From 81897d7dcbe71adbaddbc38d7eb85efe02238822 Mon Sep 17 00:00:00 2001
From: "Tadd.Bindas" <Tadd.N.Bindas@rtx.com>
Date: Sun, 31 Aug 2025 16:44:26 -0400
Subject: [PATCH 1/2] NGWPC 7009: update hydrovis with changes to work with
 t-route PR #30

---
 Source/Ingest/docker/Dockerfile.ingest        |   2 +-
 Source/RnR/dist/README.md                     |  87 ------------------
 ...cefabric_manage-0.1.0-py2.py3-none-any.whl | Bin 2207 -> 0 bytes
 ...icefabric_tools-0.1.0-py2.py3-none-any.whl | Bin 4600 -> 0 bytes
 Source/RnR/docker/Dockerfile.process_flows    |  30 ------
 Source/RnR/docker/Dockerfile.troute           |  31 ++-----
 Source/data/warehouse/.gitkeep                |   0
 Source/docker/README.md                       |  48 ++++++++--
 Source/docker/compose.yaml                    |  15 ---
 Source/{docs => docker}/rnr_workflow.png      | Bin
 Source/docker/run_post_process.sh             |   4 +-
 Source/docker/start.sh                        |   2 +-
 Source/docs/workflow.md                       |  48 ----------
 13 files changed, 51 insertions(+), 216 deletions(-)
 delete mode 100644 Source/RnR/dist/README.md
 delete mode 100644 Source/RnR/dist/icefabric_manage-0.1.0-py2.py3-none-any.whl
 delete mode 100644 Source/RnR/dist/icefabric_tools-0.1.0-py2.py3-none-any.whl
 delete mode 100644 Source/RnR/docker/Dockerfile.process_flows
 delete mode 100644 Source/data/warehouse/.gitkeep
 rename Source/{docs => docker}/rnr_workflow.png (100%)
 delete mode 100644 Source/docs/workflow.md

diff --git a/Source/Ingest/docker/Dockerfile.ingest b/Source/Ingest/docker/Dockerfile.ingest
index 91b54bdfc..7cd632ba5 100644
--- a/Source/Ingest/docker/Dockerfile.ingest
+++ b/Source/Ingest/docker/Dockerfile.ingest
@@ -4,7 +4,7 @@ FROM python:3.12-slim
 RUN apt-get update && apt-get install -y curl
 
 # Install UV properly by copying from the official image
-COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+COPY --from=ghcr.io/astral-sh/uv:0.8.14 /uv /uvx /bin/
 
