diff --git a/docs/source/conf.py b/docs/source/conf.py index 7bb2ba21..7819a94f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -7,7 +7,7 @@ import os import sys -sys.path.insert(0, os.path.abspath("../../src")) +sys.path.insert(0, os.path.abspath("../..")) # -- Project information ----------------------------------------------------- diff --git a/pyproject.toml b/pyproject.toml index acccc353..41e9abb3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = ["CFA"] license = "Apache 2.0" readme = "README.md" packages = [ - {include = "pyrenew", from = "src"}, + {include = "pyrenew"}, ] include = [{path = "datasets/*.tsv"}] exclude = [{path = "datasets/*.rds"}] diff --git a/src/pyrenew/arrayutils.py b/pyrenew/arrayutils.py similarity index 100% rename from src/pyrenew/arrayutils.py rename to pyrenew/arrayutils.py diff --git a/src/pyrenew/convolve.py b/pyrenew/convolve.py similarity index 100% rename from src/pyrenew/convolve.py rename to pyrenew/convolve.py diff --git a/src/pyrenew/datasets/__init__.py b/pyrenew/datasets/__init__.py similarity index 100% rename from src/pyrenew/datasets/__init__.py rename to pyrenew/datasets/__init__.py diff --git a/src/pyrenew/datasets/data-raw/README.md b/pyrenew/datasets/data-raw/README.md similarity index 100% rename from src/pyrenew/datasets/data-raw/README.md rename to pyrenew/datasets/data-raw/README.md diff --git a/src/pyrenew/datasets/data-raw/generation_interval.py b/pyrenew/datasets/data-raw/generation_interval.py similarity index 98% rename from src/pyrenew/datasets/data-raw/generation_interval.py rename to pyrenew/datasets/data-raw/generation_interval.py index 1f0e1aaf..d1d92e2c 100644 --- a/src/pyrenew/datasets/data-raw/generation_interval.py +++ b/pyrenew/datasets/data-raw/generation_interval.py @@ -13,7 +13,6 @@ # Building path to save the file path = os.path.join( - "src", "pyrenew", "datasets", "gen_int.tsv", diff --git a/src/pyrenew/datasets/data-raw/infection_admission_interval.py b/pyrenew/datasets/data-raw/infection_admission_interval.py similarity index 98% rename from src/pyrenew/datasets/data-raw/infection_admission_interval.py rename to pyrenew/datasets/data-raw/infection_admission_interval.py index 56cf3e9c..3fb3c14f 100644 --- a/src/pyrenew/datasets/data-raw/infection_admission_interval.py +++ b/pyrenew/datasets/data-raw/infection_admission_interval.py @@ -13,7 +13,6 @@ # Building path to save the file path = os.path.join( - "src", "pyrenew", "datasets", "infection_admission_interval.tsv", diff --git a/src/pyrenew/datasets/data-raw/wastewater.R b/pyrenew/datasets/data-raw/wastewater.R similarity index 84% rename from src/pyrenew/datasets/data-raw/wastewater.R rename to pyrenew/datasets/data-raw/wastewater.R index 5ff804f1..1d7d33ca 100644 --- a/src/pyrenew/datasets/data-raw/wastewater.R +++ b/pyrenew/datasets/data-raw/wastewater.R @@ -1,7 +1,7 @@ load( "https://github.com/CDCgov/wastewater-informed-covid-forecasting/blob/292526383ece582f10823fc939c7e590ca349c6d/cfaforecastrenewalww/data/example_df.rda" - ) -datasets_dir <- file.path("src", "pyrenew", "datasets") +) +datasets_dir <- file.path("pyrenew", "datasets") dir.create(datasets_dir) # Saving as TSV @@ -12,4 +12,4 @@ write.table( quote = FALSE, row.names = FALSE, na = "" - ) +) diff --git a/src/pyrenew/datasets/generation_interval.py b/pyrenew/datasets/generation_interval.py similarity index 100% rename from src/pyrenew/datasets/generation_interval.py rename to pyrenew/datasets/generation_interval.py diff --git a/src/pyrenew/datasets/generation_interval.tsv b/pyrenew/datasets/generation_interval.tsv similarity index 100% rename from src/pyrenew/datasets/generation_interval.tsv rename to pyrenew/datasets/generation_interval.tsv diff --git a/src/pyrenew/datasets/infection_admission_interval.py b/pyrenew/datasets/infection_admission_interval.py similarity index 100% rename from src/pyrenew/datasets/infection_admission_interval.py rename to pyrenew/datasets/infection_admission_interval.py diff --git a/src/pyrenew/datasets/infection_admission_interval.tsv b/pyrenew/datasets/infection_admission_interval.tsv similarity index 100% rename from src/pyrenew/datasets/infection_admission_interval.tsv rename to pyrenew/datasets/infection_admission_interval.tsv diff --git a/src/pyrenew/datasets/wastewater.py b/pyrenew/datasets/wastewater.py similarity index 100% rename from src/pyrenew/datasets/wastewater.py