From 6c7dd3a0a46621a8c6b868e545fe12593d3bddd0 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Thu, 25 Nov 2021 10:53:29 +0800 Subject: [PATCH 1/6] skip the UTs on machines that do not have rdkit. fix bug in mirror-gitee --- .github/workflows/mirror_gitee.yml | 1 + tests/test_amber_sqm.py | 6 ++++++ tests/test_bond_order_system.py | 12 ++++++++++-- 3 files changed, 17 insertions(+), 2 deletions(-) diff --git a/.github/workflows/mirror_gitee.yml b/.github/workflows/mirror_gitee.yml index 97ea2e48a..985674cf5 100644 --- a/.github/workflows/mirror_gitee.yml +++ b/.github/workflows/mirror_gitee.yml @@ -8,6 +8,7 @@ concurrency: jobs: git-mirror: + if: github.repository_owner == 'deepmodeling' runs-on: ubuntu-latest steps: - uses: wearerequired/git-mirror-action@v1 diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index dc98a3167..d78972a99 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -4,6 +4,11 @@ from context import dpdata from comp_sys import CompSys, CompLabeledSys, IsNoPBC +try: + from dpdata import BondOrderSystem + skip_bond_order_system = False +except ImportError: + skip_bond_order_system = True class TestAmberSqmOut(unittest.TestCase, CompSys, IsNoPBC): def setUp (self) : @@ -33,6 +38,7 @@ def tearDown(self) : if os.path.exists('tmp.sqm.forces'): shutil.rmtree('tmp.sqm.forces') +@unittest.skipIf(skip_bond_order_system, "dpdata do not have BondOrderSystem") class TestAmberSqmIn(unittest.TestCase): def setUp(self): self.system = dpdata.BondOrderSystem("amber/methane.mol", fmt='mol', type_map=['H','C']) diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py index 06928cde2..a686e345d 100644 --- a/tests/test_bond_order_system.py +++ b/tests/test_bond_order_system.py @@ -2,12 +2,20 @@ import unittest from context import dpdata import glob -from rdkit import Chem -from rdkit.Chem import AllChem +try: + from rdkit import Chem + from rdkit.Chem import AllChem + from dpdata import BondOrderSystem + skip_bond_order_system = False +except ImportError: + skip_bond_order_system = True + import shutil import numpy as np from copy import deepcopy + +@unittest.skipIf(skip_bond_order_system, "dpdata do not have BondOrderSystem") class TestBondOrderSystem(unittest.TestCase): def test_from_rdkit_mol(self): From 407d43e80bed807e426704f2f0c0bd1128bc40dd Mon Sep 17 00:00:00 2001 From: Han Wang Date: Thu, 25 Nov 2021 14:55:39 +0800 Subject: [PATCH 2/6] Update test_amber_sqm.py --- tests/test_amber_sqm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index d78972a99..d5b5cbe50 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -38,7 +38,7 @@ def tearDown(self) : if os.path.exists('tmp.sqm.forces'): shutil.rmtree('tmp.sqm.forces') -@unittest.skipIf(skip_bond_order_system, "dpdata do not have BondOrderSystem") +@unittest.skipIf(skip_bond_order_system, "dpdata does not have BondOrderSystem") class TestAmberSqmIn(unittest.TestCase): def setUp(self): self.system = dpdata.BondOrderSystem("amber/methane.mol", fmt='mol', type_map=['H','C']) From 8ef5480faea85ae064555d200c8d7d3c2848acbf Mon Sep 17 00:00:00 2001 From: Han Wang Date: Thu, 25 Nov 2021 14:56:31 +0800 Subject: [PATCH 3/6] Update test_bond_order_system.py --- tests/test_bond_order_system.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py index a686e345d..3850b62c7 100644 --- a/tests/test_bond_order_system.py +++ b/tests/test_bond_order_system.py @@ -15,7 +15,7 @@ from copy import deepcopy -@unittest.skipIf(skip_bond_order_system, "dpdata do not have BondOrderSystem") +@unittest.skipIf(skip_bond_order_system, "dpdata does not have BondOrderSystem. One may install rdkit to fix.") class TestBondOrderSystem(unittest.TestCase): def test_from_rdkit_mol(self): From 3a7dd7d7509d4b94d37d531cdf6273b394e7f34a Mon Sep 17 00:00:00 2001 From: Han Wang Date: Thu, 25 Nov 2021 14:56:46 +0800 Subject: [PATCH 4/6] Update test_amber_sqm.py --- tests/test_amber_sqm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index d5b5cbe50..3da76831a 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -38,7 +38,7 @@ def tearDown(self) : if os.path.exists('tmp.sqm.forces'): shutil.rmtree('tmp.sqm.forces') -@unittest.skipIf(skip_bond_order_system, "dpdata does not have BondOrderSystem") +@unittest.skipIf(skip_bond_order_system, "dpdata does not have BondOrderSystem. One may install rdkit to fix.") class TestAmberSqmIn(unittest.TestCase): def setUp(self): self.system = dpdata.BondOrderSystem("amber/methane.mol", fmt='mol', type_map=['H','C']) From 622551191cdb859ae49e03d4c64f9802c992cae1 Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 1 Dec 2021 08:03:40 +0800 Subject: [PATCH 5/6] Update tests/test_amber_sqm.py Co-authored-by: Jinzhe Zeng --- tests/test_amber_sqm.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/test_amber_sqm.py b/tests/test_amber_sqm.py index 3da76831a..705e7ba9e 100644 --- a/tests/test_amber_sqm.py +++ b/tests/test_amber_sqm.py @@ -6,9 +6,10 @@ try: from dpdata import BondOrderSystem - skip_bond_order_system = False except ImportError: skip_bond_order_system = True +else: + skip_bond_order_system = False class TestAmberSqmOut(unittest.TestCase, CompSys, IsNoPBC): def setUp (self) : From 44c616a7af9a35f88b85de8043c91e13668bc80d Mon Sep 17 00:00:00 2001 From: Han Wang Date: Wed, 1 Dec 2021 08:04:05 +0800 Subject: [PATCH 6/6] Update tests/test_bond_order_system.py Co-authored-by: Jinzhe Zeng --- tests/test_bond_order_system.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/test_bond_order_system.py b/tests/test_bond_order_system.py index 3850b62c7..95c595fee 100644 --- a/tests/test_bond_order_system.py +++ b/tests/test_bond_order_system.py @@ -6,9 +6,10 @@ from rdkit import Chem from rdkit.Chem import AllChem from dpdata import BondOrderSystem - skip_bond_order_system = False except ImportError: skip_bond_order_system = True +else: + skip_bond_order_system = False import shutil import numpy as np