python3Packages.arviz: 0.23.4 -> 1.1.0 (#496016)
This commit is contained in:
Nick Cao
@@ -7,6 +7,7 @@
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flit-core,
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# dependencies
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lazy-loader,
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numpy,
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typing-extensions,
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xarray,
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@@ -23,14 +24,15 @@
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buildPythonPackage (finalAttrs: {
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pname = "arviz-base";
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version = "0.8.2";
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version = "1.1.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "arviz-devs";
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repo = "arviz-base";
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tag = "v${finalAttrs.version}";
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hash = "sha256-g2DmhYqO9dgvDZwAXXSDFn5wHU0BvxXNgOzk6mmEmsw=";
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hash = "sha256-/v1LPgM2rDw9Z0en0MYGELGiRlmwQX4ILKsBEqOhhSs=";
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};
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build-system = [
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@@ -38,6 +40,7 @@ buildPythonPackage (finalAttrs: {
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];
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dependencies = [
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lazy-loader
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numpy
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typing-extensions
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xarray
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@@ -41,14 +41,15 @@
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buildPythonPackage (finalAttrs: {
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pname = "arviz-plots";
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version = "0.8.0";
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version = "1.1.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "arviz-devs";
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repo = "arviz-plots";
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tag = "v${finalAttrs.version}";
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hash = "sha256-x4UoUSKz+MAI082afnGhfoy2ad/hPK89Y1B2oEnxhsg=";
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hash = "sha256-ti1wD/aPNCk59wkad+xkvIKTB2Wkupovlo0Hg0YqK1o=";
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};
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build-system = [
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@@ -38,14 +38,15 @@
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buildPythonPackage (finalAttrs: {
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pname = "arviz-stats";
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version = "0.8.0";
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version = "1.1.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "arviz-devs";
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repo = "arviz-stats";
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tag = "v${finalAttrs.version}";
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hash = "sha256-FAZXnKxNb/DPkcpIRJRIzSbthS8Djf75hd5WMxegdhY=";
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hash = "sha256-81duRavbPUKsqTWaeD0G6ieWLtyoZm7sRk06QkG5dKQ=";
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};
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build-system = [
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@@ -1,135 +1,48 @@
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{
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lib,
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stdenv,
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buildPythonPackage,
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fetchFromGitHub,
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# nativeBuildInputs
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writableTmpDirAsHomeHook,
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# build-system
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packaging,
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setuptools,
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flit-core,
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# dependencies
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h5netcdf,
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matplotlib,
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numpy,
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pandas,
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platformdirs,
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scipy,
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typing-extensions,
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xarray,
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xarray-einstats,
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arviz-base,
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arviz-plots,
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arviz-stats,
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# tests
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bokeh,
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cloudpickle,
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emcee,
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ffmpeg,
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h5py,
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jax,
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jaxlib,
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numba,
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numpyro,
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#, pymc3 (circular dependency)
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pyro-ppl,
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#, pystan (not packaged)
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pytestCheckHook,
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torchvision,
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zarr,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "arviz";
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version = "0.23.4";
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version = "1.1.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "arviz-devs";
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repo = "arviz";
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tag = "v${finalAttrs.version}";
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hash = "sha256-YQ5i+CSuznbWAQ29jgqrOs+zgOAS5U4wSNEIquJQkvY=";
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hash = "sha256-M9tj1X65hiLpI32X+t/gPYZHGwmAQ+9n52e8lVptg7k=";
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};
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nativeBuildInputs = [
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# Arviz wants to write a stamp file to the homedir at import time.
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# Without $HOME being writable, `pythonImportsCheck` fails.
