Fix tests and CI/CD workflows

For consistent test results, teardown code was added to the pytest setup
of the flask app.
The CI/CD workflows were updated to use the latest versions of the
actions.
The path of the colorPalette.json file was changed and the file is now
included in the setup file of the backend.

.github/workflows/build_and_test.yml

@@ -14,15 +14,15 @@ jobs:
     runs-on: "ubuntu-latest"
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Cache dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
@@ -37,16 +37,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: '19'
+          node-version: '20'
 
       - name: Cache node_modules
         id: cache-node-modules
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ./frontend/node_modules
           key: node-modules-${{ hashFiles('./frontend/package-lock.json') }}
@@ -61,27 +61,27 @@ jobs:
     needs: [ python, node ]
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Get python packages from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
         id: cache
 
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: '19'
+          node-version: '20'
       - name: Get node from cache
         id: cache-node-modules
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ./frontend/node_modules
           key: node-modules-${{ hashFiles('./frontend/package-lock.json') }}
@@ -102,7 +102,7 @@ jobs:
           kill -9 $PID
 
       - name: Upload frontend to GitHub
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           retention-days: 7
           name: frontend-${{ github.sha }}
@@ -114,15 +114,15 @@ jobs:
     needs: python
     steps:
       - name: Checking out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Get python packages from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
@@ -133,7 +133,7 @@ jobs:
         run: python -m build --sdist --wheel --outdir dist/;
 
       - name: Upload backend to GitHub
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           retention-days: 7
           name: backend-${{ github.sha }}
@@ -145,19 +145,19 @@ jobs:
     needs: build-backend
     steps:
       - name: Checking out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Get artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: backend-${{ github.sha }}
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Get python packages from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
@@ -184,23 +184,23 @@ jobs:
     needs: [ build-backend, frontend ]
     steps:
       - name: Checking out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Get backend artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: backend-${{ github.sha }}
       - name: Get frontend artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: frontend-${{ github.sha }}
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Get python packages from cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}

.github/workflows/publish_pypi.yml

@@ -64,12 +64,12 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
       - name: Cache conda env
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}

backend/setup.cfg

@@ -29,6 +29,9 @@ install_requires =
 [options.packages.find]
 where = src
 
+[options.package_data]
+viasp = server/colorPalette.json
+
 [options.entry_points]
 console_scripts =
     viasp_server = viasp.__main__:backend

backend/src/viasp/server/startup.py

@@ -15,22 +15,23 @@
 import shutil
 from subprocess import Popen
 from time import time
+import json
 
 import viasp_dash
 from dash import Dash, jupyter_dash
 from dash._jupyter import _jupyter_config
 
 from viasp import clingoApiClient
 from viasp.shared.defaults import (DEFAULT_BACKEND_HOST, DEFAULT_BACKEND_PORT,
-                                   DEFAULT_BACKEND_PROTOCOL, CLINGRAPH_PATH, 
-                                   GRAPH_PATH, PROGRAM_STORAGE_PATH, STDIN_TMP_STORAGE_PATH,
-                                   COLOR_PALETTE)
+                                   DEFAULT_BACKEND_PROTOCOL, CLINGRAPH_PATH,
+                                   GRAPH_PATH, PROGRAM_STORAGE_PATH,
+                                   STDIN_TMP_STORAGE_PATH, COLOR_PALETTE_PATH)
 
 
 
 def run(host=DEFAULT_BACKEND_HOST, port=DEFAULT_BACKEND_PORT):
     """ create the dash app, set layout and start the backend on host:port """
-       
+
     # if running in binder, get proxy information
     # and set the backend URL, which will be used
     # by the frontend
@@ -40,17 +41,16 @@ def run(host=DEFAULT_BACKEND_HOST, port=DEFAULT_BACKEND_PORT):
         _default_server_url = _jupyter_config['server_url']
 
         _default_requests_pathname_prefix = (
-            _jupyter_config['base_subpath'].rstrip('/') + '/proxy/' + str(port)
-        )
+            _jupyter_config['base_subpath'].rstrip('/') + '/proxy/' +
+            str(port))
 
-        backend_url = _default_server_url+_default_requests_pathname_prefix
+        backend_url = _default_server_url + _default_requests_pathname_prefix
     elif 'google.colab' in sys.modules:
-        from google.colab.output import eval_js # type: ignore
-        backend_url=eval_js(f"google.colab.kernel.proxyPort({port})")
+        from google.colab.output import eval_js  # type: ignore
+        backend_url = eval_js(f"google.colab.kernel.proxyPort({port})")
     else:
         backend_url = f"{DEFAULT_BACKEND_PROTOCOL}://{host}:{port}"
 
-
     command = ["viasp_server", "--host", host, "--port", str(port)]
 
     # if 'ipykernel_launcher.py' in sys.argv[0]:
@@ -60,12 +60,12 @@ def run(host=DEFAULT_BACKEND_HOST, port=DEFAULT_BACKEND_PORT):
     log = open('viasp.log', 'w', encoding="utf-8")
     viasp_backend = Popen(command, stdout=log, stderr=log)
 
+    color_palette = json.load(
+        open(COLOR_PALETTE_PATH, "r"))
     app = Dash(__name__)
-    app.layout = viasp_dash.ViaspDash(
-        id="myID",
-        backendURL=backend_url,
-        colorPalette=COLOR_PALETTE
-        )
+    app.layout = viasp_dash.ViaspDash(id="myID",
+                                      backendURL=backend_url,
+                                      colorPalette=color_palette)
     app.title = "viASP"
 
