From edb1b81a426ba678fa0033b65ad2d869597fc976 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Wed, 12 Aug 2026 10:37:37 +0000
Subject: [PATCH 1/2] python3Packages.pytensor: 3.2.4 -> 3.3.0

Diff: https://github.com/pymc-devs/pytensor/compare/rel-3.2.4...rel-3.3.0

Changelog: https://github.com/pymc-devs/pytensor/releases/tag/rel-3.3.0
---
 .../python-modules/pytensor/default.nix       | 26 ++++++++++++++++---
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/pkgs/development/python-modules/pytensor/default.nix b/pkgs/development/python-modules/pytensor/default.nix
index 4a63d60eb4f7..1f9de3b56fce 100644
--- a/pkgs/development/python-modules/pytensor/default.nix
+++ b/pkgs/development/python-modules/pytensor/default.nix
@@ -3,6 +3,7 @@
   stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+  pythonAtLeast,
 
   # build-system
   setuptools,
@@ -25,7 +26,6 @@
   pytest-benchmark,
   pytest-mock,
   pytestCheckHook,
-  tensorflow-probability,
   writableTmpDirAsHomeHook,
 
   nix-update-script,
@@ -33,7 +33,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "pytensor";
-  version = "3.2.4";
+  version = "3.3.0";
   pyproject = true;
   __structuredAttrs = true;
 
@@ -44,7 +44,7 @@ buildPythonPackage (finalAttrs: {
     postFetch = ''
       sed -i 's/git_refnames = "[^"]*"/git_refnames = " (tag: ${finalAttrs.src.tag})"/' $out/pytensor/_version.py
     '';
-    hash = "sha256-m+uAf5K7biExv8rmOsyCMAVoKSSRAgm0ugw54s2JvMs=";
+    hash = "sha256-Kq/kLjdDS/NHveeFmoy0PiHLLXviPpU2zf3lcXhx7Sk=";
   };
 
   # DeprecationWarning: scipy.linalg: the `lwork` keyword is deprecated and no longer in use as of
@@ -75,6 +75,9 @@ buildPythonPackage (finalAttrs: {
     setuptools
   ];
 
+  # `tensorflow-probability` is deliberately omitted: it only unlocks a handful of jax tests but
+  # drags in `tensorflow-bin`/`tf2onnx`, which fail to evaluate on Python 3.14 and on Darwin.
+  # Most of them are guarded upstream by `TFP_INSTALLED`, the rest are listed in `disabledTests`.
   nativeCheckInputs = [
     jax
     jaxlib
@@ -82,7 +85,6 @@ buildPythonPackage (finalAttrs: {
     pytest-benchmark
     pytest-mock
     pytestCheckHook
-    tensorflow-probability
     writableTmpDirAsHomeHook
   ];
 
@@ -98,6 +100,22 @@ buildPythonPackage (finalAttrs: {
   disabledTests = [
     # AssertionError: Not equal to tolerance rtol=0.0001, atol=0
     "test_Searchsorted"
+
+    # `det` of a singular matrix: jax returns -1.3e-116 where numpy returns 0.0
+    "test_jax_basic"
+
+    # NotImplementedError: No JAX implementation for Op {betaincinv,gammainccinv,gammaincinv}.
+    # These need `tensorflow-probability` but, unlike the other tfp tests, are not guarded
+    # upstream by `TFP_INSTALLED`.
+    "test_betaincinv"
+    "test_gammainccinv"
+    "test_gammaincinv"
+  ]
+  ++ lib.optionals (pythonAtLeast "3.14") [
+    # These hardcode `getrefcount(x) == 3`, but CPython 3.14 passes locals to calls as borrowed
+    # references, so the count is one lower.
+    "test_sparse_creation_refcount"
+    "test_sparse_passthrough_refcount"
   ]
   ++ lib.optionals stdenv.hostPlatform.isDarwin [
     # Numerical assertion error

From 9a269a3bd16f3e531f2635a61db17a8984d03a46 Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Wed, 12 Aug 2026 10:38:43 +0000
Subject: [PATCH 2/2] python3Packages.pymc: 6.2.0 -> 6.3.1

Diff: https://github.com/pymc-devs/pymc/compare/v6.2.0...v6.3.1

Changelog: https://github.com/pymc-devs/pymc/releases/tag/v6.3.1
---
 pkgs/development/python-modules/pymc/default.nix | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/pkgs/development/python-modules/pymc/default.nix b/pkgs/development/python-modules/pymc/default.nix
index 639c3608d597..be838ce4105a 100644
--- a/pkgs/development/python-modules/pymc/default.nix
+++ b/pkgs/development/python-modules/pymc/default.nix
@@ -11,6 +11,7 @@
   arviz,
   cachetools,
   cloudpickle,
+  matplotlib,
   numpy,
   pandas,
   pytensor,
@@ -22,7 +23,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "pymc";
-  version = "6.2.0";
+  version = "6.3.1";
   pyproject = true;
   __structuredAttrs = true;
 
@@ -30,7 +31,7 @@ buildPythonPackage (finalAttrs: {
     owner = "pymc-devs";
     repo = "pymc";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-90Ui3hiLzU0apYq6YNuAYbqd2JOZ3J7XMh+Lu+C729w=";
+    hash = "sha256-laLj0Dts4E/7cuhQt/1mekfi/P1L7TiOcypiADs0JAc=";
   };
 
   build-system = [
@@ -40,12 +41,14 @@ buildPythonPackage (finalAttrs: {
 
   pythonRelaxDeps = [
     "cachetools"
-    "pytensor"
   ];
   dependencies = [
     arviz
     cachetools
     cloudpickle
+    # `matplotlib` is an undeclared runtime dependency: the default (`progressbar = True`) sampling
+    # path imports it in `pymc/progress_bar/rich_progress.py`.
+    matplotlib
     numpy
     pandas
     pytensor