 # Set the working directory
 WORKDIR /app
diff --git a/Source/RnR/dist/README.md b/Source/RnR/dist/README.md
deleted file mode 100644
index 146466234..000000000
--- a/Source/RnR/dist/README.md
+++ /dev/null
@@ -1,87 +0,0 @@
-# Distributions
-
-The files in this repo are wheels from the internal NGWPC icefabric repo. Each package has a service(s) designed to extract RnR segments and format the hydrofabric v2.2
-
-## How to use:
-- These files are built in the T-Route RnR docker containers and run the `rnr.get_rnr_segment()`
-- These Wheels are required to run `troute-rnr/`
-
-## Why are there wheels instead of a github install?
-- Since the `icefabric/` repo has not been delivered at this time, we've attached wheels from a version that works with replace and route to ensure the code will run
-
-## The `get_rnr_segment()` Function used in RnR
-
-### Overview
-
-The `get_rnr_segment` function extracts a river network segment from a hydrofabric dataset based on RnR (Reach and Route) rules. It processes hydrologic data from an Iceberg catalog and exports the results as a multi-layer GeoPackage file.
-
-### Function Signature
-
-```python
-def get_rnr_segment(catalog: Catalog, reach_id: str, output_file: str) -> gpd.GeoDataFrame
-```
-
-### Parameters
-
-| Parameter | Type | Description |
-|-----------|------|-------------|
-| `catalog` | `Catalog` | The Iceberg catalog containing the hydrofabric data tables |
-| `reach_id` | `str` | The reach identifier (hf_id) from the NWPS API used to locate the target stream segment |
-| `output_file` | `str` | File path where the output GeoPackage will be saved |
-
-### Returns
-
-- **Type**: `gpd.GeoDataFrame`
-- **Description**: A GeoDataFrame containing the processed hydrofabric data
-
-### Data Sources
-
-The function accesses the following tables from the hydrofabric. These are parquet files of each layer which are available from the raytheon s3:// or can be built from the hydrofabric v2.2 gpkg file through a geopandas parquet conversion.
-
-### Processing Logic
-
-1. **Stream Identification**: Locates the target stream using the provided `reach_id`
-2. **Mainstem Filtering**: Identifies all streams on the same mainstem with hydrosequence values less than or equal to the target stream
-3. **Stream Order Matching**: Filters features to include only those with the same stream order as the target reach
-4. **Geometric Data Extraction**: Retrieves associated geometric and attribute data for:
-   - Flowpaths
-   - Nexus points
-   - Divides
-   - Points of interest
-   - Hydrolocations
-5. **Multi-layer Export**: Saves all processed data as separate layers in a single GeoPackage file
-
-### Output Structure
-
-The function creates a GeoPackage file with the following layers:
-- `flowpaths`
-- `nexus`
-- `divides`
-- `divide-attributes`
-- `network`
-- `pois`
-- `flowpath-attributes-ml`
-- `flowpath-attributes`
-- `hydrolocations`
-
-### Usage Example
-
-```python
-from icefabric_manage import build
-from icefabric_tools import rnr
-from pyiceberg.catalog import load_catalog
-
-# Builds the catalog
-data_dir = <YOUR DATA DIR>
-self.catalog_settings = {
-    "type": "sql",
-    "uri": f"sqlite:///{str(data_dir / 'warehouse/pyiceberg_catalog.db')}",
-    "warehouse": f"file://{str(data_dir.resolve())}/warehouse",
-}
-
-self.catalog = load_catalog("hydrofabric", **self.catalog_settings)
-build(self.catalog, Path(f"{self.data_dir.resolve()}/parquet"))
-
-# Extract RnR segment
-gdf = rnr.get_rnr_segment(settings.catalog, inputs.reach.id, settings.tmp_geopackage)
-```
diff --git a/Source/RnR/dist/icefabric_manage-0.1.0-py2.py3-none-any.whl b/Source/RnR/dist/icefabric_manage-0.1.0-py2.py3-none-any.whl
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diff --git a/Source/RnR/dist/icefabric_tools-0.1.0-py2.py3-none-any.whl b/Source/RnR/dist/icefabric_tools-0.1.0-py2.py3-none-any.whl
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diff --git a/Source/RnR/docker/Dockerfile.process_flows b/Source/RnR/docker/Dockerfile.process_flows
deleted file mode 100644
index 31c310892..000000000
--- a/Source/RnR/docker/Dockerfile.process_flows
+++ /dev/null
@@ -1,30 +0,0 @@
-FROM rockylinux:9.3
-RUN yum install -y epel-release
-RUN yum install -y git cmake
-
-COPY --from=ghcr.io/astral-sh/uv:0.7.8 /uv /uvx /bin/
-
-# Use UV to install Python 3.11
-RUN uv python install 3.11
-
-# Clone the repository
-RUN git clone https://github.com/NGWPC/t-route.git
-WORKDIR "/t-route/"
-RUN git checkout pi_6
-
-# Create a directory for local packages
-RUN mkdir -p /app/wheels
-
-# Copy the pre-built wheel from the build context
-COPY dist/icefabric_tools-*.whl /app/wheels/
-COPY dist/icefabric_manage-*whl /app/wheels/
-
-# Create venv and set environment to use it
-RUN uv venv --python 3.11
-ENV PATH="/app/.venv/bin:$PATH"
-
-# Install the troute-rnr package specifically
-WORKDIR "/t-route/src/troute-rnr"
-RUN uv pip install /app/wheels/icefabric_tools-*.whl
-RUN uv pip install /app/wheels/icefabric_manage-*.whl
-RUN uv pip install -e .
diff --git a/Source/RnR/docker/Dockerfile.troute b/Source/RnR/docker/Dockerfile.troute
index 8602def48..75a572ec7 100644
--- a/Source/RnR/docker/Dockerfile.troute
+++ b/Source/RnR/docker/Dockerfile.troute
@@ -7,43 +7,30 @@ RUN yum install -y gcc
 RUN yum install -y netcdf netcdf-fortran netcdf-fortran-devel netcdf-openmpi
 RUN yum install -y git cmake
 
