python3Packages.mace-torch: init at 0.3.16 (#530757)
This commit is contained in:
Peder Bergebakken Sundt
@@ -0,0 +1,78 @@
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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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# build-system
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setuptools,
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setuptools-scm,
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# dependencies
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opt-einsum-fx,
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scipy,
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sympy,
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torch,
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# tests
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pytestCheckHook,
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llvmPackages,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "e3nn";
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version = "0.6.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "e3nn";
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repo = "e3nn";
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tag = finalAttrs.version;
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hash = "sha256-gGl0DiLU8w0jqGWA/ZzvkxdZdZCvtXqtmEEZ2dIwZ2o=";
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};
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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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dependencies = [
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opt-einsum-fx
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scipy
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sympy
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torch
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];
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pythonImportsCheck = [ "e3nn" ];
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nativeCheckInputs = [
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pytestCheckHook
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];
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disabledTests = [
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# RuntimeError: torch.compile does not support compiling torch.jit.script or
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# torch.jit.freeze models directly
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"test_identity"
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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# symbol not found in flat namespace '___kmpc_barrier'
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"test_activation"
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"test_input_weights_jit"
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"test_variance"
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];
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propagatedBuildInputs = lib.optionals stdenv.hostPlatform.isDarwin [
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# Otherwise, torch will fail to include `omp.h`:
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# torch._inductor.exc.InductorError: CppCompileError: C++ compile error OpenMP support not found
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llvmPackages.openmp
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];
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meta = {
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description = "Modular framework for neural networks with Euclidean symmetry";
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homepage = "https://github.com/e3nn/e3nn";
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changelog = "https://github.com/e3nn/e3nn/releases/tag/${finalAttrs.src.tag}";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ GaetanLepage ];
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};
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})
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@@ -0,0 +1,138 @@
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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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||||
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# build-system
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setuptools,
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# dependencies
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ase,
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configargparse,
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e3nn,
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gitpython,
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h5py,
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lmdb,
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matplotlib,
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matscipy,
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numpy,
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opt-einsum,
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orjson,
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pandas,
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prettytable,
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python-hostlist,
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pyyaml,
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torch,
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torch-ema,
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torchmetrics,
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tqdm,
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# tests
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pytestCheckHook,
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writableTmpDirAsHomeHook,
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}:
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buildPythonPackage (finalAttrs: {
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pname = "mace-torch";
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version = "0.3.16";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "acesuit";
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repo = "mace";
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tag = "v${finalAttrs.version}";
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hash = "sha256-sJ/3c7kPe99vkliixUMqqQi2OiL3CCUdlcgpDZ/PUHA=";
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};
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build-system = [
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setuptools
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];
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pythonRelaxDeps = [
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"e3nn"
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];
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dependencies = [
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ase
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configargparse
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e3nn
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gitpython
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h5py
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lmdb
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matplotlib
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matscipy
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numpy
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opt-einsum
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orjson
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pandas
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prettytable
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python-hostlist
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pyyaml
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torch
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torch-ema
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torchmetrics
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tqdm
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];
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pythonImportsCheck = [ "mace" ];
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nativeCheckInputs = [
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pytestCheckHook
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writableTmpDirAsHomeHook
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];
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disabledTests = [
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# _pickle.PickleError: ScriptFunction cannot be pickled
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"test_run_eval_fail_with_wrong_model"
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# ValueError: too many values to unpack (expected 2)
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"test_mace_mp"
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# AssertionError (tensors not close)
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"test_run_train_dipole"
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"test_run_train_dipole_polar"
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# RuntimeError: Model download failed and no local model found
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"test_calculator_descriptor"
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"test_compile_foundation"
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"test_extract_config"
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"test_finite_difference_hessian"
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"test_foundations"
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"test_initial_metrics_replay_head_mh0"
