python312Packages.monty: cleanup & add missing test dependency (#382662)
This commit is contained in:
Nick Cao
@@ -2,18 +2,37 @@
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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msgpack,
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numpy,
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pandas,
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pydantic,
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pymongo,
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pytestCheckHook,
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pythonOlder,
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ruamel-yaml,
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# build-system
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setuptools,
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setuptools-scm,
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# dependencies
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msgpack,
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ruamel-yaml,
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# optional-dependencies
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coverage,
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pymongo,
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pytest,
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pytest-cov,
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types-requests,
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sphinx,
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sphinx-rtd-theme,
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orjson,
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pandas,
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pydantic,
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pint,
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torch,
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tqdm,
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invoke,
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requests,
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# tests
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ipython,
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numpy,
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pytestCheckHook,
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}:
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buildPythonPackage rec {
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@@ -21,8 +40,6 @@ buildPythonPackage rec {
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version = "2025.1.9";
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pyproject = true;
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disabled = pythonOlder "3.9";
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src = fetchFromGitHub {
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owner = "materialsvirtuallab";
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repo = "monty";
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@@ -30,44 +47,63 @@ buildPythonPackage rec {
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hash = "sha256-+9nxuvrtl04Fb+GQJUn+fxg4sq1pXK59UkUTkKH16YQ=";
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};
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postPatch = ''
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substituteInPlace tests/test_os.py \
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--replace 'self.assertEqual("/usr/bin/find", which("/usr/bin/find"))' '#'
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'';
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nativeBuildInputs = [
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build-system = [
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setuptools
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setuptools-scm
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];
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propagatedBuildInputs = [
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dependencies = [
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msgpack
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ruamel-yaml
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tqdm
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];
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optional-dependencies = rec {
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ci = [
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coverage
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pymongo
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pytest
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pytest-cov
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types-requests
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] ++ optional;
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dev = [ ipython ];
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docs = [
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sphinx
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sphinx-rtd-theme
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];
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json =
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[
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orjson
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pandas
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pydantic
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pymongo
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]
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++ lib.optionals (pythonOlder "3.13") [
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pint
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torch
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];
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multiprocessing = [ tqdm ];
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optional = dev ++ json ++ multiprocessing ++ serialization;
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serialization = [ msgpack ];
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task = [
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invoke
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requests
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];
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};
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nativeCheckInputs = [
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ipython
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numpy
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pandas
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pydantic
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pymongo
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pytestCheckHook
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torch
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tqdm
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];
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pythonImportsCheck = [ "monty" ];
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disabledTests = [
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# Test file was removed and re-added after 2022.9.9
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"test_reverse_readfile_gz"
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"test_Path_objects"
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"test_zopen"
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"test_zpath"
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# flaky, precision/rounding error
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"TestJson.test_datetime"
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];
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meta = with lib; {
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meta = {
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description = "Serves as a complement to the Python standard library by providing a suite of tools to solve many common problems";
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longDescription = "
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Monty implements supplementary useful functions for Python that are not part of the
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@@ -75,8 +111,8 @@ buildPythonPackage rec {
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patterns such as singleton and cached_class, and many more.