-
 # Install UV by copying the binaries directly from the official image
-COPY --from=ghcr.io/astral-sh/uv:0.7.8 /uv /uvx /bin/
-
-# Use UV to install Python 3.11
+COPY --from=ghcr.io/astral-sh/uv:0.8.14 /uv /uvx /bin/
 RUN uv python install 3.11
 
-# Clone the repository
 RUN git clone https://github.com/NGWPC/t-route.git
 WORKDIR "/t-route/"
-RUN git checkout pi_6
+RUN git checkout NGWPC-7009
 
-# Create netcdf symlink with error handling
+# # Create netcdf symlink with error handling
 RUN ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/openmpi-x86_64/netcdf.mod || echo "NetCDF module link creation failed but continuing"
 
-# Create venv and set environment to use it
+# # Create venv and set environment to use it
 RUN uv venv --python 3.11
 ENV PATH="/app/.venv/bin:$PATH"
 
-# Create a directory for local packages
-RUN mkdir -p /app/wheels
-
-# Copy the pre-built wheel from the build context
-COPY dist/icefabric_tools-*.whl /app/wheels/
-COPY dist/icefabric_manage-*whl /app/wheels/
-
-# Install the main package in development mode
+# # Install the main package in development mode
 RUN uv pip install -e .
 
-# Run the compiler script
-RUN ./compiler_uv.sh no-e
+# # Run the compiler script
+RUN ./compiler.sh no-e --uv
 
-# Install the troute-rnr package specifically
+# # Install the troute-rnr package specifically
 WORKDIR "/t-route/src/troute-rnr"
-RUN uv pip install /app/wheels/icefabric_tools-*.whl
-RUN uv pip install /app/wheels/icefabric_manage-*.whl
 RUN uv pip install -e .
 
-# Increase max open files soft limit with error handling
+# # Increase max open files soft limit with error handling
 RUN ulimit -n 10000
diff --git a/Source/data/warehouse/.gitkeep b/Source/data/warehouse/.gitkeep
deleted file mode 100644
index e69de29bb..000000000
diff --git a/Source/docker/README.md b/Source/docker/README.md
index 70c85d4f1..f31e091df 100644
--- a/Source/docker/README.md
+++ b/Source/docker/README.md
@@ -1,20 +1,48 @@
-# Docker scripts
+# Replace and Route (v2025.6.0)
 
-The provided compose files are meant to spin up replace and route as a container for developmental testing
+Replace and route is a service which routes streamflow forecasts from the [NWPS API](https://api.water.noaa.gov/nwps/v1/docs/#/) through T-Route to propogate flow through a river segment. Outputs are shown at [water.noaa.gov](water.noaa.gov). This `Source/` dir contains a collection of code, docker management scripts, and IaC to run the full collection of services. 
 
