🚀 Added pre-commit config for gh workflow

Author: amilworks

.gitignore

@@ -1,3 +1,3 @@
 **/__pycache__/**
 *.bak
-**/.ruff_cache/**
+**/.ruff_cache/**

.pre-commit-config.yaml

@@ -11,17 +11,15 @@ repos:
       - id: isort
         language_version: python3
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0  # Update as needed
-    hooks:
-      - id: flake8
-        additional_dependencies: [flake8-bugbear]  # optional extra checks
+          #  - repo: https://github.com/PyCQA/flake8
+          #    rev: 6.1.0  # Update as needed
+          #    hooks:
+          #      - id: flake8
+          #        additional_dependencies: [flake8-bugbear]  # optional extra checks
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0  # Update as needed
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
-      - id: debug-statements  # Optional: fails if there are print() or debugger statements
-

README.md

@@ -23,7 +23,7 @@ from bqapi.util import fetch_blob
 
 For development, follow [this guide](https://towardsdatascience.com/how-to-upload-your-python-package-to-pypi-de1b363a1b3) and [this repo](https://github.com/gmyrianthous/example-publish-pypi).
 
-## Added GitHub Action 
+## Added GitHub Action
 
 ### Summary
 
@@ -34,4 +34,3 @@ For development, follow [this guide](https://towardsdatascience.com/how-to-uploa
 5. Make sure to have PyPi account credentials
 6. run `twine upload dist/*` from  main folder
 7. Enter username and password
-

pyproject.toml

@@ -2,6 +2,6 @@
 # Follow Flake8's behavior
 lint.select = ["E", "F", "W", "C90"]  # Enables Flake8-compatible rules
 lint.ignore = []                      # Add rules to ignore
-line-length = 79                 
-exclude = ["venv", ".git", "__pycache__", "**/tests/**"] 
-lint.mccabe.max-complexity = 25  # Set your desired threshold
+line-length = 79
+exclude = ["venv", ".git", "__pycache__", "**/tests/**"]
+lint.mccabe.max-complexity = 25  # Set your desired threshold

setup.py

@@ -1,17 +1,19 @@
-from setuptools import setup, find_packages
-
+from setuptools import find_packages, setup
 
 setup(
-    name='bqapi-ucsb',
-    version='1.0.6',
+    name="bqapi-ucsb",
+    version="1.0.6",
     author="Bisque Team",
-    author_email='amil@ucsb.edu',
+    author_email="amil@ucsb.edu",
     description="""Python API for interacting with BisQue""",
-    packages=find_packages('src'),
-    package_dir={'': 'src'},
-    keywords='API Bisque',
-    url='https://github.com/UCSB-VRL/bisqueUCSB',
+    packages=find_packages("src"),
+    package_dir={"": "src"},
+    keywords="API Bisque",
+    url="https://github.com/UCSB-VRL/bisqueUCSB",
     install_requires=[
-          'six', 'lxml', 'requests==2.32.3', 'requests-toolbelt',
-      ],
+        "six",
+        "lxml",
+        "requests==2.32.3",
+        "requests-toolbelt",
+    ],
 )

src/bqapi/RequestsMonkeyPatch/__init__.py

@@ -1 +1 @@
-#empty
+# empty

src/bqapi/RequestsMonkeyPatch/requests_patch.py

@@ -7,24 +7,25 @@
 """
 
 import email.utils
-
 # import mimetypes
 import warnings
 
 import requests
 import requests.packages.urllib3 as urllib3
 import six
-from .monkeypatch import monkeypatch_method
 
+from .monkeypatch import monkeypatch_method
 
 REQUESTS_V = [int(s) for s in requests.__version__.split(".")]
 
