Unify marimo apps

.github/workflows/conda.yaml

@@ -20,13 +20,12 @@ jobs:
         init-shell: bash powershell
         micromamba-version: 1.5.6-0
         post-cleanup: all
-    - run: |-
-        echo "Testing package import"
-        python -c 'import fractopo'
-        echo "Testing module entrypoint"
-        python -m fractopo --help
-        echo "Running unittests with pytest"
-        pytest -v
+    - name: Test package import
+      run: python -c 'import fractopo'
+    - name: Test module entrypoint
+      run: python -m fractopo --help
+    - name: Run unittests with pytest
+      run: pytest -v
     strategy:
       fail-fast: false
       matrix:

.github/workflows/main.yaml

@@ -20,6 +20,21 @@ jobs:
         name: nialov
     - name: Load image to docker
       run: nix run .#load-fractopo-image
+    - name: Test run of loaded fractopo-app container
+      run: nix run .#run-fractopo-image -- -d --name fractopo-test -p 2718:2718
+    - name: Wait for API to be ready
+      run: |-
+        for i in {1..60}; do
+          if curl -s http://localhost:2718/; then
+            echo "API is up!"
+            exit 0
+          fi
+          sleep 1
+        done
+        echo "API did not start in time" >&2
+        exit 1
+    - name: Test API root endpoint
+      run: curl -f http://localhost:2718/
     - env:
         PUSHER_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       if: github.event_name == 'push'

.gitignore

@@ -36,6 +36,7 @@ trace_validator.egg-info
 venv/
 paper/allrefs.bib
 .null-ls_*
+__marimo__
 
 # We do not want to include requirements.txt
 # It is merely for backwards compatible pip installs

README.rst

@@ -81,33 +81,29 @@ supported:
 container
 ~~~~~~~~~
 
-Two `marimo <https://github.com/marimo-team/marimo>`__ apps exist in
-``./marimos``, ``validation.py`` and ``network.py``. These are both
-included in the ``ghcr.io/nialov/fractopo-app:latest`` image. By
-default, when the image is run, the network analysis app is run. To run
-the validation app, add an environment variable ``RUN_MODE`` to the
-container with a value of ``validation``.
+A `marimo <https://github.com/marimo-team/marimo>`__ +
+`FastAPI <https://github.com/fastapi/fastapi>`__ app exists in
+``./marimos``, ``api.py``. This is included in the
+``ghcr.io/nialov/fractopo-app:latest`` image. By default, when the image
+is run, the network analysis app is run accessible at root (``/``). To
+access validation functinality, use path ``/validation``. Network
+analysis is also available at ``/network``.
 
 The app host and port can be chosen with ``HOST`` (default is
 ``0.0.0.0``) and ``PORT`` (default is ``2718``) environment variables.
 With ``docker`` you can, of course, expose in whichever port you choose.
 
 Example ``docker`` invocations are below.
 
-To run network analysis:
+To run app:
 
 .. code:: bash
 
-   # RUN_MODE=network specified explicitly even if it is the default
-   docker run --rm --interactive --tty --publish 2718:2718 --env RUN_MODE=network ghcr.io/nialov/fractopo-app:latest
+   docker run --rm --interactive --tty --publish 2718:2718 ghcr.io/nialov/fractopo-app:latest
 
-To run validation:
-
-.. code:: bash
-
-   docker run --rm --interactive --tty --publish 2718:2718 --env RUN_MODE=validation ghcr.io/nialov/fractopo-app:latest
-
-The app should be available at http://localhost:2718
+The network analysis functionality should be available at
+http://localhost:2718/network and validation functionality at
+http://localhost:2718/validation.
 
 Usage
 -----

docs_src/index.rst

@@ -98,33 +98,29 @@ supported:
 container
 ~~~~~~~~~
 
-Two `marimo <https://github.com/marimo-team/marimo>`__ apps exist in
-``./marimos``, ``validation.py`` and ``network.py``. These are both
-included in the ``ghcr.io/nialov/fractopo-app:latest`` image. By
-default, when the image is run, the network analysis app is run. To run
-the validation app, add an environment variable ``RUN_MODE`` to the
-container with a value of ``validation``.
+A `marimo <https://github.com/marimo-team/marimo>`__ +
+`FastAPI <https://github.com/fastapi/fastapi>`__ app exists in
+``./marimos``, ``api.py``. This is included in the
+``ghcr.io/nialov/fractopo-app:latest`` image. By default, when the image
+is run, the network analysis app is run accessible at root (``/``). To
+access validation functinality, use path ``/validation``. Network
+analysis is also available at ``/network``.
 