rename to pyrenew/datasets/wastewater.py diff --git a/src/pyrenew/datasets/wastewater.tsv b/pyrenew/datasets/wastewater.tsv similarity index 100% rename from src/pyrenew/datasets/wastewater.tsv rename to pyrenew/datasets/wastewater.tsv diff --git a/src/pyrenew/deterministic/__init__.py b/pyrenew/deterministic/__init__.py similarity index 100% rename from src/pyrenew/deterministic/__init__.py rename to pyrenew/deterministic/__init__.py diff --git a/src/pyrenew/deterministic/deterministic.py b/pyrenew/deterministic/deterministic.py similarity index 100% rename from src/pyrenew/deterministic/deterministic.py rename to pyrenew/deterministic/deterministic.py diff --git a/src/pyrenew/deterministic/deterministicpmf.py b/pyrenew/deterministic/deterministicpmf.py similarity index 100% rename from src/pyrenew/deterministic/deterministicpmf.py rename to pyrenew/deterministic/deterministicpmf.py diff --git a/src/pyrenew/deterministic/nullrv.py b/pyrenew/deterministic/nullrv.py similarity index 100% rename from src/pyrenew/deterministic/nullrv.py rename to pyrenew/deterministic/nullrv.py diff --git a/src/pyrenew/deterministic/process.py b/pyrenew/deterministic/process.py similarity index 100% rename from src/pyrenew/deterministic/process.py rename to pyrenew/deterministic/process.py diff --git a/src/pyrenew/distutil.py b/pyrenew/distutil.py similarity index 100% rename from src/pyrenew/distutil.py rename to pyrenew/distutil.py diff --git a/src/pyrenew/latent/__init__.py b/pyrenew/latent/__init__.py similarity index 100% rename from src/pyrenew/latent/__init__.py rename to pyrenew/latent/__init__.py diff --git a/src/pyrenew/latent/hospitaladmissions.py b/pyrenew/latent/hospitaladmissions.py similarity index 100% rename from src/pyrenew/latent/hospitaladmissions.py rename to pyrenew/latent/hospitaladmissions.py diff --git a/src/pyrenew/latent/infection_functions.py b/pyrenew/latent/infection_functions.py similarity index 100% rename from src/pyrenew/latent/infection_functions.py rename to pyrenew/latent/infection_functions.py diff --git a/src/pyrenew/latent/infection_initialization_method.py b/pyrenew/latent/infection_initialization_method.py similarity index 100% rename from src/pyrenew/latent/infection_initialization_method.py rename to pyrenew/latent/infection_initialization_method.py diff --git a/src/pyrenew/latent/infection_initialization_process.py b/pyrenew/latent/infection_initialization_process.py similarity index 100% rename from src/pyrenew/latent/infection_initialization_process.py rename to pyrenew/latent/infection_initialization_process.py diff --git a/src/pyrenew/latent/infections.py b/pyrenew/latent/infections.py similarity index 100% rename from src/pyrenew/latent/infections.py rename to pyrenew/latent/infections.py diff --git a/src/pyrenew/latent/infectionswithfeedback.py b/pyrenew/latent/infectionswithfeedback.py similarity index 100% rename from src/pyrenew/latent/infectionswithfeedback.py rename to pyrenew/latent/infectionswithfeedback.py diff --git a/src/pyrenew/math.py b/pyrenew/math.py similarity index 100% rename from src/pyrenew/math.py rename to pyrenew/math.py diff --git a/src/pyrenew/mcmcutils.py b/pyrenew/mcmcutils.py similarity index 100% rename from src/pyrenew/mcmcutils.py rename to pyrenew/mcmcutils.py diff --git a/src/pyrenew/metaclass.py b/pyrenew/metaclass.py similarity index 100% rename from src/pyrenew/metaclass.py rename to pyrenew/metaclass.py diff --git a/src/pyrenew/model/__init__.py b/pyrenew/model/__init__.py similarity index 100% rename from src/pyrenew/model/__init__.py rename to pyrenew/model/__init__.py diff --git a/src/pyrenew/model/admissionsmodel.py b/pyrenew/model/admissionsmodel.py similarity index 100% rename from src/pyrenew/model/admissionsmodel.py rename to pyrenew/model/admissionsmodel.py diff --git a/src/pyrenew/model/rtinfectionsrenewalmodel.py b/pyrenew/model/rtinfectionsrenewalmodel.py similarity index 100% rename from src/pyrenew/model/rtinfectionsrenewalmodel.py rename to pyrenew/model/rtinfectionsrenewalmodel.py diff --git a/src/pyrenew/observation/__init__.py b/pyrenew/observation/__init__.py similarity index 100% rename from src/pyrenew/observation/__init__.py rename to pyrenew/observation/__init__.py diff --git a/src/pyrenew/observation/negativebinomial.py b/pyrenew/observation/negativebinomial.py similarity index 100% rename from