build(deps): support py3.13, drop caps on trusted deps, fix CI tornado drift

- add Python 3.13 classifier + CI matrix leg (libroadrunner ships cp313 wheels)
- drop upper caps on paramiko/msgpack/libroadrunner/numpy/scipy
- setup-pybnf action: tornado>=6.1 to match pyproject (was stale <7)

Author: wshlavacek

.github/actions/setup-pybnf/action.yml

@@ -59,14 +59,14 @@ runs:
         uv pip install \
           'dask>=2024.1.0' \
           'distributed>=2024.1.0' \
-          'libroadrunner>=1.6.0,<3' \
-          'msgpack>=0.6.2,<2' \
-          'numpy>=1.24,<3' \
-          'paramiko>=2.7,<5' \
+          'libroadrunner>=1.6.0' \
+          'msgpack>=0.6.2' \
+          'numpy>=1.24' \
+          'paramiko>=2.7' \
           'pydantic>=2,<3' \
           'pyparsing>=2.4,<4' \
-          'scipy>=1.10,<2' \
-          'tornado>=6.1,<7' \
+          'scipy>=1.10' \
+          'tornado>=6.1' \
           'pytest>=7,<10' \
           'hypothesis>=6,<7' \
           'pytest-xdist' \

.github/workflows/tests.yml

@@ -11,9 +11,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # Min and max of the supported range (requires-python >= 3.10;
-        # classifiers list through 3.12).
-        python-version: ['3.10', '3.12']
+        # Spans the supported range (requires-python >= 3.10; classifiers list
+        # through 3.13).
+        python-version: ['3.10', '3.12', '3.13']
     name: pytest (py${{ matrix.python-version }})
     steps:
       - uses: actions/checkout@v6

pyproject.toml

@@ -26,19 +26,20 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = [
     "bngsim>=0.5.0,<1",
     "dask>=2024.1.0",
     "distributed>=2024.1.0",
-    "libroadrunner>=1.6.0,<3",
-    "msgpack>=0.6.2,<2",
-    "numpy>=1.24,<3",
-    "paramiko>=2.7,<5",
+    "libroadrunner>=1.6.0",
+    "msgpack>=0.6.2",
+    "numpy>=1.24",
+    "paramiko>=2.7",
     "pydantic>=2,<3",
     "pyparsing>=2.4,<4",
-    "scipy>=1.10,<2",
+    "scipy>=1.10",
     "tornado>=6.1",
 ]