fixing tests

Author: matthiaskoenig

release-notes/0.1.14.md

@@ -28,3 +28,4 @@ of timecourse definitions in multiple simulations. E.g. repeated timecourse `[tc
 - adding mypy configuration and initial mypy fixes
 - many flake8 fixes and type annotations
 - Fix #91, support hex colors in plot
+- Fix #92, update `xarray>=0.17.0`

setup.cfg

@@ -52,7 +52,7 @@ install_requires =
 	sympy>=1.7.1
 	pandas>=1.2.1
 	tables>=3.6.1
-	xarray>=0.16.1
+	xarray>=0.17.0
 	bottleneck>=1.3.2
 	pint>=0.16.1
 	Jinja2>=2.11.2

src/sbmlsim/diff.py

@@ -94,9 +94,9 @@ def __init__(
                 # apply factors
                 fs = factors.get(key, [1.0] * len(sel_keys))
                 for k, sel in enumerate(sel_keys):
-                    print(f"scaling: '{sel}' * {fs[k]}")
+                    print(f"scaling: '{sel}' * {fs[k]}")  # type: ignore
                     # df_new[sel] = fs[k] * df_new[sel]
-                    df_new.loc[:, sel] *= fs[k]
+                    df_new.loc[:, sel] *= fs[k]  # type: ignore
 
                 # do renaming
                 df_new = df_new.rename(columns=dict(zip(sel_keys, colnames)))

src/sbmlsim/experiment/runner.py

@@ -10,7 +10,7 @@
 
 import logging
 from pathlib import Path
-from typing import Iterable, List, Optional
+from typing import Dict, Iterable, List, Optional
 
 from sbmlsim.experiment import ExperimentResult, SimulationExperiment
 from sbmlsim.model import RoadrunnerSBMLModel

src/sbmlsim/model/model_resources.py

@@ -58,7 +58,7 @@ def from_source(cls, source: str, base_dir: Path = None) -> "Source":
             if is_urn(source):
                 content = model_from_urn(source)
             elif is_http(source):
-                content = model_from_url()
+                content = model_from_url(url=source)
 
         # is path
         if content is None:

src/sbmlsim/result/xresult.py

@@ -103,10 +103,11 @@ def from_dfs(
         if scan is None:
             dimensions = [Dimension("_dfs", index=np.arange(num_dfs))]
         else:
-            dimensions = scan.dimensions
+            dimensions = scan.dimensions  # type: ignore
 
         # add additional dimensions
-        for dimension in dimensions:  # type: Dimension
+        dimension: Dimension
+        for dimension in dimensions:
             shape.append(len(dimension))
             dim_id = dimension.dimension
             coords[dim_id] = dimension.index

src/sbmlsim/serialization.py

@@ -15,7 +15,7 @@ def from_json(json_info: Union[str, Path]) -> Dict:
         with open(json_info, "r") as f_json:
             d = json.load(f_json)
     else:
-        d = json.loads(json_info)
+        d: Dict = json.loads(json_info)
     return d
 
 

src/sbmlsim/simulator/simulation_serial.py

@@ -35,7 +35,7 @@ def __init__(self, model=None, **kwargs):
         }
         self.integrator_settings.update(kwargs)
         self.set_model(model)
-        self.model: Optional[AbstractModel, RoadrunnerSBMLModel] = None
+        # self.model: Optional[AbstractModel, RoadrunnerSBMLModel] = None
 
     def set_model(self, model):
         """Set model for simulator and updates the integrator settings.