run pre-commit formatting

CONTRIBUTING.rst

@@ -120,4 +120,3 @@ Then run::
     $ bump2version patch # possible: major / minor / patch
     $ git push
     $ git push --tags
-

docs/source/conf.py

@@ -42,7 +42,7 @@
     "IPython.sphinxext.ipython_console_highlighting",
     "nbsphinx",
     "pywps.ext_autodoc",
- ]
+]
 
 # To avoid having to install these and burst memory limit on ReadTheDocs.
 # List of all tested working mock imports from all birds so new birds can
@@ -102,7 +102,7 @@
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-source_suffix = {'.rst': 'restructuredtext'}
+source_suffix = {".rst": "restructuredtext"}
 
 # The master toctree document.
 master_doc = "index"

rook/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Top-level package for rook."""
 from .__version__ import __author__, __email__, __version__  # noqa: F401
 

rook/__version__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # This information is located in its own file so that it can be loaded
 # without importing the main package when its dependencies are not installed.
 # See: https://packaging.python.org/guides/single-sourcing-package-version

rook/catalog/db.py

@@ -15,7 +15,7 @@
 
 class DBCatalog(Catalog):
     def __init__(self, project, url=None):
-        super(DBCatalog, self).__init__(project)
+        super().__init__(project)
         self.table_name = f"rook_catalog_{self.project}".replace("-", "_")
         self.intake_catalog = IntakeCatalog(project, url)
 

rook/cli.py

@@ -51,7 +51,7 @@ def run_process_action(action=None):
     and return a status message."""
     action = action or "status"
     try:
-        with open(PID_FILE, "r") as fp:
+        with open(PID_FILE) as fp:
             pid = int(fp.read())
             p = psutil.Process(pid)
             if action == "stop":
@@ -65,7 +65,7 @@ def run_process_action(action=None):
                 )
         if action == "stop":
             os.remove(PID_FILE)
-    except IOError:
+    except OSError:
         msg = 'No PID file found. Service not running? Try "netstat -nlp | grep :5000".'
     except psutil.NoSuchProcess as e:
         msg = e.msg
@@ -172,8 +172,16 @@ def stop():
     default="sqlite:///pywps-logs.sqlite",
     help="database in PyWPS configuration",
 )
-@click.option('--outputurl', default='', help='base URL for file downloads')
-@click.option('--outputpath', default='', help='base directory where outputs are written')
+@click.option(
+    "--outputurl",
+    default="",
+    help="base URL for file downloads"
+)
+@click.option(
+    "--outputpath",
+    default="",
+    help="base directory where outputs are written"
+)
 def start(
     config,
     bind_host,
@@ -206,8 +214,8 @@ def start(
             wps_log_level=log_level,
             wps_log_file=log_file,
             wps_database=database,
-            wps_outputurl = outputurl,
-            wps_outputpath = outputpath
+            wps_outputurl=outputurl,
+            wps_outputpath=outputpath,
         )
     )
     if config:

rook/dashboard/templates/dashboard.html

@@ -49,4 +49,4 @@ <h3>Data Transfer</h3>
 {{ script_t1 | safe }}
 {{ script_t2 | safe }}
 
-{% endblock %}
+{% endblock %}

rook/operator.py

@@ -17,7 +17,7 @@
 from roocs_utils.utils.file_utils import is_file_list, FileMapper
 
 
-class Operator(object):
+class Operator:
     # Sub-classes require "prefix" property
     prefix = NotImplemented
 

rook/processes/wps_average_dim.py

@@ -87,7 +87,7 @@ def __init__(self):
             ),
         ]
 
-        super(AverageByDimension, self).__init__(
+        super().__init__(
             self._handler,
             identifier="average",
             title="Average by Dimensions",

rook/processes/wps_average_shape.py

@@ -31,7 +31,7 @@ def __init__(self):
                 "shape",
                 "Vector Shape",
                 abstract="An ESRI Shapefile, GML, GeoPackage, JSON or GeoJSON file."
-                         " The ESRI Shapefile must be zipped and contain the .shp, .shx, and .dbf.",
+                " The ESRI Shapefile must be zipped and contain the .shp, .shx, and .dbf.",
                 supported_formats=[
                     FORMATS.GML,
                     FORMATS.GEOJSON,
@@ -87,7 +87,7 @@ def __init__(self):
             ),
         ]
 
