From 03fceba1616ca4d537209cc735b4b4f70c378ff8 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 28 Apr 2024 19:52:44 +0100 Subject: [PATCH 1/3] pin to version of rdkit that works with mypy (#4580) --- .github/workflows/linters.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml index 8352c00b629..0c7ac6d2739 100644 --- a/.github/workflows/linters.yaml +++ b/.github/workflows/linters.yaml @@ -146,6 +146,7 @@ jobs: micromamba: true full-deps: true numpy: numpy=1.23.2 + rdkit: rdkit=2023.09.3 - name: install run: | From 45fb664a4e053772c3d5cf541b2705e270a7f2a6 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Sun, 28 Apr 2024 19:56:27 +0100 Subject: [PATCH 2/3] Fix testsuite packaging discovery (#4508) --- testsuite/pyproject.toml | 23 +++-------------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/testsuite/pyproject.toml b/testsuite/pyproject.toml index 88c31d34893..62f311edb02 100644 --- a/testsuite/pyproject.toml +++ b/testsuite/pyproject.toml @@ -54,26 +54,6 @@ include-package-data = true [tool.setuptools.packages.find] namespaces = false -include=[ - "MDAnalysisTests", - "MDAnalysisTests.data", - "MDAnalysisTests.data.Amber", - "MDAnalysisTests.data.capping", - "MDAnalysisTests.data.coordinates", - "MDAnalysisTests.data.gms", - "MDAnalysisTests.data.gromos11", - "MDAnalysisTests.data.merge", - "MDAnalysisTests.data.tprs", - "MDAnalysisTests.data.tprs.all_bonded", - "MDAnalysisTests.data.tprs.virtual_sites", - "MDAnalysisTests.data.analysis", - "MDAnalysisTests.data.contacts", - "MDAnalysisTests.data.dlpoly", - "MDAnalysisTests.data.gromacs", - "MDAnalysisTests.data.lammps", - "MDAnalysisTests.data.mol2", - "MDAnalysisTests.data.windows", -] [tool.setuptools.package-data] MDAnalysisTests = [ @@ -84,6 +64,9 @@ MDAnalysisTests = [ "data/tprs/all_bonded/*.gro", "data/tprs/all_bonded/*.top", "data/tprs/all_bonded/*.mdp", + "data/tprs/virtual_sites/*.mdp", + "data/tprs/virtual_sites/*.top", + "data/tprs/virtual_sites/*.gro", "data/*.tpr", "data/tprs/*/*.tpr", "data/*.gro", From ad6981906a241d6e2e2a51fb9fc38b1313dc85a4 Mon Sep 17 00:00:00 2001 From: Yuxuan Zhuang Date: Wed, 1 May 2024 12:53:12 -0700 Subject: [PATCH 3/3] Update test_encore.py --- testsuite/MDAnalysisTests/analysis/test_encore.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index bc07c21af73..3409696a5b3 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -137,7 +137,8 @@ def test_parallel_calculation(self): r[1], arguments[i][0]**2, err_msg="Unexpected results from ParallelCalculation") - + + @pytest.mark.skip(reason='test to see if it times out') def test_rmsd_matrix_with_superimposition(self, ens1): conf_dist_matrix = encore.confdistmatrix.conformational_distance_matrix( ens1, @@ -155,6 +156,7 @@ def test_rmsd_matrix_with_superimposition(self, ens1): for i, rmsd in enumerate(reference.results.rmsd): assert_allclose(conf_dist_matrix[0, i], rmsd[2], rtol=0, atol=1.5e-3, err_msg=err_msg) + @pytest.mark.skip(reason='test to see if it times out') def test_rmsd_matrix_with_superimposition_custom_weights(self, ens1): conf_dist_matrix = encore.confdistmatrix.conformational_distance_matrix( ens1, @@ -175,6 +177,7 @@ def test_rmsd_matrix_with_superimposition_custom_weights(self, ens1): for i in range(conf_dist_matrix_custom.size): assert_allclose(conf_dist_matrix_custom[0, i], conf_dist_matrix[0, i], rtol=0, atol=1.5e-7) + @pytest.mark.skip(reason='test to see if it times out') def test_rmsd_matrix_without_superimposition(self, ens1): selection_string = "name CA" selection = ens1.select_atoms(selection_string)