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| """Citation class for handling theory calculation citations""" | ||
| # citations.py is based on code from the PyBaMM project | ||
| # Inspired by pybamm.citations | ||
| # https://github.com/pybamm-team/PyBaMM | ||
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| # Copyright (c) 2018-2020, the PyBaMM team. | ||
| # All rights reserved. | ||
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| # Redistribution and use in source and binary forms, with or without | ||
| # modification, are permitted provided that the following conditions are met: | ||
| from multiprocessing import Array | ||
| import flavio | ||
| import sys | ||
| from itertools import compress | ||
| import ctypes | ||
| import yaml | ||
| import pkgutil | ||
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| # * Redistributions of source code must retain the above copyright notice, this | ||
| # list of conditions and the following disclaimer. | ||
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| # * Redistributions in binary form must reproduce the above copyright notice, | ||
| # this list of conditions and the following disclaimer in the documentation | ||
| # and/or other materials provided with the distribution. | ||
| class CitationScope: | ||
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| # * Neither the name of the copyright holder nor the names of its | ||
| # contributors may be used to endorse or promote products derived from | ||
| # this software without specific prior written permission. | ||
| def __enter__(self): | ||
| self._citations_global = flavio.citations | ||
| flavio.citations = Citations() | ||
| return flavio.citations | ||
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| # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE | ||
| # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE | ||
| # FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
| # DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR | ||
| # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER | ||
| # CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, | ||
| # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
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| import flavio | ||
| def __exit__(self, type, value, traceback): | ||
| flavio.citations = self._citations_global | ||
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| class Citations: | ||
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| """Entry point to citations management. | ||
| This object may be used to register a citation is relevant for a particular | ||
| implementation. It can then also then print out a list of papers to be cited. | ||
| Examples | ||
| -------- | ||
| >>> import flavio | ||
| >>> flavio.sm_prediction("DeltaM_s") | ||
| >>> print(flavio.default_citations) | ||
| """ | ||
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| def __init__(self): | ||
| self._reset() | ||
| collect = CitationScope | ||
| __all_citations = set(yaml.safe_load( | ||
| pkgutil.get_data('flavio', 'data/citations.yml') | ||
| )) | ||
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| def __init__(self, initial_citations=[]): | ||
| self._initial_citations = set(initial_citations) | ||
| self._all_citations = { | ||
| k:i for i,k in | ||
| enumerate(sorted(self.__all_citations | self._initial_citations)) | ||
| } | ||
| self._array = Array(ctypes.c_bool, len(self._all_citations)) | ||
| for inspire_key in self._initial_citations: | ||
| self.register(inspire_key) | ||
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| def __iter__(self): | ||
| for citation in self._papers_to_cite: | ||
| for citation in self.set: | ||
| yield citation | ||
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| def __str__(self): | ||
| return ",".join(self._papers_to_cite) | ||
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| def _reset(self): | ||
| "Reset citations to empty" | ||
| self._papers_to_cite = set() | ||
| return ",".join(self.set) | ||
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| @property | ||
| def tostring(self): | ||
| return str(self) | ||
| def set(self): | ||
| return set(compress(sorted(self._all_citations.keys()), self._array)) | ||
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| @property | ||
| def toset(self): | ||
| return self._papers_to_cite | ||
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| def register(self, key): | ||
| """Register a paper to be cited. The intended use is that this method | ||
| should be called only when the referenced functionality is actually being used. | ||
| def string(self): | ||
| return str(self) | ||
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| Parameters | ||
| ---------- | ||
| key : str | ||
| The INSPIRE texkey for the paper to be cited | ||
| """ | ||
| self._papers_to_cite.add(key) | ||
| def register(self, inspire_key): | ||
| self._array[self._all_citations[inspire_key]] = True | ||
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| def clear(self): | ||
| self._array[:] = [False]*len(self._array) | ||
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| def reset(self): | ||
| self.clear() | ||
| for inspire_key in self._initial_citations: | ||
| self.register(inspire_key) | ||
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| default_citations = Citations() | ||
| # Register the flavio paper | ||
| default_citations.register("Straub:2018kue") | ||
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| def register_citation(inspire_key): | ||
| flavio.default_citations.register(inspire_key) | ||
| sys.modules[__name__] = Citations(["Straub:2018kue"]) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| - Antonelli:2010yf | ||
| - Asatrian:2003vq | ||
| - Awramik:2003rn | ||
| - Beneke:2001at | ||
| - Beneke:2003az | ||
| - Beneke:2004dp | ||
| - Benson:2003kp | ||
| - Bernard:2009zm | ||
| - Bjorn:2016zlr | ||
| - Bobeth:2013uxa | ||
| - Boer:2014kda | ||
| - Bourrely:2008za | ||
| - Brignole:2004ah | ||
| - Brivio:2017vri | ||
| - Brod:2010hi | ||
| - Buras:2006gb | ||
| - Buras:2015yba | ||
| - Caprini:1997mu | ||
| - Chobanova:2017rkj | ||
| - Cirigliano:2007ga | ||
| - Descotes-Genon:2015hea | ||
| - Falkowski:2019hvp | ||
| - Freitas:2014hra | ||
| - Gambino:2011cq | ||
| - Gonzalez-Alonso:2018omy | ||
| - Gorbahn:2006bm | ||
| - Greub:2008cy | ||
| - Guadagnoli:2016erb | ||
| - Gubernari:2018wyi | ||
| - Huber:2015sra | ||
| - Inami:1980fz | ||
| - Kitano:2002mt | ||
| - Kozachuk:2017mdk | ||
| - Kruger:2002gf | ||
| - Kuno:1999jp | ||
| - Melikhov:2004mk | ||
| - Misiak:2006ab | ||
| - Misiak:2015xwa | ||
| - Pich:2013lsa | ||
| - Seidel:2004jh | ||
| - Straub:2015ica | ||
| - fakename:2020abc |
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| #! /usr/bin/env python3 | ||
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| """Standalone helper script to update the list of citations referenced in the | ||
| flavio source code.""" | ||
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| import argparse | ||
| import logging | ||
| import sys | ||
| import yaml | ||
| import pkgutil | ||
| logging.basicConfig(level=logging.INFO) | ||
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| def main(argv): | ||
| parser = argparse.ArgumentParser(description='Update the list of citations referenced in the flavio source code.') | ||
| args = parser.parse_args() | ||
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| from flavio.util import get_datapath, extract_citations | ||
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| filename = get_datapath('flavio', 'data/citations.yml') | ||
| with open(filename, 'w') as f: | ||
| f.write(yaml.dump(sorted(extract_citations()))) | ||
| logging.info(f"Saved updated citations to {filename}") | ||
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| if __name__ == '__main__': | ||
| main(sys.argv) |
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