From 342ef5d0d1bc7bb664583b1d40c46af913c39fc8 Mon Sep 17 00:00:00 2001
From: Tadd Bindas <tkb5476@psu.edu>
Date: Sun, 18 Feb 2024 20:44:17 -0500
Subject: [PATCH] Fixed Streamflow outputs that cause a NaN (#12)

* added lower bound to streamflow predictions
---
 .idea/marquette.iml                                 | 2 +-
 .idea/misc.xml                                      | 2 +-
 README.md                                           | 9 ++++-----
 marquette/merit/_streamflow_conversion_functions.py | 6 ++++--
 4 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/.idea/marquette.iml b/.idea/marquette.iml
index 2bd4486..a81d4e2 100644
--- a/.idea/marquette.iml
+++ b/.idea/marquette.iml
@@ -2,7 +2,7 @@
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="jdk" jdkName="marquette_env" jdkType="Python SDK" />
+    <orderEntry type="jdk" jdkName="Remote Python 3.10.9 (sftp://tkb5476@suntzu.cee.psu.edu:22/data/tkb5476/projects/marquette/.venv/bin/python3.10) (2)" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
 </module>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
index 39c947b..d37b035 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -3,7 +3,7 @@
   <component name="Black">
     <option name="sdkName" value="$USER_HOME$/mambaforge/envs/marquette" />
   </component>
-  <component name="ProjectRootManager" version="2" project-jdk-name="marquette_env" project-jdk-type="Python SDK" />
+  <component name="ProjectRootManager" version="2" project-jdk-name="Remote Python 3.10.9 (sftp://tkb5476@suntzu.cee.psu.edu:22/data/tkb5476/projects/marquette/.venv/bin/python3.10) (2)" project-jdk-type="Python SDK" />
   <component name="PyCharmProfessionalAdvertiser">
     <option name="shown" value="true" />
   </component>
diff --git a/README.md b/README.md
index e26a60d..c3b89ad 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,12 @@
 # Marquette
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Python](https://img.shields.io/pypi/pyversions/msmhelper)]()
-
 ![image](https://github.com/taddyb/marquette/assets/16233925/4a7b8745-7576-4150-bf4a-9469d44a9425)
 
 A river mapping library to take .shp files and create River Network CSVs
 
-## Quick Start
-1. clone
-2. set up env from `environment.yml`
-3. put your data files into the `data/` folder (if it's not there, then create it), then reference them from your config
+## Quick Start:
+1. `conda create -n marquette python=3.11`
+2. `conda activate marquette`
+3. `pip install -r requirements.txt`
 
diff --git a/marquette/merit/_streamflow_conversion_functions.py b/marquette/merit/_streamflow_conversion_functions.py
index 37d33e8..c8b132d 100644
--- a/marquette/merit/_streamflow_conversion_functions.py
+++ b/marquette/merit/_streamflow_conversion_functions.py
@@ -124,6 +124,7 @@ def calculate_merit_flow(cfg: DictConfig) -> None:
     streamflow_predictions_root = zarr.open(
         Path(cfg.create_streamflow.predictions), mode="r"
     )
+    log.info("Reading Zarr Store")
     runoff = streamflow_predictions_root.Runoff[:]
 
     log.info("Creating areas areas_array")
@@ -139,8 +140,9 @@ def calculate_merit_flow(cfg: DictConfig) -> None:
 
     log.info("Converting runoff data")
     streamflow_m3_s_data = runoff * areas_array
-    mask = np.any(np.isnan(runoff), axis=0)
-    streamflow_m3_s_data[:, mask] = 0.0
+    streamflow_m3_s_data = np.nan_to_num(
+        streamflow_m3_s_data, nan=1e-6, posinf=1e-6, neginf=1e-6
+    )
 
     date_range = pd.date_range(
         start=cfg.create_streamflow.start_date,