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Run doctests via pytest and update docstring examples (#299)
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* Run doctest via pytest

* Update or fix docstring examples
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@eduardo-rodrigues
eduardo-rodrigues authored Feb 1, 2023
1 parent d23a548 commit b6f8d79
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Showing 4 changed files with 52 additions and 44 deletions.
6 changes: 5 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -55,12 +55,16 @@ jobs:
run: python -m pip install pytest-github-actions-annotate-failures

- name: Test package
run: python -m pytest ./tests --doctest-modules --cov=src/decaylanguage --cov-report=xml
run: python -m pytest ./tests --cov=src/decaylanguage --cov-report=xml

- name: Test coverage with Codecov
if: "runner.os != 'Windows' && matrix.python-version != 3.7"
uses: codecov/codecov-action@v3

- name: Test docstrings with doctest
if: "runner.os == 'Linux' && matrix.python-version == 3.11"
run: python -m pytest --doctest-modules src/decaylanguage

notebooks:
runs-on: ubuntu-latest

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52 changes: 28 additions & 24 deletions src/decaylanguage/dec/dec.py
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Expand Up @@ -74,8 +74,8 @@ class DecFileParser:
Example
-------
>>> dfp = DecFileParser('my-decay-file.dec')
>>> dfp.parse()
>>> dfp = DecFileParser('my-decay-file.dec') # doctest: +SKIP
>>> dfp.parse() # doctest: +SKIP
"""

__slots__ = (
Expand Down Expand Up @@ -693,10 +693,11 @@ def list_decay_modes(self, mother: str, pdg_name: bool = False) -> list[list[str
Example
-------
>>> parser = DecFileParser('my-decay-file.dec')
>>> parser.parse()
>>> parser.list_decay_mother_names() # Inspect what decays are defined
>>> parser.list_decay_modes('pi0')
>>> parser = DecFileParser('my-decay-file.dec') # doctest: +SKIP
>>> parser.parse() # doctest: +SKIP
>>> # Inspect what decays are defined
>>> parser.list_decay_mother_names() # doctest: +SKIP
>>> parser.list_decay_modes('pi0') # doctest: +SKIP
"""
if pdg_name:
mother = PDG2EvtGenNameMap[mother]
Expand Down Expand Up @@ -928,9 +929,9 @@ def build_decay_chains(
Examples
--------
>>> parser = DecFileParser('a-Dplus-decay-file.dec')
>>> parser.parse()
>>> parser.build_decay_chains('D+')
>>> parser = DecFileParser('a-Dplus-decay-file.dec') # doctest: +SKIP
>>> parser.parse() # doctest: +SKIP
>>> parser.build_decay_chains('D+') # doctest: +SKIP
{'D+': [{'bf': 1.0,
'fs': ['K-',
'pi+',
Expand All @@ -950,7 +951,7 @@ def build_decay_chains(
{'bf': 6.5e-08, 'fs': ['e+', 'e-'], 'model': 'PHSP', 'model_params': ''}]}],
'model': 'PHSP',
'model_params': ''}]}
>>> p.build_decay_chains('D+', stable_particles=['pi0'])
>>> p.build_decay_chains('D+', stable_particles=['pi0']) # doctest: +SKIP
{'D+': [{'bf': 1.0, 'fs': ['K-', 'pi+', 'pi+', 'pi0'], 'model': 'PHSP', 'model_params': ''}]}
"""
keys = ("bf", "fs", "model", "model_params")
Expand Down Expand Up @@ -1067,19 +1068,21 @@ class DecayModelParamValueReplacement(Visitor): # type: ignore[misc]
Examples
--------
>>> from lark import Tree, Token
>>> ...
>>> ... # doctest: +SKIP
>>> t = Tree('decay', [Tree('particle', [Token('LABEL', 'Upsilon(4S)')]),
... Tree('decayline', [Tree('value', [Token('SIGNED_NUMBER', '1.0')]),
... Tree('particle', [Token('LABEL', 'B0')]),
... Tree('particle', [Token('LABEL', 'anti-B0')]),
... Tree('model', [Token('MODEL_NAME', 'VSS_BMIX'),
... Tree('model_options', [Token('LABEL', 'dm')])])])])
>>> dict_define_defs = {'dm': 0.507e12}
>>> DecayModelParamValueReplacement(define_defs=dict_define_defs).visit(t)
Tree(decay, [Tree(particle, [Token(LABEL, 'Upsilon(4S)')]), Tree(decayline,
[Tree(value, [Token(SIGNED_NUMBER, '1.0')]), Tree(particle, [Token(LABEL, 'B0')]),
Tree(particle, [Token(LABEL, 'anti-B0')]), Tree(model, [Token(MODEL_NAME, 'VSS_BMIX'),
Tree(model_options, [Token(LABEL, 507000000000.0)])])])])
>>> DecayModelParamValueReplacement(define_defs=dict_define_defs).visit(t) # doctest: +NORMALIZE_WHITESPACE
Tree('decay', [Tree('particle', [Token('LABEL', 'Upsilon(4S)')]),
Tree('decayline', [Tree('value', [Token('SIGNED_NUMBER', '1.0')]),
Tree('particle', [Token('LABEL', 'B0')]),
Tree('particle', [Token('LABEL', 'anti-B0')]),
Tree('model', [Token('MODEL_NAME', 'VSS_BMIX'),
Tree('model_options', [Token('LABEL', 507000000000.0)])])])])
"""