src/pyrenew/observation/negativebinomial.py rename to pyrenew/observation/negativebinomial.py diff --git a/src/pyrenew/observation/poisson.py b/pyrenew/observation/poisson.py similarity index 100% rename from src/pyrenew/observation/poisson.py rename to pyrenew/observation/poisson.py diff --git a/src/pyrenew/process/__init__.py b/pyrenew/process/__init__.py similarity index 100% rename from src/pyrenew/process/__init__.py rename to pyrenew/process/__init__.py diff --git a/src/pyrenew/process/ar.py b/pyrenew/process/ar.py similarity index 100% rename from src/pyrenew/process/ar.py rename to pyrenew/process/ar.py diff --git a/src/pyrenew/process/differencedprocess.py b/pyrenew/process/differencedprocess.py similarity index 100% rename from src/pyrenew/process/differencedprocess.py rename to pyrenew/process/differencedprocess.py diff --git a/src/pyrenew/process/iidrandomsequence.py b/pyrenew/process/iidrandomsequence.py similarity index 100% rename from src/pyrenew/process/iidrandomsequence.py rename to pyrenew/process/iidrandomsequence.py diff --git a/src/pyrenew/process/periodiceffect.py b/pyrenew/process/periodiceffect.py similarity index 100% rename from src/pyrenew/process/periodiceffect.py rename to pyrenew/process/periodiceffect.py diff --git a/src/pyrenew/process/randomwalk.py b/pyrenew/process/randomwalk.py similarity index 100% rename from src/pyrenew/process/randomwalk.py rename to pyrenew/process/randomwalk.py diff --git a/src/pyrenew/process/rtperiodicdiffar.py b/pyrenew/process/rtperiodicdiffar.py similarity index 100% rename from src/pyrenew/process/rtperiodicdiffar.py rename to pyrenew/process/rtperiodicdiffar.py diff --git a/src/pyrenew/regression.py b/pyrenew/regression.py similarity index 100% rename from src/pyrenew/regression.py rename to pyrenew/regression.py diff --git a/src/pyrenew/transformation/__init__.py b/pyrenew/transformation/__init__.py similarity index 100% rename from src/pyrenew/transformation/__init__.py rename to pyrenew/transformation/__init__.py diff --git a/src/pyrenew/transformation/builtin.py b/pyrenew/transformation/builtin.py similarity index 100% rename from src/pyrenew/transformation/builtin.py rename to pyrenew/transformation/builtin.py diff --git a/src/test/__init__.py b/test/__init__.py similarity index 100% rename from src/test/__init__.py rename to test/__init__.py diff --git a/src/test/test_ar_process.py b/test/test_ar_process.py similarity index 100% rename from src/test/test_ar_process.py rename to test/test_ar_process.py diff --git a/src/test/test_arrayutils.py b/test/test_arrayutils.py similarity index 100% rename from src/test/test_arrayutils.py rename to test/test_arrayutils.py diff --git a/src/test/test_assert_sample_and_rtype.py b/test/test_assert_sample_and_rtype.py similarity index 100% rename from src/test/test_assert_sample_and_rtype.py rename to test/test_assert_sample_and_rtype.py diff --git a/src/test/test_assert_type.py b/test/test_assert_type.py similarity index 100% rename from src/test/test_assert_type.py rename to test/test_assert_type.py diff --git a/src/test/test_broadcaster.py b/test/test_broadcaster.py similarity index 100% rename from src/test/test_broadcaster.py rename to test/test_broadcaster.py diff --git a/src/test/test_convolve_scanners.py b/test/test_convolve_scanners.py similarity index 100% rename from src/test/test_convolve_scanners.py rename to test/test_convolve_scanners.py diff --git a/src/test/test_datasets.py b/test/test_datasets.py similarity index 100% rename from src/test/test_datasets.py rename to test/test_datasets.py diff --git a/src/test/test_deterministic.py b/test/test_deterministic.py similarity index 100% rename from src/test/test_deterministic.py rename to test/test_deterministic.py diff --git a/src/test/test_differenced_process.py b/test/test_differenced_process.py similarity index 100% rename from src/test/test_differenced_process.py rename to test/test_differenced_process.py diff --git a/src/test/test_distributional_rv.py b/test/test_distributional_rv.py similarity index 100% rename from src/test/test_distributional_rv.py rename to test/test_distributional_rv.py diff --git a/src/test/test_forecast.py b/test/test_forecast.py similarity index 100% rename from src/test/test_forecast.py rename to test/test_forecast.py diff --git a/src/test/test_iid_random_sequence.py b/test/test_iid_random_sequence.py