From fb90a194cd5b31d10cd27c7475d2545684133c2c Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Thu, 25 May 2023 12:15:38 +0200 Subject: [PATCH 1/6] Fix CMake not adding some tests --- CMakeLists.txt | 34 ++++++++++++++++++++++++---------- 1 file changed, 24 insertions(+), 10 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index d372bdfc..b88158ad 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -56,25 +56,39 @@ foreach(TEST_PATH ${TEST_PATHS}) add_test(${TEST_NAME} ${TEST_NAME}) endforeach() +# List of directories containing test scripts +set(PYTHON_TEST_DIRS + ${CMAKE_SOURCE_DIR}/src/pytorch/ + ${CMAKE_SOURCE_DIR}/src/pytorch/neighbors +) + # Move test scripts to a test folder in the build directory, create test folder if necessary add_custom_target(copy_test ALL COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/test - COMMAND ${CMAKE_COMMAND} -E copy - ${CMAKE_SOURCE_DIR}/src/pytorch/Test*.py - ${CMAKE_SOURCE_DIR}/src/pytorch/neighbors/Test*.py - ${CMAKE_SOURCE_DIR}/src/pytorch/neighbors/getNeighborPairs.py - ${CMAKE_BINARY_DIR}/test +) + +# Add the data directory as well +add_custom_command( + TARGET copy_test POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/pytorch/molecules ${CMAKE_BINARY_DIR}/test/molecules ) -# Add tests for all scripts in the test directory -file(GLOB_RECURSE PYTHON_TEST_PATHS ${CMAKE_BINARY_DIR}/test/Test*.py) -foreach(TEST_PATH ${PYTHON_TEST_PATHS}) - cmake_path(GET TEST_PATH STEM TEST_NAME) - add_test(${TEST_NAME} pytest -v ${CMAKE_BINARY_DIR}/test/${TEST_NAME}.py) +# Copy each test to the binary dir and add it +foreach(TEST_DIR ${PYTHON_TEST_DIRS}) + file(GLOB TEST_SCRIPTS ${TEST_DIR}/Test*.py) + foreach(TEST_SCRIPT ${TEST_SCRIPTS}) + get_filename_component(TEST_NAME ${TEST_SCRIPT} NAME_WE) + file(RELATIVE_PATH RELATIVE_TEST_PATH ${CMAKE_SOURCE_DIR}/src/pytorch ${TEST_SCRIPT}) + add_custom_command( + TARGET copy_test POST_BUILD + COMMAND ${CMAKE_COMMAND} -E copy ${TEST_SCRIPT} ${CMAKE_BINARY_DIR}/test/${RELATIVE_TEST_PATH} + ) + add_test(NAME ${TEST_NAME} COMMAND pytest -v ${CMAKE_BINARY_DIR}/test/${RELATIVE_TEST_PATH}) + endforeach() endforeach() + add_test(TestGetNeighborPairs pytest -v --doctest-modules ${CMAKE_BINARY_DIR}/test/getNeighborPairs.py) # Installation From cd7cf5353c65b929fe2075b88ad46289ff4821fd Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Thu, 25 May 2023 12:32:25 +0200 Subject: [PATCH 2/6] Forgot to copy one script --- CMakeLists.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index b88158ad..fe70b32a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -89,6 +89,11 @@ foreach(TEST_DIR ${PYTHON_TEST_DIRS}) endforeach() endforeach() +add_custom_command( + TARGET copy_test POST_BUILD + COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/src/pytorch/neighbors/getNeighborPairs.py ${CMAKE_BINARY_DIR}/test/getNeighborPairs.py +) + add_test(TestGetNeighborPairs pytest -v --doctest-modules ${CMAKE_BINARY_DIR}/test/getNeighborPairs.py) # Installation From b9009fea439076becc34ee825fede8d539afa315 Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Mon, 29 May 2023 10:00:38 +0200 Subject: [PATCH 3/6] Remove non-ascii characters in a mol2 file --- src/pytorch/molecules/1hvj_ligand.mol2 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/pytorch/molecules/1hvj_ligand.mol2 b/src/pytorch/molecules/1hvj_ligand.mol2 index c51a4e8f..b6122f42 100644 --- a/src/pytorch/molecules/1hvj_ligand.mol2 +++ b/src/pytorch/molecules/1hvj_ligand.mol2 @@ -7,8 +7,8 @@ USER_CHARGES @ATOM 1 C1 3.4440 3.3887 10.7035 zw 1 A78 0.766100 - 2 O2 3.2004 4.2657 11.5137 z‚ 1 A78 -0.669100 - 3 N3 4.0410 3.6349 9.4679 z€ 1 A78 -0.445800 + 2 O2 3.2004 4.2657 11.5137 z 1 A78 -0.669100 + 3 N3 4.0410 3.6349 9.4679 z 1 A78 -0.445800 4 C4 4.2905 2.5750 8.4667 c3 1 A78 0.072300 5 C5 4.5571 4.9758 9.1200 za 1 A78 0.046700 6 C6 6.0491 5.1114 9.4017 zo 1 A78 0.372600 @@ -20,7 +20,7 @@ USER_CHARGES 12 N22 3.1777 2.0550 10.9450 z| 1 A78 -0.557900 13 C23 2.6353 1.5314 12.2140 zb 1 A78 0.044700 14 C24 3.6764 0.5489 12.7936 zx 1 A78 0.653100 - 15 O25 3.4215 -0.6062 13.0869 z‚ 1 A78 -0.634100 + 15 O25 3.4215 -0.6062 13.0869 z 1 A78 -0.634100 16 C26 1.1960 0.9387 12.0510 zh 1 A78 -0.074700 17 C27 0.5342 0.6636 13.4290 zi 1 A78 -0.094600 18 C28 0.2755 1.8727 11.2187 zi 1 A78 -0.094600 @@ -34,7 +34,7 @@ USER_CHARGES 26 C45 6.5634 -0.7826 9.1129 ca 1 A78 -0.133000 27 C46 6.6724 -0.6210 10.5037 zr 1 A78 -0.123000 28 C47 6.3818 0.6114 14.8979 zj 1 A78 -0.123400 - 29 O48 5.4918 0.6100 17.1615 zƒ 1 A78 -0.608800 + 29 O48 5.4918 0.6100 17.1615 z 1 A78 -0.608800 30 C49 5.2282 0.1487 15.8325 zk 1 A78 0.125100 31 N50 6.1967 -2.0921 16.4025 z~ 1 A78 -0.538900 32 C51 5.0294 -1.3972 15.8311 zm 1 A78 0.103700 @@ -45,16 +45,16 @@ USER_CHARGES 37 C56 3.1116 -6.1003 16.4218 ca 1 A78 -0.136000 38 C57 2.8290 -5.3098 15.2970 ca 1 A78 -0.132500 39 C58 3.0128 -3.9187 15.3507 zt 1 A78 -0.123500 - 40 N81 7.1331 -5.5620 16.8647 z 1 A78 -0.539900 + 40 N81 7.1331 -5.5620 16.8647 z 1 A78 -0.539900 41 C82 7.4436 -4.1278 17.0194 zc 1 A78 0.034700 42 C83 6.6091 -3.3476 15.9854 zy 1 A78 0.658100 - 43 O84 6.2884 -3.8198 14.9065 z‚ 1 A78 -0.633100 + 43 O84 6.2884 -3.8198 14.9065 z 1 A78 -0.633100 44 C85 8.9768 -3.8384 16.8891 ze 1 A78 -0.086700 45 C86 9.3055 -2.3257 16.9980 zf 1 A78 -0.095100 46 C87 9.8090 -4.6280 17.9340 zf 1 A78 -0.095100 47 C97 6.9688 -6.4414 17.9188 zz 1 A78 0.754100 - 48 O98 7.1154 -6.1080 19.0818 z‚ 1 A78 -0.657100 - 49 N99 6.6109 -7.7343 17.5371 z 1 A78 -0.445800 + 48 O98 7.1154 -6.1080 19.0818 z 1 A78 -0.657100 + 49 N99 6.6109 -7.7343 17.5371 z 1 A78 -0.445800 50 C2 6.4191 -8.1324 16.1243 c3 1 A78 0.059300 51 C3 6.3450 -8.7797 18.5509 zd 1 A78 0.038700 52 C8 4.9082 -8.7509 19.0589 zu 1 A78 0.359600 From bc4d83bdc6b6c18989c9896c9e4a53234b0285bd Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Fri, 7 Jul 2023 18:01:43 +0200 Subject: [PATCH 4/6] Add PME tests in CMakeLists.txt --- CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/CMakeLists.txt b/CMakeLists.txt index 16b3b668..89f34917 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -63,6 +63,7 @@ endforeach() set(PYTHON_TEST_DIRS ${CMAKE_SOURCE_DIR}/src/pytorch/ ${CMAKE_SOURCE_DIR}/src/pytorch/neighbors + ${CMAKE_SOURCE_DIR}/src/pytorch/pme ) # Move test scripts to a test folder in the build directory, create test folder if necessary From 66c3f6078685fb422d4994255b0b709074e0e899 Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Fri, 7 Jul 2023 18:34:31 +0200 Subject: [PATCH 5/6] Trigger a rerun --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 9db9ae23..6525d627 100644 --- a/environment.yml +++ b/environment.yml @@ -12,3 +12,4 @@ dependencies: - python 3.10.* - pytorch-gpu 2.0.* - sysroot_linux-64 2.17 + From 2601eace63bef64c80cd486d78040d5d96b12692 Mon Sep 17 00:00:00 2001 From: RaulPPealez Date: Fri, 7 Jul 2023 18:34:43 +0200 Subject: [PATCH 6/6] Trigger a rerun --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 6525d627..1a6455c3 100644 --- a/environment.yml +++ b/environment.yml @@ -12,4 +12,4 @@ dependencies: - python 3.10.* - pytorch-gpu 2.0.* - sysroot_linux-64 2.17 - +