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"test_initial_metrics_replay_head_mh1"
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"test_initial_metrics_replay_head_omol"
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"test_mace_mh_1_elements_subset_reproduces_energy_forces"
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"test_mace_mp_energies"
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"test_mace_mp_stresses"
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"test_mace_off"
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"test_mace_omol_elements_subset_reproduces_energy_forces"
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"test_multi_reference"
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"test_multihead_finetuning_different_formats"
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"test_multihead_finetuning_does_not_modify_default_keyspec"
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"test_potential_energy_and_hessian"
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"test_remove_pt_head_omol_multihead"
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"test_run_train_foundation"
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"test_run_train_foundation_elements"
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"test_run_train_foundation_elements_multihead"
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"test_run_train_foundation_multihead"
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"test_run_train_foundation_multihead_json"
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"test_run_train_foundation_multihead_pseudolabeling"
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"test_run_train_freeze"
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"test_run_train_mh_foundation"
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"test_run_train_soft_freeze"
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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# symbol not found in flat namespace '___kmpc_barrier'
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"test_mace"
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"test_mace_compile_stress"
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];
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meta = {
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description = "Fast and accurate machine learning interatomic potentials with higher order equivariant message passing";
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homepage = "https://github.com/acesuit/mace";
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changelog = "https://github.com/acesuit/mace/releases/tag/${finalAttrs.src.tag}";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ GaetanLepage ];
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};
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})
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@@ -0,0 +1,186 @@
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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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pythonAtLeast,
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fetchpatch,
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# build-system
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meson-python,
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ninja,
|
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numpy,
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# dependencies
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ase,
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||||
packaging,
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||||
scipy,
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||||
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# optional-dependencies
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# cli:
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argcomplete,
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# dislocation:
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atomman,
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nglview,
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ovito,
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||||
# docs:
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||||
jupytext,
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||||
myst-nb,
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numpydoc,
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pydata-sphinx-theme,
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sphinx,
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sphinx-copybutton,
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sphinx-rtd-theme,
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sphinxcontrib-spelling,
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# tests
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pytest-subtests,
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pytest-timeout,
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pytest-xdist,
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sympy,
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# tests
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pytestCheckHook,
|
||||
}:
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buildPythonPackage (finalAttrs: {
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pname = "matscipy";
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version = "1.2.0";
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pyproject = true;
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__structuredAttrs = true;
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src = fetchFromGitHub {
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owner = "libAtoms";
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repo = "matscipy";
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tag = "v${finalAttrs.version}";
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hash = "sha256-XmY13B5S8tXYiUaec9gL6e0E3bSnbaMteHHiX2ij2sw=";
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};
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patches = [
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# API: Fix compatibility with ASE 3.27.0
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# https://github.com/libAtoms/matscipy/pull/301
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(fetchpatch {
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url = "https://github.com/libAtoms/matscipy/commit/6a91a4646e30796abe51ef3efa4b479d4471aae0.patch";
|
||||
hash = "sha256-PH9I+7+nN6fSkugVbxPCs3LqjhP/fQ5NZjiNQ7F70YU=";
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||||
})
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(fetchpatch {
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url = "https://github.com/libAtoms/matscipy/commit/f6478347bbceeab8ec177042b6ed1243e742d55f.patch";
|
||||
hash = "sha256-DKk+1TlP+OngcmycsCIE+7s2h/7wa7Gxv9APbuIAoZg=";
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||||
})
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];
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postPatch =
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# Otherwise the script fails as it can't resolve the version with git
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''
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substituteInPlace discover_version.py \
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--replace-fail \
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"version = get_version_from_git()" \
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"version = '${finalAttrs.version}'"
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''
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# Failed: [pytest] section in setup.cfg files is no longer supported, change to [tool:pytest] instead.
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+ ''
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substituteInPlace setup.cfg \
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--replace-fail \
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"[pytest]" \
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"[tool:pytest]"
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'';
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build-system = [
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||||
# meson
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||||
meson-python
|
||||
ninja
|
||||
numpy
|
||||
];
|
||||
|
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dependencies = [
|
||||
ase
|
||||
numpy
|
||||
packaging
|
||||
scipy
|
||||
];
|
||||
|
||||
optional-dependencies = {
|
||||
cli = [
|
||||
argcomplete
|
||||
];
|
||||
dislocation = [
|
||||
atomman
|
||||
nglview
|
||||
ovito
|
||||
];
|
||||
docs = [
|
||||
jupytext
|
||||
# matscipy
|
||||
myst-nb
|
||||
numpydoc
|
||||
pydata-sphinx-theme
|
||||
sphinx
|
||||
sphinx-copybutton
|
||||
sphinx-rtd-theme
|
||||
sphinxcontrib-spelling
|
||||
];
|
||||
};
|
||||
|
||||
pythonImportsCheck = [ "matscipy" ];
|
||||
|
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nativeCheckInputs = [
|
||||
pytest-subtests
|
||||
pytest-timeout
|
||||
pytest-xdist
|
||||
pytestCheckHook
|
||||
sympy
|
||||
];
|
||||
|
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preCheck = ''
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rm -rf matscipy
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'';
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disabledTestPaths = [
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# The CLI tests look for the source scripts under `../matscipy/cli` relative to the test
|
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# directory, which we remove in `preCheck` so that tests run against the installed package.
