test available properties for plotting (#782)

* test with pytest-cov

* test `model_json_schema_from_atoms`

* refactor into function

* bump version

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* sleep longer

* increase wait timeout

* increase timeout

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: PythonFZ

.github/workflows/test.yaml

@@ -48,9 +48,13 @@ jobs:
       - name: Pytest
         run: |
           uv run python --version
-          uv run coverage run -m pytest -vv
-          uv run coverage xml
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          uv run pytest --cov --junitxml=junit.xml -o junit_family=legacy
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "zndraw"
-version = "0.5.8a1"
+version = "0.5.8"
 description = "Display and Edit Molecular Structures and Trajectories in the Browser."
 authors = [
     { name = "Fabian Zills", email = "[email protected]" },
@@ -63,9 +63,9 @@ skip = "*.svg,*.lock"
 
 [dependency-groups]
 dev = [
-    "coverage>=7.6.10",
     "mdanalysis>=2.8.0",
     "pytest>=8.3.4",
+    "pytest-cov>=6.0.0",
     "rdkit2ase>=0.1.4",
     "tidynamics>=1.1.2",
     "znh5md>=0.4.4",

tests/test_analysis.py

@@ -1,6 +1,8 @@
+import numpy as np
 import znsocket
 
 from zndraw import ZnDraw
+from zndraw.analyse import Properties1D
 
 
 def run_queue(vis, key, msg: dict):
@@ -11,7 +13,7 @@ def run_queue(vis, key, msg: dict):
     )
     modifier_queue.update(msg)
     vis.socket.emit("room:worker:run")
-    vis.socket.sleep(7)
+    vis.socket.sleep(10)
 
 
 def test_run_analysis_distance(server, s22_energy_forces):
@@ -68,3 +70,26 @@ def test_run_analysis_DihedralAngle(server, s22_energy_forces):
     fig = vis.figures["DihedralAngle"]
     # assert that the x-axis label is "step"
     assert fig.layout.xaxis.title.text == "step"
+
+
+def test_analysis_Properties1D_json_schema(s22_energy_forces):
+    # add custom info keys
+    for atoms in s22_energy_forces:
+        atoms.info["custom"] = 42
+        atoms.info["custom2"] = np.random.rand(10)
+        atoms.info["custom3"] = np.random.rand(10, 5)
+        atoms.calc.results["custom4"] = np.random.rand(10)
+        atoms.arrays["arr"] = np.zeros_like(atoms.get_positions())
+
+    schema = Properties1D.model_json_schema_from_atoms(s22_energy_forces[0])
+    assert set(schema["properties"]["value"]["enum"]) == {
+        "energy",
+        "forces",
+        "custom",
+        "numbers",
+        "positions",
+        "arr",
+        "custom2",
+        "custom3",
+        "custom4",
+    }

tests/test_geometries.py

@@ -48,7 +48,7 @@ def test_geometry_selection_position(server):
         "height": 10,
     }
     vis.socket.emit("room:worker:run")
-    vis.socket.sleep(5)
+    vis.socket.sleep(8)
 
     assert len(vis.geometries) == 1
     assert vis.geometries[0].position == [0, 0, 0]
@@ -66,7 +66,7 @@ def test_geometry_selection_position(server):
         "height": 10,
     }
     vis.socket.emit("room:worker:run")
-    vis.socket.sleep(5)
+    vis.socket.sleep(8)
 
     assert len(vis.geometries) == 2
     assert vis.geometries[1].position == vis.atoms.positions[1].tolist()
@@ -85,7 +85,7 @@ def test_geometry_selection_position(server):
         "height": 10,
     }
     vis.socket.emit("room:worker:run")
-    vis.socket.sleep(5)
+    vis.socket.sleep(8)
 
     assert len(vis.geometries) == 3
     assert (

tests/test_modifier.py

@@ -16,7 +16,7 @@ def run_queue(vis, key, msg: dict):
     )
     modifier_queue.update(msg)
     vis.socket.emit("room:worker:run")
-    vis.socket.sleep(5)
+    vis.socket.sleep(10)
 
 
 def test_run_selection(server, s22):

uv.lock

@@ -19,6 +19,14 @@
     pass
 
 
+def _get_available_properties(atoms: ase.Atoms) -> list[str]:
+    available_properties = list(atoms.arrays.keys())
+    available_properties += list(atoms.info.keys())
+    if atoms.calc is not None:
+        available_properties += list(atoms.calc.results.keys())
+    return available_properties
+
+
 log = logging.getLogger(__name__)
 
 
@@ -130,10 +138,7 @@ class Properties2D(AnaylsisMethod):
     def model_json_schema_from_atoms(cls, atoms: ase.Atoms) -> dict:
         schema = cls.model_json_schema()
 
-        available_properties = list(atoms.arrays.keys())
-        available_properties += list(atoms.info.keys())
-        if atoms.calc is not None:
-            available_properties += list(atoms.calc.results.keys())  # global ATOMS object
+        available_properties = _get_available_properties(atoms)
 
         available_properties += ["step"]
         schema["properties"]["x_data"]["enum"] = available_properties
@@ -195,10 +200,7 @@ class ForceCorrelation(AnaylsisMethod):
     def model_json_schema_from_atoms(cls, atoms: ase.Atoms) -> dict:
         schema = cls.model_json_schema()
 
-        available_properties = list(atoms.arrays.keys())
-        available_properties += list(atoms.info.keys())
-        if atoms.calc is not None:
-            available_properties += list(atoms.calc.results.keys())
+        available_properties = _get_available_properties(atoms)
         schema["properties"]["x_data"]["enum"] = available_properties
         schema["properties"]["y_data"]["enum"] = available_properties
 
@@ -254,11 +256,7 @@ class Properties1D(AnaylsisMethod):
     def model_json_schema_from_atoms(cls, atoms: ase.Atoms) -> dict:
         schema = cls.model_json_schema()
 
-        available_properties = list(atoms.arrays.keys())
-        available_properties += list(atoms.info.keys())
-        if atoms.calc is not None:
-            available_properties += list(atoms.calc.results.keys())
-        log.critical(f"AVAILABLE PROPERTIES: {available_properties=}")
+        available_properties = _get_available_properties(atoms)
         schema["properties"]["value"]["enum"] = available_properties
 
         return schema