github-actions[bot]
commented
2 weeks ago Coverage Report
| Name | Stmts | Miss | ∆ Miss | Cover |
|---|---|---|---|---|
edsnlp/training/optimizer.pyNew missing coverage at line 256 ! def state(self, value):
- self.optim.state = value
| 131 | 1 | 1 | 99.24% |
| TOTAL | 10327 | 213 | 0 | 97.94% |
Files without new missing coverage
| Name | Stmts | Miss | ∆ Miss | Cover |
|---|---|---|---|---|
edsnlp/utils/span_getters.pyWas already missing at lines 52-55 else:
- for span in candidates:
- if span.label_ in span_filter:
- yield span
Was already missing at lines 59-61 if span_getter is None:
- yield doc[:], None
- return
if callable(span_getter):Was already missing at lines 62-64 if callable(span_getter):
- yield from span_getter(doc)
- return
for key, span_filter in span_getter.items():Was already missing at line 66 if key == "*":
- candidates = (
(span, group) for group in doc.spans.values() for span in groupWas already missing at lines 75-78 else:
- for span, group in candidates:
- if span.label_ in span_filter:
- yield span, group
Was already missing at line 82 if callable(span_setter):
- span_setter(doc, matches)
else:Was already missing at line 124 elif isinstance(v, str):
- new_value[k] = [v]
elif isinstance(v, list) and all(isinstance(i, str) for i in v):Was already missing at line 162 elif isinstance(v, str):
- new_value[k] = [v]
elif isinstance(v, list) and all(isinstance(i, str) for i in v): | 149 | 14 | 0 | 90.60% |
edsnlp/utils/resources.pyWas already missing at line 33 if not verbs:
- return conjugated_verbs
| 24 | 1 | 0 | 95.83% |
edsnlp/utils/numbers.pyWas already missing at line 34 else:
- string = s
string = string.lower().strip()Was already missing at lines 38-41 return int(string)
- except ValueError:
- parsed = DIGITS_MAPPINGS.get(string, None)
- return parsed | 16 | 4 | 0 | 75.00% |
edsnlp/utils/lazy_module.pyWas already missing at line 46 ):
- continue
for import_node in node.body: | 31 | 1 | 0 | 96.77% |
edsnlp/utils/filter.pyWas already missing at line 206 if isinstance(label, int):
- return [span for span in spans if span.label == label]
else: | 74 | 1 | 0 | 98.65% |
edsnlp/utils/bindings.pyWas already missing at line 23 return "." + path
- return path
| 65 | 1 | 0 | 98.46% |
edsnlp/utils/batching.pyWas already missing at line 288 else: # drop
- continue
batch.append(item)Was already missing at line 347 else: # drop
- continue
batch.append(item) | 187 | 2 | 0 | 98.93% |
edsnlp/training/trainer.pyWas already missing at line 74 if result is None:
- result = {}
if isinstance(x, dict):Was already missing at line 91 if p not in current:
- break
current = current[p] | 200 | 2 | 0 | 99.00% |
edsnlp/processing/spark.pyWas already missing at line 50 getActiveSession = SparkSession.getActiveSession
- except AttributeError:
| 47 | 1 | 0 | 97.87% |
edsnlp/processing/deprecated_pipe.pyWas already missing at lines 207-209 def converter(doc):
- res = results_extractor(doc)
- return (
[{"note_id": doc._.note_id, **row} for row in res] | 57 | 2 | 0 | 96.49% |
edsnlp/pipes/trainable/span_linker/span_linker.pyWas already missing at lines 402-404 if self.reference_mode == "synonym":
- embeds = embeds.to(new_lin.weight)
- new_lin.weight.data = embeds
else: | 173 | 2 | 0 | 98.84% |
edsnlp/pipes/trainable/span_classifier/span_classifier.pyWas already missing at line 345 if not all(keep_bindings):
- logger.warning(
"Some attributes have no labels or values and have been removed:" | 159 | 1 | 0 | 99.37% |
edsnlp/pipes/trainable/ner_crf/ner_crf.pyWas already missing at line 254 if self.labels is not None and not self.infer_span_setter:
- return
Was already missing at lines 262-264 if callable(self.target_span_getter):