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";
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homepage = "https://github.com/materialsvirtuallab/monty";
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changelog = "https://github.com/materialsvirtuallab/monty/releases/tag/${src.tag}";
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license = licenses.mit;
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maintainers = with maintainers; [ psyanticy ];
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changelog = "https://github.com/materialsvirtuallab/monty/releases/tag/v${version}";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ psyanticy ];
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};
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}
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@@ -1,46 +1,65 @@
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{
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lib,
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ase,
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stdenv,
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buildPythonPackage,
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cython,
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pythonAtLeast,
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fetchFromGitHub,
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# build-system
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setuptools,
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# nativeBuildInputs
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cython,
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glibcLocales,
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# dependencies
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joblib,
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matplotlib,
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monty,
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networkx,
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oldest-supported-numpy,
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numpy,
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palettable,
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pandas,
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plotly,
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pybtex,
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pydispatcher,
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pytest-xdist,
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pytestCheckHook,
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pythonOlder,
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requests,
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ruamel-yaml,
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scipy,
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seekpath,
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setuptools,
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spglib,
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sympy,
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tabulate,
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tqdm,
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uncertainties,
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# optional-dependencies
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netcdf4,
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ase,
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pytest,
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pytest-cov,
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invoke,
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sphinx,
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sphinx-rtd-theme,
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numba,
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vtk,
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# tests
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addBinToPathHook,
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pytest-xdist,
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pytestCheckHook,
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}:
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buildPythonPackage rec {
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pname = "pymatgen";
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version = "2025.1.9";
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version = "2025.1.24";
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pyproject = true;
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disabled = pythonOlder "3.8";
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disabled = pythonAtLeast "3.13";
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src = fetchFromGitHub {
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owner = "materialsproject";
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repo = "pymatgen";
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tag = "v${version}";
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hash = "sha256-mbXnuqgve8YjktJ2PSaMNk8ADioaGe+W12bYm/chpzE=";
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hash = "sha256-0P3/M6VI2RKPArMwXD95sjW7dYOTXxUeu4tOliN0IGk=";
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};
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build-system = [ setuptools ];
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@@ -51,49 +70,107 @@ buildPythonPackage rec {
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];
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dependencies = [
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joblib
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matplotlib
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monty
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networkx
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oldest-supported-numpy
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numpy
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palettable
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pandas
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plotly
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pybtex
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pydispatcher
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requests
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ruamel-yaml
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scipy
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spglib
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sympy
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tabulate
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tqdm
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uncertainties
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];
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optional-dependencies = {
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abinit = [ netcdf4 ];
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ase = [ ase ];
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joblib = [ joblib ];
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seekpath = [ seekpath ];
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ci = [
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pytest
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pytest-cov
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# pytest-split
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];
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docs = [
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invoke
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sphinx
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# sphinx_markdown_builder
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sphinx-rtd-theme
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];
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electronic_structure = [
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# fdint
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];
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mlp = [
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# chgnet
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# matgl
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];
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numba = [ numba ];
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vis = [ vtk ];
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};
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pythonImportsCheck = [ "pymatgen" ];
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nativeCheckInputs = [
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addBinToPathHook
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pytestCheckHook
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pytest-xdist
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] ++ lib.flatten (builtins.attrValues optional-dependencies);
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preCheck = ''
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preCheck =
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# ensure tests can find these
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export PMG_TEST_FILES_DIR="$(realpath ./tests/files)"
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# some tests cover the command-line scripts
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export PATH=$out/bin:$PATH
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'';
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''
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export PMG_TEST_FILES_DIR="$(realpath ./tests/files)"
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'';
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pythonImportsCheck = [ "pymatgen" ];
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disabledTests =
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[
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# Flaky
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"test_numerical_eos_values"
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"test_pca"
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"test_static_si_no_kgrid"
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"test_thermal_conductivity"
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]
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++ lib.optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [
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# AttributeError: 'NoneType' object has no attribute 'items'
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"test_mean_field"
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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# Fatal Python error: Aborted
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# matplotlib/backend_bases.py", line 2654 in create_with_canvas
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"test_angle"
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"test_as_dict_from_dict"
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"test_attributes"
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"test_basic"
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"test_core_state_eigen"
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"test_eos_func"
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"test_get_info_cohps_to_neighbors"
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"test_get_plot"
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"test_get_point_group_operations"
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"test_matplotlib_plots"
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"test_ph_plot_w_gruneisen"
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"test_plot"
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"test_proj_bandstructure_plot"
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"test_structure"
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"test_structure_environments"
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];
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meta = with lib; {
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disabledTestPaths = lib.optionals stdenv.hostPlatform.isDarwin [
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# Crash when running the pmg command
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# Critical error: required built-in appearance SystemAppearance not found
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"tests/cli/test_pmg_plot.py"
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];
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meta = {
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description = "Robust materials analysis code that defines core object representations for structures and molecules";
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homepage = "https://pymatgen.org/";
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changelog = "https://github.com/materialsproject/pymatgen/releases/tag/${src.tag}";
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license = licenses.mit;
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maintainers = with maintainers; [ psyanticy ];
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changelog = "https://github.com/materialsproject/pymatgen/releases/tag/v${version}";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ psyanticy ];
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};
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}
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