 print(REQUESTS_V)
 if REQUESTS_V < [2, 4, 0] or REQUESTS_V > [2, 32, 3]:
-    warnings.warn("""\
+    warnings.warn(
+        """\
 We need to patch requests 2.4.0 up to 2.32.3, make sure your version of
 requests needs this patch, greater than 2.4.3 we do not know if this
-patch applys.""")
+patch applys."""
+    )
     raise ImportError("Requests 2.4.0 to 2.32.3 is required!")
 # elif requests_v > [3, 0, 0]:
 #    #does not require this patch

src/bqapi/blockable_module.py

@@ -1,11 +1,8 @@
-import sys
 import collections
-
-from bqapi import BQSession
-
-
 import logging
+import sys
 
+from bqapi import BQSession
 
 # logging.basicConfig(filename='BlockableModule.log',level=logging.DEBUG) #!!!
 log = logging.getLogger("bqapi.blockable_module")
@@ -21,17 +18,13 @@ def main(self, mex_url=None, auth_token=None, bq=None, **kw):
 
         # check for list parameters
         params = bq.get_mex_inputs()
-        if isinstance(params, dict) or not isinstance(
-            params, collections.Iterable
-        ):
+        if isinstance(params, dict) or not isinstance(params, collections.Iterable):
             params = [params]
         # pass values directly as args
         for single_params in params:
             for param_name in single_params:
                 if "value" in single_params[param_name]:
-                    single_params[param_name] = single_params[param_name].get(
-                        "value"
-                    )
+                    single_params[param_name] = single_params[param_name].get("value")
 
         # TODO: measure block startup time
         self.start_block(bq, params)

src/bqapi/bqclass.py

@@ -51,25 +51,23 @@
 __version__ = "0.1"
 __revision__ = "$Rev$"
 __date__ = "$Date$"
-__copyright__ = (
-    "Center for BioImage Informatics, University California, Santa Barbara"
-)
+__copyright__ = "Center for BioImage Informatics, University California, Santa Barbara"
 
-import os
-import sys
-import math
-import io
+import collections
 import inspect
+import io
 import logging
+import math
+import os
+import sys
 import tempfile
-import collections
 
 try:
     from lxml import etree
 except ImportError:
     import xml.etree.ElementTree as etree
-from .xmldict import xml2nv
 
+from .xmldict import xml2nv
 
 log = logging.getLogger("bqapi.class")
 
@@ -148,9 +146,7 @@ def __repr__(self):
     def __str__(self):
         return "(%s:%s)" % (
             self.xmltag,
-            ",".join(
-                ["%s=%s" % (f, getattr(self, f, "")) for f in self.xmlfields]
-            ),
+            ",".join(["%s=%s" % (f, getattr(self, f, "")) for f in self.xmlfields]),
         )
 
     def toTuple(self):
@@ -429,9 +425,7 @@ def fetch(self, path=None, stream=False):
         response = image_service.fetch(url, stream=stream)
         if path is not None:
             with open(path, "wb") as fb:
-                for block in response.iter_content(
-                    chunk_size=16 * 1024 * 1024
-                ):  # 16MB
+                for block in response.iter_content(chunk_size=16 * 1024 * 1024):  # 16MB
                     fb.write(block)
                 response.close()
         else:
@@ -476,9 +470,7 @@ def asarray(self):
             # response.raw.decode_content = True
             return tifffile.imread(io.BytesIO(response.content))
 
-    def savearray(
-        self, fname, imdata=None, imshape=None, dtype=None, **kwargs
-    ):
+    def savearray(self, fname, imdata=None, imshape=None, dtype=None, **kwargs):
         try:
             import tifffile
         except ImportError:

src/bqapi/bqfeature.py

@@ -1,21 +1,22 @@
 # import threading
-from threading import Thread
-import socket
 import errno
-import tempfile
-import urllib.request
-import urllib.parse
-import urllib.error
+import logging
 import os
-from math import ceil
 import queue
-import logging
+import socket
+import tempfile
+import urllib.error
+import urllib.parse
+import urllib.request
 import warnings
 from collections import namedtuple
+from math import ceil
+from threading import Thread
+
+from .exception import BQCommError
 
