From f2f41d0109bec2f16614c22525b83ecb90730cac Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Fri, 10 Jul 2026 21:15:39 +0000 Subject: [PATCH 1/6] python3Packages.jax-tap: init at 0.3.0 --- .../python-modules/jax-tap/default.nix | 62 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 64 insertions(+) create mode 100644 pkgs/development/python-modules/jax-tap/default.nix diff --git a/pkgs/development/python-modules/jax-tap/default.nix b/pkgs/development/python-modules/jax-tap/default.nix new file mode 100644 index 000000000000..1a4dcb5e2972 --- /dev/null +++ b/pkgs/development/python-modules/jax-tap/default.nix @@ -0,0 +1,62 @@ +{ + lib, + buildPythonPackage, + fetchFromGitHub, + + # build-system + hatch-vcs, + hatchling, + + # dependencies + jax, + + # optional-dependencies + pandas, + + # tests + pytestCheckHook, +}: + +buildPythonPackage (finalAttrs: { + pname = "jax-tap"; + version = "0.3.0"; + pyproject = true; + __structuredAttrs = true; + + src = fetchFromGitHub { + owner = "arcueil"; + repo = "jax-tap"; + tag = "v${finalAttrs.version}"; + hash = "sha256-B6Y8+9FXLhHZwQ9ayomffP3P7Uz7zuL52oxzJwCE2hM="; + }; + + build-system = [ + hatch-vcs + hatchling + ]; + + dependencies = [ + jax + ]; + + optional-dependencies = { + pandas = [ + pandas + ]; + }; + + pythonImportsCheck = [ "jaxtap" ]; + + nativeCheckInputs = [ + pandas + pytestCheckHook + ]; + + meta = { + description = "Make print-debugging great again"; + homepage = "https://github.com/arcueil/jax-tap"; + changelog = "https://github.com/arcueil/jax-tap/blob/${finalAttrs.src.tag}/CHANGELOG.md"; + license = lib.licenses.asl20; + maintainers = with lib.maintainers; [ GaetanLepage ]; + }; +}) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 7b11f4638909..eaeff52bca6f 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -8369,6 +8369,8 @@ self: super: with self; { jax-jumpy = callPackage ../development/python-modules/jax-jumpy { }; + jax-tap = callPackage ../development/python-modules/jax-tap { }; + jaxlib = jaxlib-bin; jaxlib-bin = callPackage ../development/python-modules/jaxlib/bin.nix { }; From 792815c4edd9cdbe33e3f21c40e0be83b403df92 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Fri, 10 Jul 2026 21:11:58 +0000 Subject: [PATCH 2/6] python3Packages.blackjax: 1.5 -> 1.6 Diff: https://github.com/blackjax-devs/blackjax/compare/1.5...1.6 Changelog: https://github.com/blackjax-devs/blackjax/releases/tag/1.6 --- pkgs/development/python-modules/blackjax/default.nix | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/blackjax/default.nix b/pkgs/development/python-modules/blackjax/default.nix index df2e518d70e1..21bcd14d54fe 100644 --- a/pkgs/development/python-modules/blackjax/default.nix +++ b/pkgs/development/python-modules/blackjax/default.nix @@ -17,7 +17,8 @@ typing-extensions, # optional-dependencies - fastprogress, + jax-tap, + tqdm, # checks chex, @@ -27,14 +28,15 @@ buildPythonPackage (finalAttrs: { pname = "blackjax"; - version = "1.5"; + version = "1.6"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "blackjax-devs"; repo = "blackjax"; tag = finalAttrs.version; - hash = "sha256-tKJfukTqSiW2Xg3/8DakxtxlwGpJ14S/7qUE1OGM97I="; + hash = "sha256-qLOAmUQxr1xtlJB/TMnjFkvvHUwh0XKpPN+FVD8ju8Y="; }; build-system = [ @@ -53,7 +55,8 @@ buildPythonPackage (finalAttrs: { optional-dependencies = { progress = [ - fastprogress + jax-tap + tqdm ]; }; @@ -77,6 +80,7 @@ buildPythonPackage (finalAttrs: { # AssertionError on numerical values "test_barker" + "test_imm_shrinkage_seed_influence_persists_diagonal" "test_laps" "test_mclmc" "test_mcse4" From a26dc104b57e770bd84f27518a6cd669ec7cea8d Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Fri, 