-        super(AverageByShape, self).__init__(
+        super().__init__(
             self._handler,
             identifier="average_shape",
             title="Average over polygonal shape",

rook/processes/wps_average_time.py

@@ -81,7 +81,7 @@ def __init__(self):
             ),
         ]
 
-        super(AverageByTime, self).__init__(
+        super().__init__(
             self._handler,
             identifier="average_time",
             title="Average by Time",

rook/processes/wps_average_weighted.py

@@ -54,7 +54,7 @@ def __init__(self):
             ),
         ]
 
-        super(WeightedAverage, self).__init__(
+        super().__init__(
             self._handler,
             identifier="weighted_average",
             title="Weighted Average",

rook/processes/wps_concat.py

@@ -114,7 +114,7 @@ def __init__(self):
             ),
         ]
 
-        super(Concat, self).__init__(
+        super().__init__(
             self._handler,
             identifier="concat",
             title="Concat",

rook/processes/wps_dashboard.py

@@ -45,7 +45,7 @@ def __init__(self):
             ),
         ]
 
-        super(DashboardProcess, self).__init__(
+        super().__init__(
             self._handler,
             identifier="dashboard",
             title="Dashboard",

rook/processes/wps_orchestrate.py

@@ -49,7 +49,7 @@ def __init__(self):
             ),
         ]
 
-        super(Orchestrate, self).__init__(
+        super().__init__(
             self._handler,
             identifier="orchestrate",
             title="Orchestrate",

rook/processes/wps_regrid.py

@@ -52,7 +52,7 @@ def __init__(self):
                     "0pt75deg",
                     "1deg",
                     "1pt25deg",
-                    "2pt5deg"
+                    "2pt5deg",
                 ],
                 default="auto",
             ),
@@ -83,7 +83,7 @@ def __init__(self):
             ),
         ]
 
-        super(Regrid, self).__init__(
+        super().__init__(
             self._handler,
             identifier="regrid",
             title="Regrid",

rook/processes/wps_subset.py

@@ -120,7 +120,7 @@ def __init__(self):
             ),
         ]
 
-        super(Subset, self).__init__(
+        super().__init__(
             self._handler,
             identifier="subset",
             title="Subset",

rook/processes/wps_usage.py

@@ -46,7 +46,7 @@ def __init__(self):
             ),
         ]
 
-        super(Usage, self).__init__(
+        super().__init__(
             self._handler,
             identifier="usage",
             title="Usage",

rook/provenance.py

@@ -28,7 +28,7 @@
 ROOCS = Namespace("roocs", uri="urn:roocs:")
 
 
-class Provenance(object):
+class Provenance:
     def __init__(self, output_dir):
         if isinstance(output_dir, pathlib.Path):
             self.output_dir = output_dir

rook/workflow.py

@@ -65,7 +65,7 @@ def build_tree(wfdoc):
     return tree
 
 
-class WorkflowRunner(object):
+class WorkflowRunner:
     def __init__(self, output_dir):
         self.workflow = Workflow(output_dir)
 
@@ -80,7 +80,7 @@ def provenance(self):
         return self.workflow.prov
 
 
-class BaseWorkflow(object):
+class BaseWorkflow:
     def __init__(self, output_dir):
         self.concat_op = Concat(output_dir)
         self.subset_op = Subset(output_dir)

setup.py

@@ -12,11 +12,11 @@
 REQUIRES_PYTHON = ">=3.9.0"
 
 about = {}
-with open(os.path.join(here, "rook", "__version__.py"), "r") as f:
+with open(os.path.join(here, "rook", "__version__.py")) as f:
     exec(f.read(), about)
 
-requirements = [line.strip() for line in open('requirements.txt')]
-dev_reqs = [line.strip() for line in open('requirements_dev.txt')]
+requirements = [line.strip() for line in open("requirements.txt")]
+dev_reqs = [line.strip() for line in open("requirements_dev.txt")]
 
