Update tests / paths etc

coverage.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
-<coverage version="7.4.3" timestamp="1729480086814" lines-valid="319" lines-covered="302" line-rate="0.9467" branches-valid="96" branches-covered="82" branch-rate="0.8542" complexity="0">
+<coverage version="7.4.3" timestamp="1730151898557" lines-valid="319" lines-covered="302" line-rate="0.9467" branches-valid="96" branches-covered="82" branch-rate="0.8542" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.4.3 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>

data/processed/df_paths.txt

@@ -1,33 +1,33 @@
-data/raw/economic/GDP/gdp_current_dollars.csv
-data/raw/economic/UI/ar203_output.csv
-data/raw/economic/consumption/consumption.csv
-data/raw/economic/consumption_durable_goods/consumption_durable_goods.csv
-data/raw/economic/consumption_nondurable_goods/consumption_nondurable_goods.csv
-data/raw/economic/consumption_services/consumption_services.csv
-data/raw/economic/consumption_total_goods/consumption_total_goods.csv
-data/raw/economic/employment/CE16OV_output.csv
-data/raw/economic/employment/PAYEMS_output.csv
-data/raw/economic/inflation/CPIAUCSL_output.csv
-data/raw/economic/inflation/PCEPILFE_output.csv
-data/raw/economic/inflation/PCEPI_output.csv
-data/raw/economic/interest_rates/rates_output.csv
-data/raw/economic/investment/K1TTOTL1ES000_output.csv
-data/raw/economic/investment/RPFI_output.csv
-data/raw/economic/productivity/labor-productivity-by-state-and-region_output.csv
-data/raw/economic/unemployment/ststdsadata_output.csv
-data/raw/intervention/american_rescue_plan/fiscalrecoveryfunds-statefunding1-CSV_output.csv
-data/raw/intervention/cares/cares_state_allocation_output.csv
-data/raw/intervention/ppp/PPP_states_and_territories_output.csv
-data/raw/pandemic/cases/CDC_state_cases_and_deaths_output.csv
-data/raw/pandemic/cases/JHU_time_series_cases_output.csv
-data/raw/pandemic/deaths/time_series_covid19_deaths_US_output_FIXED - time_series_covid19_deaths_US_output.csv
-data/raw/pandemic/vaccinations/19_Vaccinations_in_the_United_States_Jurisdiction_output_output.csv
-data/raw/pandemic/vaccinations/time_series_covid19_vaccine_us_output.csv
-data/raw/state_mandates/UWashington/USstatesCov19distancingpolicyBETA_complete_output.csv
-data/raw/state_mandates/mask_mandates/U.S._State_and_Territorial_Public_Mask_Mandates_From_April_8__2020_through_August_15__2021_by_State_by_Day_output.csv
-data/raw/economic/inflation/pcpiMvMd.csv
-data/raw/economic/interest_rates/FEDFUNDS_output.csv
-data/raw/economic/inflation/pcpiMvMd.csv
-data/raw/economic/interest_rates/FEDFUNDS_output.csv
-data/raw/state_mandates/shelter_in_place/U.S._State_and_Territorial_Stay-At-Home_Orders__March_15__2020___August_15__2021_by_County_by_Day_output.csv
-data/raw/pandemic/cases/CDC_Case_Surveillance.csv
+../data/raw/economic/GDP/gdp_current_dollars.csv
+../data/raw/economic/UI/ar203_output.csv
+../data/raw/economic/consumption/consumption.csv
+../data/raw/economic/consumption_durable_goods/consumption_durable_goods.csv
+../data/raw/economic/consumption_nondurable_goods/consumption_nondurable_goods.csv
+../data/raw/economic/consumption_services/consumption_services.csv
+../data/raw/economic/consumption_total_goods/consumption_total_goods.csv
+../data/raw/economic/employment/CE16OV_output.csv
+../data/raw/economic/employment/PAYEMS_output.csv
+../data/raw/economic/inflation/CPIAUCSL_output.csv
+../data/raw/economic/inflation/PCEPILFE_output.csv
+../data/raw/economic/inflation/PCEPI_output.csv
+../data/raw/economic/interest_rates/rates_output.csv
+../data/raw/economic/investment/K1TTOTL1ES000_output.csv
+../data/raw/economic/investment/RPFI_output.csv
+../data/raw/economic/productivity/labor-productivity-by-state-and-region_output.csv
+../data/raw/economic/unemployment/ststdsadata_output.csv
+../data/raw/intervention/american_rescue_plan/fiscalrecoveryfunds-statefunding1-CSV_output.csv
+../data/raw/intervention/cares/cares_state_allocation_output.csv
+../data/raw/intervention/ppp/PPP_states_and_territories_output.csv
+../data/raw/pandemic/cases/CDC_state_cases_and_deaths_output.csv
+../data/raw/pandemic/cases/JHU_time_series_cases_output.csv
+../data/raw/pandemic/deaths/time_series_covid19_deaths_US_output_FIXED - time_series_covid19_deaths_US_output.csv
+../data/raw/pandemic/vaccinations/19_Vaccinations_in_the_United_States_Jurisdiction_output_output.csv
+../data/raw/pandemic/vaccinations/time_series_covid19_vaccine_us_output.csv
+../data/raw/state_mandates/UWashington/USstatesCov19distancingpolicyBETA_complete_output.csv
+../data/raw/state_mandates/mask_mandates/U.S._State_and_Territorial_Public_Mask_Mandates_From_April_8__2020_through_August_15__2021_by_State_by_Day_output.csv
+../data/raw/economic/inflation/pcpiMvMd.csv
+../data/raw/economic/interest_rates/FEDFUNDS_output.csv
+../data/raw/economic/inflation/pcpiMvMd.csv
+../data/raw/economic/interest_rates/FEDFUNDS_output.csv
+../data/raw/state_mandates/shelter_in_place/U.S._State_and_Territorial_Stay-At-Home_Orders__March_15__2020___August_15__2021_by_County_by_Day_output.csv
+../data/raw/pandemic/cases/CDC_Case_Surveillance.csv

