Format with black

tests/conftest.py

@@ -101,7 +101,10 @@ def __init__(self):
         }
         inputs = [
             LiteralInput(
-                "string", "String", abstract="Enter string.", data_type="string",
+                "string",
+                "String",
+                abstract="Enter string.",
+                data_type="string",
             )
         ]
         outputs = [

tests/test_R.py

@@ -14,7 +14,8 @@
 
 
 @pytest.mark.parametrize(
-    ("package"), [("base"), ("utils")],
+    ("package"),
+    [("base"), ("utils")],
 )
 def test_get_package(package):
     pkg = get_package(package)
@@ -41,7 +42,9 @@ def test_load_rdata_to_python(r_file, r_object_name):
 
 @pytest.mark.parametrize(
     ("file_", "obj_name"),
-    [(resource_filename("tests", "data/expected_days_data.rda"), "autumn_days"),],
+    [
+        (resource_filename("tests", "data/expected_days_data.rda"), "autumn_days"),
+    ],
 )
 def test_load_rdata_to_python_err(file_, obj_name):
     with pytest.raises(ProcessError) as e:
@@ -53,7 +56,11 @@ def test_load_rdata_to_python_err(file_, obj_name):
 
 
 @pytest.mark.parametrize(
-    ("r_name", "py_var"), [("str_ex", "string"), ("int_ex", 300),],
+    ("r_name", "py_var"),
+    [
+        ("str_ex", "string"),
+        ("int_ex", 300),
+    ],
 )
 def test_save_python_to_rdata(r_name, py_var):
     with NamedTemporaryFile(
@@ -68,14 +75,16 @@ def test_save_python_to_rdata(r_name, py_var):
 
 
 @pytest.mark.parametrize(
-    ("name"), [("hello.world"), ("r_name")],
+    ("name"),
+    [("hello.world"), ("r_name")],
 )
 def test_r_valid_name(name):
     r_valid_name(name)
 
 
 @pytest.mark.parametrize(
-    ("name"), [(".2"), ("if"), ("two words")],
+    ("name"),
+    [(".2"), ("if"), ("two words")],
 )
 def test_r_valid_name_err(name):
     with pytest.raises(ProcessError) as e:

tests/test_file_handling.py

@@ -26,7 +26,11 @@
 
 @pytest.mark.online
 @pytest.mark.parametrize(
-    ("url"), [url_path(nc_file, "opendap"), local_path(nc_file),],
+    ("url"),
+    [
+        url_path(nc_file, "opendap"),
+        local_path(nc_file),
+    ],
 )
 def test_is_opendap_url(url):
     if "docker" in url:
@@ -38,7 +42,8 @@ def test_is_opendap_url(url):
 
 
 @pytest.mark.parametrize(
-    ("nc_input"), [[NCInput(file=local_path(nc_file))]],
+    ("nc_input"),
+    [[NCInput(file=local_path(nc_file))]],
 )
 def test_get_filepaths_local(nc_input):
     paths = get_filepaths(nc_input)
@@ -52,7 +57,10 @@ def test_get_filepaths_local(nc_input):
     ("nc_input"),
     [
         [NCInput(url=url_path(nc_file, "opendap"))],
-        [NCInput(file=local_path(nc_file)), NCInput(url=url_path(nc_file, "opendap")),],
+        [
+            NCInput(file=local_path(nc_file)),
+            NCInput(url=url_path(nc_file, "opendap")),
+        ],
     ],
 )
 def test_get_filepaths_online(nc_input):
@@ -119,7 +127,10 @@ def test_copy_http_content(http, expected):
 @pytest.mark.online
 @pytest.mark.parametrize(
     ("url_type", "url"),
-    [("http", url_path(nc_file, "http")), ("opendap", url_path(nc_file, "opendap")),],
+    [
+        ("http", url_path(nc_file, "http")),
+        ("opendap", url_path(nc_file, "opendap")),
+    ],
 )
 def test_url_handler(url_type, url):
     processed = url_handler("/tmp", url)

tests/test_io.py

@@ -19,7 +19,10 @@ def run_args_collection(wps_test_process_multi_input, file, csv, argc):
     ("file", "argc"),
     [
         (
-            [local_path("tiny_daily_pr.nc"), local_path("tiny_daily_prsn.nc"),],
+            [
+                local_path("tiny_daily_pr.nc"),
+                local_path("tiny_daily_prsn.nc"),
+            ],
             {"file": 2, "csv_input": 1, "argc": 1},
         )
     ],

tests/test_output_handling.py

@@ -27,7 +27,8 @@ def test_nc_to_dataset(url):
 
 
 @pytest.mark.parametrize(
-    ("url"), [local_path("gsl.json")],
+    ("url"),
+    [local_path("gsl.json")],
 )
 def test_json_to_dict(url):
     output_dict = json_to_dict(url)
@@ -85,7 +86,13 @@ def test_auto_construct_outputs_online(outputs, expected_types):
 
