decaylanguage 0.2.0__tar.gz → 0.3.0__tar.gz

{decaylanguage-0.2.0 → decaylanguage-0.3.0}/.coveragerc

@@ -8,6 +8,9 @@ branch = true
 source =
     decaylanguage
 parallel = true
+omit =
+    # omit certain files
+    decaylanguage/__main__.py
 
 [report]
 show_missing = true

{decaylanguage-0.2.0 → decaylanguage-0.3.0}/AUTHORS.rst

@@ -3,3 +3,4 @@ Authors
 =======
 
 * Henry Fredrick Schreiner III - https://iscinumpy.gitlab.io
+* Eduardo Rodrigues - https://github.com/eduardo-rodrigues/

decaylanguage-0.3.0/CHANGELOG.md

@@ -0,0 +1,39 @@
+# Changelog
+
+## Version 0.3.0 (2019-06-26)
+
+* Decays modelling:
+  - Updates to Mint related particle data files.
+* Parsing of decay files (aka .dec files):
+  - Lark parser files added, for ``.dec`` decay files.
+  - ``DecFileParser`` class introduced, with documentation and test suite.
+  - Various ``.dec`` test decay files added.
+* Visualisation of decay chains:
+  - ``DecayChainViewer`` class introduced, with documentation and test suite.
+* Universal representation of decay chains:
+  - First "building block" classes ``DaughtersDict`` and ``DecayMode`` introduced,
+    with documentation and test suite.
+* Package dependencies:
+  - Package made dependent on Scikit-HEP's ``Particle`` package.
+  - Redundant code removed.
+* Continuous integration:
+  - CI with Azure pipelines introduced.
+  - CI with Travis and AppVeyor removed.
+* Miscellaneous:
+  - Demo notebook added, with a launcher for Binder.
+  -Copyright statements added to repository files.
+  - General clean-up and minor bug fixes.
+
+
+## Version 0.2.0 (2018-08-02)
+
+* First release as part of Scikit-HEP.
+* Using new data package with ``importlib_resources`` (or ``importlib.resources`` on Python 3.7).
+* Better docs and examples.
+* Some method renaming.
+* Generalized converter script.
+
+
+## Version 0.1.0 (2018-03-13)
+
+* First release on PyPI.

{decaylanguage-0.2.0 → decaylanguage-0.3.0}/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018, the decaylanguage developers
+Copyright (c) 2018-2019, Eduardo Rodrigues and Henry Schreiner.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following

{decaylanguage-0.2.0 → decaylanguage-0.3.0}/MANIFEST.in

@@ -25,6 +25,7 @@ include tox.ini .travis.yml .appveyor.yml
 recursive-include decaylanguage *.py
 recursive-include decaylanguage *.csv
 recursive-include decaylanguage *.txt
+recursive-include decaylanguage *.lark
 
 recursive-include images *.pdf
 recursive-include images *.png

decaylanguage-0.3.0/PKG-INFO

@@ -0,0 +1,203 @@
+Metadata-Version: 2.1
+Name: decaylanguage
+Version: 0.3.0
+Summary: A language to describe particle decays, and tools to work with them.
+Home-page: https://github.com/scikit-hep/decaylanguage
+Author: Henry Fredrick Schreiner III
+Author-email: henry.schreiner@cern.ch
+Maintainer: The Scikit-HEP admins
+Maintainer-email: scikit-hep-admins@googlegroups.com
+License: BSD 3-Clause License
+Description: 
+            ![[DecayLanguage](https://github.com/scikit-hep/decaylanguage)](https://github.com/scikit-hep/decaylanguage/raw/master/images/DecayLanguage.png)
+        
+            
+        
+        DecayLanguage implements a language to describe and convert particle decays
+        between digital representations, effectively making it possible to interoperate
+        several fitting programs. Particular interest is given to programs dedicated
+        to amplitude analyses.
+        
+        DecayLanguage provides tools to parse so-called .dec decay files,
+        and manipulate and visualize decay chains.
+        
+        
+        ### Installation
+        
+        Just run the following:
+        
+        ```bash
+        pip install decaylanguage
+        ```
+        
+        You can use a virtual environment through pipenv or with `--user` if you know
+        what those are. [Python 2.7 and 3.4+](http://docs.python-guide.org/en/latest/starting/installation) are supported.
+        
+        <details><summary>Dependencies: (click to expand)</summary><p>
+        
+        Required and compatibility dependencies will be automatically installed by pip.
+        
+        #### Required dependencies:
+        
+        -   [particle](https://github.com/scikit-hep/particle): PDG particle data and identification codes
+        -   [Numpy](https://scipy.org/install.html): The numerical library for Python
+        -   [pandas](https://pandas.pydata.org/): Tabular data in Python
+        -   [attrs](https://github.com/python-attrs/attrs): DataClasses for Python
+        -   [plumbum](https://github.com/tomerfiliba/plumbum): Command line tools
+        -   [lark-parser](https://github.com/lark-parser/lark): A modern parsing library for Python
+        
+        #### Python compatibility:
+        -   [six](https://github.com/benjaminp/six): Compatibility library
+        -   [pathlib2](https://github.com/mcmtroffaes/pathlib2) backport if using Python 2.7
+        -   [enum34](https://bitbucket.org/stoneleaf/enum34) backport if using Python /< 3.5
+        -   [importlib_resources](http://importlib-resources.readthedocs.io/en/latest/) backport if using Python /< 3.7
+        
+        
+        #### Recommended dependencies:
+        -   [graphviz](https://gitlab.com/graphviz/graphviz/) to render (DOT
+            language) graph descriptions of decay chains.
+        -   [pydot](https://github.com/pydot/pydot), a Python interface to
+            Graphviz's Dot language, used to visualize particle decay chains.
+        </p></details>
+        
+        
+        ### Usage
+        
+        This is a quick user guide. For a full API docs, go [here](https://decaylanguage.readthedocs.io/en/latest/).
+        
+        ``DecayLanguage`` is a set of tools for building and transforming particle
+        decays. The parts are:
+        
+        #### Particles
+        
+        Particles are a key component when dealing with decays.
+        Refer to the [particle package](https://github.com/scikit-hep/particle)
+        for how to deal with particles and PDG identification codes.
+        
+        #### Decay files
+        
+        Decay .dec files can be parsed simply with
+        
+        ```python
+        from decaylanguage import DecFileParser
+        
+        parser = DecFileParser('my-decay-file.dec')
+        parser.parse()
+        
+        # Inspect what decays are defined
+        parser.list_decay_mother_names()
+        
+        # Print decay modes, etc. ...
+        ```
+        
+        A copy of the master DECAY.DEC file used by the LHCb experiment is provided