- for span in get_spans(doc, self.target_span_getter):
- inferred_labels.add(span.label_)
else: | 160 | 3 | 0 | 98.12% |
edsnlp/pipes/trainable/layers/crf.pyWas already missing at line 21 # out: 2 * N * O
- return (log_A.unsqueeze(-1) + log_B.unsqueeze(-3)).logsumexp(-2)
Was already missing at line 29 # out: 2 * N * O
- return (log_A.unsqueeze(-1) + log_B.unsqueeze(-3)).max(-2)
Was already missing at line 98 if learnable_transitions:
- self.transitions = torch.nn.Parameter(
torch.zeros_like(forbidden_transitions, dtype=torch.float)Was already missing at line 108 if learnable_transitions and with_start_end_transitions:
- self.start_transitions = torch.nn.Parameter(
torch.zeros(num_tags, dtype=torch.float)Was already missing at line 117 if learnable_transitions and with_start_end_transitions:
- self.end_transitions = torch.nn.Parameter(
torch.zeros(num_tags, dtype=torch.float) | 137 | 5 | 0 | 96.35% |
edsnlp/pipes/trainable/embeddings/transformer/transformer.pyWas already missing at line 165 if quantization is not None:
- kwargs["quantization_config"] = quantization
| 160 | 1 | 0 | 99.38% |
edsnlp/pipes/qualifiers/reported_speech/reported_speech.pyWas already missing at lines 24-28 return "REPORTED"
- elif token._.rspeech is False:
- return "DIRECT"
- else:
- return None
| 99 | 3 | 0 | 96.97% |
edsnlp/pipes/qualifiers/negation/negation.pyWas already missing at line 28 else:
- return None
| 99 | 1 | 0 | 98.99% |
edsnlp/pipes/qualifiers/hypothesis/hypothesis.pyWas already missing at line 27 else:
- return None
| 96 | 1 | 0 | 98.96% |
edsnlp/pipes/qualifiers/history/history.pyWas already missing at lines 26-32 def history_getter(token: Union[Token, Span]) -> Optional[str]:
- if token._.history is True:
- return "ATCD"
- elif token._.history is False:
- return "CURRENT"
- else:
- return None
Was already missing at lines 337-343 )
- except ValueError:
...
- note_datetime = None
Was already missing at lines 352-358 )
- except ValueError:
...
- birth_datetime = None
Was already missing at lines 424-427 )
- except ValueError as e:
- absolute_date = None
- logger.warning(
"In doc {}, the following date {} raises this error: {}. " | 177 | 14 | 0 | 92.09% |
edsnlp/pipes/qualifiers/family/family.pyWas already missing at line 27 else:
- return None
| 81 | 1 | 0 | 98.77% |
edsnlp/pipes/qualifiers/base.pyWas already missing at line 178 def __call__(self, doc: Doc) -> Doc:
- results = self.process(doc)
raise NotImplementedError(f"{type(results)} should be used to tag the document") | 50 | 1 | 0 | 98.00% |
edsnlp/pipes/ner/tnm/model.pyWas already missing at line 147 def __str__(self):
- return self.norm()
Was already missing at line 171 )
- exclude_unset = skip_defaults
| 110 | 2 | 0 | 98.18% |
edsnlp/pipes/ner/scores/sofa/sofa.pyWas already missing at line 32 if not assigned:
- continue
if assigned.get("method_max") is not None:Was already missing at line 40 else:
- method = "Non précisée"
| 25 | 2 | 0 | 92.00% |
edsnlp/pipes/ner/scores/elston_ellis/patterns.pyWas already missing at line 26 if x <= 5:
- return 1
Was already missing at lines 32-36 else:
- return 3
-
- except ValueError:
- return None | 21 | 4 | 0 | 80.95% |
edsnlp/pipes/ner/scores/charlson/patterns.pyWas already missing at lines 21-23 return int(extracted_score)
- except ValueError:
- return None | 13 | 2 | 0 | 84.62% |
edsnlp/pipes/ner/scores/base_score.pyWas already missing at line 154 if value is None:
- continue
normalized_value = self.score_normalization(value) | 47 | 1 | 0 | 97.87% |
edsnlp/pipes/ner/disorders/solid_tumor/solid_tumor.pyWas already missing at lines 130-136 for span in spans:
- span.label_ = "solid_tumor"
...
