Merge pull request NeuroML#386 from NeuroML/feat/coverage

Feat/coverage

.github/workflows/ci.yml

@@ -50,8 +50,3 @@ jobs:
         pynml -h
 
         ./test-ghactions.sh -neuron
-
-    - name: Lint with ruff
-      run: |
-        pip install ruff
-        ruff . --exit-zero --show-source

.github/workflows/ruff.yml

@@ -0,0 +1,16 @@
+name: Ruff
+on:
+  pull_request:
+    branches:
+      - master
+      - development
+      - experimental
+      - 'test*'
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          changed-files: 'true'

pyneuroml/channelml/__init__.py

@@ -13,17 +13,15 @@
 Copyright 2023 NeuroML contributors
 """
 
-
 import argparse
 import logging
-import typing
 import pathlib
-from lxml.etree import parse, XSLT, tostring
+import typing
+from typing import Optional
 
+from lxml.etree import XSLT, parse, tostring
 
 from pyneuroml.utils.cli import build_namespace
-from typing import Optional
-
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -53,7 +51,7 @@ def channelml2nml(
     """
     try:
         dom = parse(channelmlfile)
-    except:
+    except Exception:
         logger.error(f"Cannot parse channelml file: {channelmlfile}")
         return None
     if not xsltfile:
@@ -62,7 +60,7 @@ def channelml2nml(
 
     try:
         xslt = parse(xsltfile)
-    except:
+    except Exception:
         logger.error(f"Cannot parse XSL: {xsltfile}")
         return None
 

pyneuroml/lems/LEMSSimulation.py

@@ -3,26 +3,25 @@
 Helper class for generating LEMS xml files for simulations
 """
 
-import os.path
 import logging
-import typing
-import random
 import os
+import os.path
+import random
+import typing
+from typing import Optional
 
 import airspeed
-from pyneuroml import __version__ as pynml_ver
 from neuroml import __version__ as libnml_ver
-from pyneuroml.pynml import read_neuroml2_file
-from pyneuroml.pynml import read_lems_file
+
+from pyneuroml import __version__ as pynml_ver
+from pyneuroml.pynml import read_lems_file, read_neuroml2_file
 from pyneuroml.utils.plot import get_next_hex_color
 from pyneuroml.utils.units import convert_to_units
-from typing import Optional
 
 logger = logging.getLogger(__name__)
 
 
 class LEMSSimulation:
-
     """
     Helper class for creating LEMS Simulations for running NeuroML2 models.
     """
@@ -88,7 +87,7 @@ def __init__(
         :type meta: dict
         """
 
-        if type(duration) is str:
+        if isinstance(duration, str):
             # is this just the magnitude in the string?
             try:
                 duration_mag_ms = float(duration)
@@ -97,7 +96,7 @@ def __init__(
         else:
             duration_mag_ms = float(duration)
 
-        if type(dt) is str:
+        if isinstance(dt, str):
             # is this just the magnitude in the string?
             try:
                 dt_mag_ms = float(dt)

pyneuroml/neuron/__init__.py

@@ -18,11 +18,6 @@
 import airspeed
 import yaml
 
-try:
-    from yaml import CDumper as Dumper
-except ImportError:
-    from yaml import Dumper
-
 from pyneuroml.pynml import validate_neuroml1, validate_neuroml2
 
 pp = pprint.PrettyPrinter(depth=4)

pyneuroml/plot/PlotTimeSeries.py

@@ -13,10 +13,11 @@
 import typing
 
 import numpy
-import pyneuroml.lems as pynmll
-import pyneuroml.plot.Plot as pynmlplt
 from matplotlib import pyplot as plt
 from matplotlib_scalebar.scalebar import ScaleBar
+
+import pyneuroml.lems as pynmll
+import pyneuroml.plot.Plot as pynmlplt
 from pyneuroml.utils.cli import build_namespace
 
 logger = logging.getLogger(__name__)
@@ -77,7 +78,7 @@ def plot_time_series(
     :raises ValueError: if a 't' (time) key is not found in the traces data
 
     """
-    if type(trace_data) is dict:
+    if isinstance(trace_data, dict):
         trace_data = [trace_data]
 
     num_traces = 0
@@ -217,7 +218,7 @@ def plot_time_series_from_data_files(
 
     """
     all_traces = []
-    if type(data_file_names) is str:
+    if isinstance(data_file_names, str):
         data_file_names = [data_file_names]
 
     for f in data_file_names:

pyneuroml/runners.py

@@ -7,7 +7,6 @@
 Copyright 2024 NeuroML contributors
 """
 
