-emplace,
+modernize-use-override,
+modernize-use-using,
+*performance*,
+readability-avoid-const-params-in-decls,
+readability-const-return-type,
+readability-container-size-empty,
+readability-delete-null-pointer,
+readability-else-after-return,
+readability-implicit-bool-conversion,
+readability-make-member-function-const,
+readability-misplaced-array-index,
+readability-non-const-parameter,
+readability-redundant-function-ptr-dereference,
+readability-redundant-smartptr-get,
+readability-redundant-string-cstr,
+readability-simplify-subscript-expr,
+readability-static-accessed-through-instance,
+readability-static-definition-in-anonymous-namespace,
+readability-string-compare,
+readability-uniqueptr-delete-release,
+-bugprone-exception-escape,
+-bugprone-reserved-identifier,
+-bugprone-unused-raii,
+'
+
+CheckOptions:
+- key:             performance-for-range-copy.WarnOnAllAutoCopies
+  value:           true
+- key:             performance-unnecessary-value-param.AllowedTypes
+  value:           'exception_ptr$;'
+- key:             readability-implicit-bool-conversion.AllowPointerConditions
+  value:           true
+
+HeaderFilterRegex: 'pybind11/.*h'
+
+WarningsAsErrors: '*'

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.cmake-format.yaml

@@ -0,0 +1,73 @@
+parse:
+  additional_commands:
+    pybind11_add_module:
+      flags:
+        - THIN_LTO
+        - MODULE
+        - SHARED
+        - NO_EXTRAS
+        - EXCLUDE_FROM_ALL
+        - SYSTEM
+
+format:
+  line_width: 99
+  tab_size: 2
+
+  # If an argument group contains more than this many sub-groups
+  # (parg or kwarg groups) then force it to a vertical layout.
+  max_subgroups_hwrap: 2
+
+  # If a positional argument group contains more than this many
+  # arguments, then force it to a vertical layout.
+  max_pargs_hwrap: 6
+
+  # If a cmdline positional group consumes more than this many
+  # lines without nesting, then invalidate the layout (and nest)
+  max_rows_cmdline: 2
+  separate_ctrl_name_with_space: false
+  separate_fn_name_with_space: false
+  dangle_parens: false
+
+  # If the trailing parenthesis must be 'dangled' on its on
+  # 'line, then align it to this reference: `prefix`: the start'
+  # 'of the statement,  `prefix-indent`: the start of the'
+  # 'statement, plus one indentation  level, `child`: align to'
+  # the column of the arguments
+  dangle_align: prefix
+  # If the statement spelling length (including space and
+  # parenthesis) is smaller than this amount, then force reject
+  # nested layouts.
+  min_prefix_chars: 4
+
+  # If the statement spelling length (including space and
+  # parenthesis) is larger than the tab width by more than this
+  # amount, then force reject un-nested layouts.
+  max_prefix_chars: 10
+
+  # If a candidate layout is wrapped horizontally but it exceeds
+  # this many lines, then reject the layout.
+  max_lines_hwrap: 2
+
+  line_ending: unix
+
+  # Format command names consistently as 'lower' or 'upper' case
+  command_case: canonical
+
+  # Format keywords consistently as 'lower' or 'upper' case
+  # unchanged is valid too
+  keyword_case: 'upper'
+
+  # A list of command names which should always be wrapped
+  always_wrap: []
+
+  # If true, the argument lists which are known to be sortable
+  # will be sorted lexicographically
+  enable_sort: true
+
+  # If true, the parsers may infer whether or not an argument
+  # list is sortable (without annotation).
+  autosort: false
+
+# Causes a few issues - can be solved later, possibly.
+markup:
+  enable_markup: false

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.git

@@ -0,0 +1 @@
+gitdir: ../../../../../../.git/modules/xcoll/scattering_routines/geant4/collimasim/modules/pybind11

xcoll/scattering_routines/geant4/collimasim/lib/pybind11/.github/CODEOWNERS

@@ -0,0 +1,9 @@
+*.cmake @henryiii
+CMakeLists.txt @henryiii
+*.yml @henryiii
+*.yaml @henryiii
+/tools/ @henryiii
+/pybind11/ @henryiii
+noxfile.py @henryiii
+.clang-format @henryiii
+.clang-tidy @henryiii