From 25eb3afcd683bf051758c1d5135d0fb84ee61238 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:00:20 +0000 Subject: [PATCH 01/10] Bump scipy from 1.14.1 to 1.15.0 Bumps [scipy](https://github.com/scipy/scipy) from 1.14.1 to 1.15.0. - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](https://github.com/scipy/scipy/compare/v1.14.1...v1.15.0) --- updated-dependencies: - dependency-name: scipy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 74aeec798..0d60e4292 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,7 @@ dependencies = [ "pyiron_snippets==0.1.4", "pylammpsmpi==0.2.26", "pyscal3==3.2.7", - "scipy==1.14.1", + "scipy==1.15.0", "scikit-learn==1.6.0", "seekpath==2.1.0", "spglib==2.5.0", From 718fa4760310e20bc79b96496d983bda181dcc23 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 8 Jan 2025 19:03:54 +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 dfe2613b3..9905096c0 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -22,7 +22,7 @@ dependencies: - pylammpsmpi =0.2.26 - pyscal3 =3.2.7 - scikit-learn =1.6.0 -- scipy =1.14.1 +- scipy =1.15.0 - seekpath =2.1.0 - spglib =2.5.0 - structuretoolkit =0.0.29 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 5a7222c91..7a38fb2c9 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -20,7 +20,7 @@ dependencies: - pylammpsmpi =0.2.26 - pyscal3 =3.2.7 - scikit-learn =1.6.0 -- scipy =1.14.1 +- scipy =1.15.0 - seekpath =2.1.0 - spglib =2.5.0 - structuretoolkit =0.0.29 diff --git a/binder/environment.yml b/binder/environment.yml index 1dc7bff5c..546c6164b 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -18,7 +18,7 @@ dependencies: - pylammpsmpi =0.2.26 - pyscal3 =3.2.7 - scikit-learn =1.6.0 -- scipy =1.14.1 +- scipy =1.15.0 - seekpath =2.1.0 - spglib =2.5.0 - structuretoolkit =0.0.29 From 2cd99ec8bcbda943c0c7b2c45f4bcfed0de5cb05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 20:37:14 +0100 Subject: [PATCH 03/10] fix tests --- tests/sphinx/test_base.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index 47ebc80e5..36ae29174 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -157,7 +157,7 @@ def test_write_input(self): "\t}\n", "}\n", "structure {\n", - "\tcell = [[4.913287924027003, 0.0, 0.0], [0.0, 4.913287924027003, 0.0], [0.0, 0.0, 4.913287924027003]];\n", + "\tcell = [[4.913287927360235, 0.0, 0.0], [0.0, 4.913287927360235, 0.0], [0.0, 0.0, 4.913287927360235]];\n", "\tspecies {\n", '\t\telement = "Fe";\n', "\t\tatom {\n", @@ -167,7 +167,7 @@ def test_write_input(self): "\t\t}\n", "\t\tatom {\n", '\t\t\tlabel = "spin_0.5";\n', - "\t\t\tcoords = [2.4566439620135014, 2.4566439620135014, 2.4566439620135014];\n", + "\t\t\tcoords = [2.4566439636801176, 2.4566439636801176, 2.4566439636801176];\n", "\t\t}\n", "\t}\n", "\tsymmetry {\n", @@ -590,7 +590,7 @@ def test_write_structure(self): "\t}\n", "\tatom {\n", '\t\tlabel = "spin_0.5";\n', - "\t\tcoords = [2.4566439620135014, 2.4566439620135014, 2.4566439620135014];\n", + "\t\tcoords = [2.4566439636801176, 2.4566439636801176, 2.4566439636801176];\n", "\t}\n", "}\n", "symmetry {\n", From 4456993a9dadab5e8c8afa7632f9b25055e5106b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 20:54:58 +0100 Subject: [PATCH 04/10] another fix --- tests/sphinx/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index 36ae29174..c31ecdc69 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -177,7 +177,7 @@ def test_write_input(self): "\t}\n", "}\n", "basis {\n", - "\teCut = 24.989539079445393;\n", + "\teCut = 24.98953907945182;\n", "\tkPoint {\n", "\t\tcoords = [0.5, 0.5, 0.5];\n", "\t\tweight = 1;\n", From 71141c1459b4b8b2b9554107352598bb971d24b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 21:01:47 +0100 Subject: [PATCH 05/10] and another --- tests/sphinx/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index c31ecdc69..ba0640943 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -211,7 +211,7 @@ def