python package updates (#74)

* update package versions

* ruff updates

* update pybind11

* exact pin

CMakeLists.txt

@@ -8,7 +8,7 @@ ExternalProject_Add(
         pybind11
         PREFIX .
         GIT_REPOSITORY "https://github.com/pybind/pybind11.git"
-        GIT_TAG "80dc998efced8ceb2be59756668a7e90e8bef917" # v2.10.4
+        GIT_TAG "a2e59f0e7065404b44dfe92a28aca47ba1378dc4" # v2.13.6
         SOURCE_DIR "${CMAKE_BINARY_DIR}/third-party/pybind11"
         # Override default steps with no action, we just want the clone step.
         UPDATE_COMMAND ""
@@ -80,7 +80,7 @@ set(FETCHCONTENT_QUIET FALSE)
 
 FetchContent_Declare(
   pybind11
-  URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.4.tar.gz
+  URL https://github.com/pybind/pybind11/archive/refs/tags/v2.13.6.tar.gz
 )
 
 FetchContent_GetProperties(pybind11)

pyproject.toml

@@ -31,31 +31,31 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-  "coverage~=7.5.1",
-  "mypy~=1.10.0",
-  "pybind11~=2.10.4",
+  "coverage~=7.6.4",
+  "mypy~=1.13.0",
+  "pybind11==2.13.6",
   "pytest-mpl~=0.17.0",
-  "pytest~=8.2.1",
-  "ruff~=0.5.7",
-  "setuptools~=67.7.2",
-  "wheel~=0.43.0",
+  "pytest~=8.3.3",
+  "ruff~=0.7.1",
+  "setuptools~=75.3.0",
+  "wheel~=0.44.0",
 ]
 docs = [
-  "Sphinx~=7.4.7",
-  "myst-nb~=1.1.1",
-  "myst-parser~=3.0.1",
-  "furo==2024.7.18",
-  "sphinx_design==0.6.0",
-  "sphinx-autobuild~=2024.4.16",
+  "Sphinx~=8.1.3",
+  "myst-nb~=1.1.2",
+  "myst-parser~=4.0.0",
+  "furo==2024.8.6",
+  "sphinx_design~=0.6.1",
+  "sphinx-autobuild~=2024.10.3",
 ]
 
 [project.scripts]
 "bmds-priors-report" = "pybmds.cli.priors_report:main"
 
 [build-system]
 requires = [
-  "pybind11~=2.10.4",
-  "setuptools~=67.7.2",
+  "pybind11==2.13.6",
+  "setuptools~=75.3.0",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -119,6 +119,7 @@ addopts = "--mpl-baseline-path=tests/data/mpl"
 python_files = ["test_*.py"]
 
 [tool.ruff]
+exclude = ["docs"]
 line-length = 100
 lint.select = ["F", "E", "W", "I", "UP", "S", "B", "T20", "ERA", "NPY", "RUF", "PTH"]
 lint.ignore = ["E501"]

src/pybmds/types/common.py

@@ -72,7 +72,7 @@ def inspect_cpp_obj(lines: list[str], obj: Any, depth: int):
     depth += 1
     indent = "  " * depth + "- "
     for attr, value in inspect.getmembers(obj):
-        if attr.startswith("__"):
+        if attr.startswith("__") or attr.startswith("_pybind11"):
             continue
         elif attr == "models" and "multitumor" in obj.__class__.__name__:
             lines.append(f"{indent}{attr}:")

tests/test_bmdscore/testCont.py

@@ -1,6 +1,7 @@
-import bmdscore
 import numpy as np
 
+import bmdscore
+
 pyAnal = bmdscore.python_continuous_analysis()
 pyAnal.model = bmdscore.cont_model.exp_5
 # isIncreasing needed if detectAdvDir is set to false

tests/test_bmdscore/testDicho.py

@@ -1,6 +1,7 @@
-import bmdscore
 import numpy as np
 
+import bmdscore
+
 pyAnal = bmdscore.python_dichotomous_analysis()
 pyAnal.model = bmdscore.dich_model.d_weibull
 pyAnal.n = 4

tests/test_bmdscore/testDichoMA.py

@@ -1,6 +1,7 @@
-import bmdscore
 import numpy as np
 
+import bmdscore
+
 pyMA = bmdscore.python_dichotomousMA_analysis()
 pyMA.nmodels = 9
 pyMA.actual_parms = np.array([4, 3, 2, 3, 3, 4, 2, 2, 3])

tests/test_bmdscore/testMultitumor.py

@@ -1,6 +1,7 @@
-import bmdscore
 import numpy as np
 
+import bmdscore
+
 
 def getMultitumorPrior(degree, prior_cols):
     prG = np.array([0, -17, 0, -18, 18])

tests/test_bmdscore/testNested.py

@@ -1,8 +1,9 @@
 import sys
 
-import bmdscore
 import numpy as np
 
+import bmdscore
+
 
 def getNLogisticPrior(ngrp, prior_cols, restricted):
     prG = np.array([0, 1])