-
 import inspect
 import logging
 import math
@@ -107,9 +106,12 @@ def run_lems_with_jneuroml(
         return False
 
     if load_saved_data:
-        if verbose: logger.info(
-            "Reloading data generated by: {}, plotting: {}".format(lems_file_name, plot)
-        )
+        if verbose:
+            logger.info(
+                "Reloading data generated by: {}, plotting: {}".format(
+                    lems_file_name, plot
+                )
+            )
         return reload_saved_data(
             lems_file_name,
             base_dir=exec_in_dir,
@@ -676,15 +678,15 @@ def _gui_string(nogui: bool) -> str:
 
 
 def _include_string(
-    paths_to_include: typing.Union[str, typing.Tuple[str], typing.List[str]]
+    paths_to_include: typing.Union[str, typing.Tuple[str], typing.List[str]],
 ) -> str:
     """Convert a path or list of paths into an include string to be used by jnml.
     :param paths_to_include: path or list or tuple of paths to be included
     :type paths_to_include: str or list(str) or tuple(str)
     :returns: include string to be used with jnml.
     """
     if paths_to_include:
-        if type(paths_to_include) is str:
+        if isinstance(paths_to_include, str):
             paths_to_include = [paths_to_include]
     if type(paths_to_include) in (tuple, list):
         result = " -I '%s'" % ":".join(paths_to_include)
@@ -847,7 +849,7 @@ def run_jneuroml_with_realtime_output(
 
     except KeyboardInterrupt as e:
         raise e
-    except:
+    except Exception:
         logger.error("*** Execution of jnml has failed! ***")
         logger.error("*** Command: %s ***" % command)
         if exit_on_fail:

pyneuroml/tellurium/__init__.py

@@ -2,10 +2,10 @@
 run a model using the tellurium engine
 """
 
-import os
 import logging
-from pyneuroml.sedml import validate_sedml_files
+import os
 
+from pyneuroml.sedml import validate_sedml_files
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -51,7 +51,7 @@ def run_from_sedml_file(input_files, args):
     if "-outputdir" in args:
         try:
             outputdir = args[args.index("-outputdir") + 1]
-        except:
+        except Exception:
             raise ValueError("Incorrectly specified outputdir")
 
         if outputdir == "none":

pyneuroml/tune/NeuroMLTuner.py

@@ -646,7 +646,7 @@ def _run_optimisation(a: argparse.Namespace) -> typing.Optional[dict]:
         added = []
         # print("Plotting saved data from %s which are relevant for targets: %s"%(best_candidate_v.keys(), a.target_data.keys()))
 
-        fig = plt.figure()
+        plt.figure()
         plt.get_current_fig_manager().set_window_title(
             "Simulation of fittest individual from run: %s" % ref
         )

pyneuroml/utils/plot.py

@@ -18,7 +18,7 @@
 from matplotlib.lines import Line2D
 from matplotlib.patches import Rectangle
 from matplotlib_scalebar.scalebar import ScaleBar
-from neuroml import Cell, NeuroMLDocument
+from neuroml import Cell, NeuroMLDocument, Segment
 from neuroml.loaders import read_neuroml2_file
 
 logger = logging.getLogger(__name__)
@@ -317,9 +317,9 @@ def get_cell_bound_box(cell: Cell):
     :returns: tuple (min view, max view)
 
     """
-    seg0 = cell.morphology.segments[0]  # type: Segment
+    seg0: Segment = cell.morphology.segments[0]
     ex1 = numpy.array([seg0.distal.x, seg0.distal.y, seg0.distal.z])
-    seg1 = cell.morphology.segments[-1]  # type: Segment
+    seg1: Segment = cell.morphology.segments[-1]
     ex2 = numpy.array([seg1.distal.x, seg1.distal.y, seg1.distal.z])
     center = (ex1 + ex2) / 2
     diff = numpy.linalg.norm(ex2 - ex1)

pyneuroml/xppaut/__init__.py

@@ -4,7 +4,6 @@
 import argparse
 import logging
 import os
-import sys
 import typing
 from pprint import pprint
 

pyproject.toml

@@ -4,3 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [tool.ruff.lint]
 ignore = ["F403", "F405"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=pyneuroml"
+markers = [
+    "localonly", # test to not be run on GH actions: they segfault.
+]

tests/plot/test_PlotSpikes.py

@@ -49,7 +49,7 @@ def test_plot_spikes_from_data_single(self):
             pyplts.plot_spikes(
                 title=f"spikes from data - {data['name']}",
                 spike_data=[data],
-                show_plots_already=True,
+                show_plots_already=False,
                 save_spike_plot_to=f"spike-plot-test-{data['name']}.png",
             )
             self.assertIsFile(f"spike-plot-test-{data['name']}.png")
@@ -62,7 +62,7 @@ def test_plot_spikes_from_data_multi(self):
         pyplts.plot_spikes(
             title="spikes from data",
             spike_data=self.spike_data,
-            show_plots_already=True,
+            show_plots_already=False,
             save_spike_plot_to="spike-plot-test-multi.png",
         )
         self.assertIsFile("spike-plot-test-multi.png")
@@ -93,7 +93,7 @@ def test_plot_spikes_from_files(self, max_spikes_per_population=100):
             filelist,
             format_="id_t",
             title="spikes from data files",
-            show_plots_already=True,
+            show_plots_already=False,
             save_spike_plot_to="spike-plot-from-file-test.png",
         )
 
@@ -199,7 +199,7 @@ def test_plot_spikes_from_lems_file(self):
         pyplts.plot_spikes_from_lems_file(
             lems_file_name=lems_file.name,
             base_dir=".",
-            show_plots_already=True,
+            show_plots_already=False,
             save_spike_plot_to="spikes-test-from-lems-file.png",
             rates=False,
             # rate_window=50,