def __init__(self, define_defs: dict[str, Any] | None = None) -> None:
Expand Down Expand Up @@ -1126,15 +1129,16 @@ class ChargeConjugateReplacement(Visitor): # type: ignore[misc]
Examples
--------
>>> from lark import Tree, Token
>>> ...
>>> ... # doctest: +SKIP
>>> t = Tree('decay', [Tree('particle', [Token('LABEL', 'D0')]), Tree('decayline', [Tree
... ('value', [Token('SIGNED_NUMBER', '1.0')]), Tree('particle', [Token('LABEL', 'K-')])
... , Tree('particle', [Token('LABEL', 'pi+')]), Tree('model', [Token('MODEL_NAME', 'PHS
... P')])])])
>>> ChargeConjugateReplacement().visit(t)
Tree(decay, [Tree(particle, [Token(LABEL, 'D~0')]), Tree(decayline,
[Tree(value, [Token(SIGNED_NUMBER, '1.0')]), Tree(particle, [Token(LABEL, 'K+')]),
Tree(particle, [Token(LABEL, 'pi-')]), Tree(model, [Token(MODEL_NAME, 'PHSP')])])])
... ('value', [Token('SIGNED_NUMBER', '1.0')]), Tree('particle', [Token('LABEL', 'K-')]),
... Tree('particle', [Token('LABEL', 'pi+')]), Tree('model', [Token('MODEL_NAME', 'PHSP')])])])
>>> ChargeConjugateReplacement().visit(t) # doctest: +NORMALIZE_WHITESPACE
Tree('decay', [Tree('particle', [Token('LABEL', 'anti-D0')]),
Tree('decayline', [Tree('value', [Token('SIGNED_NUMBER', '1.0')]),
Tree('particle', [Token('LABEL', 'K+')]),
Tree('particle', [Token('LABEL', 'pi-')]),
Tree('model', [Token('MODEL_NAME', 'PHSP')])])])
"""

