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Release 0.0.0a17 #173

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merged 17 commits into from
Dec 4, 2019
Merged

Release 0.0.0a17 #173

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6884a82
Add helper function and test case to deal with timepoint-specific par…
Oct 4, 2019
ec0bd35
Add functionality to create data summary report (#140) (#141)
dweindl Oct 22, 2019
f63ace7
Fix get_noise_distributions: so far we got 'normal' everywhere due to…
dweindl Nov 29, 2019
82ff3dc
Fix create_parameter_df: Exclude rule targets (#149)
dweindl Nov 29, 2019
12f75a1
Verify condition table column names occur as model parameters (Closes…
dweindl Nov 29, 2019
90d8545
Fixup #151: ignore conditionName column (#153)
dweindl Nov 29, 2019
8fab85e
More informative error messages in case of wrongly set observable and…
dweindl Nov 29, 2019
92e3366
Update doc for copasi import and github installation (#158)
dweindl Dec 2, 2019
eca81a5
Extend validator to check if all required parameters are present in p…
dweindl Dec 2, 2019
ed1ec91
Setup documentation for RTD (#161)
dweindl Dec 3, 2019
79b7c88
Handle None in petab.core.split_parameter_replacement_list (Closes #121)
dweindl Dec 1, 2019
5dce8d2
Fix(lint) correct handling of optional columns. Check before access.
dweindl Nov 30, 2019
ebef1fc
Visualization, allow empty column observableParameters (measurement-f…
erikadudki Dec 3, 2019
60d5e1f
Cleanup (#167)
dweindl Dec 4, 2019
5c399c9
Add CHANGELOG (Closes #137)
dweindl Dec 4, 2019
7eec68e
Remove obsolete generate_experiment_id.py (Closes #111)
dweindl Dec 3, 2019
a6a304f
Bump version number to 0.0.0a17 and update ChangeLog
dweindl Dec 4, 2019
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Fix(lint) correct handling of optional columns. Check before access.
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@dweindl
dweindl committed Dec 3, 2019
commit 5dce8d24ca2fe19518b559aded6fd21af5e04535
19 changes: 14 additions & 5 deletions petab/lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,17 +56,26 @@ def check_condition_df(df: pd.DataFrame, sbml_model: libsbml.Model):


def check_measurement_df(df):
req_cols = [
"observableId", "preequilibrationConditionId", "simulationConditionId",
"measurement", "time", "observableParameters", "noiseParameters"
required_columns = [
"observableId", "simulationConditionId", "measurement", "time"
]
optional_columns = [
"preequilibrationConditionId",
"observableParameters", "noiseParameters"
]

for column_name in req_cols:
_check_df(df, required_columns, "measurement")

for column_name in required_columns:
if not np.issubdtype(df[column_name].dtype, np.number):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name)

_check_df(df, req_cols, "measurement")
for column_name in optional_columns:
if column_name in df \
and not np.issubdtype(df[column_name].dtype, np.number):
assert_no_leading_trailing_whitespace(
df[column_name].values, column_name)


def check_parameter_df(
Expand Down