From a0add4bd67254be242786e179b7f400849702999 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jul 2024 08:01:45 +0000 Subject: [PATCH 01/10] Bump structuretoolkit from 0.0.26 to 0.0.27 Bumps [structuretoolkit](https://github.com/pyiron/structuretoolkit) from 0.0.26 to 0.0.27. - [Release notes](https://github.com/pyiron/structuretoolkit/releases) - [Commits](https://github.com/pyiron/structuretoolkit/compare/structuretoolkit-0.0.26...structuretoolkit-0.0.27) --- updated-dependencies: - dependency-name: structuretoolkit dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 97306a2d6..8a5cbbdfc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,7 @@ dependencies = [ "scikit-learn==1.5.1", "seekpath==2.1.0", "spglib==2.4.0", - "structuretoolkit==0.0.26", + "structuretoolkit==0.0.27", ] dynamic = ["version"] From 0af45b33aa8d7c7dfc0395da7e16af6ed6b449c3 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 11 Jul 2024 08:02:04 +0000 Subject: [PATCH 02/10] [dependabot skip] Update environment --- .ci_support/environment-docs.yml | 2 +- .ci_support/environment.yml | 2 +- binder/environment.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index f694e5818..fae102892 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -25,6 +25,6 @@ dependencies: - scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.26 +- structuretoolkit =0.0.27 - pyxtal =0.6.2 - jupyter-book =1.0.0 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 0c289c193..a0b45cafa 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -23,5 +23,5 @@ dependencies: - scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.26 +- structuretoolkit =0.0.27 - pyxtal =0.6.2 diff --git a/binder/environment.yml b/binder/environment.yml index a93439874..74be72bb7 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -21,7 +21,7 @@ dependencies: - scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.26 +- structuretoolkit =0.0.27 - pyxtal =0.6.2 - pyiron-data >=0.0.22 - sqsgenerator From 7b937a6cfbc9db350b055318292a708ffbd6afbd Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 11:32:30 +0200 Subject: [PATCH 03/10] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index a0b45cafa..ae43e2b32 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -18,7 +18,7 @@ dependencies: - pyiron_base =0.9.6 - pyiron_snippets =0.1.2 - pylammpsmpi =0.2.20 -- pyscal =2.10.18 +- pyscal3 =3.2.5 - scikit-learn =1.5.1 - scipy =1.14.0 - seekpath =2.1.0 From 1d7081db73c9f09d18a82f6dc432e457fdd7f18f Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 11:32:45 +0200 Subject: [PATCH 04/10] Update environment-docs.yml --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index fae102892..40da10af4 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -20,7 +20,7 @@ dependencies: - pyiron_base =0.9.6 - pyiron_snippets =0.1.2 - pylammpsmpi =0.2.20 -- pyscal =2.10.18 +- pyscal3 =3.2.5 - scikit-learn =1.5.1 - scipy =1.14.0 - seekpath =2.1.0 From d7fa716478f7a1c43a03a2e3e51df26188f4e83d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 11:33:05 +0200 Subject: [PATCH 05/10] Update environment.yml --- binder/environment.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/binder/environment.yml b/binder/environment.yml index 74be72bb7..12b418b79 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -16,7 +16,7 @@ dependencies: - pyiron_base =0.9.6 - pyiron_snippets =0.1.2 - pylammpsmpi =0.2.20 -- pyscal =2.10.18 +- pyscal3 =3.2.5 - scikit-learn =1.5.1 - scipy =1.14.0 - seekpath =2.1.0 @@ -32,4 +32,3 @@ dependencies: - sphinxdft-data - nglview - seaborn -- pyscal From 6fb450d49eea6c6cf0239bd8b95e94defd38f9ed Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 11:33:37 +0200 Subject: [PATCH 06/10] Update pyproject.toml --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 8a5cbbdfc..9a9b00eee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,6 +38,7 @@ dependencies = [ "pyiron_base==0.9.6", "pyiron_snippets==0.1.2", "pylammpsmpi==0.2.20", + "pyscal3==3.2.5", "scipy==1.14.0", "scikit-learn==1.5.1", "seekpath==2.1.0", From 7709781c633b851713dac024287100aa7136448e Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 11:52:40 +0200 Subject: [PATCH 07/10] Update test_pyscal.py --- tests/atomic/structure/test_pyscal.