Precommit config

.github/workflows/pre-commit.yml

@@ -0,0 +1,31 @@
+name: Pre-commit Checks
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Install pre-commit if not already available in your dependencies
+          pip install pre-commit
+          # Optionally install your API package dependencies if needed
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Run pre-commit checks
+        run: pre-commit run

.gitignore

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

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.7.0  # Use the latest stable version available
+    hooks:
+      - id: black
+        language_version: python3
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0  # Update as appropriate
+    hooks:
+      - 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/pre-commit/pre-commit-hooks
+    rev: v4.6.0  # Update as needed
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml

README.md

@@ -1,31 +1,33 @@
 # Bisque API for Python 3
 
 [![Upload Python Package](https://github.com/UCSB-VRL/bqapi/actions/workflows/python-publish.yml/badge.svg)](https://github.com/UCSB-VRL/bqapi/actions/workflows/python-publish.yml)
+[![Pre-commit Checks](https://github.com/UCSB-VRL/bqapi/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/UCSB-VRL/bqapi/actions/workflows/pre-commit.yml)
+[![PyPI](https://img.shields.io/pypi/v/bqapi-ucsb?style=flat-square)](https://pypi.org/project/bqapi-ucsb/)
+[![Documentation](https://img.shields.io/badge/Documentation-View%20here-brightgreen?style=flat-square)](https://bisque.gitbook.io/docs)
+[![PyPi Installs](https://pepy.tech/badge/bqapi-ucsb?style=flat-square)](https://pepy.tech/project/bqapi-ucsb)
 
-[Full Documentation](https://github.com/UCSB-VRL/bisqueUCSB)
 
-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).
 
-# Installing
+## Install
 ```
 pip install bqapi-ucsb
 ```
 
-[Pypi link](https://pypi.org/project/bqapi-ucsb)
+## Usage
 
-# Usage
-```python
-from bqapi.comm import BQSession
-from bqapi.util import fetch_blob
-```
+### Upload Image
+
+Upload your first image to BisQue using our tutorial!
 
-# Development
+[Upload an Image to BisQue](https://bisque.gitbook.io/docs/bisque-api/upload-an-image)
+
+
+## Development
 
 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 
 
-### Summary
+## Contribute
 
 1. Clone repo
 2. Make any necessary changes to source code, setup.py, and setup.cfg
@@ -34,4 +36,3 @@ 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
@@ -46,7 +47,7 @@ def format_header_param(name, value):
             The value of the parameter, provided as a unicode string.
         """
         if not any(ch in value for ch in '"\\\r\n'):
-            result = '%s="%s"' % (name, value)
+            result = '{}="{}"'.format(name, value)
             try:
                 result.encode("ascii")
             except UnicodeEncodeError:
@@ -58,7 +59,7 @@ def format_header_param(name, value):
         if not six.PY3:  # Python 2:
             value_encode = value.encode("utf-8")
 
-        value = '%s="%s"; %s*=%s' % (
+        value = '{}="{}"; {}*={}'.format(
             name,
             value,
             name,

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: