From 44d3834454ae972cedc614f7641613cf4b9ee048 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Mon, 2 Mar 2026 23:53:11 +0000 Subject: [PATCH 1/6] python3Packages.arviz-base: 0.8.2 -> 1.1.0 Diff: https://github.com/arviz-devs/arviz-base/compare/v0.8.2...v1.1.0 Changelog: https://github.com/arviz-devs/arviz-base/blob/v1.1.0/CHANGELOG.md --- pkgs/development/python-modules/arviz-base/default.nix | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/arviz-base/default.nix b/pkgs/development/python-modules/arviz-base/default.nix index 2b673f93e9cb..32f7a70f191f 100644 --- a/pkgs/development/python-modules/arviz-base/default.nix +++ b/pkgs/development/python-modules/arviz-base/default.nix @@ -7,6 +7,7 @@ flit-core, # dependencies + lazy-loader, numpy, typing-extensions, xarray, @@ -23,14 +24,15 @@ buildPythonPackage (finalAttrs: { pname = "arviz-base"; - version = "0.8.2"; + version = "1.1.0"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "arviz-devs"; repo = "arviz-base"; tag = "v${finalAttrs.version}"; - hash = "sha256-g2DmhYqO9dgvDZwAXXSDFn5wHU0BvxXNgOzk6mmEmsw="; + hash = "sha256-/v1LPgM2rDw9Z0en0MYGELGiRlmwQX4ILKsBEqOhhSs="; }; build-system = [ @@ -38,6 +40,7 @@ buildPythonPackage (finalAttrs: { ]; dependencies = [ + lazy-loader numpy typing-extensions xarray From 07e8c3e71b3c8d4ba7db02060b10b6e5de93fedc Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Mon, 2 Mar 2026 23:54:20 +0000 Subject: [PATCH 2/6] python3Packages.arviz-stats: 0.8.0 -> 1.1.0 Diff: https://github.com/arviz-devs/arviz-stats/compare/v0.8.0...v1.1.0 Changelog: https://github.com/arviz-devs/arviz-stats/blob/v1.1.0/CHANGELOG.md --- pkgs/development/python-modules/arviz-stats/default.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/arviz-stats/default.nix b/pkgs/development/python-modules/arviz-stats/default.nix index f3627df9b35d..490f7bdacb23 100644 --- a/pkgs/development/python-modules/arviz-stats/default.nix +++ b/pkgs/development/python-modules/arviz-stats/default.nix @@ -38,14 +38,15 @@ buildPythonPackage (finalAttrs: { pname = "arviz-stats"; - version = "0.8.0"; + version = "1.1.0"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "arviz-devs"; repo = "arviz-stats"; tag = "v${finalAttrs.version}"; - hash = "sha256-FAZXnKxNb/DPkcpIRJRIzSbthS8Djf75hd5WMxegdhY="; + hash = "sha256-81duRavbPUKsqTWaeD0G6ieWLtyoZm7sRk06QkG5dKQ="; }; build-system = [ From 791731a3271413c90d94e10c01b8e6cbae4788a5 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Mon, 2 Mar 2026 23:53:42 +0000 Subject: [PATCH 3/6] python3Packages.arviz-plots: 0.8.0 -> 1.1.0 Diff: https://github.com/arviz-devs/arviz-plots/compare/v0.8.0...v1.1.0 Changelog: https://github.com/arviz-devs/arviz-plots/blob/v1.1.0/CHANGELOG.md --- pkgs/development/python-modules/arviz-plots/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/arviz-plots/default.nix b/pkgs/development/python-modules/arviz-plots/default.nix index c0f2a3649117..77c0eaf4a6a8 100644 --- a/pkgs/development/python-modules/arviz-plots/default.nix +++ b/pkgs/development/python-modules/arviz-plots/default.nix @@ -41,14 +41,14 @@ buildPythonPackage (finalAttrs: { pname = "arviz-plots"; - version = "0.8.0"; + version = "1.1.0"; pyproject = true; src = fetchFromGitHub { owner = "arviz-devs"; repo = "arviz-plots"; tag = "v${finalAttrs.version}"; - hash = "sha256-x4UoUSKz+MAI082afnGhfoy2ad/hPK89Y1B2oEnxhsg="; + hash = "sha256-ti1wD/aPNCk59wkad+xkvIKTB2Wkupovlo0Hg0YqK1o="; }; build-system = [ From b39810cd26500e0af5c3bd3401111b0a76787fab Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Mon, 2 Mar 2026 23:47:50 +0000 Subject: [PATCH 4/6] python3Packages.arviz: 0.23.4 -> 1.1.0 Diff: https://github.com/arviz-devs/arviz/compare/v0.23.4...v1.1.0 Changelog: https://github.com/arviz-devs/arviz/blob/v1.1.0/CHANGELOG.md --- .../python-modules/arviz-plots/default.nix | 1 + .../python-modules/arviz/default.nix | 113 ++---------------- 2 files changed, 14 insertions(+), 100 deletions(-) diff --git a/pkgs/development/python-modules/arviz-plots/default.nix b/pkgs/development/python-modules/arviz-plots/default.nix index 77c0eaf4a6a8..5e7a4a87e052 100644 --- a/pkgs/development/python-modules/arviz-plots/default.nix +++ b/pkgs/development/python-modules/arviz-plots/default.nix @@ -43,6 +43,7 @@ buildPythonPackage (finalAttrs: { pname = "arviz-plots"; version = "1.1.0"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "arviz-devs"; diff --git a/pkgs/development/python-modules/arviz/default.nix b/pkgs/development/python-modules/arviz/default.nix index 098d412a1908..abfabf9053ae 100644 --- a/pkgs/development/python-modules/arviz/default.nix +++ b/pkgs/development/python-modules/arviz/default.nix @@ -1,135 +1,48 @@ { lib, - stdenv, buildPythonPackage, fetchFromGitHub, - # nativeBuildInputs - writableTmpDirAsHomeHook, - # build-system - packaging, - setuptools, + flit-core, # dependencies - h5netcdf, - matplotlib, - numpy, - pandas, - platformdirs, - scipy, - typing-extensions, - xarray, - xarray-einstats, + arviz-base, + arviz-plots, + arviz-stats, # tests - bokeh, - cloudpickle, - emcee, - ffmpeg, - h5py, - jax, - jaxlib, - numba, - numpyro, - #, pymc3 (circular dependency) - pyro-ppl, - #, pystan (not packaged) pytestCheckHook, - torchvision, - zarr, }: buildPythonPackage (finalAttrs: { pname = "arviz"; - version = "0.23.4"; + version = "1.1.0"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "arviz-devs"; repo = "arviz"; tag = "v${finalAttrs.version}"; - hash = "sha256-YQ5i+CSuznbWAQ29jgqrOs+zgOAS5U4wSNEIquJQkvY="; + hash = "sha256-M9tj1X65hiLpI32X+t/gPYZHGwmAQ+9n52e8lVptg7k="; }; - nativeBuildInputs = [ - # Arviz wants to write a stamp file to the homedir at import time. - # Without $HOME being writable, `pythonImportsCheck` fails. - # https://github.com/arviz-devs/arviz/commit/4db612908f588d89bb5bfb6b83a08ada3d54fd02 - writableTmpDirAsHomeHook - ]; - build-system = [ - packaging - setuptools + flit-core ]; dependencies = [ - h5netcdf - h5py - matplotlib - numpy - pandas - platformdirs - scipy - typing-extensions - xarray - xarray-einstats - ]; + arviz-base + arviz-plots + arviz-stats + ] + ++ arviz-stats.optional-dependencies.xarray; nativeCheckInputs = [ - bokeh - cloudpickle - emcee - ffmpeg - jax - jaxlib - numba - numpyro - # pymc3 (circular dependency) - pyro-ppl - # pystan (not packaged) pytestCheckHook - torchvision - zarr ]; - enabledTestPaths = [ - "arviz/tests/base_tests/" - ]; - - disabledTestPaths = [ - # AttributeError: module 'zarr.storage' has no attribute 'DirectoryStore' - # https://github.com/arviz-devs/arviz/issues/2357 - "arviz/tests/base_tests/test_data_zarr.py::TestDataZarr::test_io_function" - "arviz/tests/base_tests/test_data_zarr.py::TestDataZarr::test_io_method" - ]; - - disabledTests = [ - # TypeError: only 0-dimensional arrays can be converted to Python scalars - "test_deterministic" - "test_mcse_array" - "test_mcse_dataset" - "test_mcse_nan" - "test_multichain_summary_array" - "test_numba_mcse" - "test_plot_mcse" - - # Tests require network access - "test_plot_ppc_transposed" - "test_plot_separation" - "test_plot_trace_legend" - "test_cov" - - # countourpy is not available at the moment - "test_plot_kde" - "test_plot_kde_2d" - "test_plot_pair" - ]; - - # Tests segfault on darwin - doCheck = !stdenv.hostPlatform.isDarwin; - pythonImportsCheck = [ "arviz" ]; meta = { From 06649792db3251091a4eb591548eaf7d1a8c219b Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Mon, 4 May 2026 12:04:41 +0000 Subject: [PATCH 5/6] python3Packages.pytensor: 2.38.3 -> 3.0.2 Diff: https://github.com/pymc-devs/pytensor/compare/rel-2.38.3...rel-3.0.2 Changelog: https://github.com/pymc-devs/pytensor/releases/tag/rel-3.0.2 --- .../python-modules/pytensor/default.nix | 18 ++++-------------- 1 file changed, 4 insertions(+), 14 deletions(-) diff --git a/pkgs/development/python-modules/pytensor/default.nix b/pkgs/development/python-modules/pytensor/default.nix index 33648a0dc369..47080bc41830 100644 --- a/pkgs/development/python-modules/pytensor/default.nix +++ b/pkgs/development/python-modules/pytensor/default.nix @@ -33,8 +33,9 @@ buildPythonPackage (finalAttrs: { pname = "pytensor"; - version = "2.38.3"; + version = "3.0.2"; pyproject = true; + __structuredAttrs = true; src = fetchFromGitHub { owner = "pymc-devs"; @@ -43,7 +44,7 @@ buildPythonPackage (finalAttrs: { postFetch = '' sed -i 's/git_refnames = "[^"]*"/git_refnames = " (tag: ${finalAttrs.src.tag})"/' $out/pytensor/_version.py ''; - hash = "sha256-+yfALDxNIjQUgzEJ3/ZtvLIGNmx6bPYRQ9zGXFbcMNM="; + hash = "sha256-JPBNqgNrd892aVVEVipehMjZwQ4fktf9/gM/eAohD3Y="; }; build-system = [ @@ -84,18 +85,7 @@ buildPythonPackage (finalAttrs: { rm -rf pytensor ''; - disabledTests = [ - # TypeError: jax_funcified_fgraph() takes 2 positional arguments but 3 were given - "test_jax_Reshape_shape_graph_input" - - # AssertionError: equal_computations failed - "test_infer_shape_db_handles_xtensor_lowering" - - # Crashes with jax>=0.9.0 - # in .../jax/_src/compiler.py", line 362 in backend_compile_and_load - "test_higher_order_derivatives" - ] - ++ lib.optionals stdenv.hostPlatform.isDarwin [ + disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [ # Numerical assertion error # tests.unittest_tools.WrongValue: WrongValue "test_op_sd" From f87cee814a2e483338b596f6b43cf8db1d6aa9d7 Mon Sep 17 00:00:00 2001 From: Gaetan Lepage Date: Wed, 13 May 2026 08:53:25 +0000 Subject: [PATCH 6/6] python3Packages.pymc: 5.28.5 -> 6.0.0 Diff: https://github.com/pymc-devs/pymc/compare/v5.28.5...v6.0.0 Changelog: https://github.com/pymc-devs/pymc/releases/tag/v6.0.0 --- pkgs/development/python-modules/pymc/default.nix | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/pkgs/development/python-modules/pymc/default.nix b/pkgs/development/python-modules/pymc/default.nix index 8be9f8e322c9..3b351ccaabd7 100644 --- a/pkgs/development/python-modules/pymc/default.nix +++ b/pkgs/development/python-modules/pymc/default.nix @@ -2,7 +2,6 @@ lib, buildPythonPackage, fetchFromGitHub, - writableTmpDirAsHomeHook, # build-system setuptools, @@ -23,7 +22,7 @@ buildPythonPackage (finalAttrs: { pname = "pymc"; - version = "5.28.5"; + version = "6.0.0"; pyproject = true; __structuredAttrs = true; @@ -31,7 +30,7 @@ buildPythonPackage (finalAttrs: { owner = "pymc-devs"; repo = "pymc"; tag = "v${finalAttrs.version}"; - hash = "sha256-neySWgFxnebW9v0Fa6+ZaxQeFQ0v6wpRvQrBj0zOHJs="; + hash = "sha256-djioOgEtfKxXcbxYJGjPjCQOxcXi54xXNowJJhUWjE4="; }; build-system = [ @@ -52,13 +51,6 @@ buildPythonPackage (finalAttrs: { typing-extensions ]; - nativeBuildInputs = [ - # Arviz (imported by pymc) wants to write a stamp file to the homedir at import time. - # Without $HOME being writable, `pythonImportsCheck` fails. - # https://github.com/arviz-devs/arviz/commit/4db612908f588d89bb5bfb6b83a08ada3d54fd02 - writableTmpDirAsHomeHook - ]; - # The test suite is computationally intensive and test failures are not # indicative for package usability hence tests are disabled by default. doCheck = false;