Fix CI

Author: GianlucaFicarelli

.github/workflows/run-tox.yml

@@ -22,6 +22,10 @@ jobs:
           tox-env: py311
         - python-version: '3.12'
           tox-env: py312
+        - python-version: '3.13'
+          tox-env: py313
+        - python-version: '3.12'
+          tox-env: coverage
           codecov: codecov
         - python-version: '3.12'
           tox-env: lint

.gitignore

@@ -12,3 +12,4 @@ dist
 htmlcov
 dask-worker-space
 venv
+_version.py

.pylintrc

@@ -1,3 +1,7 @@
+[MAIN]
+# Files or directories to be skipped. They should be base names, not paths.
+ignore=_version.py
+
 [MESSAGES CONTROL]
 disable=fixme,invalid-name,len-as-condition,no-else-return
 
@@ -8,6 +12,8 @@ max-line-length=100
 [DESIGN]
 # Maximum number of arguments for function / method
 max-args=8
+# Maximum number of positional arguments for function / method.
+max-positional-arguments=11
 # Argument names that match this expression will be ignored. Default to name
 # with leading underscore
 ignored-argument-names=_.*
@@ -48,3 +54,6 @@ ignore-docstrings=yes
 ignored-classes=numpy,list
 
 extension-pkg-whitelist=numpy,lxml
+
+# Files or directories to be skipped. They should be base names, not paths.
+ignore=_version.py

connectome_tools/apps/s2f_recipe.py

@@ -10,6 +10,7 @@
 import yaml
 from bluepysnap import Circuit
 
+from connectome_tools import __version__
 from connectome_tools.s2f_recipe import (
     BOUTON_REDUCTION_FACTOR,
     CV_SYNS_CONNECTION,
@@ -33,7 +34,6 @@
     timed,
     validate_config,
 )
-from connectome_tools.version import __version__
 
 L = logging.getLogger("s2f-recipe")
 

connectome_tools/equation.py

@@ -15,6 +15,12 @@ def evaluate(expression, context=None):
         expression(str): math expression.
         context: optional dict of variables.
 
+    Returns:
+        the calculated value.
+
+    Raises:
+        NameError: if an unexpected name is present in the given expression.
+
     Examples:
         >>> evaluate("1 + 2 * 3")
         7
@@ -28,4 +34,11 @@ def evaluate(expression, context=None):
     for name in code.co_names:
         if name not in allowed_names:
             raise NameError(f"The use of '{name}' is not allowed")
-    return eval(code, {"__builtins__": {}}, allowed_names)
+    # Add `__import__` to the `__builtins__` dict, because numpy may print a RuntimeWarning,
+    # and this causes `__import__('warnings')` to be explicitly called in Python >= 3.13,
+    # raising the exception KeyError: '__import__' if __import__ is not found in globals.
+    # For example, the following instruction raises with numpy 2.1.3 and Python 3.13.0:
+    # >>> eval('n ** 0.5', {'__builtins__': {}}, {'n': np.float64(-1)})
+    return eval(  # pylint: disable=eval-used
+        code, {"__builtins__": {"__import__": __import__}}, allowed_names
+    )

connectome_tools/merge.py

@@ -20,9 +20,9 @@
 import submitit
 import yaml
 
+from connectome_tools import __version__
 from connectome_tools.apps import s2f_recipe
 from connectome_tools.utils import DEFAULT_CONFIG_PATH, load_yaml, setup_logging, validate_config
-from connectome_tools.version import __version__
 
 L = logging.getLogger(__name__)
 

connectome_tools/s2f_recipe/estimate_syns_con.py

@@ -134,7 +134,8 @@ def _execute(pathway, estimate, formulae, syn_class_map, max_value):
         return []
     L.info("nsyn estimate for pathway %s: %.3g", pathway, value)
     expression = _choose_formula(formulae, pathway, syn_class_map)
-    value = equation.evaluate(expression, context={"n": value})
+    # ensure that n is np.float64, to get consistent results
+    value = equation.evaluate(expression, context={"n": np.float64(value)})
     # NSETM-1137 consider nan as 1.0
     if value < 1.0 or np.isnan(value):
         value = 1.0

pyproject.toml

@@ -26,7 +26,10 @@ dependencies = [
     "morphio>=3.0.1,<4.0.0",
     "voxcell>=3.0,<4.0",
     # setuptools needed because of https://github.com/facebookincubator/submitit/issues/1765
-    'setuptools;python_version>="3.12"',
+    "setuptools",
+    # pynrrd>=1.1.0 needed because of https://github.com/mhe/pynrrd/issues/152
+    # this dependency can be removed after pynrrd 1.1.0 is released
+    "pynrrd @ git+https://github.com/mhe/pynrrd.git@e92a82dd12b6fa99405dc655c4374415367cb778",
 ]
 license = {text = "Apache-2.0"}
 classifiers=[
@@ -63,7 +66,8 @@ s2f-recipe = "connectome_tools.apps.s2f_recipe:app"
 s2f-recipe-merge = "connectome_tools.apps.s2f_recipe_merge:cli"
 