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# https://github.com/arviz-devs/arviz/commit/4db612908f588d89bb5bfb6b83a08ada3d54fd02
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writableTmpDirAsHomeHook
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];
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build-system = [
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packaging
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setuptools
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flit-core
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];
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dependencies = [
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h5netcdf
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h5py
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matplotlib
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numpy
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pandas
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platformdirs
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scipy
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typing-extensions
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xarray
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xarray-einstats
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];
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arviz-base
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arviz-plots
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arviz-stats
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]
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++ arviz-stats.optional-dependencies.xarray;
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nativeCheckInputs = [
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bokeh
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cloudpickle
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emcee
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ffmpeg
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jax
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jaxlib
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numba
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numpyro
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# pymc3 (circular dependency)
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pyro-ppl
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# pystan (not packaged)
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pytestCheckHook
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torchvision
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zarr
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];
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enabledTestPaths = [
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"arviz/tests/base_tests/"
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];
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disabledTestPaths = [
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# AttributeError: module 'zarr.storage' has no attribute 'DirectoryStore'
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# https://github.com/arviz-devs/arviz/issues/2357
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"arviz/tests/base_tests/test_data_zarr.py::TestDataZarr::test_io_function"
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"arviz/tests/base_tests/test_data_zarr.py::TestDataZarr::test_io_method"
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];
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disabledTests = [
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# TypeError: only 0-dimensional arrays can be converted to Python scalars
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"test_deterministic"
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"test_mcse_array"
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"test_mcse_dataset"
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"test_mcse_nan"
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"test_multichain_summary_array"
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"test_numba_mcse"
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"test_plot_mcse"
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# Tests require network access
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"test_plot_ppc_transposed"
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"test_plot_separation"
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"test_plot_trace_legend"
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"test_cov"
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# countourpy is not available at the moment
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"test_plot_kde"
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"test_plot_kde_2d"
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"test_plot_pair"
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];
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# Tests segfault on darwin
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doCheck = !stdenv.hostPlatform.isDarwin;
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pythonImportsCheck = [ "arviz" ];
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meta = {
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@@ -2,7 +2,6 @@
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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writableTmpDirAsHomeHook,
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# build-system
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setuptools,
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@@ -23,7 +22,7 @@
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buildPythonPackage (finalAttrs: {
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pname = "pymc";
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version = "5.28.5";
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version = "6.0.0";
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pyproject = true;
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__structuredAttrs = true;
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@@ -31,7 +30,7 @@ buildPythonPackage (finalAttrs: {
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owner = "pymc-devs";
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repo = "pymc";
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tag = "v${finalAttrs.version}";
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hash = "sha256-neySWgFxnebW9v0Fa6+ZaxQeFQ0v6wpRvQrBj0zOHJs=";
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hash = "sha256-djioOgEtfKxXcbxYJGjPjCQOxcXi54xXNowJJhUWjE4=";
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};
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build-system = [
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@@ -52,13 +51,6 @@ buildPythonPackage (finalAttrs: {
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typing-extensions
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];
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nativeBuildInputs = [
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# Arviz (imported by pymc) wants to write a stamp file to the homedir at import time.
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# Without $HOME being writable, `pythonImportsCheck` fails.
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# https://github.com/arviz-devs/arviz/commit/4db612908f588d89bb5bfb6b83a08ada3d54fd02
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writableTmpDirAsHomeHook
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];
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# The test suite is computationally intensive and test failures are not
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# indicative for package usability hence tests are disabled by default.
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doCheck = false;
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@@ -33,8 +33,9 @@
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buildPythonPackage (finalAttrs: {
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pname = "pytensor";
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version = "2.38.3";
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version = "3.0.2";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "pymc-devs";
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@@ -43,7 +44,7 @@ buildPythonPackage (finalAttrs: {
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postFetch = ''
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sed -i 's/git_refnames = "[^"]*"/git_refnames = " (tag: ${finalAttrs.src.tag})"/' $out/pytensor/_version.py
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'';
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hash = "sha256-+yfALDxNIjQUgzEJ3/ZtvLIGNmx6bPYRQ9zGXFbcMNM=";
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hash = "sha256-JPBNqgNrd892aVVEVipehMjZwQ4fktf9/gM/eAohD3Y=";
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};
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build-system = [
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@@ -84,18 +85,7 @@ buildPythonPackage (finalAttrs: {
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rm -rf pytensor
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'';
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disabledTests = [
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# TypeError: jax_funcified_fgraph() takes 2 positional arguments but 3 were given
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"test_jax_Reshape_shape_graph_input"
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# AssertionError: equal_computations failed
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"test_infer_shape_db_handles_xtensor_lowering"
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# Crashes with jax>=0.9.0
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# in .../jax/_src/compiler.py", line 362 in backend_compile_and_load
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"test_higher_order_derivatives"
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [
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# Numerical assertion error
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# tests.unittest_tools.WrongValue: WrongValue
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"test_op_sd"
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