reorganized dockerfiles

doc/api/api_docs.md

@@ -6,7 +6,7 @@ The following doc is meant to explain the T-Route FastAPI implementation using d
 
 T-Route is used in many contexts for hydrological river routing:
 - NGEN 
-- Scientific Python 
+- Scientific Python Projects
 - Replace and Route (RnR)
 
 In the latest PR for RnR (https://github.com/NOAA-OWP/hydrovis/pull/865), there is an requirement to run T-Route as a service. This service requires an easy way to dynamically create config files, restart flow from Initial Conditions, and run T-Route. To satisfy this requirement, a FastAPI endpoint was created in `/src/app` along with code to dynamically create t-route endpoints. 
@@ -76,7 +76,7 @@ docker login --username ${GH_USERNAME} --password ${GH_TOKEN} ghcr.io
 - This command will log the user into the GitHub container registry using their credentials
 
 ```shell
-docker build -t ghcr.io/NOAA-OWP/t-route/t-route-api:${TAG} -f Dockerfile.troute_api
+docker build -t ghcr.io/NOAA-OWP/t-route/t-route-api:${TAG} -f docker/Dockerfile.troute_api
 ```
 - This command builds the T-Route API container using a defined version `${TAG}`
 
@@ -99,7 +99,39 @@ If you want to build this off a forked version, change the container registry (`
 
 ## Testing:
 
-### Testing the RnR Extension: 
+### Set up Using a Dockerfile:
+
+To build the T-Route api from a dockerfile, you can use the following commands from the t-route root repo:
+
+```shell
+docker build -t troute_api -f docker/Dockerfile.troute_api .
+```
+
+```shell
+docker run -p 8000:8000   \
+--env-file docker/test_troute_api.env  \
+-v ${OUTPUT_VOLUME_SOURCE}:${OUTPUT_VOLUME_TARGET}  \
+-v ${DATA_VOLUME_SOURCE}:${DATA_VOLUME_TARGET}  \
+-v ${CORE_VOLUME_SOURCE}:${CORE_VOLUME_TARGET}  \
+-v ${TEST_SOURCE}:${TEST_TARGET}   troute_api
+```
+
+### Set up Docker Compose:
+
+Docker Compose uses a YAML file to configure docker containers and execution. To install compose, you can follow the examples on docker's docs: https://docs.docker.com/compose/install/linux/
+
+To run compose, you can use the following command from the root directory:
+
+```shell
+docker compose --env-file docker/test_troute_api.env -f docker/compose.yaml up --build
+```
+
+if you want to build a compose container to mimic what is used in RnR, you can run the following steps
+```shell
+docker compose --env-file docker/rnr_compose.env -f docker/compose.yaml up --build
+```
+
+#### Testing the RnR endpoint in the API: 
 The following folder contains data files that are to be used to test the T-Route FastAPI code within src/app
 
 To use these files, follow the steps below:
@@ -117,8 +149,8 @@ To use these files, follow the steps below:
 5. Click execute
 6. A Status 201 code means the run ran, and test/api/data/troute_output will be populated in the `{lid}/` folder
 
-### Testing the LowerColorado test cases:
+#### Testing the LowerColorado test cases through docker compose:
 1. Run the compose.yaml file from the base dir using: `docker compose --env-file ./compose.env up --build`
 2. visit `localhost:8000/docs` in your browser
-3. Execute the `/api/v1/flow_routing/v4/tests/LowerColorado` endpoint using the default parameter file path
+3. Execute the `/api/v1/flow_routing/v4/tests/LowerColorado` endpoint using the default parameter file path for LowerColorado_TX_v4 
 4. A Status 201 code means the run ran, and the defined yaml output will be populated

Dockerfile.troute_api → docker/Dockerfile.compose

@@ -4,8 +4,8 @@ RUN yum install -y netcdf netcdf-fortran netcdf-fortran-devel netcdf-openmpi
 
 RUN yum install -y git cmake python python-devel pip 
 
-WORKDIR "/t-route/"
-COPY . "/t-route/"
+WORKDIR /t-route/
+COPY . /t-route/
 
 RUN ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/openmpi-x86_64/netcdf.mod
 
@@ -16,11 +16,11 @@ RUN uv venv
 ENV VIRTUAL_ENV=/t-route/.venv
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
-RUN uv pip install --no-cache-dir -r requirements.txt
+RUN uv pip install --no-cache-dir -r /t-route/requirements.txt
 
 RUN ./compiler.sh no-e
 
-RUN uv pip install --no-cache-dir -r requirements-app.txt
+RUN uv pip install --no-cache-dir -r /t-route/requirements-app.txt
 