test_write_input(self): "\tscfDiag {\n", "\t\trhoMixing = 1.0;\n", "\t\tspinMixing = 1.0;\n", - "\t\tdEnergy = 3.674932217565499e-06;\n", + "\t\tdEnergy = 3.6749322175664444e-06;\n", "\t\tmaxSteps = 100;\n", "\t\tpreconditioner {\n", "\t\t\ttype = KERKER;\n", From 8e8456b80d80493fb267ff7c2a283424e37809c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 21:58:31 +0100 Subject: [PATCH 06/10] compare as dict --- tests/sphinx/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index ba0640943..fba914744 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -383,7 +383,7 @@ def test_get_scf_group(self): self.sphinx_band_structure.input["nSloppy"] = 0 self.sphinx_band_structure.input["WriteWaves"] = False test_scf = self.sphinx_band_structure.get_scf_group() - self.assertEqual(test_scf, ref_scf) + self.assertEqual(test_scf.to_builtin(), ref_scf) def test_check_setup(self): self.assertFalse(self.sphinx.check_setup()) From 2de5c18a5999153ada0959650809b15a070441eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 22:04:26 +0100 Subject: [PATCH 07/10] compare as dict --- tests/sphinx/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index fba914744..23290d59e 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -363,7 +363,7 @@ def test_get_scf_group(self): "maxSteps": "100", "blockCCG": {}, } - self.assertEqual(test_scf, ref_scf) + self.assertEqual(test_scf.to_builtin(), ref_scf) ref_scf = { "rhoMixing": "1.0", From 4ed1e483b1b3aa16ff8e2bc81b7a961b0e77421e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 22:11:50 +0100 Subject: [PATCH 08/10] more fixes --- tests/sphinx/test_base.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index 23290d59e..f00730cac 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -363,13 +363,13 @@ def test_get_scf_group(self): "maxSteps": "100", "blockCCG": {}, } - self.assertEqual(test_scf.to_builtin(), ref_scf) + self.assertEqual(test_scf, ref_scf) ref_scf = { "rhoMixing": "1.0", "spinMixing": "1.0", "nPulaySteps": "0", - "dEnergy": 3.674932217565499e-06, + "dEnergy": 3.6749322175664444e-06, "maxSteps": "100", "preconditioner": {"type": 0}, "blockCCG": {"maxStepsCCG": 0, "blockSize": 0, "nSloppy": 0}, @@ -383,7 +383,7 @@ def test_get_scf_group(self): self.sphinx_band_structure.input["nSloppy"] = 0 self.sphinx_band_structure.input["WriteWaves"] = False test_scf = self.sphinx_band_structure.get_scf_group() - self.assertEqual(test_scf.to_builtin(), ref_scf) + self.assertEqual(test_scf, ref_scf) def test_check_setup(self): self.assertFalse(self.sphinx.check_setup()) From 4307a50ffdb78762d2f4a96c96d80ea8c7caf2b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 22:23:47 +0100 Subject: [PATCH 09/10] consistency --- tests/sphinx/test_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/sphinx/test_base.py b/tests/sphinx/test_base.py index f00730cac..cf0839489 100644 --- a/tests/sphinx/test_base.py +++ b/tests/sphinx/test_base.py @@ -354,7 +354,7 @@ def test_get_scf_group(self): ref_scf = { "rhoMixing": "1.0", "spinMixing": "1.0", - "dEnergy": 3.674932217565499e-06, + "dEnergy": 3.6749322175664444e-06, "preconditioner": { "type": "KERKER", "scaling": 1.0, From b7b0bb293aca93cf4d37434c67749587f1f818c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 8 Jan 2025 22:30:44 +0100 Subject: [PATCH 10/10] update lower bound --- .ci_support/environment-old.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-old.yml b/.ci_support/environment-old.yml index 8448ba2e7..189b7183b 100644 --- a/.ci_support/environment-old.yml +++ b/.ci_support/environment-old.yml @@ -3,7 +3,7 @@ channels: dependencies: - aimsgb =1.0.2 - ase =3.22.1 -- atomistics =0.1.27 +- atomistics =0.1.33 - defusedxml =0.7.0 - h5py =3.9.0 - matplotlib-base =3.5.3 @@ -20,7 +20,7 @@ dependencies: - monty =2024.3.31 - pyxtal =0.6.1 - scikit-learn =1.2.1 -- scipy =1.11.1 +- scipy =1.15.0 - seekpath =1.9.5 - spglib =2.0.2 -- structuretoolkit =0.0.27 +- structuretoolkit =0.0.29