 [tool.setuptools.packages.find]
-include = ["connectome_tools"]
+include = ["connectome_tools*"]
+namespaces = true
 
 [tool.setuptools_scm]
 version_file = "connectome_tools/_version.py"
@@ -91,3 +95,8 @@ pythonpath = [
 filterwarnings = [
     "ignore::DeprecationWarning:nptyping",
 ]
+
+[tool.coverage.run]
+omit = [
+    "connectome_tools/_version.py",
+]

tests/test_dataset.py

@@ -17,10 +17,10 @@
             mtypes=None,
             expected=pd.DataFrame(
                 [
-                    ["*", 42.0, np.NaN, np.NaN, np.NaN],
-                    ["L1_DAC", 10.0, 0.0, 1.0, np.NaN],
-                    ["L23_MC", 30.0, 0.0, 1.0, np.NaN],
-                    ["SO_OLM", 50.0, 0.0, 1.0, np.NaN],
+                    ["*", 42.0, np.nan, np.nan, np.nan],
+                    ["L1_DAC", 10.0, 0.0, 1.0, np.nan],
+                    ["L23_MC", 30.0, 0.0, 1.0, np.nan],
+                    ["SO_OLM", 50.0, 0.0, 1.0, np.nan],
                 ],
                 columns=["mtype", "mean", "std", "size", "sample"],
             ),
@@ -29,7 +29,7 @@
             _="filter_mtypes",
             mtypes={"L1_DAC"},
             expected=pd.DataFrame(
-                [["L1_DAC", 10.0, 0.0, 1.0, np.NaN]],
+                [["L1_DAC", 10.0, 0.0, 1.0, np.nan]],
                 columns=["mtype", "mean", "std", "size", "sample"],
             ),
         ),
@@ -51,7 +51,7 @@ def test_read_bouton_density(_, mtypes, expected):
             expected=pd.DataFrame(
                 [
                     ["SLM_PPA", "SLM_PPA", 16.2, 8.77, 5.0, "1,16,16,20,28"],
-                    ["SLM_PPA", "SO_BP", np.NaN, np.NaN, np.NaN, np.NaN],
+                    ["SLM_PPA", "SO_BP", np.nan, np.nan, np.nan, np.nan],
                     ["SLM_PPA", "SP_AA", 3.0, 1.63, 3.0, "1,3,5"],
                 ],
                 columns=["from", "to", "mean", "std", "size", "sample"],

tests/test_equation.py

@@ -13,6 +13,8 @@
         ("sin(n * pi)", {"n": 0.5}, 1.0),
         ("n * 3", {"n": np.nan}, np.nan),
         ("1 / n", {"n": np.nan}, np.nan),
+        ("6 * ((n - 2) ** 0.5) - 1", {"n": 1.5}, (-1 + 4.242640687119286j)),  # float -> complex
+        ("6 * ((n - 2) ** 0.5) - 1", {"n": np.float64(1.5)}, np.nan),  # np.float64 -> np.nan
     ],
 )
 def test_evaluate(expression, context, expected):
@@ -23,9 +25,9 @@ def test_evaluate(expression, context, expected):
 @pytest.mark.parametrize(
     ("expression", "error", "match"),
     [
-        ("1 + 2 *", SyntaxError, "invalid syntax"),
+        ("1 + 2 *", SyntaxError, "invalid syntax|unexpected EOF while parsing"),
         ("sqrt(-1)", ValueError, "math domain error"),
-        ("1 / 0", ValueError, "math domain error"),
+        ("1 / 0", ZeroDivisionError, "division by zero"),
         ("sum([1, 2])", NameError, "The use of 'sum' is not allowed"),
         ("open('/etc/passwd')", NameError, "The use of 'open' is not allowed"),
         (

tests/test_merge.py

@@ -6,9 +6,9 @@
 from utils import TEST_DATA_DIR, canonicalize_xml, tmp_cwd, xml_to_regular_dict
 
 import connectome_tools.merge as test_module
+from connectome_tools import __version__
 from connectome_tools.merge import RECIPES_DIR, SLURM_DIR, WORKDIR
 from connectome_tools.utils import load_yaml
-from connectome_tools.version import __version__
 
 
 def test_execute_pending_tasks_success():

tox.ini

@@ -22,8 +22,6 @@ ignore_basepython_conflict = true
 basepython=python3.11
 deps = {[base]testdeps}
 commands = pytest -v tests {posargs}
-setenv =
-    PIP_INDEX_URL = https://bbpteam.epfl.ch/repository/devpi/simple
 
 [testenv:check-version]
 skip_install = true