 # import numpy as np
 
-from .exception import BQCommError
 
 try:  # checks for lxml if not found uses python xml
     from lxml import etree
@@ -36,11 +37,13 @@
 FeatureResource = namedtuple("FeatureResource", ["image", "mask", "gobject"])
 FeatureResource.__new__.__defaults__ = (None, None, None)
 
+
 class FeatureError(Exception):
     """
     Feature Communication Exception
     """
 
+
 class Feature(object):
     def fetch(self, session, name, resource_list, path=None):
         """
@@ -74,8 +77,7 @@ def fetch(self, session, name, resource_list, path=None):
             query = "&".join(query)
             sub.attrib["uri"] = "%s?%s" % (url, query)
 
-        log.debug("Fetch Feature %s for %s resources" % (name,
-                            len(resource_list)))
+        log.debug("Fetch Feature %s for %s resources" % (name, len(resource_list)))
 
         if path is None:
             f = tempfile.NamedTemporaryFile(
@@ -130,8 +132,7 @@ def fetch_vector(self, session, name, resource_list):
             status = status[index[0]][0]
             hdf5.close()
             os.remove(hdf5.filename)  # remove file from temp directory
-            raise FeatureError("%s:Error occured during feature calculations"
-                                                % status)
+            raise FeatureError("%s:Error occured during feature calculations" % status)
         table = hdf5.root.values
         # status_table = hdf5.root.status # to get the status
         feature_vector = table[:]["feature"]
@@ -150,8 +151,8 @@ def length(session, name):
         @return: feature length
         """
         xml = session.fetchxml("/features/%s" % name)
-        return int(xml.find(
-                    'feature/tag[@name="feature_length"]').attrib.get("value"))
+        return int(xml.find('feature/tag[@name="feature_length"]').attrib.get("value"))
+
 
 class ParallelFeature(Feature):
     MaxThread = 8
@@ -200,8 +201,7 @@ def run(self):
                 else:
                     break
 
-    def request_thread_pool(self, request_queue, errorcb=None,
-                                    thread_count=MaxThread):
+    def request_thread_pool(self, request_queue, errorcb=None, thread_count=MaxThread):
         """
         Runs the BQRequestThread
 
@@ -293,8 +293,7 @@ def fetch(self, session, name, resource_list, path=None):
             log.warning("Warning no resources were provided")
             return
 
-        log.debug("Exctracting %s on %s resources" % (name,
-                                              len(resource_list)))
+        log.debug("Exctracting %s on %s resources" % (name, len(resource_list)))
 
         if path is None:
             f = tempfile.TemporaryFile(suffix=".h5", dir=tempfile.gettempdir())
@@ -338,8 +337,7 @@ def run(self):
                                     temp_status_table = hdf5temp.root.status
                                     if not hasattr(hdf5.root, "values"):
                                         temp_table.copy(hdf5.root, "values")
-                                        temp_status_table.copy(hdf5.root,
-                                                                "status")
+                                        temp_status_table.copy(hdf5.root, "status")
                                     else:
                                         table = hdf5.root.values
                                         status_table = hdf5.root.status
@@ -420,8 +418,7 @@ def request():
         else:
             thread_num, chunk_size = self.calculate_request_plan(resource_list)
 
-        for partial_resource_list in self.chunk(resource_list,
-                                                int(chunk_size)):
+        for partial_resource_list in self.chunk(resource_list, int(chunk_size)):
             request_queue.put(request_factory(partial_resource_list))
 
         w = WriteHDF5Thread(write_queue)
@@ -462,5 +459,4 @@ def fetch_vector(self, session, name, resource_list):
 
         @return: a list of features as numpy array
         """
-        return super(ParallelFeature, self).fetch_vector(session, name,
-                                                         resource_list)
+        return super(ParallelFeature, self).fetch_vector(session, name, resource_list)