 The app host and port can be chosen with ``HOST`` (default is
 ``0.0.0.0``) and ``PORT`` (default is ``2718``) environment variables.
 With ``docker`` you can, of course, expose in whichever port you choose.
 
 Example ``docker`` invocations are below.
 
-To run network analysis:
+To run app:
 
 .. code:: bash
 
-   # RUN_MODE=network specified explicitly even if it is the default
-   docker run --rm --interactive --tty --publish 2718:2718 --env RUN_MODE=network ghcr.io/nialov/fractopo-app:latest
+   docker run --rm --interactive --tty --publish 2718:2718 ghcr.io/nialov/fractopo-app:latest
 
-To run validation:
-
-.. code:: bash
-
-   docker run --rm --interactive --tty --publish 2718:2718 --env RUN_MODE=validation ghcr.io/nialov/fractopo-app:latest
-
-The app should be available at http://localhost:2718
+The network analysis functionality should be available at
+http://localhost:2718/network and validation functionality at
+http://localhost:2718/validation.
 
 Usage
 -----
@@ -437,7 +433,7 @@ Copyright © 2020-2026, Nikolas Ovaskainen.
    :target: https://mybinder.org/v2/gh/nialov/fractopo/HEAD?filepath=docs_src%2Fnotebooks%2Ffractopo_network_1.ipynb
 .. |Zenodo| image:: https://zenodo.org/badge/297451015.svg
    :target: https://zenodo.org/badge/latestdoi/297451015
-.. [[[end]]] (checksum: 03b8bc905d987b2f0346263e2055bca2)
+.. [[[end]]] (checksum: 0fed91a430072b847114ba600a6aec78)
 
 .. toctree::
    :hidden:

marimos/api.py

@@ -0,0 +1,23 @@
+import marimo
+from fastapi import FastAPI
+
+# Create a marimo asgi app
+server = (
+    marimo.create_asgi_app()
+    .with_app(path="/", root="./marimos/network.py")
+    .with_app(path="/network", root="./marimos/network.py")
+    .with_app(path="/validation", root="./marimos/validation.py")
+)
+
+# Create a FastAPI app
+app = FastAPI()
+
+app.mount("/", server.build())
+
+# Run the server using command-line:
+# uvicorn marimos.api:app --host localhost --port 56000
+# Run the file as script:
+if __name__ == "__main__":
+    import uvicorn
+
+    uvicorn.run(app, host="localhost", port=8000)

nix/ci.nix

@@ -157,6 +157,8 @@ in
                       };
                     };
 
+                  dockerPort = builtins.toString 2718;
+
                 in
                 baseNixSteps
                 ++ [
@@ -165,6 +167,28 @@ in
                     run = "nix run .#load-fractopo-image";
 
                   }
+                  {
+                    name = "Test run of loaded fractopo-app container";
+                    run = "nix run .#run-fractopo-image -- -d --name fractopo-test -p ${dockerPort}:${dockerPort}";
+                  }
+                  {
+                    name = "Wait for API to be ready";
+                    run = ''
+                      for i in {1..60}; do
+                        if curl -s http://localhost:${dockerPort}/; then
+                          echo "API is up!"
+                          exit 0
+                        fi
+                        sleep 1
+                      done
+                      echo "API did not start in time" >&2
+                      exit 1
+                    '';
+                  }
+                  {
+                    name = "Test API root endpoint";
+                    run = "curl -f http://localhost:${dockerPort}/";
+                  }
                   (mkPushStep {
                     rev = "$(git rev-parse --short HEAD)";
                     name = "Push to ghcr.io from all branches";
@@ -200,6 +224,7 @@ in
               strategy = {
                 fail-fast = false;
                 matrix = {
+                  # Test same Python versions as for poetry job
                   inherit (config.workflows.".github/workflows/main.yaml".jobs.poetry.strategy.matrix)
                     python-version
                     ;
@@ -228,12 +253,20 @@ in
                   };
                 }
                 {
+                  name = "Test package import";
                   run = ''
-                    echo "Testing package import"
                     python -c 'import fractopo'
-                    echo "Testing module entrypoint"
+                  '';
+                }
+                {
+                  name = "Test module entrypoint";
+                  run = ''
                     python -m fractopo --help
-                    echo "Running unittests with pytest"
+                  '';
+                }
+                {
+                  name = "Run unittests with pytest";
+                  run = ''
                     pytest -v
                   '';
                 }