+        [here](https://github.com/scikit-hep/decaylanguage/tree/master/decaylanguage/data)
+        for convenience.
+        
+        The `DecFileParser` class implements a series of methods giving access to all
+        information stored in decay files: the decays themselves, particle name aliases,
+        definitions of charge-conjugate particles, variable and Pythia-specific
+        definitions, etc.
+        
+        #### Decay modeling
+        
+        The most common way to create a decay chain is to read in an [AmpGen]
+        style syntax from a file or a string. You can use:
+        
+        ```python
+        from decaylanguage.modeling import AmplitudeChain
+        lines, parameters, constants, states = AmplitudeChain.read_ampgen(text='''
+        EventType D0 K- pi+ pi+ pi-
+        
+        D0[D]{K*(892)bar0{K-,pi+},rho(770)0{pi+,pi-}}                            0 1 0.1 0 1 0.1
+        
+        K(1460)bar-_mass  0 1460 1
+        K(1460)bar-_width 0  250 1
+        
+        a(1)(1260)+::Spline::Min 0.18412
+        a(1)(1260)+::Spline::Max 1.86869
+        a(1)(1260)+::Spline::N 34
+        ''')
+        ```
+        
+        Here, `lines` will be a list of AmplitudeChain lines (pretty print supported in Jupyter notebooks),
+        `parameters` will be a table of parameters (ranged parameters not yet supported),
+        `constants` will be a table of constants,
+        and `states` will be the list of known states (EventType).
+        
+        #### Converters
+        
+        You can output to a format (currently only [GooFit] supported, feel free
+        to make a PR to add more). Use a subclass of DecayChain, in this case,
+        GooFitChain. To use the [GooFit] output, type from the shell:
+        
+        ```bash
+        python -m decaylanguage -G goofit myinput.opts
+        ```
+        
+        ### Acknowledgements
+        
+        DecayLanguage is free software released under a BSD 3-Clause License.
+        It was originally developed by Henry Schreiner.
+        
+        [AmpGen]: https://gitlab.cern.ch/lhcb/Gauss/tree/LHCBGAUSS-1058.AmpGenDev/Gen/AmpGen
+        [GooFit]: https://GooFit.github.io
+        
+        
+        # Changelog
+        
+        ## Version 0.3.0 (2019-06-26)
+        
+        * Decays modelling:
+          - Updates to Mint related particle data files.
+        * Parsing of decay files (aka .dec files):
+          - Lark parser files added, for ``.dec`` decay files.
+          - ``DecFileParser`` class introduced, with documentation and test suite.
+          - Various ``.dec`` test decay files added.
+        * Visualisation of decay chains:
+          - ``DecayChainViewer`` class introduced, with documentation and test suite.
+        * Universal representation of decay chains:
+          - First "building block" classes ``DaughtersDict`` and ``DecayMode`` introduced,
+            with documentation and test suite.
+        * Package dependencies:
+          - Package made dependent on Scikit-HEP's ``Particle`` package.
+          - Redundant code removed.
+        * Continuous integration:
+          - CI with Azure pipelines introduced.
+          - CI with Travis and AppVeyor removed.
+        * Miscellaneous:
+          - Demo notebook added, with a launcher for Binder.
+          -Copyright statements added to repository files.
+          - General clean-up and minor bug fixes.
+        
+        
+        ## Version 0.2.0 (2018-08-02)
+        
+        * First release as part of Scikit-HEP.
+        * Using new data package with ``importlib_resources`` (or ``importlib.resources`` on Python 3.7).
+        * Better docs and examples.
+        * Some method renaming.
+        * Generalized converter script.
+        
+        
+        ## Version 0.1.0 (2018-03-13)
+        
+        * First release on PyPI.
+        
+Keywords: particle,decay,HEP
+Platform: Any
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Topic :: Scientific/Engineering
+Description-Content-Type: text/markdown
+Provides-Extra: test
+Provides-Extra: notebook