 WORKDIR "/t-route/src/"
 RUN mkdir -p /t-route/data/troute_restart/

docker/Dockerfile.troute_api

@@ -0,0 +1,39 @@
+FROM rockylinux:9.2 as rocky-base
+
+RUN yum install -y epel-release 
+RUN yum install -y netcdf netcdf-fortran netcdf-fortran-devel netcdf-openmpi
+
+RUN yum install -y git cmake python python-devel pip 
+
+WORKDIR "/t-route/"
+
+# Copy the contents of the parent directory (repository root) into the container
+COPY . /t-route/
+
+RUN ln -s /usr/lib64/gfortran/modules/netcdf.mod /usr/include/openmpi-x86_64/netcdf.mod
+
+ENV PYTHONPATH=/t-route:$PYTHONPATH
+RUN pip install uv==0.2.5
+RUN uv venv
+
+ENV VIRTUAL_ENV=/t-route/.venv
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+RUN uv pip install --no-cache-dir -r /t-route/requirements.txt
+
+RUN ./compiler.sh no-e
+
+RUN uv pip install --no-cache-dir -r /t-route/requirements-app.txt
+
+WORKDIR "/t-route/src/"
+RUN mkdir -p /t-route/data/troute_restart/
+
+# Create volume mount points
+RUN mkdir -p ${OUTPUT_VOLUME_TARGET} ${DATA_VOLUME_TARGET} ${CORE_VOLUME_TARGET} /t-route/test
+
+# Set the command to run the application
+CMD sh -c ". /t-route/.venv/bin/activate && uvicorn app.main:app --host 0.0.0.0 --port ${PORT}"
+
+# Add healthcheck
+HEALTHCHECK --interval=30s --timeout=5s --start-period=5s --retries=3 \
+  CMD curl --fail -I http://localhost:${PORT}/health || exit 1

compose.yaml → docker/compose.yaml

@@ -1,8 +1,8 @@
 services:
   troute:
     build: 
-      context: .
-      dockerfile: Dockerfile.troute_api
+      context: ..
+      dockerfile: docker/Dockerfile.compose
     ports:
       - "${PORT}:${PORT}"
     volumes:
@@ -16,8 +16,8 @@ services:
         source: ${CORE_VOLUME_SOURCE}
         target: ${CORE_VOLUME_TARGET}
       - type: bind
-        source: ./test
-        target: /t-route/test
+        source: ${TEST_SOURCE}
+        target: ${TEST_TARGET}
     command: sh -c ". /t-route/.venv/bin/activate && uvicorn app.main:app --host 0.0.0.0 --port ${PORT}"
     healthcheck:
       test: curl --fail -I http://localhost:${PORT}/health || exit 1

compose.env → docker/rnr_compose.env

@@ -9,13 +9,18 @@ PORT=8000
 # The following variables are used in the compose.yaml file to define the shared volume mount with T-Route
 
 # For saving output from the container
-OUTPUT_VOLUME_SOURCE=./data/troute_output 
+OUTPUT_VOLUME_SOURCE=../data/troute_output 
 OUTPUT_VOLUME_TARGET=/t-route/output
 
 # For mounting the data directory
-DATA_VOLUME_SOURCE=./data
+DATA_VOLUME_SOURCE=../data
 DATA_VOLUME_TARGET=/t-route/data
 
 # For mounting all core files within T-Route (Used for sharing template config files)
-CORE_VOLUME_SOURCE=./src/app/core
+CORE_VOLUME_SOURCE=../src/app/core
 CORE_VOLUME_TARGET=/t-route/src/app/core
+
+# For uploading test data scripts
+TEST_SOURCE=../test
+TEST_TARGET=/t-route/test
+

docker/test_troute_api.env

@@ -0,0 +1,25 @@
+# Port mapping
+#-------------
+# The following port will be used for spinning up the API server
+
+PORT=8000
+
+# Volume bindings
+# ---------------
+# The following variables are used in the compose.yaml file to define the shared volume mount with T-Route
+
+# For saving output from the container
+OUTPUT_VOLUME_SOURCE=../test/api/data/troute_output 
+OUTPUT_VOLUME_TARGET=/t-route/output
+
+# For mounting the data directory
+DATA_VOLUME_SOURCE=../test/api/data
+DATA_VOLUME_TARGET=/t-route/data
+
+# For mounting all core files within T-Route (Used for sharing template config files)
+CORE_VOLUME_SOURCE=../src/app/core
+CORE_VOLUME_TARGET=/t-route/src/app/core
+
+# For uploading test data scripts
+TEST_SOURCE=../test
+TEST_TARGET=/t-route/test