-## How to run:
+## Overview
 
-Run:
+There are two versions of Replace and Route contained in `hydrovis/`
+- The Docker Development Version
+    - This version is what can be spun up locally within a User's environment if they were to clone the repo
+- IaC version
+    - This is the production version which will is designed to scale efficiently to handle many t-route containers running in parallel
+    - This code is contained in `Source/terraform`
 
-```sh
-docker compose -f docker/compose.yaml up
-```
+Both versions are the same code, but the terraform IaC is what is designed to scale. The docker version is meant to be a localized testing version
 
+## Requirements
 
-The services require a data directory. By default, it uses the `data` directory at the root of this repository. 
+The following data is required to run RnR locally
+- the v2.2 hydrofabric layers stored as parquet files
+    - These are located at `s3://hydrofabric-data/icefabric` from the Raytheon private S3 bucket. Please contact @taddyb for these files if you do not have access
+- `docker compose` installed on your system
 
-You can override this by setting the `RNR_DATA_PATH` environment variable before running docker-compose:
+## Parts
+![RnR Workflow](rnr_workflow.png)
 
+There are three parts to replace and route
+1. The HML Ingestion 
+    - This code reads in HML files from the public [weather api](https://api.weather.gov/) and queues them into a Rabbit MQ. Redis is used to cache previously read forecasts. This code is located in `Source/Ingest`
+    - To run this, run `./run_ingest.sh` after starting the containers
+2. T-Route
+    - This is the routing code which will propograte forecasted flow downstream. All code is located in `src/troute-rnr` directory and the `Source/RnR` contains the docker scripts to run T-Route.
+    - To run this, run `./run_rnr.sh` after starting the containers
+3. Post-processing
+    - This is the code which will read T-Route outputs and create and `output-inundation.csv` file
+    - To run this, run `./run_post_process.sh` after starting the containers
+
+### How to run
+To run RnR you can run the following scripts:
 ```sh
-RNR_DATA_PATH=/path/to/your/data 
+cd Source/docker
+./start.sh
+./run_ingest.sh
+./run_rnr.sh
+./run_post_process.sh
+./stop.sh
 ```
+and you can view the logs through `./logs.sh`
+
diff --git a/Source/docker/compose.yaml b/Source/docker/compose.yaml
index 27df8acb6..2bdb9e31f 100644
--- a/Source/docker/compose.yaml
+++ b/Source/docker/compose.yaml
@@ -57,21 +57,6 @@ services:
         condition: service_healthy
     command: ["tail", "-f", "/dev/null"]
 
-  process_flows:
-    build:
-      context: ../RnR
-      dockerfile: docker/Dockerfile.process_flows
-    volumes:
-      - ../data:/t-route/data
-    networks:
-      - app-network
-    depends_on:
-      redis:
-        condition: service_healthy
-      rabbitmq:
-        condition: service_healthy
-    command: ["tail", "-f", "/dev/null"]
-  
 networks:
   app-network:
     driver: bridge
diff --git a/Source/docs/rnr_workflow.png b/Source/docker/rnr_workflow.png
similarity index 100%
rename from Source/docs/rnr_workflow.png
rename to Source/docker/rnr_workflow.png
diff --git a/Source/docker/run_post_process.sh b/Source/docker/run_post_process.sh
index 5ea98fa6a..1ea2efeb3 100755
--- a/Source/docker/run_post_process.sh
+++ b/Source/docker/run_post_process.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# run_rnr.sh - Formats the .nc files to create output csvs
+# run_post_process.sh - Formats the .nc files to create output csvs
 
 # Goes into the container, activates the .venv/, runs the read script
-docker exec docker-process_flows-1 bash -c "source ../../.venv/bin/activate && python post_process.py"
+docker exec docker-rnr-1 bash -c "source ../../.venv/bin/activate && python post_process.py"
diff --git a/Source/docker/start.sh b/Source/docker/start.sh
index 301b94756..bfc308b9e 100755
--- a/Source/docker/start.sh
+++ b/Source/docker/start.sh
@@ -54,7 +54,7 @@ check_service_health "Redis" 6379 10 2 || { echo "Redis failed to start properly
 