def __init__(self, charge_conj_defs: dict[str, str] | None = None) -> None:
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25 changes: 12 additions & 13 deletions src/decaylanguage/decay/decay.py
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Original file line number Diff line number Diff line change
Expand Up @@ -236,8 +236,8 @@ def __init__(
>>> # Decay mode with decay model information
>>> dd = DaughtersDict('pi- pi0 nu_tau')
>>> dm = DecayMode(0.2551, dd,
model='TAUHADNU',
model_params=[-0.108, 0.775, 0.149, 1.364, 0.400])
... model='TAUHADNU',
... model_params=[-0.108, 0.775, 0.149, 1.364, 0.400])
>>> # Decay mode with user metadata
>>> dd = DaughtersDict('K+ K-')
Expand All @@ -246,6 +246,7 @@ def __init__(
>>> # Decay mode with metadata for generators such as zfit's phasespace
>>> dm = DecayMode(0.5, "K+ K-", zfit={"B0": "gauss"})
>>> dm.metadata['zfit'] == {'B0': 'gauss'}
True
"""
self.bf = bf
self.daughters = DaughtersDict(daughters)
Expand Down Expand Up @@ -273,16 +274,15 @@ def from_dict(
Examples
--------
>>> Simplest construction
>>> DecayMode.from_dict({'bf': 0.98823,
'fs': ['gamma', 'gamma']})
>>> # Simplest construction
>>> DecayMode.from_dict({'bf': 0.98823, 'fs': ['gamma', 'gamma']})
<DecayMode: daughters=gamma gamma, BF=0.98823>
>>> # Decay mode with decay model details
>>> DecayMode.from_dict({'bf': 0.98823,
'fs': ['gamma', 'gamma'],
'model': 'PHSP',
'model_params': ''})
... 'fs': ['gamma', 'gamma'],
... 'model': 'PHSP',
... 'model_params': ''})
<DecayMode: daughters=gamma gamma, BF=0.98823>
>>> # Decay mode with metadata for generators such as zfit's phasespace
Expand Down Expand Up @@ -384,9 +384,8 @@ def to_dict(self) -> dict[str, int | float | str | list[str]]:
Examples
--------
>>> dm = DecayMode(0.5, 'K+ K- K- pi- pi0 nu_tau',
model='PHSP', study='toy', year=2019)
>>> dm.to_dict()
>>> dm = DecayMode(0.5, 'K+ K- K- pi- pi0 nu_tau', model='PHSP', study='toy', year=2019)
>>> dm.to_dict() # doctest: +NORMALIZE_WHITESPACE
{'bf': 0.5,
'fs': ['K+', 'K-', 'K-', 'nu_tau', 'pi-', 'pi0'],
'model': 'PHSP',
Expand Down Expand Up @@ -693,7 +692,7 @@ def to_dict(self) -> dict[str, list[dict[str, float | str | list[Any]]]]:
>>> dm1 = DecayMode(0.028, 'K_S0 pi+ pi-')
>>> dm2 = DecayMode(0.692, 'pi+ pi-')
>>> dc = DecayChain('D0', {'D0':dm1, 'K_S0':dm2})
>>> dc.to_dict()
>>> dc.to_dict() # doctest: +NORMALIZE_WHITESPACE
{'D0': [{'bf': 0.028,
'fs': [{'K_S0': [{'bf': 0.692,
'fs': ['pi+', 'pi-'],
Expand Down Expand Up @@ -750,7 +749,7 @@ def flatten(
>>>
>>> dc.flatten()
<DecayChain: D0 -> gamma gamma pi+ pi- (0 sub-decays), BF=0.008479803984>
>>> dc.flatten().to_dict()
>>> dc.flatten().to_dict() # doctest: +NORMALIZE_WHITESPACE
{'D0': [{'bf': 0.008479803984,
'fs': ['gamma', 'gamma', 'pi+', 'pi-'],
'model': 'PHSP',
Expand Down
13 changes: 7 additions & 6 deletions src/decaylanguage/decay/viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,15 +34,16 @@ class DecayChainViewer:
Examples
--------
>>> dfp = DecFileParser('my-Dst-decay-file.dec')
>>> dfp.parse()
>>> chain = dfp.build_decay_chains('D*+')
>>> dcv = DecayChainViewer(chain)
>>> dcv # display the SVG figure in a notebook
>>> dfp = DecFileParser('my-Dst-decay-file.dec') # doctest: +SKIP
>>> dfp.parse() # doctest: +SKIP
>>> chain = dfp.build_decay_chains('D*+') # doctest: +SKIP
>>> dcv = DecayChainViewer(chain) # doctest: +SKIP
>>> # display the SVG figure in a notebook
>>> dcv # doctest: +SKIP
When not in notebooks the graph can easily be visualized with the
`graphviz.Digraph.render` or `graphviz.Digraph.view` functions, e.g.:
>>> dcv.graph.render(filename="test", format="pdf", view=True, cleanup=True)
>>> dcv.graph.render(filename="test", format="pdf", view=True, cleanup=True) # doctest: +SKIP
"""

__slots__ = ("_chain", "_graph", "_graph_attributes")
Expand Down

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