Elevate contents of src to root directory (#409)

* move src to root * remove src references in code * restore deleted tsv
CDCgov · Aug 22, 2024 · 648e69b · 648e69b
1 parent a793417
commit 648e69b
Show file tree

Hide file tree

Showing 82 changed files with 5 additions and 7 deletions.
diff --git 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
@@ -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 → pyrenew/arrayutils.py b/src/pyrenew/arrayutils.py → pyrenew/arrayutils.py
diff --git a/src/pyrenew/convolve.py → pyrenew/convolve.py b/src/pyrenew/convolve.py → pyrenew/convolve.py
diff --git a/src/pyrenew/datasets/__init__.py → pyrenew/datasets/__init__.py b/src/pyrenew/datasets/__init__.py → pyrenew/datasets/__init__.py
diff --git a/src/pyrenew/datasets/data-raw/README.md → pyrenew/datasets/data-raw/README.md b/src/pyrenew/datasets/data-raw/README.md → pyrenew/datasets/data-raw/README.md
diff --git a/.../datasets/data-raw/generation_interval.py → .../datasets/data-raw/generation_interval.py b/.../datasets/data-raw/generation_interval.py → .../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/.../data-raw/infection_admission_interval.py → .../data-raw/infection_admission_interval.py b/.../data-raw/infection_admission_interval.py → .../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 → pyrenew/datasets/data-raw/wastewater.R b/src/pyrenew/datasets/data-raw/wastewater.R → 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 → pyrenew/datasets/generation_interval.py b/src/pyrenew/datasets/generation_interval.py → pyrenew/datasets/generation_interval.py
diff --git a/src/pyrenew/datasets/generation_interval.tsv → pyrenew/datasets/generation_interval.tsv b/src/pyrenew/datasets/generation_interval.tsv → pyrenew/datasets/generation_interval.tsv
diff --git a/.../datasets/infection_admission_interval.py → .../datasets/infection_admission_interval.py b/.../datasets/infection_admission_interval.py → .../datasets/infection_admission_interval.py
diff --git a/...datasets/infection_admission_interval.tsv → ...datasets/infection_admission_interval.tsv b/...datasets/infection_admission_interval.tsv → ...datasets/infection_admission_interval.tsv
diff --git a/src/pyrenew/datasets/wastewater.py → pyrenew/datasets/wastewater.py b/src/pyrenew/datasets/wastewater.py → pyrenew/datasets/wastewater.py
diff --git a/src/pyrenew/datasets/wastewater.tsv → pyrenew/datasets/wastewater.tsv b/src/pyrenew/datasets/wastewater.tsv → pyrenew/datasets/wastewater.tsv
diff --git a/src/pyrenew/deterministic/__init__.py → pyrenew/deterministic/__init__.py b/src/pyrenew/deterministic/__init__.py → pyrenew/deterministic/__init__.py
diff --git a/src/pyrenew/deterministic/deterministic.py → pyrenew/deterministic/deterministic.py b/src/pyrenew/deterministic/deterministic.py → pyrenew/deterministic/deterministic.py
diff --git a/...pyrenew/deterministic/deterministicpmf.py → pyrenew/deterministic/deterministicpmf.py b/...pyrenew/deterministic/deterministicpmf.py → pyrenew/deterministic/deterministicpmf.py
diff --git a/src/pyrenew/deterministic/nullrv.py → pyrenew/deterministic/nullrv.py b/src/pyrenew/deterministic/nullrv.py → pyrenew/deterministic/nullrv.py
diff --git a/src/pyrenew/deterministic/process.py → pyrenew/deterministic/process.py b/src/pyrenew/deterministic/process.py → pyrenew/deterministic/process.py
diff --git a/src/pyrenew/distutil.py → pyrenew/distutil.py b/src/pyrenew/distutil.py → pyrenew/distutil.py
diff --git a/src/pyrenew/latent/__init__.py → pyrenew/latent/__init__.py b/src/pyrenew/latent/__init__.py → pyrenew/latent/__init__.py
diff --git a/src/pyrenew/latent/hospitaladmissions.py → pyrenew/latent/hospitaladmissions.py b/src/pyrenew/latent/hospitaladmissions.py → pyrenew/latent/hospitaladmissions.py
diff --git a/src/pyrenew/latent/infection_functions.py → pyrenew/latent/infection_functions.py b/src/pyrenew/latent/infection_functions.py → pyrenew/latent/infection_functions.py
diff --git a/...latent/infection_initialization_method.py → ...latent/infection_initialization_method.py b/...latent/infection_initialization_method.py → ...latent/infection_initialization_method.py