- yield span
| 37 | 6 | 0 | 83.78% |
edsnlp/pipes/ner/disorders/peripheral_vascular_disease/peripheral_vascular_disease.pyWas already missing at line 107 if "peripheral" not in span._.assigned.keys():
- continue
| 15 | 1 | 0 | 93.33% |
edsnlp/pipes/ner/disorders/diabetes/diabetes.pyWas already missing at line 131 # Mostly FP
- continue
Was already missing at line 134 elif self.has_far_complications(span):
- span._.status = 2
Was already missing at line 146 if next(iter(self.complication_matcher(context)), None) is not None:
- return True
return False | 31 | 3 | 0 | 90.32% |
edsnlp/pipes/ner/disorders/connective_tissue_disease/connective_tissue_disease.pyWas already missing at line 103 # Huge change of FP / Title section
- continue
| 14 | 1 | 0 | 92.86% |
edsnlp/pipes/ner/disorders/ckd/ckd.pyWas already missing at lines 120-123 dfg_value = float(dfg_span.text.replace(",", ".").strip())
- except ValueError:
- logger.trace(f"DFG value couldn't be extracted from {dfg_span.text}")
- return False
| 29 | 3 | 0 | 89.66% |
edsnlp/pipes/ner/disorders/cerebrovascular_accident/cerebrovascular_accident.pyWas already missing at lines 111-113 if span._.source == "ischemia":
- if "brain" not in span._.assigned.keys():
- continue
| 17 | 2 | 0 | 88.24% |
edsnlp/pipes/ner/adicap/models.pyWas already missing at line 15 def norm(self) -> str:
- return self.code
Was already missing at line 18 def __str__(self):
- return self.norm()
| 16 | 2 | 0 | 87.50% |
edsnlp/pipes/misc/split/split.pyWas already missing at lines 175-177 if max_length <= 0 and self.regex is None:
- yield doc
- return
| 70 | 2 | 0 | 97.14% |
edsnlp/pipes/misc/sections/sections.pyWas already missing at line 126 if sections is None:
- sections = patterns.sections
sections = dict(sections) | 45 | 1 | 0 | 97.78% |
edsnlp/pipes/misc/quantities/quantities.pyWas already missing at lines 147-149 def __getitem__(self, item: int):
- assert isinstance(item, int)
- return [self][item]
Was already missing at lines 160-163 def __eq__(self, other: Any):
- if isinstance(other, SimpleQuantity):
- return self.convert_to(other.unit) == other.value
- return False
Was already missing at line 166 if other.unit == self.unit:
- return self.__class__(self.value + other.value, self.unit, self.registry)
return self.__class__(Was already missing at line 193 return self.convert_to(other_unit)
- except KeyError:
raise AttributeError(f"Unit {other_unit} not found")Was already missing at line 198 def verify(cls, ent):
- return True
Was already missing at line 237 def __lt__(self, other: Union[SimpleQuantity, "RangeQuantity"]):
- return max(self.convert_to(other.unit)) < min((part.value for part in other))
Was already missing at line 248 return self.convert_to(other.unit) == other.value
- return False
Was already missing at line 262 def verify(cls, ent):
- return True
Was already missing at line 861 if snippet.end != last and doclike.doc[last: snippet.end].text.strip() == "":
- pseudo.append("w")
pseudo = "".join(pseudo)Was already missing at line 1042 if start_line is None:
- continue
Was already missing at lines 1073-1075 unit_norm = self.unit_followers[unit_before.label_]
- except (KeyError, AttributeError, IndexError):
- pass
Was already missing at line 1118 ):
- ent = doc[unit_text.start: number.end]
else:Was already missing at lines 1125-1127 dims = self.unit_registry.parse_unit(unit_norm)[0]
- except KeyError:
- continue
Was already missing at lines 1233-1235 last._.set(last.label_, new_value)
- except (AttributeError, TypeError):
- merged.append(ent)
else: | 432 | 20 | 0 | 95.37% |
edsnlp/pipes/misc/dates/models.pyWas already missing at line 156 else:
- d["month"] = note_datetime.month
if self.day is None:Was already missing at lines 160-166 else:
- if self.year is None:
...
