Elevate contents of src to root directory (#409)

* move src to root

* remove src references in code

* restore deleted tsv

Author: damonbayer

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 -----------------------------------------------------

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"}]

src/pyrenew/arrayutils.py pyrenew/arrayutils.pysrc/pyrenew/arrayutils.py renamed to pyrenew/arrayutils.py

@@ -13,7 +13,6 @@
 
 # Building path to save the file
 path = os.path.join(
-    "src",
     "pyrenew",
     "datasets",
     "gen_int.tsv",

src/pyrenew/convolve.py pyrenew/convolve.pysrc/pyrenew/convolve.py renamed to pyrenew/convolve.py

@@ -13,7 +13,6 @@
 
 # Building path to save the file
 path = os.path.join(
-    "src",
     "pyrenew",
     "datasets",
     "infection_admission_interval.tsv",

src/pyrenew/datasets/__init__.py pyrenew/datasets/__init__.pysrc/pyrenew/datasets/__init__.py renamed to pyrenew/datasets/__init__.py

@@ -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 = ""
-  )
+)