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"tests/test_electrochemistry_cli.py"
|
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]
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++ lib.optionals (pythonAtLeast "3.14") [
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# ValueError: cannot resize an array that may be referenced by another object
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"tests/manybody/test_newmb.py"
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"tests/test_neighbours.py"
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||||
];
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||||
|
||||
disabledTests = [
|
||||
# Numerical assertion failure
|
||||
"test_birch_constants"
|
||||
|
||||
# numpy 2 / ase 3.28 incompatibilities in matscipy 1.2.0
|
||||
# `ase.phonons` finite-difference reference no longer matches
|
||||
"test_hessian_monoatomic"
|
||||
"test_hessian_amorphous_alloy"
|
||||
"test_hessian_crystalline_alloy"
|
||||
|
||||
# TypeError: only 0-dimensional arrays can be converted to Python scalars
|
||||
"test_eam_read_write"
|
||||
|
||||
# AttributeError: 'Log' object has no attribute 'close'
|
||||
"test_logger"
|
||||
"test_usage"
|
||||
]
|
||||
++ lib.optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [
|
||||
# AssertionError: assert np.False (numerical precision)
|
||||
"test_fixed_line_atoms"
|
||||
]
|
||||
++ lib.optionals (pythonAtLeast "3.14") [
|
||||
# ValueError: cannot resize an array that may be referenced by another object
|
||||
"test_harmonic_bond"
|
||||
"test_read_molecules_from_atoms"
|
||||
"test_read_molecules_from_lammps_data"
|
||||
"test_read_write_lammps_data"
|
||||
];
|
||||
|
||||
meta = {
|
||||
description = "Materials science with Python at the atomic-scale";
|
||||
homepage = "https://github.com/libAtoms/matscipy";
|
||||
changelog = "https://github.com/libAtoms/matscipy/blob/${finalAttrs.src.tag}/ChangeLog.md";
|
||||
license = lib.licenses.lgpl21Only;
|
||||
maintainers = with lib.maintainers; [ GaetanLepage ];
|
||||
};
|
||||
})
|
||||
@@ -0,0 +1,52 @@
|
||||
{
|
||||
lib,
|
||||
buildPythonPackage,
|
||||
fetchFromGitHub,
|
||||
|
||||
# build-system
|
||||
setuptools,
|
||||
|
||||
# dependencies
|
||||
opt-einsum,
|
||||
torch,
|
||||
|
||||
# tests
|
||||
pytestCheckHook,
|
||||
}:
|
||||
|
||||
buildPythonPackage (finalAttrs: {
|
||||
pname = "opt-einsum-fx";
|
||||
version = "0.1.4";
|
||||
pyproject = true;
|
||||
__structuredAttrs = true;
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "Linux-cpp-lisp";
|
||||
repo = "opt_einsum_fx";
|
||||
tag = "v${finalAttrs.version}";
|
||||
hash = "sha256-HamDghqmdX4Q+4zXQvCly588p3TaYFCSnzgEKLVMXSo=";
|
||||
};
|
||||
|
||||
build-system = [
|
||||
setuptools
|
||||
];
|
||||
|
||||
dependencies = [
|
||||
opt-einsum
|
||||
torch
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "opt_einsum_fx" ];
|
||||
|
||||
nativeCheckInputs = [
|
||||
pytestCheckHook
|
||||
];
|
||||
|
||||
meta = {
|
||||
description = "Einsum optimization using opt_einsum and PyTorch FX graph rewriting";
|
||||
homepage = "https://github.com/Linux-cpp-lisp/opt_einsum_fx";
|
||||
changelog = "https://github.com/Linux-cpp-lisp/opt_einsum_fx/blob/${finalAttrs.src.tag}/CHANGELOG.md";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ GaetanLepage ];
|
||||
};
|
