From 9e2a51017477464336f370f6e70043876e508b6b Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Fri, 1 Apr 2022 13:23:11 +0200
Subject: [PATCH] MAINT: Linting tests run through now.
Issue for real fix: #80
---
pylintrc | 16 +++++++++++---
src/caosadvancedtools/cfood.py | 10 +++++++--
src/caosadvancedtools/cfoods/h5.py | 1 +
.../converter/labfolder_api.py | 2 +-
src/caosadvancedtools/models/parser.py | 4 ++--
.../scifolder/simulation_cfood.py | 10 ++++-----
src/caosadvancedtools/scifolder/withreadme.py | 22 +++++++++----------
.../serverside/generic_analysis.py | 3 +--
src/caosadvancedtools/serverside/helper.py | 2 +-
9 files changed, 43 insertions(+), 27 deletions(-)
diff --git a/pylintrc b/pylintrc
index 8a12125d..625f83ce 100644
--- a/pylintrc
+++ b/pylintrc
@@ -2,8 +2,18 @@
[FORMAT]
# Good variable names which should always be accepted, separated by a comma
-good-names=ii,rt
-
+good-names=ii,rt,df
[TYPECHECK]
-ignored-modules=etree
+# List of module names for which member attributes should not be checked
+# (useful for modules/projects where namespaces are manipulated during runtime
+# and thus existing member attributes cannot be deduced by static analysis
+ignored-modules=etree,h5py,labfolder
+
+[MASTER]
+# TODO: The max_inferred size is necessary for https://github.com/PyCQA/pylint/issues/4577,
+# otherwise pandas.read_csv's return value would be inferred as TextFileReader.
+init-hook=
+ import sys; sys.path.extend(["src/caosadvancedtools"]);
+ import astroid; astroid.context.InferenceContext.max_inferred = 500;
+
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 3c2d5408..f060bed5 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -841,8 +841,14 @@ class CMeal(object):
matching_groups = []
def __init__(self):
+ self.item = None
+ self.match = None
self.__class__.existing_instances.append(self)
+ @staticmethod
+ def get_re():
+ raise NotImplementedError("Subclasses must implement this function.")
+
@classmethod
def all_groups_equal(cls, m1, m2):
equal = True
@@ -878,5 +884,5 @@ class CMeal(object):
if match is None:
return False
- else:
- return self.all_groups_equal(match, self.match)
+
+ return self.all_groups_equal(match, self.match)
diff --git a/src/caosadvancedtools/cfoods/h5.py b/src/caosadvancedtools/cfoods/h5.py
index 6c68edd3..cbf9d0ba 100644
--- a/src/caosadvancedtools/cfoods/h5.py
+++ b/src/caosadvancedtools/cfoods/h5.py
@@ -124,6 +124,7 @@ class H5CFood(AbstractFileCFood):
"""CFood which consumes HDF5 files."""
super().__init__(*args, **kwargs)
self.h5file = None
+ self.identifiable_root = None
self.root_name = "root"
self.hdf5Container = db.Container()
self.em = EntityMapping()
diff --git a/src/caosadvancedtools/converter/labfolder_api.py b/src/caosadvancedtools/converter/labfolder_api.py
index a29d965b..cf57c015 100644
--- a/src/caosadvancedtools/converter/labfolder_api.py
+++ b/src/caosadvancedtools/converter/labfolder_api.py
@@ -28,7 +28,7 @@ import time
import html2text
import caosdb as db
-from labfolder.connection import configure_connection
+from labfolder.connection import configure_connection # pylint: disable=import-error
class Importer(object):
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index b290b1b7..48fc1e72 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/src/caosadvancedtools/models/parser.py
@@ -566,9 +566,9 @@ class Parser(object):
db.BOOLEAN]:
if is_list:
- value.datatype = db.LIST(db.__getattribute__(dtype))
+ value.datatype = db.LIST(db.__getattribute__(dtype)) # pylint: disable=no-member
else:
- value.datatype = db.__getattribute__(dtype)
+ value.datatype = db.__getattribute__(dtype) # pylint: disable=no-member
continue
diff --git a/src/caosadvancedtools/scifolder/simulation_cfood.py b/src/caosadvancedtools/scifolder/simulation_cfood.py
index ae129e6a..c8f23f14 100644
--- a/src/caosadvancedtools/scifolder/simulation_cfood.py
+++ b/src/caosadvancedtools/scifolder/simulation_cfood.py
@@ -88,22 +88,22 @@ class SimulationCFood(AbstractFileCFood, WithREADME):
self.to_be_updated,
datatype=db.LIST(db.REFERENCE))
- if SOURCES.key in self.header:
+ if SOURCES.key in self.header: # pylint: disable=unsupported-membership-test
reference_records_corresponding_to_files(
record=self.simulation,
recordtypes=["Experiment", "Publication", "Simulation",
"Analysis"],
- globs=get_glob(self.header[SOURCES.key]),
+ globs=get_glob(self.header[SOURCES.key]), # pylint: disable=unsubscriptable-object