 # Step 5: Start the rest of the services in detached mode
 echo "Starting application services..."
-docker compose up -d process_flows rnr ingest
+docker compose up -d rnr ingest
 
 echo "All services have been started successfully!"
 echo "Use './run_ingest.sh', './run_rnr.sh', or './run_post_process.sh' to run specific services individually."
diff --git a/Source/docs/workflow.md b/Source/docs/workflow.md
deleted file mode 100644
index f31e091df..000000000
--- a/Source/docs/workflow.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# Replace and Route (v2025.6.0)
-
-Replace and route is a service which routes streamflow forecasts from the [NWPS API](https://api.water.noaa.gov/nwps/v1/docs/#/) through T-Route to propogate flow through a river segment. Outputs are shown at [water.noaa.gov](water.noaa.gov). This `Source/` dir contains a collection of code, docker management scripts, and IaC to run the full collection of services. 
-
-## Overview
-
-There are two versions of Replace and Route contained in `hydrovis/`
-- The Docker Development Version
-    - This version is what can be spun up locally within a User's environment if they were to clone the repo
-- IaC version
-    - This is the production version which will is designed to scale efficiently to handle many t-route containers running in parallel
-    - This code is contained in `Source/terraform`
-
-Both versions are the same code, but the terraform IaC is what is designed to scale. The docker version is meant to be a localized testing version
-
-## Requirements
-
-The following data is required to run RnR locally
-- the v2.2 hydrofabric layers stored as parquet files
-    - These are located at `s3://hydrofabric-data/icefabric` from the Raytheon private S3 bucket. Please contact @taddyb for these files if you do not have access
-- `docker compose` installed on your system
-
-## Parts
-![RnR Workflow](rnr_workflow.png)
-
-There are three parts to replace and route
-1. The HML Ingestion 
-    - This code reads in HML files from the public [weather api](https://api.weather.gov/) and queues them into a Rabbit MQ. Redis is used to cache previously read forecasts. This code is located in `Source/Ingest`
-    - To run this, run `./run_ingest.sh` after starting the containers
-2. T-Route
-    - This is the routing code which will propograte forecasted flow downstream. All code is located in `src/troute-rnr` directory and the `Source/RnR` contains the docker scripts to run T-Route.
-    - To run this, run `./run_rnr.sh` after starting the containers
-3. Post-processing
-    - This is the code which will read T-Route outputs and create and `output-inundation.csv` file
-    - To run this, run `./run_post_process.sh` after starting the containers
-
-### How to run
-To run RnR you can run the following scripts:
-```sh
-cd Source/docker
-./start.sh
-./run_ingest.sh
-./run_rnr.sh
-./run_post_process.sh
-./stop.sh
-```
-and you can view the logs through `./logs.sh`
-

From 028b437142876a924ad4bb8093279ba41b8a74d8 Mon Sep 17 00:00:00 2001
From: "Tadd.Bindas" <Tadd.N.Bindas@rtx.com>
Date: Tue, 2 Sep 2025 17:08:46 -0400
Subject: [PATCH 2/2] changed t-route branch reference

---
 Source/RnR/docker/Dockerfile.troute | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/RnR/docker/Dockerfile.troute b/Source/RnR/docker/Dockerfile.troute
index 75a572ec7..181a5ce00 100644
--- a/Source/RnR/docker/Dockerfile.troute
+++ b/Source/RnR/docker/Dockerfile.troute
@@ -13,7 +13,7 @@ RUN uv python install 3.11
 
 RUN git clone https://github.com/NGWPC/t-route.git
 WORKDIR "/t-route/"
-RUN git checkout NGWPC-7009
+RUN git checkout pi-7-NGWPC-6258
 
 # # Create netcdf symlink with error handling
 RUN ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/openmpi-x86_64/netcdf.mod || echo "NetCDF module link creation failed but continuing"