- d["day"] = default_day
Was already missing at lines 174-176 return dt
- except ValueError:
- return None
Was already missing at line 192 else:
- return None
Was already missing at line 208 if self.second:
- norm += f"{self.second:02}s"
| 199 | 11 | 0 | 94.47% |
edsnlp/pipes/misc/dates/dates.pyWas already missing at line 249 if isinstance(absolute, str):
- absolute = [absolute]
if isinstance(relative, str):Was already missing at line 251 if isinstance(relative, str):
- relative = [relative]
if isinstance(duration, str):Was already missing at line 253 if isinstance(duration, str):
- relative = [duration]
if isinstance(false_positive, str):Was already missing at lines 357-366 if self.merge_mode == "align":
- alignments = align_spans(matches, spans, sort_by_overlap=True)
...
- matches.append(span)
Was already missing at line 451 elif d1 in seen or v1.bound is None or v2.bound is None:
- continue
Was already missing at lines 462-464 if v1.mode == Mode.DURATION:
- m1 = Bound.FROM if v2.bound == Bound.UNTIL else Bound.UNTIL
- m2 = v2.mode or Bound.FROM
elif v2.mode == Mode.DURATION: | 153 | 15 | 0 | 90.20% |
edsnlp/pipes/misc/consultation_dates/consultation_dates.pyWas already missing at line 131 else:
- self.date_matcher = None
Was already missing at line 134 if not consultation_mention:
- consultation_mention = []
elif consultation_mention is True: | 48 | 2 | 0 | 95.83% |
edsnlp/pipes/core/normalizer/__init__.pyWas already missing at line 7 def excluded_or_space_getter(t):
- return t.is_space or t.tag_ == "EXCLUDED"
| 5 | 1 | 0 | 80.00% |
edsnlp/pipes/core/endlines/endlines.pyWas already missing at lines 156-160 if end_lines_model is None:
- path = build_path(__file__, "base_model.pkl")
-
- with open(path, "rb") as inp:
- self.model = pickle.load(inp)
elif isinstance(end_lines_model, str):Was already missing at lines 163-165 self.model = pickle.load(inp)
- elif isinstance(end_lines_model, EndLinesModel):
- self.model = end_lines_model
else:Was already missing at line 196 ):
- return "ENUMERATION"
Was already missing at line 283 if np.isnan(sigma):
- sigma = 1
| 87 | 7 | 0 | 91.95% |
edsnlp/pipes/core/contextual_matcher/models.pyWas already missing at lines 28-32 if isinstance(v, list):
- assert (
- len(v) == 2
- ), "`window` should be a tuple/list of two integer, or a single integer"
- v = tuple(v)
if isinstance(v, int): | 138 | 2 | 0 | 98.55% |
edsnlp/pipes/core/contextual_matcher/contextual_matcher.pyWas already missing at line 94 )
- label = label_name
if label is None:Was already missing at line 343 if assigned is None:
- continue
if replace_entity: | 143 | 2 | 0 | 98.60% |
edsnlp/patch_spacy.pyWas already missing at lines 67-69 # if module is reloaded.
- existing_func = registry.factories.get(internal_name)
- if not util.is_same_func(factory_func, existing_func):
raise ValueError( | 31 | 2 | 0 | 93.55% |
edsnlp/package.pyWas already missing at lines 475-477 version = version or pyproject["project"]["version"]
- except (KeyError, TypeError):
- version = "0.1.0"
name = name or pyproject["project"]["name"]Was already missing at line 481 else:
- main_package = None
model_package = snake_case(name.lower()) | 207 | 3 | 0 | 98.55% |
edsnlp/metrics/span_attributes.pyWas already missing at lines 56-58 )
- assert attributes is None
- attributes = kwargs.pop("qualifiers")
if attributes is None: | 71 | 2 | 0 | 97.18% |
edsnlp/matchers/simstring.pyWas already missing at line 280 if custom:
- attr = attr[1:].lower()
Was already missing at line 295 if custom:
- token_text = getattr(token._, attr)
else: | 146 | 2 | 0 | 98.63% |
edsnlp/language.pyWas already missing at line 103 if last != begin:
- logger.warning(
"Missed some characters during" | 51 | 1 | 0 | 98.04% |
edsnlp/data/standoff.pyWas already missing at line 38 def __init__(self, ann_file, line):
- super().__init__(f"File {ann_file}, unrecognized Brat line {line}")
Was already missing at line 192 )