property_name=dm.sources,
path=self.crawled_path,
to_be_updated=self.to_be_updated)
self.reference_files_from_header(record=self.simulation)
- if REVISIONOF.key in self.header:
+ if REVISIONOF.key in self.header: # pylint: disable=unsupported-membership-test
reference_records_corresponding_to_files(
record=self.simulation,
- recordtypes=[dm.Software],
+ recordtypes=[dm.Software], # pylint: disable=no-member
property_name=dm.revisionOf,
- globs=get_glob(self.header[dm.revisionOf]),
+ globs=get_glob(self.header[dm.revisionOf]), # pylint: disable=unsubscriptable-object
path=self.crawled_path,
to_be_updated=self.to_be_updated)
diff --git a/src/caosadvancedtools/scifolder/withreadme.py b/src/caosadvancedtools/scifolder/withreadme.py
index 8a63e1f6..e1968ba4 100644
--- a/src/caosadvancedtools/scifolder/withreadme.py
+++ b/src/caosadvancedtools/scifolder/withreadme.py
@@ -121,12 +121,12 @@ class WithREADME(object):
@property
def header(self):
if self._header is None:
- if self.crawled_path.lower().endswith(".md"):
+ if self.crawled_path.lower().endswith(".md"): # pylint: disable=no-member
self._header = get_md_header(
- fileguide.access(self.crawled_path))
- elif self.crawled_path.lower().endswith(".xlsx"):
+ fileguide.access(self.crawled_path)) # pylint: disable=no-member
+ elif self.crawled_path.lower().endswith(".xlsx"): # pylint: disable=no-member
self._header = get_xls_header(
- fileguide.access(self.crawled_path))
+ fileguide.access(self.crawled_path)) # pylint: disable=no-member
else:
raise RuntimeError("Readme format not recognized.")
self.convert_win_paths()
@@ -145,7 +145,7 @@ class WithREADME(object):
globs = get_glob(self.header[field.key])
files = get_files_referenced_by_field(
- globs, prefix=os.path.dirname(self.crawled_path))
+ globs, prefix=os.path.dirname(self.crawled_path)) # pylint: disable=no-member
description = [get_description(val) for val in
self.header[field.key]]
@@ -160,7 +160,7 @@ class WithREADME(object):
LOGGER.warn("ATTENTION: the field {} does not reference any "
"known files".format(field.key))
- self.attached_filenames.extend(flat_list)
+ self.attached_filenames.extend(flat_list) # pylint: disable=no-member
def convert_path(self, el):
""" converts the path in el to unix type
@@ -185,7 +185,7 @@ class WithREADME(object):
return win_path_converter(el)
def convert_win_paths(self):
- for field in self.win_paths:
+ for field in self.win_paths: # pylint: disable=no-member
if field in self.header:
if isinstance(self.header[field], list):
@@ -245,7 +245,7 @@ class WithREADME(object):
references[ref_type],
record,
ref_type,
- to_be_updated=self.to_be_updated,
+ to_be_updated=self.to_be_updated, # pylint: disable=no-member
)
def reference_included_records(self, record, fields, to_be_updated):
@@ -255,16 +255,16 @@ class WithREADME(object):
for field in fields:
- if field.key not in self.header:
+ if field.key not in self.header: # pylint: disable=no-member
continue
included = []
- for item in self.header[field.key]:
+ for item in self.header[field.key]: # pylint: disable=no-member
if INCLUDE.key in item:
try:
included.extend(
get_entity_ids_from_include_file(
- os.path.dirname(self.crawled_path),
+ os.path.dirname(self.crawled_path), # pylint: disable=no-member
item[INCLUDE.key]))
except ValueError:
al = logging.getLogger("caosadvancedtools")
diff --git a/src/caosadvancedtools/serverside/generic_analysis.py b/src/caosadvancedtools/serverside/generic_analysis.py
index 66bec8a7..85d0c860 100644
--- a/src/caosadvancedtools/serverside/generic_analysis.py
+++ b/src/caosadvancedtools/serverside/generic_analysis.py
@@ -210,5 +210,4 @@ def main():
if __name__ == "__main__":
- args = _parse_arguments()
- sys.exit(main(args))
+ sys.exit(main())
diff --git a/src/caosadvancedtools/serverside/helper.py b/src/caosadvancedtools/serverside/helper.py
index 33deb8cc..ba75739e 100644
--- a/src/caosadvancedtools/serverside/helper.py
+++ b/src/caosadvancedtools/serverside/helper.py
@@ -394,7 +394,7 @@ def send_mail(from_addr, to, subject, body, cc=None, bcc=None,
err_msg = ("No sendmail executable configured. "
"Please configure `Misc.sendmail` "
"in your pycaosdb.ini.")
- raise db.ConfigurationException(err_msg)
+ raise db.ConfigurationError(err_msg)
sendmail = caosdb_config["Misc"]["sendmail"]
# construct sendmail command
--
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