[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.coveragerc

@@ -3,5 +3,5 @@ omit =
     tests/*
 
 [report]
-exclude_also = 
+exclude_also =
     if __name__ == .__main__.:

.readthedocs.yaml

@@ -31,5 +31,3 @@ python:
    install:
      - method: pip
        path: .[docs]
-
-

adtl/__init__.py

@@ -86,12 +86,14 @@ def get_value_unhashed(row: StrDict, rule: Rule, ctx: Context = None) -> Any:
                         params.append(row[rule["apply"]["params"][i][1:]])
                     elif isinstance(rule["apply"]["params"][i], list):
                         param = [
-                            row[rule["apply"]["params"][i][j][1:]]
-                            if (
-                                isinstance(rule["apply"]["params"][i][j], str)
-                                and rule["apply"]["params"][i][j].startswith("$")
+                            (
+                                row[rule["apply"]["params"][i][j][1:]]
+                                if (
+                                    isinstance(rule["apply"]["params"][i][j], str)
+                                    and rule["apply"]["params"][i][j].startswith("$")
+                                )
+                                else rule["apply"]["params"][i][j]
                             )
-                            else rule["apply"]["params"][i][j]
                             for j in range(len(rule["apply"]["params"][i]))
                         ]
                         params.append(param)
@@ -590,9 +592,11 @@ def ctx(self, attribute: str):
             "defaultDateFormat": self.header.get(
                 "defaultDateFormat", DEFAULT_DATE_FORMAT
             ),
-            "skip_pattern": re.compile(self.header.get("skipFieldPattern"))
-            if self.header.get("skipFieldPattern")
-            else False,
+            "skip_pattern": (
+                re.compile(self.header.get("skipFieldPattern"))
+                if self.header.get("skipFieldPattern")
+                else False
+            ),
         }
 
     def validate_spec(self):
@@ -793,12 +797,14 @@ def parse(self, file: str, encoding: str = "utf-8", skip_validation=False):
         with open(file, encoding=encoding) as fp:
             reader = csv.DictReader(fp)
             return self.parse_rows(
-                tqdm(
-                    reader,
-                    desc=f"[{self.name}] parsing {Path(file).name}",
-                )
-                if not self.quiet
-                else reader,
+                (
+                    tqdm(
+                        reader,
+                        desc=f"[{self.name}] parsing {Path(file).name}",
+                    )
+                    if not self.quiet
+                    else reader
+                ),
                 skip_validation=skip_validation,
             )
 

docs/_static/style.css

@@ -111,4 +111,3 @@ div.bodywrapper h4 {
     padding-right: 0;
   }
 }
-

docs/adtl.rst

@@ -3,4 +3,4 @@ Module reference
 =====================
 
 .. autoclass:: adtl.Parser
-  :members:
+  :members:

docs/conf.py

@@ -38,12 +38,12 @@
 
 html_theme = "better"
 html_static_path = ["_static"]
-html_theme_path=[better.better_theme_path]
+html_theme_path = [better.better_theme_path]
 html_short_title = "Home"
 
 html_theme_options = {
     "rightsidebar": True,
     "sidebarwidth": "25rem",
     "cssfiles": ["_static/style.css"],
     "showheader": False,
-}
+}

docs/getting_started/installation.md

@@ -26,4 +26,3 @@ If you are writing code which depends on adtl (instead of using
 the command-line program), then it is best to add a dependency on
 `git+https://github.com/globaldothealth/adtl` to your Python build tool of
 choice.
-

docs/index.md

@@ -47,4 +47,4 @@ maxdepth: 1
 
 adtl
 transformations
-```
+```

docs/transformations.rst

@@ -3,4 +3,4 @@ Transformations
 =====================
 
 .. automodule:: adtl.transformations
-  :members:
+  :members:

schemas/dev.schema.json

@@ -226,4 +226,4 @@
       }
     }
   }
-}
+}

tests/parsers/epoch-web-schema.json

@@ -24,4 +24,4 @@
       "field": "Text"
     }
   }
-}
+}

tests/parsers/epoch.yml

@@ -8,4 +8,4 @@ table:
   id: { field: Entry_ID }
   epoch: { field: Epoch }
   some_date: { field: SomeDate }
-  text: { field: Text }
+  text: { field: Text }

tests/parsers/skip_field.json

@@ -31,4 +31,4 @@
       "can_skip": true
     }
   }
-}
+}

tests/parsers/stop-overwriting.toml

@@ -12,13 +12,13 @@
   [visit.subject_id]
     field = "subjid"
     description = "Subject ID"
-  
+
   [visit.earliest_admission]
     combinedType = "min"
     fields = [
       { field = "first_admit" },
     ]
-  
+
   [visit.start_date]
     combinedType = "firstNonNull"
     fields = [
@@ -44,4 +44,3 @@
       { field = "overall_antiviral_dc___2", values = { 1 = "Lopinavir" } },
       { field = "overall_antiviral_dc___3", values = { 1 = "Interferon" } },
       ]
-

tests/schemas/epoch-data.schema.json

@@ -29,4 +29,4 @@
       "description": "Follow-up cough field"
     }
   }
-}
+}

tests/schemas/epoch-oneOf.schema.json

@@ -58,4 +58,4 @@
       "description": "sex"
     }
   }
-}
+}

tests/schemas/observation_defaultif.schema.json

@@ -72,4 +72,4 @@
             ]
         }
     }
-}
+}

tests/sources/oneToMany.csv

@@ -1,2 +1,2 @@
 dt,headache_cmyn,cough_cmyn,dyspnea_cmyn
-2022-02-05,1,1,0
+2022-02-05,1,1,0

tests/sources/stop-overwriting.csv

@@ -8,4 +8,4 @@ subjid,redcap,first_admit,enrolment,icu_admission_date,daily_antiviral_type___1,
 2,day1,,,2020-11-30,0,1,0,0,0,0
 3,admit,,2020-02-20,,0,0,0,0,0,0
 3,discharge,,,,0,0,0,0,1,1
-3,day1,,,,1,0,0,0,0,0
+3,day1,,,,1,0,0,0,0,0