10 Jul 2026 22:18:23 +0000 Subject: [PATCH 3/6] python3Packages.minikanren: fix, cleanup --- .../python-modules/minikanren/default.nix | 39 ++++++++++++------- 1 file changed, 24 insertions(+), 15 deletions(-) diff --git a/pkgs/development/python-modules/minikanren/default.nix b/pkgs/development/python-modules/minikanren/default.nix index ecfc66738735..457587e272b8 100644 --- a/pkgs/development/python-modules/minikanren/default.nix +++ b/pkgs/development/python-modules/minikanren/default.nix @@ -2,27 +2,35 @@ lib, buildPythonPackage, fetchFromGitHub, - toolz, - cons, - multipledispatch, - etuples, - logical-unification, - py, - pytestCheckHook, - pytest-html, + + # build-system setuptools, setuptools-scm, + + # dependencies + cons, + etuples, + logical-unification, + multipledispatch, + toolz, + typing-extensions, + + # tests + py, + pytest-html, + pytestCheckHook, }: -buildPythonPackage rec { +buildPythonPackage (finalAttrs: { pname = "minikanren"; version = "1.0.5"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "pythological"; repo = "kanren"; - tag = "v${version}"; + tag = "v${finalAttrs.version}"; hash = "sha256-lCQ0mKT99zK5A74uoo/9bP+eFdm3MC43Fh8+P2krXrs="; }; @@ -32,17 +40,18 @@ buildPythonPackage rec { ]; dependencies = [ - toolz cons - multipledispatch etuples logical-unification + multipledispatch + toolz + typing-extensions ]; nativeCheckInputs = [ py - pytestCheckHook pytest-html + pytestCheckHook ]; pytestFlags = [ @@ -55,8 +64,8 @@ buildPythonPackage rec { meta = { description = "Relational programming in Python"; homepage = "https://github.com/pythological/kanren"; - changelog = "https://github.com/pythological/kanren/releases/tag/${src.tag}"; + changelog = "https://github.com/pythological/kanren/releases/tag/${finalAttrs.src.tag}"; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ Etjean ]; }; -} +}) From 309eeecb42582febef85d44e605e93f8ec895297 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Fri, 10 Jul 2026 22:33:38 +0000 Subject: [PATCH 4/6] python3Packages.arviz-base: ignore failing warning --- pkgs/development/python-modules/arviz-base/default.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pkgs/development/python-modules/arviz-base/default.nix b/pkgs/development/python-modules/arviz-base/default.nix index 99c5e909f275..814e3b911a0d 100644 --- a/pkgs/development/python-modules/arviz-base/default.nix +++ b/pkgs/development/python-modules/arviz-base/default.nix @@ -67,6 +67,11 @@ buildPythonPackage (finalAttrs: { writableTmpDirAsHomeHook ]; + pytestFlags = [ + # DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. + "-Wignore::DeprecationWarning" + ]; + meta = { description = "Base ArviZ features and converters"; homepage = "https://github.com/arviz-devs/arviz-base"; From e409745df771e9dcc11ffb002f118731bf3e4e4a Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Fri, 10 Jul 2026 22:47:53 +0000 Subject: [PATCH 5/6] python3Packages.corner: 2.2.3 -> 2.3.0 Diff: https://github.com/dfm/corner.py/compare/v2.2.3...v2.3.0 Changelog: https://github.com/dfm/corner.py/releases/tag/v2.3.0 --- .../python-modules/corner/default.nix | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/pkgs/development/python-modules/corner/default.nix b/pkgs/development/python-modules/corner/default.nix index 6fb5d809ddf6..1c891a66d4b3 100644 --- a/pkgs/development/python-modules/corner/default.nix +++ b/pkgs/development/python-modules/corner/default.nix @@ -2,7 +2,6 @@ lib, buildPythonPackage, fetchFromGitHub, - writableTmpDirAsHomeHook, # build-system hatch-vcs, @@ -13,6 +12,7 @@ # optional-dependencies arviz, + arviz-base, ipython, myst-nb, pandoc, @@ -23,28 +23,20 @@ # tests