     # make sure the backend is up, before continuing with other modules

backend/src/viasp/shared/defaults.py

@@ -1,6 +1,5 @@
 import pathlib
 import os
-import json
 
 DEFAULT_BACKEND_PROTOCOL = "http"
 DEFAULT_BACKEND_HOST = "localhost"
@@ -9,8 +8,9 @@
 DEFAULT_BACKEND_URL = f"{DEFAULT_BACKEND_PROTOCOL}://{DEFAULT_BACKEND_HOST}:{DEFAULT_BACKEND_PORT}"
 SHARED_PATH = pathlib.Path(__file__).parent.resolve()
 GRAPH_PATH = SHARED_PATH / "viasp_graph_storage.db"
-STATIC_PATH =  pathlib.Path(__file__).parent.parent.resolve() / "server/static/"
+SERVER_PATH =  pathlib.Path(__file__).parent.parent.resolve() / "server/"
+STATIC_PATH =  os.path.join(SERVER_PATH, "static")
 CLINGRAPH_PATH = os.path.join(STATIC_PATH, "clingraph")
 PROGRAM_STORAGE_PATH = SHARED_PATH / "prg.lp"
 STDIN_TMP_STORAGE_PATH = SHARED_PATH / "viasp_stdin_tmp.lp"
-COLOR_PALETTE = json.load(open(os.path.join(STATIC_PATH, "colorPalette.json"), "r"))
+COLOR_PALETTE_PATH = SERVER_PATH / "colorPalette.json"

backend/test/conftest.py

@@ -146,23 +146,40 @@ def client_with_a_single_node_graph(get_sort_program_and_get_all_graphs, a_1) ->
 
 
 @pytest.fixture(params=["program_simple", "program_multiple_sorts", "program_recursive"])
-def client_with_a_graph(request, get_sort_program_and_get_all_graphs) -> Generator[Tuple[FlaskClient, ProgramAnalyzer, List[Tuple[Mapping, str, str, int]], str], Any, Any]:
+def client_with_a_graph(
+    request, get_sort_program_and_get_all_graphs
+) -> Generator[Tuple[FlaskClient, ProgramAnalyzer, List[Tuple[
+        Mapping, str, str, int]], str], Any, Any]:
     app = create_app_with_registered_blueprints(app_bp, api_bp, dag_bp)
 
     program = request.getfixturevalue(request.param)
-    serializable_graphs, analyzer = get_sort_program_and_get_all_graphs(program)
+    serializable_graphs, analyzer = get_sort_program_and_get_all_graphs(
+        program)
     with app.test_client() as client:
         for serializable_graph, hash, sorted_program, _ in serializable_graphs:
-            client.post("graph", json={"data": serializable_graph, "hash": hash, "sort": sorted_program})
+            client.post("graph",
+                        json={
+                            "data": serializable_graph,
+                            "hash": hash,
+                            "sort": sorted_program
+                        })
         yield client, analyzer, serializable_graphs, program
+        _ = client.delete("/control/clingraph")
+        _ = client.post("/control/models/clear")
+        _ = client.delete("/graph/clear")
 
 @pytest.fixture
-def client_with_a_clingraph(client_with_a_graph, get_clingo_stable_models) -> Generator[Tuple[FlaskClient, ProgramAnalyzer, List[Tuple[Mapping, str, str, int]], str], Any, Any]:
+def client_with_a_clingraph(
+    client_with_a_graph, get_clingo_stable_models
+) -> Generator[Tuple[FlaskClient, ProgramAnalyzer, List[Tuple[
+        Mapping, str, str, int]], str], Any, Any]:
     client, analyzer, serializable_graphs, program = client_with_a_graph
 
-    _ = client.delete("/control/clingraph")
     serialized = get_clingo_stable_models(program)
-    _ = client.post("/control/models", json=serialized, headers={'Content-Type': 'application/json'})
+    print(f"Marking models: {serialized}", flush=True)
+    _ = client.post("/control/models",
+                    json=serialized,
+                    headers={'Content-Type': 'application/json'})
 
     yield client, analyzer, serializable_graphs, program
 

backend/test/test_clingraph.py

@@ -98,13 +98,15 @@ def test_clingraph_edges(client_with_a_clingraph):
     assert res.status_code == 200
     assert res.data == b'ok'
 
+    res = client.post(f"/graph/edges",
+                        json={
+                            "shownRecursion": [],
+                            "usingClingraph": "true"
+                        })
+    assert res.status_code == 200
+    assert type(res.json) == list
     if "{b(X)}" in program:
-        res = client.post(f"/graph/edges",
-                          json={
-                              "shownRecursion": [],
-                              "usingClingraph": "true"
-                          })
-        assert res.status_code == 200
-        assert type(res.json) == list
         # program_simple and program_multiple_sorts
         assert len(res.json) == 12
+    else:
+        assert len(res.json) == 2

docs/viasp/colorPalette.rst

@@ -2,7 +2,7 @@
 Color Palette
 =================
 
-The color Palette of viASP's frontend is defined by the file `/server/static/colorPalette.json`.
+The color Palette of viASP's frontend is defined by the file `/server/colorPalette.json`.
 
 The default file contains the following JSON object:
 

examples/quickstart.py

@@ -19,6 +19,10 @@ def main():
             ctl.viasp.mark(m)
         print(handle.get())
     ctl.viasp.show()
+    ctl.viasp.clingraph(viz_encoding="viz_hamiltonian.lp",
+                        engine="dot",
+                        graphviz_type="graph")
+
 
 
 app = startup.run()

frontend/src/demo/App.js

@@ -1,6 +1,6 @@
 /* eslint no-magic-numbers: 0 */
 import React from 'react';
-import colorPaletteData from '../../../backend/src/viasp/server/static/colorPalette.json';
+import colorPaletteData from '../../../backend/src/viasp/server/colorPalette.json';
 
 import { ViaspDash } from '../lib';