add poetry package env simple, incomplete; edit README

CDCgov · Aug 26, 2024 · fc58b6a · fc58b6a
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diff --git a/README.md b/README.md
@@ -4,7 +4,15 @@
 
 _`pyrenew-flu-light` is an instantiation of an [Epidemia](https://imperialcollegelondon.github.io/epidemia/) influenza forecasting model in [PyRenew](https://github.com/CDCgov/PyRenew)._
 
-NOTE: Presently, this `pyrenew-flu-light` cannot be installed and used with current NHSN, as its author is validating it on historical influenza data, which is .
+NOTE: Presently, this `pyrenew-flu-light` cannot be installed and used with current NHSN, as its author is validating it on historical influenza data.
+
+Run command typically used:
+
+```
+poetry run python tut_epim_port_msr.py --reporting_date 2024-01-20 --regions NY --historical --forecast
+
+python3 tut_epim_port_msr.py --reporting_date 2024-01-20 --regions NY --historical --forecast
+```
 
 ## ...Contained Within This Repository
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,22 @@
+[tool.poetry]
+name = "pyrenew-flu-light"
+version = "0.0.1"
+description = "An instantiation of an Epidemia influenza forecasting model in PyRenew."
+authors = ["CFA"]
+license = "Apache-2.0"
+readme = "README.md"
+packages = [{include = "pyrenew_flu_light"}]
+
+
+[tool.poetry.dependencies]
+python = "^3.11"
+polars = "^1.5.0"
+numpyro = "^0.15.2"
+arviz = "^0.19.0"
+
+[tool.poetry.group.dev.dependencies]
+rpy2 = "^3.5.16"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/src/utils/checks.py → pyrenew_flu_light/checks.py b/src/utils/checks.py → pyrenew_flu_light/checks.py
diff --git a/src/utils/compare.py → pyrenew_flu_light/compare.py b/src/utils/compare.py → pyrenew_flu_light/compare.py
diff --git a/src/model/inf.py → pyrenew_flu_light/inf.py b/src/model/inf.py → pyrenew_flu_light/inf.py
diff --git a/src/model/model.py → pyrenew_flu_light/model.py b/src/model/model.py → pyrenew_flu_light/model.py
diff --git a/src/model/obs.py → pyrenew_flu_light/obs.py b/src/model/obs.py → pyrenew_flu_light/obs.py
diff --git a/src/utils/pad.py → pyrenew_flu_light/pad.py b/src/utils/pad.py → pyrenew_flu_light/pad.py
diff --git a/src/utils/plot_data.py → pyrenew_flu_light/plot_data.py b/src/utils/plot_data.py → pyrenew_flu_light/plot_data.py
diff --git a/src/utils/plot_for.py → pyrenew_flu_light/plot_for.py b/src/utils/plot_for.py → pyrenew_flu_light/plot_for.py
diff --git a/src/utils/plot_mcmc.py → pyrenew_flu_light/plot_mcmc.py b/src/utils/plot_mcmc.py → pyrenew_flu_light/plot_mcmc.py
diff --git a/src/utils/reports.py → pyrenew_flu_light/reports.py b/src/utils/reports.py → pyrenew_flu_light/reports.py
diff --git a/src/model/rt.py → pyrenew_flu_light/rt.py b/src/model/rt.py → pyrenew_flu_light/rt.py
diff --git a/src/run.py → pyrenew_flu_light/run.py b/src/run.py → pyrenew_flu_light/run.py
diff --git a/src/model/tut_epim_port_msr.py → pyrenew_flu_light/tut_epim_port_msr.py b/src/model/tut_epim_port_msr.py → pyrenew_flu_light/tut_epim_port_msr.py
@@ -298,7 +298,7 @@ def ensure_output_directory(args: dict[str, any]):  # numpydoc ignore=GL08
 def assert_historical_data_files_exist(
     reporting_date: str,
 ):  # numpydoc ignore=GL08
-    data_directory = f"../../data/{reporting_date}/"
+    data_directory = f"../data/{reporting_date}/"
     assert os.path.exists(
         data_directory
     ), f"Data directory {data_directory} does not exist."
@@ -1744,7 +1744,7 @@ def main(args):  # numpydoc ignore=GL08
 
         # load historical configuration file (modified from cfaepim)
         config = load_config(
-            config_path=f"../../config/params_{args.reporting_date}_historical.toml"
+            config_path=f"../config/params_{args.reporting_date}_historical.toml"
         )
         logging.info("Configuration (historical) loaded.")
 

diff --git a/src/model/__init__.py b/src/model/__init__.py
diff --git a/src/utils/__init__.py b/src/utils/__init__.py