pytestCheckHook, - corner, }: -buildPythonPackage rec { +buildPythonPackage (finalAttrs: { pname = "corner"; - version = "2.2.3"; + version = "2.3.0"; pyproject = true; src = fetchFromGitHub { owner = "dfm"; repo = "corner.py"; - tag = "v${version}"; - hash = "sha256-gK2yylteI3VLVJ0p7NB7bR7cirCo2BvFKnYIH3kfyh4="; + tag = "v${finalAttrs.version}"; + hash = "sha256-H59IVXKPT4CLApn4kUuSuiYA9EWdOaH88Rd4YXf0VlQ="; }; - nativeBuildInputs = [ - # During `pythonImportsCheck`, `corner` imports `arviz` which wants to write a stamp file to the - # homedir. It then needs to be writable. - # https://github.com/arviz-devs/arviz/commit/4db612908f588d89bb5bfb6b83a08ada3d54fd02 - writableTmpDirAsHomeHook - ]; - build-system = [ hatch-vcs hatchling @@ -53,9 +45,13 @@ buildPythonPackage rec { dependencies = [ matplotlib ]; optional-dependencies = { - arviz = [ arviz ]; + arviz = [ + arviz + arviz-base + ]; docs = [ arviz + arviz-base ipython myst-nb pandoc @@ -71,10 +67,14 @@ buildPythonPackage rec { pythonImportsCheck = [ "corner" ]; - nativeCheckInputs = [ pytestCheckHook ] ++ corner.optional-dependencies.test; + nativeCheckInputs = [ + arviz + pytestCheckHook + scipy + ]; - # matplotlib.testing.exceptions.ImageComparisonFailure: images not close disabledTests = [ + # matplotlib.testing.exceptions.ImageComparisonFailure: images not close "test_1d_fig_argument" "test_arviz" "test_basic" @@ -110,8 +110,8 @@ buildPythonPackage rec { meta = { description = "Make some beautiful corner plots"; homepage = "https://github.com/dfm/corner.py"; - changelog = "https://github.com/dfm/corner.py/releases/tag/v${version}"; + changelog = "https://github.com/dfm/corner.py/releases/tag/${finalAttrs.src.tag}"; license = lib.licenses.bsd2; maintainers = with lib.maintainers; [ GaetanLepage ]; }; -} +}) From 13f27af73b4687fa1b4497b36443698c53da31a2 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Sat, 11 Jul 2026 20:29:25 +0000 Subject: [PATCH 6/6] python3Packages.pytensor: 3.1.2 -> 3.1.3 Diff: https://github.com/pymc-devs/pytensor/compare/rel-3.1.2...rel-3.1.3 Changelog: https://github.com/pymc-devs/pytensor/releases/tag/rel-3.1.3 --- .../python-modules/pytensor/default.nix | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/pkgs/development/python-modules/pytensor/default.nix b/pkgs/development/python-modules/pytensor/default.nix index c6115797ae12..0741e59af6ba 100644 --- a/pkgs/development/python-modules/pytensor/default.nix +++ b/pkgs/development/python-modules/pytensor/default.nix @@ -33,7 +33,7 @@ buildPythonPackage (finalAttrs: { pname = "pytensor"; - version = "3.1.2"; + version = "3.1.3"; pyproject = true; __structuredAttrs = true; @@ -44,9 +44,16 @@ buildPythonPackage (finalAttrs: { postFetch = '' sed -i 's/git_refnames = "[^"]*"/git_refnames = " (tag: ${finalAttrs.src.tag})"/' $out/pytensor/_version.py ''; - hash = "sha256-kKfbVSWsaA9ytii4GXeEmE+Oq8Qi7QNUOozgemqJI+k="; + hash = "sha256-9Apjyg+wmAWrK7hMSF54b1u/3TT0GGitDlyF6rQA4OY="; }; + # DeprecationWarning: scipy.linalg: the `lwork` keyword is deprecated and no longer in use as of + # SciPy 1.18.0 and will be removed in SciPy 1.20.0 + postPatch = '' + substituteInPlace pytensor/link/numba/dispatch/linalg/decomposition/qr.py \ + --replace-fail "lwork=lwork," "" + ''; + build-system = [ setuptools cython @@ -85,7 +92,11 @@ buildPythonPackage (finalAttrs: { rm -rf pytensor ''; - disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [ + disabledTests = [ + # AssertionError: Not equal to tolerance rtol=0.0001, atol=0 + "test_Searchsorted" + ] + ++ lib.optionals stdenv.hostPlatform.isDarwin [ # Numerical assertion error # tests.unittest_tools.WrongValue: WrongValue "test_op_sd"