similarity index 100% rename from src/test/test_iid_random_sequence.py rename to test/test_iid_random_sequence.py diff --git a/src/test/test_infection_functions.py b/test/test_infection_functions.py similarity index 100% rename from src/test/test_infection_functions.py rename to test/test_infection_functions.py diff --git a/src/test/test_infection_initialization_method.py b/test/test_infection_initialization_method.py similarity index 100% rename from src/test/test_infection_initialization_method.py rename to test/test_infection_initialization_method.py diff --git a/src/test/test_infection_initialization_process.py b/test/test_infection_initialization_process.py similarity index 100% rename from src/test/test_infection_initialization_process.py rename to test/test_infection_initialization_process.py diff --git a/src/test/test_infectionsrtfeedback.py b/test/test_infectionsrtfeedback.py similarity index 100% rename from src/test/test_infectionsrtfeedback.py rename to test/test_infectionsrtfeedback.py diff --git a/src/test/test_latent_admissions.py b/test/test_latent_admissions.py similarity index 100% rename from src/test/test_latent_admissions.py rename to test/test_latent_admissions.py diff --git a/src/test/test_latent_infections.py b/test/test_latent_infections.py similarity index 100% rename from src/test/test_latent_infections.py rename to test/test_latent_infections.py diff --git a/src/test/test_leslie_matrix.py b/test/test_leslie_matrix.py similarity index 100% rename from src/test/test_leslie_matrix.py rename to test/test_leslie_matrix.py diff --git a/src/test/test_logistic_susceptibility_adjustment.py b/test/test_logistic_susceptibility_adjustment.py similarity index 100% rename from src/test/test_logistic_susceptibility_adjustment.py rename to test/test_logistic_susceptibility_adjustment.py diff --git a/src/test/test_model_basic_renewal.py b/test/test_model_basic_renewal.py similarity index 100% rename from src/test/test_model_basic_renewal.py rename to test/test_model_basic_renewal.py diff --git a/src/test/test_model_hosp_admissions.py b/test/test_model_hosp_admissions.py similarity index 100% rename from src/test/test_model_hosp_admissions.py rename to test/test_model_hosp_admissions.py diff --git a/src/test/test_observation_negativebinom.py b/test/test_observation_negativebinom.py similarity index 100% rename from src/test/test_observation_negativebinom.py rename to test/test_observation_negativebinom.py diff --git a/src/test/test_observation_poisson.py b/test/test_observation_poisson.py similarity index 100% rename from src/test/test_observation_poisson.py rename to test/test_observation_poisson.py diff --git a/src/test/test_periodiceffect.py b/test/test_periodiceffect.py similarity index 100% rename from src/test/test_periodiceffect.py rename to test/test_periodiceffect.py diff --git a/src/test/test_predictive.py b/test/test_predictive.py similarity index 100% rename from src/test/test_predictive.py rename to test/test_predictive.py diff --git a/src/test/test_process_asymptotics.py b/test/test_process_asymptotics.py similarity index 100% rename from src/test/test_process_asymptotics.py rename to test/test_process_asymptotics.py diff --git a/src/test/test_random_key.py b/test/test_random_key.py similarity index 100% rename from src/test/test_random_key.py rename to test/test_random_key.py diff --git a/src/test/test_random_walk.py b/test/test_random_walk.py similarity index 100% rename from src/test/test_random_walk.py rename to test/test_random_walk.py diff --git a/src/test/test_regression.py b/test/test_regression.py similarity index 100% rename from src/test/test_regression.py rename to test/test_regression.py diff --git a/src/test/test_rtperiodicdiff.py b/test/test_rtperiodicdiff.py similarity index 100% rename from src/test/test_rtperiodicdiff.py rename to test/test_rtperiodicdiff.py diff --git a/src/test/test_transformation.py b/test/test_transformation.py similarity index 100% rename from src/test/test_transformation.py rename to test/test_transformation.py diff --git a/src/test/test_transformed_rv_class.py b/test/test_transformed_rv_class.py similarity index 100% rename from src/test/test_transformed_rv_class.py rename to test/test_transformed_rv_class.py diff --git a/src/test/utils.py b/test/utils.py similarity index 100% rename from src/test/utils.py rename to test/utils.py