diff --git a/...atent/infection_initialization_process.py → ...atent/infection_initialization_process.py b/...atent/infection_initialization_process.py → ...atent/infection_initialization_process.py
diff --git a/src/pyrenew/latent/infections.py → pyrenew/latent/infections.py b/src/pyrenew/latent/infections.py → pyrenew/latent/infections.py
diff --git a/src/pyrenew/latent/infectionswithfeedback.py → pyrenew/latent/infectionswithfeedback.py b/src/pyrenew/latent/infectionswithfeedback.py → pyrenew/latent/infectionswithfeedback.py
diff --git a/src/pyrenew/math.py → pyrenew/math.py b/src/pyrenew/math.py → pyrenew/math.py
diff --git a/src/pyrenew/mcmcutils.py → pyrenew/mcmcutils.py b/src/pyrenew/mcmcutils.py → pyrenew/mcmcutils.py
diff --git a/src/pyrenew/metaclass.py → pyrenew/metaclass.py b/src/pyrenew/metaclass.py → pyrenew/metaclass.py
diff --git a/src/pyrenew/model/__init__.py → pyrenew/model/__init__.py b/src/pyrenew/model/__init__.py → pyrenew/model/__init__.py
diff --git a/src/pyrenew/model/admissionsmodel.py → pyrenew/model/admissionsmodel.py b/src/pyrenew/model/admissionsmodel.py → pyrenew/model/admissionsmodel.py
diff --git a/...pyrenew/model/rtinfectionsrenewalmodel.py → pyrenew/model/rtinfectionsrenewalmodel.py b/...pyrenew/model/rtinfectionsrenewalmodel.py → pyrenew/model/rtinfectionsrenewalmodel.py
diff --git a/src/pyrenew/observation/__init__.py → pyrenew/observation/__init__.py b/src/pyrenew/observation/__init__.py → pyrenew/observation/__init__.py
diff --git a/src/pyrenew/observation/negativebinomial.py → pyrenew/observation/negativebinomial.py b/src/pyrenew/observation/negativebinomial.py → pyrenew/observation/negativebinomial.py
diff --git a/src/pyrenew/observation/poisson.py → pyrenew/observation/poisson.py b/src/pyrenew/observation/poisson.py → pyrenew/observation/poisson.py
diff --git a/src/pyrenew/process/__init__.py → pyrenew/process/__init__.py b/src/pyrenew/process/__init__.py → pyrenew/process/__init__.py
diff --git a/src/pyrenew/process/ar.py → pyrenew/process/ar.py b/src/pyrenew/process/ar.py → pyrenew/process/ar.py
diff --git a/src/pyrenew/process/differencedprocess.py → pyrenew/process/differencedprocess.py b/src/pyrenew/process/differencedprocess.py → pyrenew/process/differencedprocess.py
diff --git a/src/pyrenew/process/iidrandomsequence.py → pyrenew/process/iidrandomsequence.py b/src/pyrenew/process/iidrandomsequence.py → pyrenew/process/iidrandomsequence.py
diff --git a/src/pyrenew/process/periodiceffect.py → pyrenew/process/periodiceffect.py b/src/pyrenew/process/periodiceffect.py → pyrenew/process/periodiceffect.py
diff --git a/src/pyrenew/process/randomwalk.py → pyrenew/process/randomwalk.py b/src/pyrenew/process/randomwalk.py → pyrenew/process/randomwalk.py
diff --git a/src/pyrenew/process/rtperiodicdiffar.py → pyrenew/process/rtperiodicdiffar.py b/src/pyrenew/process/rtperiodicdiffar.py → pyrenew/process/rtperiodicdiffar.py
diff --git a/src/pyrenew/regression.py → pyrenew/regression.py b/src/pyrenew/regression.py → pyrenew/regression.py
diff --git a/src/pyrenew/transformation/__init__.py → pyrenew/transformation/__init__.py b/src/pyrenew/transformation/__init__.py → pyrenew/transformation/__init__.py
diff --git a/src/pyrenew/transformation/builtin.py → pyrenew/transformation/builtin.py b/src/pyrenew/transformation/builtin.py → pyrenew/transformation/builtin.py
diff --git a/src/test/__init__.py → test/__init__.py b/src/test/__init__.py → test/__init__.py
diff --git a/src/test/test_ar_process.py → test/test_ar_process.py b/src/test/test_ar_process.py → test/test_ar_process.py
diff --git a/src/test/test_arrayutils.py → test/test_arrayutils.py b/src/test/test_arrayutils.py → test/test_arrayutils.py
diff --git a/src/test/test_assert_sample_and_rtype.py → test/test_assert_sample_and_rtype.py b/src/test/test_assert_sample_and_rtype.py → test/test_assert_sample_and_rtype.py
diff --git a/src/test/test_assert_type.py → test/test_assert_type.py b/src/test/test_assert_type.py → test/test_assert_type.py
diff --git a/src/test/test_broadcaster.py → test/test_broadcaster.py b/src/test/test_broadcaster.py → test/test_broadcaster.py
diff --git a/src/test/test_convolve_scanners.py → test/test_convolve_scanners.py b/src/test/test_convolve_scanners.py → test/test_convolve_scanners.py
