From e2d9f802b54b08a3977b736a6e68286c426438b6 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Wed, 9 Sep 2020 10:20:29 +1000 Subject: [PATCH 1/3] add test files --- testsuite/setup.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/testsuite/setup.py b/testsuite/setup.py index f454ba9e9cd..0bb0d73ca73 100755 --- a/testsuite/setup.py +++ b/testsuite/setup.py @@ -136,10 +136,11 @@ def run(self): 'MDAnalysisTests.plugins': 'MDAnalysisTests/plugins'}, package_data={'MDAnalysisTests': ['data/*.psf', 'data/*.dcd', 'data/*.pdb', - 'data/tprs/*.tpr', 'data/tprs/all_bonded/*.tpr', + 'data/tprs/*.tpr', 'data/tprs/all_bonded/*.gro', 'data/tprs/all_bonded/*.top', 'data/tprs/all_bonded/*.mdp', 'data/*.tpr', + 'data/tprs/*/*.tpr', 'data/*.gro', 'data/*.xtc', 'data/*.trr', 'data/*npy', 'data/*.crd', 'data/*.xyz', 'data/Amber/*.bz2', @@ -172,9 +173,12 @@ def run(self): 'data/analysis/*', 'data/*.gsd', 'data/windows/*', - 'data/*.itp', + 'data/*.itp', "data/gromacs/gromos54a7_edited.ff/*", 'data/*.coor', 'data/*.h5md', + 'data/*.in', + 'data/*.top', + 'data/*.sdf', ], }, install_requires=[ From bbc0f3cfbe20fa3f21384549f98e2867b3cc4023 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Wed, 9 Sep 2020 23:39:25 +1000 Subject: [PATCH 2/3] transfer PCA to memory --- testsuite/MDAnalysisTests/analysis/test_pca.py | 1 + 1 file changed, 1 insertion(+) diff --git a/testsuite/MDAnalysisTests/analysis/test_pca.py b/testsuite/MDAnalysisTests/analysis/test_pca.py index 18c47d649f9..2b769d21342 100644 --- a/testsuite/MDAnalysisTests/analysis/test_pca.py +++ b/testsuite/MDAnalysisTests/analysis/test_pca.py @@ -56,6 +56,7 @@ def pca(u): @pytest.fixture(scope='module') def pca_aligned(u): + u.transfer_to_memory() return PCA(u, select=SELECTION, align=True).run() From baa871f1de52e4f9aa2c6406b6363cc4f1ee5b7f Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 10 Sep 2020 06:33:18 +1000 Subject: [PATCH 3/3] Revert "transfer PCA to memory" This reverts commit bbc0f3cfbe20fa3f21384549f98e2867b3cc4023. --- testsuite/MDAnalysisTests/analysis/test_pca.py | 1 - 1 file changed, 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_pca.py b/testsuite/MDAnalysisTests/analysis/test_pca.py index 2b769d21342..18c47d649f9 100644 --- a/testsuite/MDAnalysisTests/analysis/test_pca.py +++ b/testsuite/MDAnalysisTests/analysis/test_pca.py @@ -56,7 +56,6 @@ def pca(u): @pytest.fixture(scope='module') def pca_aligned(u): - u.transfer_to_memory() return PCA(u, select=SELECTION, align=True).run()