decaylanguage-0.3.0/README.md

@@ -0,0 +1,146 @@
+[![DecayLanguage](https://github.com/scikit-hep/decaylanguage/raw/master/images/DecayLanguage.png)](http://decaylanguage.readthedocs.io/en/latest/)
+
+## DecayLanguage: describe, manipulate and convert particle decays
+
+[![PyPI Package latest release](https://img.shields.io/pypi/v/decaylanguage.svg)](https://pypi.python.org/pypi/decaylanguage)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3257423.svg)](https://doi.org/10.5281/zenodo.3257423)
+[![Documentation Status](https://readthedocs.org/projects/decaylanguage/badge/?style=flat)](https://readthedocs.org/projects/decaylanguage)
+[![Azure Build Status](https://dev.azure.com/scikit-hep/decaylanguage/_apis/build/status/scikit-hep.decaylanguage?branchName=master)](https://dev.azure.com/scikit-hep/decaylanguage/_build/latest?definitionId=3?branchName=master)
+[![Coverage Status](https://img.shields.io/azure-devops/coverage/scikit-hep/decaylanguage/3.svg)](https://dev.azure.com/scikit-hep/decaylanguage/_build/latest?definitionId=3?branchName=master)
+[![Tests Status](https://img.shields.io/azure-devops/tests/scikit-hep/decaylanguage/3.svg)](https://dev.azure.com/scikit-hep/decaylanguage/_build/latest?definitionId=3?branchName=master)
+[![Supported versions](https://img.shields.io/pypi/pyversions/decaylanguage.svg)](https://pypi.python.org/pypi/decaylanguage)
+[![Commits since latest release](https://img.shields.io/github/commits-since/scikit-hep/decaylanguage/v0.3.0.svg)](https://github.com/scikit-hep/decaylanguage/compare/v0.3.0...master)
+[![Binder demo](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/scikit-hep/decaylanguage/master?urlpath=lab/tree/notebooks/DecayLanguageDemo.ipynb)
+
+
+<!-- break -->
+
+DecayLanguage implements a language to describe and convert particle decays
+between digital representations, effectively making it possible to interoperate
+several fitting programs. Particular interest is given to programs dedicated
+to amplitude analyses.
+
+DecayLanguage provides tools to parse so-called .dec decay files,
+and manipulate and visualize decay chains.
+
+
+### Installation
+
+Just run the following:
+
+```bash
+pip install decaylanguage
+```
+
+You can use a virtual environment through pipenv or with `--user` if you know
+what those are. [Python 2.7 and 3.4+](http://docs.python-guide.org/en/latest/starting/installation) are supported.
+
+<details><summary>Dependencies: (click to expand)</summary><p>
+
+Required and compatibility dependencies will be automatically installed by pip.
+
+#### Required dependencies:
+
+-   [particle](https://github.com/scikit-hep/particle): PDG particle data and identification codes
+-   [Numpy](https://scipy.org/install.html): The numerical library for Python
+-   [pandas](https://pandas.pydata.org/): Tabular data in Python
+-   [attrs](https://github.com/python-attrs/attrs): DataClasses for Python
+-   [plumbum](https://github.com/tomerfiliba/plumbum): Command line tools
+-   [lark-parser](https://github.com/lark-parser/lark): A modern parsing library for Python
+
+#### Python compatibility:
+-   [six](https://github.com/benjaminp/six): Compatibility library
+-   [pathlib2](https://github.com/mcmtroffaes/pathlib2) backport if using Python 2.7
+-   [enum34](https://bitbucket.org/stoneleaf/enum34) backport if using Python /< 3.5
+-   [importlib_resources](http://importlib-resources.readthedocs.io/en/latest/) backport if using Python /< 3.7
+
+
+#### Recommended dependencies:
+-   [graphviz](https://gitlab.com/graphviz/graphviz/) to render (DOT
+    language) graph descriptions of decay chains.
+-   [pydot](https://github.com/pydot/pydot), a Python interface to
+    Graphviz's Dot language, used to visualize particle decay chains.
+</p></details>
+
+
+### Usage
+
+This is a quick user guide. For a full API docs, go [here](https://decaylanguage.readthedocs.io/en/latest/).
+
+``DecayLanguage`` is a set of tools for building and transforming particle
+decays. The parts are:
+
+#### Particles
+
+Particles are a key component when dealing with decays.
+Refer to the [particle package](https://github.com/scikit-hep/particle)
+for how to deal with particles and PDG identification codes.
+
+#### Decay files
+
+Decay .dec files can be parsed simply with
+
+```python
+from decaylanguage import DecFileParser
+
+parser = DecFileParser('my-decay-file.dec')
+parser.parse()
+
+# Inspect what decays are defined
+parser.list_decay_mother_names()
+
+# Print decay modes, etc. ...
+```
+
+A copy of the master DECAY.DEC file used by the LHCb experiment is provided
+[here](https://github.com/scikit-hep/decaylanguage/tree/master/decaylanguage/data)
+for convenience.
+
+The `DecFileParser` class implements a series of methods giving access to all
+information stored in decay files: the decays themselves, particle name aliases,
+definitions of charge-conjugate particles, variable and Pythia-specific
+definitions, etc.
+
+#### Decay modeling
+
+The most common way to create a decay chain is to read in an [AmpGen]
+style syntax from a file or a string. You can use:
+
+```python
+from decaylanguage.modeling import AmplitudeChain
+lines, parameters, constants, states = AmplitudeChain.read_ampgen(text='''
+EventType D0 K- pi+ pi+ pi-
+
+D0[D]{K*(892)bar0{K-,pi+},rho(770)0{pi+,pi-}}                            0 1 0.1 0 1 0.1
+
+K(1460)bar-_mass  0 1460 1
+K(1460)bar-_width 0  250 1
+
+a(1)(1260)+::Spline::Min 0.18412
+a(1)(1260)+::Spline::Max 1.86869
+a(1)(1260)+::Spline::N 34
+''')
+```
+
+Here, `lines` will be a list of AmplitudeChain lines (pretty print supported in Jupyter notebooks),
+`parameters` will be a table of parameters (ranged parameters not yet supported),
+`constants` will be a table of constants,
+and `states` will be the list of known states (EventType).
+
+#### Converters
+
+You can output to a format (currently only [GooFit] supported, feel free
+to make a PR to add more). Use a subclass of DecayChain, in this case,
+GooFitChain. To use the [GooFit] output, type from the shell:
+
+```bash
+python -m decaylanguage -G goofit myinput.opts
+```
+
+### Acknowledgements
+
+DecayLanguage is free software released under a BSD 3-Clause License.
+It was originally developed by Henry Schreiner.
+
+[AmpGen]: https://gitlab.cern.ch/lhcb/Gauss/tree/LHCBGAUSS-1058.AmpGenDev/Gen/AmpGen
+[GooFit]: https://GooFit.github.io