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -36,28 +36,28 @@
 ]
 
 setup(
-    name='roocs-rook',
-    version=about['__version__'],
+    name="roocs-rook",
+    version=about["__version__"],
     description="A WPS service for roocs.",
-    long_description=README + '\n\n' + CHANGES,
+    long_description=README + "\n\n" + CHANGES,
     long_description_content_type="text/x-rst",
-    author=about['__author__'],
-    author_email=about['__email__'],
-    url='https://github.com/roocs/rook',
+    author=about["__author__"],
+    author_email=about["__email__"],
+    url="https://github.com/roocs/rook",
     python_requires=REQUIRES_PYTHON,
     classifiers=classifiers,
     license="Apache Software License 2.0",
     zip_safe=False,
-    keywords='wps pywps birdhouse rook',
+    keywords="wps pywps birdhouse rook",
     packages=find_packages(),
     include_package_data=True,
     install_requires=requirements,
     extras_require={
         "dev": dev_reqs,  # pip install ".[dev]"
     },
     entry_points={
-        'console_scripts': [
-            'rook=rook.cli:cli',
+        "console_scripts": [
+            "rook=rook.cli:cli",
         ]
     },
 )

tests/common.py

@@ -67,7 +67,7 @@ def get(self, *args, **kwargs):
         query = "?"
         for key, value in kwargs.items():
             query += "{}={}&".format(key, value)
-        return super(WpsTestClient, self).get(query)
+        return super().get(query)
 
 
 def client_for(service):
@@ -100,6 +100,6 @@ def get_output(doc):
 
 def extract_paths_from_metalink(path):
     path = path.replace("file://", "")
-    doc = BeautifulSoup(open(path, "r").read(), "xml")
+    doc = BeautifulSoup(open(path).read(), "xml")
     paths = [el.text.replace("file://", "") for el in doc.find_all("metaurl")]
     return paths

tests/test_wps_average_shape.py

@@ -11,19 +11,23 @@
 from .common import PYWPS_CFG, get_output, extract_paths_from_metalink
 
 
-POLY = Polygon([[5.8671874999999996, 57.326521225217064],
-                [-15.468749999999998, 48.45835188280866],
-                [-16.171875, 24.84656534821976],
-                [-3.8671874999999996, 13.581920900545844],
-                [21.796875, 25.799891182088334],
-                [22.8515625, 52.482780222078226],
-                [5.8671874999999996, 57.326521225217064]])
+POLY = Polygon(
+    [
+        [5.8671874999999996, 57.326521225217064],
+        [-15.468749999999998, 48.45835188280866],
+        [-16.171875, 24.84656534821976],
+        [-3.8671874999999996, 13.581920900545844],
+        [21.796875, 25.799891182088334],
+        [22.8515625, 52.482780222078226],
+        [5.8671874999999996, 57.326521225217064],
+    ]
+)
 
 
 def test_wps_average_shape_cmip6(tmp_path):
     # Save POLY to tmpdir
     tmp_poly_path = tmp_path / "tmppoly.json"
-    gpd.GeoDataFrame([{'geometry': POLY}]).to_file(tmp_poly_path)
+    gpd.GeoDataFrame([{"geometry": POLY}]).to_file(tmp_poly_path)
 
     # test the case where the inventory is used
     client = client_for(Service(processes=[AverageByShape()], cfgfiles=[PYWPS_CFG]))

tests/test_wps_orchestrate.py

@@ -125,7 +125,7 @@ def test_wps_orchestrate_c3s_cmip6_subset_metadata():
     m_path = get_output(resp.xml)["output"]
     # print(m_path)
     # parse metalink
-    xml = open(m_path[7:], "r").read()
+    xml = open(m_path[7:]).read()
     urls = parse_metalink(xml)
     # print(urls)
     ds = xr.open_dataset(urls[0][7:], use_cftime=True)

tests/test_wps_subset.py

@@ -100,7 +100,7 @@ def test_wps_subset_c3s_cmip6_metadata():
     m_path = get_output(resp.xml)["output"]
     assert "meta4" in m_path
     # parse metalink
-    xml = open(m_path[7:], "r").read()
+    xml = open(m_path[7:]).read()
     urls = parse_metalink(xml)
     # print(urls)
     ds = xr.open_dataset(urls[0][7:], use_cftime=True)

tox.ini

@@ -23,4 +23,3 @@ deps =
 ;     -r{toxinidir}/requirements.txt
 commands =
     pytest --basetemp={envtmpdir}
-