 
 @pytest.mark.parametrize(
-    ("outputs", "expected_types"), [(["test string"], [str, str],)],
+    ("outputs", "expected_types"),
+    [
+        (
+            ["test string"],
+            [str, str],
+        )
+    ],
 )
 def test_auto_construct_outputs_local(txt_file, outputs, expected_types):
     outputs.append(f"file://{txt_file.name}")
@@ -94,7 +101,8 @@ def test_auto_construct_outputs_local(txt_file, outputs, expected_types):
 
 
 @pytest.mark.parametrize(
-    ("output"), ["https://test_metalinks.meta4"],
+    ("output"),
+    ["https://test_metalinks.meta4"],
 )
 def test_get_metalink_content(mock_metalink, output):
     for file_ in get_metalink_content(output):

tests/test_testing.py

@@ -44,23 +44,41 @@ def test_run_wps_process(wps_test_process, string):
 
 
 @pytest.mark.parametrize(
-    "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),]
+    "bird",
+    [
+        ("thunderbird"),
+        ("sandpiper"),
+        ("osprey"),
+        ("chickadee"),
+    ],
 )
 @pytest.mark.parametrize("expected", ["http://localhost:5000/wps"])
 def test_get_target_url_local(mock_local_url, bird, expected):
     assert get_target_url(bird) == expected
 
 
 @pytest.mark.parametrize(
-    "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),]
+    "bird",
+    [
+        ("thunderbird"),
+        ("sandpiper"),
+        ("osprey"),
+        ("chickadee"),
+    ],
 )
 @pytest.mark.parametrize("expected", ["http://docker-dev03.pcic.uvic.ca/somebird"])
 def test_get_target_url_dev(mock_dev_url, bird, expected):
     assert get_target_url(bird) == expected
 
 
 @pytest.mark.parametrize(
-    "bird", [("thunderbird"), ("sandpiper"), ("osprey"), ("chickadee"),]
+    "bird",
+    [
+        ("thunderbird"),
+        ("sandpiper"),
+        ("osprey"),
+        ("chickadee"),
+    ],
 )
 def test_get_target_url(bird):
     assert bird in get_target_url(bird)

wps_tools/R.py

@@ -10,14 +10,14 @@
 
 def get_package(package):
     """
-        Exposes all R objects in package as Python objects after
-        checking that it is installed.
+    Exposes all R objects in package as Python objects after
+    checking that it is installed.
 
-        Parameters:
-            package (str): the name of an R package
+    Parameters:
+        package (str): the name of an R package
 
-        Returns:
-            Exposed R package
+    Returns:
+        Exposed R package
     """
     if isinstalled(package):
         return importr(package)
@@ -27,15 +27,15 @@ def get_package(package):
 
 def load_rdata_to_python(r_file, r_object_name):
     """
-        Loads R objects from a .rda or .Rdata file into the embedded R
-        environment, then exposes that object as a Python object.
+    Loads R objects from a .rda or .Rdata file into the embedded R
+    environment, then exposes that object as a Python object.
 
-        Parameters:
-            r_file (str): path to an .rda or .rdata file
-            r_object_name (str): name of an R object from the r_file
+    Parameters:
+        r_file (str): path to an .rda or .rdata file
+        r_object_name (str): name of an R object from the r_file
 
-        Returns:
-            Exposed R object as a python object
+    Returns:
+        Exposed R object as a python object
     """
     try:
         robjects.r(f"load(file='{r_file}')")
@@ -55,12 +55,12 @@ def load_rdata_to_python(r_file, r_object_name):
 
 def save_python_to_rdata(r_name, py_var, r_file):
     """
-        Saves a Python object as an R object to a Rdata (.rda) file
+    Saves a Python object as an R object to a Rdata (.rda) file
 
-        Parameters:
-            r_name (str): name to give the oject in the R environment
-            py_var (any type): python variable to save to the R environment
-            r_file (str): path to rdata file
+    Parameters:
+        r_name (str): name to give the oject in the R environment
+        py_var (any type): python variable to save to the R environment
+        r_file (str): path to rdata file
     """
     robjects.r.assign(r_name, py_var)
     robjects.r(f"save({r_name}, file='{r_file}')")

wps_tools/file_handling.py

@@ -76,7 +76,7 @@ def get_filepaths(nc_input):
 
     Each path in nc_input is checked to determine if it is an OpenDAP url. If so,
     then the url is appended to the path list. If not, then whether or not it's a valid
-    netcdf file is checked. If so, then the path is appended to the list. If not, then 
+    netcdf file is checked. If so, then the path is appended to the list. If not, then
     a ProcessError is raised due to an invalid input.
 
     Parameters:
@@ -162,16 +162,16 @@ def build_meta_link(
 
 def copy_http_content(http, file):
     """
-        This function is implemented to copy the content of a file passed
-        as an http address to a local file.
-
-        Parameters:
-            http (str): http address containing the desired content
-            file (file object): path to the
-                file that the content will be copied to
-        Returns:
-            Path to the copied file in /tmp directory
-        """
+    This function is implemented to copy the content of a file passed
+    as an http address to a local file.
+
+    Parameters:
+        http (str): http address containing the desired content
+        file (file object): path to the
+            file that the content will be copied to
+    Returns:
+        Path to the copied file in /tmp directory
+    """
     file.write(get(http).content)
     return file.name