decaylanguage-0.3.0/decaylanguage/__init__.py

@@ -0,0 +1,14 @@
+# Copyright (c) 2018-2019, Eduardo Rodrigues and Henry Schreiner.
+#
+# Distributed under the 3-clause BSD license, see accompanying file LICENSE
+# or https://github.com/scikit-hep/decaylanguage for details.
+
+
+# Convenient access to the version number
+from ._version import __version__
+
+# Direct access to decay file parsing tools
+from .dec import DecFileParser
+
+# Direct access to decay chain visualization tools
+from .decay import DecayChainViewer

{decaylanguage-0.2.0 → decaylanguage-0.3.0}/decaylanguage/__main__.py

@@ -1,5 +1,9 @@
 #!/usr/bin/env python
 # coding: utf-8
+# Copyright (c) 2018-2019, Eduardo Rodrigues and Henry Schreiner.
+#
+# Distributed under the 3-clause BSD license, see accompanying file LICENSE
+# or https://github.com/scikit-hep/decaylanguage for details.
 
 from __future__ import absolute_import
 from __future__ import division
@@ -7,11 +11,11 @@ from __future__ import print_function
 
 from plumbum import cli
 
-from decaylanguage.decay.ampgen2goofit import ampgen2goofit
+from decaylanguage.modeling.ampgen2goofit import ampgen2goofit
 
 
 class DecayLanguageDecay(cli.Application):
-    generator = cli.SwitchAttr('-G,--generator', cli.Set('goofit'))
+    generator = cli.SwitchAttr(['-G', '--generator'], cli.Set('goofit'), mandatory=True)
 
     def main(self, filename):
         if self.generator == 'goofit':

decaylanguage-0.3.0/decaylanguage/_version.py

@@ -0,0 +1,10 @@
+# Copyright (c) 2018-2019, Eduardo Rodrigues and Henry Schreiner.
+#
+# Distributed under the 3-clause BSD license, see accompanying file LICENSE
+# or https://github.com/scikit-hep/decaylanguage for details.
+
+
+__version__ = '0.3.0'
+
+version = __version__
+version_info = __version__.split('.')