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Bump pytest-mock from 3.11.1 to 3.14.0 #310

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Bump pytest-mock from 3.11.1 to 3.14.0 #310

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0cd809e
Bump pytest-mock from 3.11.1 to 3.14.0
dependabot[bot] Mar 22, 2024
191c834
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 22, 2024
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18 changes: 9 additions & 9 deletions example/example_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,20 +41,20 @@
tasks="All",
networks="STRING",
features="SixSpeciesN2V",
sp_trn = "Human",
sp_tst = "Mouse",
gsc= "GO",
sp_trn="Human",
sp_tst="Mouse",
gsc="GO",
)

# Run through the pipeline
# First initialize the geneplexus object
myclass = geneplexus.GenePlexus(
file_loc = fp_data,
gsc = "Combined",
features = "SixSpeciesN2V",
net_type = "STRING",
sp_trn = "Human",
sp_tst = "Mouse",
file_loc=fp_data,
gsc="Combined",
features="SixSpeciesN2V",
net_type="STRING",
sp_trn="Human",
sp_tst="Mouse",
)

# Load the input genes into the class and set up positives/negatives
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6 changes: 3 additions & 3 deletions geneplexus/geneplexus.py
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Expand Up @@ -16,7 +16,8 @@
from ._config import logger
from ._config.logger_util import set_stream_level
from .download import download_select_data
from .exception import CustomDataError, ZebrafishBioGRIDError
from .exception import CustomDataError
from .exception import ZebrafishBioGRIDError


class GenePlexus:
Expand Down Expand Up @@ -88,14 +89,13 @@ def __init__(

if input_genes is not None:
self.load_genes(input_genes)

if ("Zebrafish" == (self.sp_trn or self.sp_tst)) and (self.net_type == "BioGRID"):
raise ZebrafishBioGRIDError(
f"The BioGRID network for Zebrafish is not "
"included due to it not having enough nodes "
"so this combination is not allowed.",
)


@property
def _params(self) -> List[str]:
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2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -4,4 +4,4 @@ pytest-cov==4.1.0
pytest-order==1.1.0
parameterized==0.9.0
requests-mock==1.11.0
pytest-mock==3.11.1
pytest-mock==3.14.0
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