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Fix linting for google symptoms #455

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Merged
merged 2 commits into from
Nov 6, 2020
Merged

Fix linting for google symptoms #455

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d7247f7
Fix linting
chinandrew Nov 6, 2020
c8c2408
Update google_symptoms/delphi_google_symptoms/geo.py
chinandrew Nov 6, 2020
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2 changes: 1 addition & 1 deletion google_symptoms/delphi_google_symptoms/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,4 +80,4 @@
'Wisconsin': 'wi',
'Wyoming': 'wy'}

DC_FIPS = "11001"
DC_FIPS = "11001"
10 changes: 5 additions & 5 deletions google_symptoms/delphi_google_symptoms/geo.py
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Expand Up @@ -21,7 +21,7 @@ def generate_transition_matrix(geo_res):
The first is a data frame for HRR regions and the second are MSA
regions.
"""
map_df = gmpr._load_crosswalk("fips", geo_res)
map_df = gmpr._load_crosswalk("fips", geo_res) # pylint: disable=W0212
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(this one is fine; google_symptoms is deprecated anyway)

# Add population as weights
map_df = gmpr.add_population_column(map_df, "fips")
if geo_res == "hrr":
Expand All @@ -31,7 +31,7 @@ def generate_transition_matrix(geo_res):
msa_pop, on=geo_res, how="inner", suffixes=["_raw", "_groupsum"]
)
map_df["weight"] = map_df["population_raw"] / map_df["population_groupsum"]

map_df = pd.pivot_table(
map_df, values='weight', index=["fips"], columns=[geo_res]
).fillna(0).reset_index().rename({"fips": "geo_id"}, axis = 1)
Expand All @@ -52,13 +52,13 @@ def geo_map(df, geo_res):
Returns
-------
pd.DataFrame
A dataframe with columns "geo_id", "timestamp",
and columns for signal vals.
A dataframe with columns "geo_id", "timestamp",
and columns for signal vals.
The geo_id has been converted from fips to HRRs/MSAs
"""
if geo_res in set(["county", "state"]):
return df

map_df = generate_transition_matrix(geo_res)
converted_df = pd.DataFrame(columns = df.columns)
for _date in df["timestamp"].unique():
Expand Down
4 changes: 2 additions & 2 deletions google_symptoms/delphi_google_symptoms/pull.py
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Expand Up @@ -43,7 +43,7 @@ def preprocess(df, level):
"""
# Constants
KEEP_COLUMNS = ["geo_id", "date"] + METRICS + ["combined_symptoms"]

df["combined_symptoms"] = 0
for metric in METRICS:
df.rename({"symptom:" + metric: metric}, axis = 1, inplace = True)
Expand All @@ -52,7 +52,7 @@ def preprocess(df, level):
(df["Anosmia"].isnull())
& (df["Ageusia"].isnull())
, "combined_symptoms"] = np.nan

# Delete rows with missing FIPS
null_mask = (df["geo_id"].isnull())
df = df.loc[~null_mask]
Expand Down
4 changes: 2 additions & 2 deletions google_symptoms/delphi_google_symptoms/run.py
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Expand Up @@ -23,7 +23,7 @@ def run_module():
base_url = params["base_url"]

# Pull GS data
dfs = pull_gs_data(base_url)
dfs = pull_gs_data(base_url)
for geo_res in GEO_RESOLUTIONS:
if geo_res == "state":
df_pull = dfs["state"]
Expand All @@ -48,4 +48,4 @@ def run_module():
start_date=SMOOTHERS_MAP[smoother][1](export_start_date),
metric=metric.lower(),
geo_res=geo_res,
sensor=sensor_name)
sensor=sensor_name)