dfmdash/covid19.py

@@ -10,7 +10,7 @@
 from dfmdash.constants import NAME_MAP
 
 ROOT_DIR = Path(__file__).parent.absolute()
-DATA_DIR = ROOT_DIR / "data/processed"
+DATA_DIR = ROOT_DIR / "../data/processed"
 
 
 def _get_raw_df() -> pd.DataFrame:

tests/test_cli.py

@@ -1,15 +1,13 @@
-import shutil
-import os
 from pathlib import Path
 
-import pytest
 from typer.testing import CliRunner
 
 from dfmdash.cli import app
 from dfmdash.covid19 import DATA_DIR
 
 runner = CliRunner()
 
+
 # TODO: Change to be test.h5ad with small state subset
 def test_run_dfm(tmpdir):
     result = runner.invoke(app, ["run", str(DATA_DIR / "test.h5ad"), str(tmpdir), "--batch", "State"])

tests/test_covid19.py

@@ -3,14 +3,14 @@
 
 from dfmdash.covid19 import (
     _get_raw_df,
-    get_raw,
-    get_df,
-    get_project_h5ad,
-    get_govt_fund_dist,
+    add_datetime,
     adjust_inflation,
     adjust_pandemic_response,
-    add_datetime,
     fix_names,
+    get_df,
+    get_govt_fund_dist,
+    get_project_h5ad,
+    get_raw,
 )
 
 

tests/test_dfm.py

@@ -1,9 +1,11 @@
 import shutil
 import unittest
 from pathlib import Path
-from dfmdash.dfm import ModelRunner
+
 from anndata import AnnData
+
 from dfmdash.covid19 import get_project_h5ad
+from dfmdash.dfm import ModelRunner
 
 COLUMNS = ["PCE", "CPIU", "Hosp1", "Hosp2"]
 STATES = ["AK", "CA"]

tests/test_io.py

@@ -1,18 +1,20 @@
 import shutil
-import pandas as pd
-import numpy as np
 from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import pytest
 from anndata import AnnData
-from dfmdash.io import DataLoader
+
 from dfmdash.covid19 import DATA_DIR
-import pytest
+from dfmdash.io import DataLoader
 
 
 @pytest.fixture()
 def dfs():
     data = pd.read_csv(DATA_DIR / "data.csv")
-    factors = pd.read_csv(DATA_DIR / "factors.csv", index_col=0)
-    metadata = pd.read_csv(DATA_DIR / "metadata.csv", index_col=0)
+    factors = pd.read_csv(DATA_DIR / "../factors.csv", index_col=0)
+    metadata = pd.read_csv(DATA_DIR / "../metadata.csv", index_col=0)
     return data, factors, metadata
 
 

tests/test_processing.py

@@ -1,8 +1,8 @@
 from functools import reduce
+from pathlib import Path
 
 import pandas as pd
 import pytest
-from pathlib import Path
 
 from dfmdash.covid19 import get_project_h5ad
 from dfmdash.processing import DataProcessor, is_constant

tests/test_results.py

@@ -7,7 +7,7 @@
 
 @pytest.fixture
 def runs_dir() -> pd.DataFrame:
-    return ROOT_DIR / "data" / "example-data"
+    return ROOT_DIR / "../data" / "example-data"
 
 
 @pytest.fixture