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/atomic/structure/test_pyscal.py b/tests/atomic/structure/test_pyscal.py index ae04cf5b1..1e86f697d 100644 --- a/tests/atomic/structure/test_pyscal.py +++ b/tests/atomic/structure/test_pyscal.py @@ -4,7 +4,7 @@ import unittest import numpy as np -import pyscal.core as pc +import pyscal3 as pc from pyiron_atomistics.atomistics.structure.atoms import Atoms, CrystalStructure from ase.build import bulk from pyiron_atomistics.atomistics.structure.atoms import ase_to_pyiron @@ -25,8 +25,7 @@ def test_simple_system(self): """ Test a simple ase to pyscal conversion """ - sysp = pc.System() - sysp.read_inputfile(self.structure, format="ase") + sysp = pc.System(self.structure, format="ase") self.assertEqual(len(sysp.atoms), 256) def test_steinhardt_parameters_returns(self): From bd2f968456e0a773f06d4b40513e1eea22082623 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 12:06:49 +0200 Subject: [PATCH 08/10] Fix tests --- tests/atomic/structure/test_pyscal.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tests/atomic/structure/test_pyscal.py b/tests/atomic/structure/test_pyscal.py index 1e86f697d..8bb7d9bc0 100644 --- a/tests/atomic/structure/test_pyscal.py +++ b/tests/atomic/structure/test_pyscal.py @@ -209,8 +209,7 @@ def test_analyse_pyscal_cna_adaptive(self): def test_analyse_pyscal_diamond_structure(self): pyscal_keys = [ - 'others', 'fcc', 'hcp', 'bcc', 'ico', - 'cubic diamond', 'cubic diamond 1NN', 'cubic diamond 2NN', + 'others', 'cubic diamond', 'cubic diamond 1NN', 'cubic diamond 2NN', 'hex diamond', 'hex diamond 1NN', 'hex diamond 2NN' ] ovito_keys = [ @@ -233,7 +232,7 @@ def test_analyse_pyscal_diamond_structure(self): self.assertEqual(res_dict_total[pyscal_keys[0]], len(self.ti_hcp)) res_dict_total = self.si_dia.analyse.pyscal_diamond_structure(mode="total", ovito_compatibility=False) self.assertEqual(sum([k in res_dict_total.keys() for k in pyscal_keys]), len(pyscal_keys)) - self.assertEqual(res_dict_total[pyscal_keys[5]], len(self.si_dia)) + self.assertEqual(res_dict_total[pyscal_keys[1]], len(self.si_dia)) res_numeric = self.al_fcc.analyse.pyscal_diamond_structure(mode="numeric", ovito_compatibility=False) self.assertEqual(len(res_numeric), len(self.al_fcc)) @@ -246,7 +245,7 @@ def test_analyse_pyscal_diamond_structure(self): self.assertTrue(all([v == 0 for v in res_numeric])) res_numeric = self.si_dia.analyse.pyscal_diamond_structure(mode="numeric", ovito_compatibility=False) self.assertEqual(len(res_numeric), len(self.si_dia)) - self.assertTrue(all([v == 5 for v in res_numeric])) + self.assertTrue(all([v == 1 for v in res_numeric])) res_str = self.al_fcc.analyse.pyscal_diamond_structure(mode="str", ovito_compatibility=False) self.assertEqual(len(res_str), len(self.al_fcc)) From 32b3fbc23c61c20eb0673d1b09cd2694de23483f Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 12:07:46 +0200 Subject: [PATCH 09/10] Update environment-old.yml --- .ci_support/environment-old.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml index dc4ff7dd2..eb364503b 100644 --- a/.ci_support/environment-old.yml +++ b/.ci_support/environment-old.yml @@ -16,7 +16,7 @@ dependencies: - pyiron_base =0.9.4 - pyiron_snippets =0.1.1 - pylammpsmpi =0.2.18 -- pyscal =2.10.15 +- pyscal3 =3.2.5 - monty =2024.3.31 - pyxtal =0.6.1 - scikit-learn =1.2.1 From eacc9e57b78e8f824d16c7f9216b1a3796be9756 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Thu, 11 Jul 2024 12:14:21 +0200 Subject: [PATCH 10/10] Update environment-old.yml --- .ci_support/environment-old.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml index eb364503b..731d8fae1 100644 --- a/.ci_support/environment-old.yml +++ b/.ci_support/environment-old.yml @@ -23,4 +23,4 @@ dependencies: - scipy =1.11.1 - seekpath =1.9.5 - spglib =2.0.2 -- structuretoolkit =0.0.19 +- structuretoolkit =0.0.27