diff --git a/src/test/test_datasets.py → test/test_datasets.py b/src/test/test_datasets.py → test/test_datasets.py
diff --git a/src/test/test_deterministic.py → test/test_deterministic.py b/src/test/test_deterministic.py → test/test_deterministic.py
diff --git a/src/test/test_differenced_process.py → test/test_differenced_process.py b/src/test/test_differenced_process.py → test/test_differenced_process.py
diff --git a/src/test/test_distributional_rv.py → test/test_distributional_rv.py b/src/test/test_distributional_rv.py → test/test_distributional_rv.py
diff --git a/src/test/test_forecast.py → test/test_forecast.py b/src/test/test_forecast.py → test/test_forecast.py
diff --git a/src/test/test_iid_random_sequence.py → test/test_iid_random_sequence.py b/src/test/test_iid_random_sequence.py → test/test_iid_random_sequence.py
diff --git a/src/test/test_infection_functions.py → test/test_infection_functions.py b/src/test/test_infection_functions.py → test/test_infection_functions.py
diff --git a/...t/test_infection_initialization_method.py → test/test_infection_initialization_method.py b/...t/test_infection_initialization_method.py → test/test_infection_initialization_method.py
diff --git a/.../test_infection_initialization_process.py → .../test_infection_initialization_process.py b/.../test_infection_initialization_process.py → .../test_infection_initialization_process.py
diff --git a/src/test/test_infectionsrtfeedback.py → test/test_infectionsrtfeedback.py b/src/test/test_infectionsrtfeedback.py → test/test_infectionsrtfeedback.py
diff --git a/src/test/test_latent_admissions.py → test/test_latent_admissions.py b/src/test/test_latent_admissions.py → test/test_latent_admissions.py
diff --git a/src/test/test_latent_infections.py → test/test_latent_infections.py b/src/test/test_latent_infections.py → test/test_latent_infections.py
diff --git a/src/test/test_leslie_matrix.py → test/test_leslie_matrix.py b/src/test/test_leslie_matrix.py → test/test_leslie_matrix.py
diff --git a/...est_logistic_susceptibility_adjustment.py → ...est_logistic_susceptibility_adjustment.py b/...est_logistic_susceptibility_adjustment.py → ...est_logistic_susceptibility_adjustment.py
diff --git a/src/test/test_model_basic_renewal.py → test/test_model_basic_renewal.py b/src/test/test_model_basic_renewal.py → test/test_model_basic_renewal.py
diff --git a/src/test/test_model_hosp_admissions.py → test/test_model_hosp_admissions.py b/src/test/test_model_hosp_admissions.py → test/test_model_hosp_admissions.py
diff --git a/src/test/test_observation_negativebinom.py → test/test_observation_negativebinom.py b/src/test/test_observation_negativebinom.py → test/test_observation_negativebinom.py
diff --git a/src/test/test_observation_poisson.py → test/test_observation_poisson.py b/src/test/test_observation_poisson.py → test/test_observation_poisson.py
diff --git a/src/test/test_periodiceffect.py → test/test_periodiceffect.py b/src/test/test_periodiceffect.py → test/test_periodiceffect.py
diff --git a/src/test/test_predictive.py → test/test_predictive.py b/src/test/test_predictive.py → test/test_predictive.py
diff --git a/src/test/test_process_asymptotics.py → test/test_process_asymptotics.py b/src/test/test_process_asymptotics.py → test/test_process_asymptotics.py
diff --git a/src/test/test_random_key.py → test/test_random_key.py b/src/test/test_random_key.py → test/test_random_key.py
diff --git a/src/test/test_random_walk.py → test/test_random_walk.py b/src/test/test_random_walk.py → test/test_random_walk.py
diff --git a/src/test/test_regression.py → test/test_regression.py b/src/test/test_regression.py → test/test_regression.py
diff --git a/src/test/test_rtperiodicdiff.py → test/test_rtperiodicdiff.py b/src/test/test_rtperiodicdiff.py → test/test_rtperiodicdiff.py
diff --git a/src/test/test_transformation.py → test/test_transformation.py b/src/test/test_transformation.py → test/test_transformation.py
diff --git a/src/test/test_transformed_rv_class.py → test/test_transformed_rv_class.py b/src/test/test_transformed_rv_class.py → test/test_transformed_rv_class.py
diff --git a/src/test/utils.py → test/utils.py b/src/test/utils.py → test/utils.py