build(env): adopt the PyMC 6.2 shared baseline

environment.yml

@@ -6,33 +6,33 @@ dependencies:
   # Must match dse-research-utils' data/environment-core.yml exactly. Verify:
   #   dse-check-env environment.yml
   - python=3.14.6
-  - numpy>=2.4.6,<2.5 # pymc>=6.1.0 -> pytensor 3.1.x -> numba<=0.65.1 -> numpy<2.5
+  - numpy>=2.4.6,<2.5 # pymc -> pytensor 3.x -> numba -> numpy<2.5; numba 0.66.0 still pins <2.5, so lifting this needs a numba release that supports 2.5
   - scipy>=1.18.0
-  - pandas>=3.0.3
+  - pandas>=3.0.5
   - pyarrow>=24.0.0 # pandas 3.x's default `str` dtype is Arrow-backed; floor held at 24 by jaxlib's libabseil pin
-  - numba>=0.58,<=0.65.1 # pytensor 3.x caps numba; this is what pymc>=6.1.0 commits us to
-  - matplotlib>=3.11.0
+  - numba>=0.58,<=0.65.1 # every pytensor 3.x caps numba here (verified through 3.2.3); this is what pymc>=6.2.0 commits us to
+  - matplotlib>=3.11.1
   - scikit-learn>=1.9.0
   - statsmodels>=0.14.6
-  - pymc>=6.1.0 # pulls pytensor + a C toolchain from conda-forge; forces pytensor >=3.1.2 -> numba <=0.65.1 -> numpy <2.5
+  - pymc>=6.2.0 # pulls pytensor + a C toolchain from conda-forge; requires pytensor >=3.2.2,<3.3 -> numba <=0.65.1 -> numpy <2.5
   - nutpie>=0.16.11
   - numpyro>=0.21.0
   - jax>=0.10.2 # CPU build; GPU acceleration via an environment-gpu.yml overlay
   - arviz>=1.2.0
   - arviz-base>=1.2.0
   - arviz-stats>=1.2.0
   - arviz-plots>=1.2.0
-  - preliz>=0.27.0
-  - h5py>=3.12.0
-  - h5netcdf>=1.3.0
+  - preliz>=0.27.1
+  - h5py>=3.16.0
+  - h5netcdf>=1.8.1
   - graphviz>=14.1.2
-  - python-graphviz>=0.20
+  - python-graphviz>=0.21
   # ── LRP add-ons (gradient boosting, graphs, array storage) ────────────────
-  - lightgbm>=4.6.0
+  - lightgbm>=4.7.0
   - xgboost>=3.3.0
   - shap>=0.52.0
   - networkx # DAG plotting via dse_research_utils.plot.graphs (uses python-graphviz)
-  - xarray>=2026.4.0
+  - xarray>=2026.7.0
   - pip
   - pip:
       # Shared library from the public git tag (no auth; PyPI is a later
@@ -43,7 +43,7 @@ dependencies:
       # rich, psutil, pyyaml, …) — no need to list them here. Graph plotting
       # (graphviz/networkx) is served by the conda-forge core + add-ons, so the
       # `graphs` extra is intentionally omitted.
-      - dse-research-utils[viz,notebook,dependence,tuning,io] @ git+https://github.com/dseinternational/research.git@v0.8.0#subdirectory=src/python
+      - dse-research-utils[viz,notebook,dependence,tuning,io] @ git+https://github.com/dseinternational/research.git@v0.9.0#subdirectory=src/python
       - -e ./
       # Local-dev override — to develop against a sibling checkout of research,
       # comment the git line above and uncomment this instead:
@@ -54,6 +54,6 @@ dependencies:
       - hatch
       - build
       - pytest>=9.1.1
-      - ruff>=0.15.20
+      - ruff>=0.16.1
       - mypy>=1.18.2
-      - setuptools>=82.0.1
+      - setuptools>=83.0.0

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling>=1.30.1"]
+requires = ["hatchling>=1.31.0"]
 build-backend = "hatchling.build"
 
 [project]
@@ -15,35 +15,35 @@ dependencies = [
   "arviz-plots>=1.2.0",
   "arviz-stats>=1.2.0",
   "arviz>=1.2.0",
-  "dse-research-utils>=0.8.0",
+  "dse-research-utils>=0.9.0",
   "graphviz",
-  "lightgbm>=4.6.0",
-  "matplotlib>=3.10.8",
+  "lightgbm>=4.7.0",
+  "matplotlib>=3.11.1",
   "networkx",
-  "numpy>=2.4.3",
-  "pandas>=3.0.2",
-  "preliz>=0.27.0",
-  "pymc>=6.0.1",
+  "numpy>=2.4.6,<2.5",  # pymc -> pytensor -> numba pins numpy <2.5; matches the shared conda core
+  "pandas>=3.0.5",
+  "preliz>=0.27.1",
+  "pymc>=6.2.0",
   "rich>=15.0.0",
   "scikit-learn>=1.9.0",
   "seaborn>=0.13.2",
   "shap>=0.52.0",
   "scipy>=1.18.0",
-  "xarray>=2026.4.0"
+  "xarray>=2026.7.0"
 ]
 
 [project.optional-dependencies]
 dev = [
   "jupyter>=1.1.1",
   "mypy>=1.18.2",
-  "pytest>=9.0.3"
+  "pytest>=9.1.1"
 ]
 
 [tool.uv.sources]
 # dse-research-utils isn't published to PyPI — resolve it from the public git
 # tag. (The conda env in environment.yml installs it from the same tag in its
 # pip layer; this entry is only consumed by uv.)
-dse-research-utils = { git = "https://github.com/dseinternational/research.git", subdirectory = "src/python", tag = "v0.8.0" }
+dse-research-utils = { git = "https://github.com/dseinternational/research.git", subdirectory = "src/python", tag = "v0.9.0" }
 
 [tool.hatch.version]
 path = "src/language_reading_predictors/__init__.py"