||||
})
|
||||
@@ -0,0 +1,52 @@
|
||||
{
|
||||
lib,
|
||||
buildPythonPackage,
|
||||
fetchFromGitHub,
|
||||
|
||||
# build-system
|
||||
setuptools,
|
||||
setuptools-scm,
|
||||
|
||||
# dependencies
|
||||
attrs,
|
||||
pytest,
|
||||
}:
|
||||
|
||||
buildPythonPackage (finalAttrs: {
|
||||
pname = "pytest-subtests";
|
||||
version = "0.15.0";
|
||||
pyproject = true;
|
||||
__structuredAttrs = true;
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "pytest-dev";
|
||||
repo = "pytest-subtests";
|
||||
tag = "v${finalAttrs.version}";
|
||||
hash = "sha256-KJbTxhheEkvH/Xnje45dSb57526bVoi8N6GSKfUfCYA=";
|
||||
};
|
||||
|
||||
build-system = [
|
||||
setuptools
|
||||
setuptools-scm
|
||||
];
|
||||
|
||||
dependencies = [
|
||||
attrs
|
||||
pytest
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "pytest_subtests" ];
|
||||
|
||||
# The self-tests assert on exact pytest terminal output. pytest 9 ships its
|
||||
# own bundled subtests support and changed how subtest failures are reported,
|
||||
# so these output-matching tests no longer match. The plugin itself works.
|
||||
doCheck = false;
|
||||
|
||||
meta = {
|
||||
description = "Unittest subTest() support and subtests fixture";
|
||||
homepage = "https://github.com/pytest-dev/pytest-subtests";
|
||||
changelog = "https://github.com/pytest-dev/pytest-subtests/blob/${finalAttrs.src.tag}/CHANGELOG.rst";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ GaetanLepage ];
|
||||
};
|
||||
})
|
||||
@@ -0,0 +1,39 @@
|
||||
{
|
||||
lib,
|
||||
buildPythonPackage,
|
||||
fetchurl,
|
||||
|
||||
# build-system
|
||||
setuptools,
|
||||
|
||||
# tests
|
||||
pytestCheckHook,
|
||||
}:
|
||||
buildPythonPackage (finalAttrs: {
|
||||
pname = "python-hostlist";
|
||||
version = "2.3.0";
|
||||
pyproject = true;
|
||||
__structuredAttrs = true;
|
||||
|
||||
src = fetchurl {
|
||||
url = "https://www.nsc.liu.se/~kent/python-hostlist/python_hostlist-${finalAttrs.version}.tar.gz";
|
||||
hash = "sha256-4aCxjlJaX8pXPLmGJ5nxGz8r07p67HDE7Ni5U0G7ceo=";
|
||||
};
|
||||
|
||||
build-system = [
|
||||
setuptools
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "hostlist" ];
|
||||
|
||||
nativeCheckInputs = [
|
||||
pytestCheckHook
|
||||
];
|
||||
|
||||
meta = {
|
||||
description = "Python module for hostlist handling";
|
||||
homepage = "https://www.nsc.liu.se/~kent/python-hostlist/";
|
||||
license = lib.licenses.gpl3Plus;
|
||||
maintainers = with lib.maintainers; [ GaetanLepage ];
|
||||
};
|
||||
})
|
||||
@@ -0,0 +1,58 @@
|
||||
{
|
||||
lib,
|
||||
stdenv,
|
||||
buildPythonPackage,
|
||||
fetchFromGitHub,
|
||||
|
||||
# build-system
|
||||
setuptools,
|
||||
|
||||
# dependencies
|
||||
torch,
|
||||
|
||||
# tests
|
||||
pytestCheckHook,
|
||||
}:
|
||||
|
||||
buildPythonPackage (finalAttrs: {
|
||||
pname = "torch-ema";
|
||||
version = "0.3.0";
|
||||
pyproject = true;
|
||||
__structuredAttrs = true;
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = "fadel";
|
||||
repo = "pytorch_ema";
|
||||
tag = "v${finalAttrs.version}";
|
||||
hash = "sha256-OOF5Lb3HEIBXc1WXoUp7y44pheDc5oX/7L1vTrwNS2o=";
|
||||
};
|
||||
|
||||
build-system = [
|
||||
setuptools
|
||||
];
|
||||
|
||||
dependencies = [
|
||||
torch
|
||||
];
|
||||
|
||||
pythonImportsCheck = [ "torch_ema" ];
|
||||
|
||||
nativeCheckInputs = [
|
||||
pytestCheckHook
|
||||
];