- except Exception:
raise Exception( | 185 | 2 | 0 | 98.92% |
edsnlp/data/polars.pyWas already missing at line 35 if hasattr(data, "collect"):
- data = data.collect()
assert isinstance(data, pl.DataFrame) | 54 | 1 | 0 | 98.15% |
edsnlp/data/json.pyWas already missing at line 87 return records
- except Exception as e:
raise Exception(f"Cannot read {file}: {e}") | 113 | 1 | 0 | 99.12% |
edsnlp/data/converters.pyWas already missing at line 140 if "tokenizer" in CONTEXT[0]:
- return CONTEXT[0]["tokenizer"]
if _DEFAULT_TOKENIZER is None:Was already missing at line 669 if isinstance(converter, type) or kwargs_to_init:
- return converter(**kwargs), {}
return converter, validate_kwargs(converter, kwargs) | 204 | 2 | 0 | 99.02% |
edsnlp/core/torch_component.pyWas already missing at line 392 if hasattr(self, "compiled"):
- res = self.compiled(batch)
else:Was already missing at line 438 """
- return self.preprocess(doc)
Was already missing at line 463 if object.__repr__(self) in exclude:
- return
exclude.add(object.__repr__(self)) | 179 | 3 | 0 | 98.32% |
edsnlp/core/stream.pyWas already missing at lines 190-192 if isinstance(batch, StreamSentinel):
- yield batch
- continue
results = []Was already missing at lines 994-996 elif op.batch_fn is None:
- batch_size = op.size
- batch_fn = batchify
else: | 353 | 4 | 0 | 98.87% |
edsnlp/core/registries.pyWas already missing at line 95 if obj.error is not None:
- raise obj.error
| 164 | 1 | 0 | 99.39% |
edsnlp/core/pipeline.pyWas already missing at lines 487-489 if a is not b and pipe_to_params[a] & pipe_to_params[b]:
- current.append(b)
- remaining_pipes[j] = None
remaining_pipes = [p for p in remaining_pipes if p is not None]Was already missing at line 610 if name in exclude:
- continue
if name not in components:Was already missing at lines 721-724 """
- res = Stream.ensure_stream(docs)
- res = res.map(functools.partial(self.preprocess, supervision=supervision))
- return res
| 443 | 6 | 0 | 98.65% |
edsnlp/connectors/omop.pyWas already missing at line 69 if not isinstance(row.ents, list):
- continue
Was already missing at line 87 else:
- doc.spans[span.label_].append(span)
Was already missing at line 127 if df.note_id.isna().any():
- df["note_id"] = range(len(df))
Was already missing at line 171 if i > 0:
- df.term_modifiers += ";"
df.term_modifiers += ext + "=" + df[ext].astype(str) | 84 | 4 | 0 | 95.24% |
edsnlp/processing/multiprocessing.pyWas already missing at line 246 def save_align_devices_hook(pickler: Any, obj: Any):
- pickler.save_reduce(load_align_devices_hook, (obj.__dict__,), obj=obj)
Was already missing at lines 249-256 def load_align_devices_hook(state):
- state["execution_device"] = MAP_LOCATION
...
- AlignDevicesHook = None
Was already missing at lines 448-453 self.on_stop()
- except BaseException as e:
...
- self.main_control_queue.put(e)
finally:Was already missing at lines 457-459 pass
- except StopSignal:
- pass
for name, queue in self.consumer_queues(stage):Was already missing at line 593 while schedule[task_idx] is None:
- task_idx = (task_idx + 1) % len(schedule)
Was already missing at lines 657-659 if isinstance(docs, StreamSentinel):
- self.active_batches[stage].append([None, None, None, docs])
- continue
batch_id = str(hash(tuple(id(x) for x in docs)))[-8:] + "-" + self.uidWas already missing at line 815 if self.stop and not stop_mode:
- raise StopSignal()
Was already missing at lines 1128-1135 if out[0].kind == requires_sentinel:
- missing_sentinels -= 1
...
- continue
if requires_sentinel:Was already missing at line 1154 if idx % world_size != local_rank:
- continue
| 635 | 24 | -1 | 96.22% |
263 files skipped due to complete coverage.
Coverage success: total of 97.94% is above 97.90% 🎉
sonarcloud[bot]
Improve docs and drop
edsnlp.training.optimization.create_optimizerin favor of the underlyingedsnlp.training.optimizer.ScheduledOptimizerdirectlyChecklist