nix/overlays.nix

@@ -23,6 +23,7 @@
             cp ${../marimos/utils.py} ./app/marimos/utils.py
             cp ${../marimos/validation.py} ./app/marimos/validation.py
             cp ${../marimos/network.py} ./app/marimos/network.py
+            cp ${../marimos/api.py} ./app/marimos/api.py
             chmod -R 777 ./app
           '';
           # Add for debugging
@@ -35,43 +36,21 @@
               "/bin/bash"
               "-c"
               (lib.concatStringsSep " " [
-                "${final.fractopoEnv}/bin/marimo"
-                "run"
+                "${final.fractopo-api-run}/bin/fractopo-api-run"
                 "--host"
                 "$HOST"
                 "--port"
                 "$PORT"
-                "--redirect-console-to-browser"
-                "/app/marimos/$RUN_MODE.py"
               ])
             ];
             WorkingDir = "/app";
             Env = [
               "HOME=/app"
               "HOST=0.0.0.0"
               "PORT=2718"
-              "RUN_MODE=network"
             ];
           };
         };
-        mkMarimoRun =
-          {
-            name,
-            script,
-            marimosDir ? ../marimos,
-          }:
-          prev.writeShellApplication {
-            inherit name;
-            runtimeInputs = [ final.fractopoEnv ];
-            text =
-              let
-                scriptPath = "${marimosDir}/${script}";
-              in
-              ''
-                marimo run ${scriptPath} "$@"
-              '';
-
-          };
 
       in
       {
@@ -95,20 +74,22 @@
           in
           prev.buildFHSEnv (lib.recursiveUpdate base config);
 
-        pythonEnv = final.python3.withPackages (p: p.fractopo.passthru.optional-dependencies.dev);
-        fractopoEnv = final.python3.withPackages (
+        pythonEnv = final.python3.withPackages (
           p:
-          # TODO: Should check.
-          [ p.fractopo.passthru.no-check ] ++ p.fractopo.passthru.optional-dependencies.dev
+          [ p.fractopo.passthru.no-check ]
+          ++ p.fractopo.optional-dependencies.dev
+          ++ p.fractopo.optional-dependencies.api
         );
-        fractopo-validation-run = mkMarimoRun {
-          name = "fractopo-validation-run";
-          script = "validation.py";
-        };
 
-        fractopo-network-run = mkMarimoRun {
-          name = "fractopo-network-run";
-          script = "network.py";
+        fractopo-api-env = final.python3.withPackages (
+          p: [ p.fractopo.passthru.no-check ] ++ p.fractopo.passthru.optional-dependencies.api
+        );
+
+        fractopo-api-run = prev.writeShellApplication {
+          name = "fractopo-api-run";
+          text = ''
+            ${final.fractopo-api-env}/bin/uvicorn marimos.api:app "$@"
+          '';
         };
 
         fractopo-app-image = prev.dockerTools.buildLayeredImage fractopoImageConfig;
@@ -124,6 +105,16 @@
             docker image list
           '';
         };
+        run-fractopo-image = prev.writeShellApplication {
+          name = "run-fractopo-image";
+          text =
+            let
+              inherit (final.fractopo-app-image-stream) imageName imageTag;
+            in
+            ''
+              docker run "$@" ${imageName}:${imageTag}
+            '';
+        };
         push-fractopo-image = prev.writeShellApplication {
           name = "push-fractopo-image";
           text =