|
||||
|
||||
disabledTests = lib.optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [
|
||||
# aarch64-linux fails cpuinfo test, because /sys/devices/system/cpu/ does not exist in the sandbox:
|
||||
# RuntimeError: Failed to initialize cpuinfo!
|
||||
"test_state_dict_types"
|
||||
"test_to"
|
||||
];
|
||||
|
||||
meta = {
|
||||
description = "Tiny PyTorch library for maintaining a moving average of a collection of parameters";
|
||||
homepage = "https://github.com/fadel/pytorch_ema";
|
||||
changelog = "https://github.com/fadel/pytorch_ema/blob/${finalAttrs.src.tag}/CHANGELOG.md";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ GaetanLepage ];
|
||||
};
|
||||
})
|
||||
@@ -4903,6 +4903,8 @@ self: super: with self; {
|
||||
|
||||
e3-testsuite = callPackage ../development/python-modules/e3-testsuite { };
|
||||
|
||||
e3nn = callPackage ../development/python-modules/e3nn { };
|
||||
|
||||
eagle100 = callPackage ../development/python-modules/eagle100 { };
|
||||
|
||||
earn-e-p1 = callPackage ../development/python-modules/earn-e-p1 { };
|
||||
@@ -9574,6 +9576,8 @@ self: super: with self; {
|
||||
|
||||
macaddress = callPackage ../development/python-modules/macaddress { };
|
||||
|
||||
mace-torch = callPackage ../development/python-modules/mace-torch { };
|
||||
|
||||
macfsevents = callPackage ../development/python-modules/macfsevents { };
|
||||
|
||||
macholib = callPackage ../development/python-modules/macholib { };
|
||||
@@ -9748,6 +9752,8 @@ self: super: with self; {
|
||||
|
||||
matrix-nio = callPackage ../development/python-modules/matrix-nio { };
|
||||
|
||||
matscipy = callPackage ../development/python-modules/matscipy { };
|
||||
|
||||
matter-ble-proxy = callPackage ../development/python-modules/matter-ble-proxy { };
|
||||
|
||||
matter-python-client = callPackage ../development/python-modules/matter-python-client { };
|
||||
@@ -12050,6 +12056,8 @@ self: super: with self; {
|
||||
|
||||
opt-einsum = callPackage ../development/python-modules/opt-einsum { };
|
||||
|
||||
opt-einsum-fx = callPackage ../development/python-modules/opt-einsum-fx { };
|
||||
|
||||
optax = callPackage ../development/python-modules/optax { };
|
||||
|
||||
optiland = callPackage ../development/python-modules/optiland { };
|
||||
@@ -15791,6 +15799,8 @@ self: super: with self; {
|
||||
|
||||
pytest-subtesthack = callPackage ../development/python-modules/pytest-subtesthack { };
|
||||
|
||||
pytest-subtests = callPackage ../development/python-modules/pytest-subtests { };
|
||||
|
||||
pytest-sugar = callPackage ../development/python-modules/pytest-sugar { };
|
||||
|
||||
pytest-tap = callPackage ../development/python-modules/pytest-tap { };
|
||||
@@ -16019,6 +16029,8 @@ self: super: with self; {
|
||||
|
||||
python-homewizard-energy = callPackage ../development/python-modules/python-homewizard-energy { };
|
||||
|
||||
python-hostlist = callPackage ../development/python-modules/python-hostlist { };
|
||||
|
||||
python-hosts = callPackage ../development/python-modules/python-hosts { };
|
||||
|
||||
python-hpilo = callPackage ../development/python-modules/python-hpilo { };
|
||||
@@ -19903,6 +19915,8 @@ self: super: with self; {
|
||||
|
||||
torch-einops-utils = callPackage ../development/python-modules/torch-einops-utils { };
|
||||
|
||||
torch-ema = callPackage ../development/python-modules/torch-ema { };
|
||||
|
||||
torch-geometric = callPackage ../development/python-modules/torch-geometric { };
|
||||
|
||||
torch-memory-saver = callPackage ../development/python-modules/torch-memory-saver { };
|
||||
|
||||
Reference in New Issue
Block a user