From b71935f2e84fc6d7567a4052c0bb9b632be84428 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Wed, 14 Feb 2024 17:08:03 +0100
Subject: [PATCH] CI: add compound lib
This enables tests that depend on the compound lib.
Squashed commit of the following:
commit b5bbb4451ef1270cdc1ccb153126d60e00fc691f
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 15:45:21 2024 +0100
Revert "CI: test a CI failure"
This reverts commit 494222f9dd8ec0efcb7c9862c1b33a30ad88fde8.
commit 494222f9dd8ec0efcb7c9862c1b33a30ad88fde8
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 15:40:47 2024 +0100
CI: test a CI failure
This worfklow is expected to fail with an error in
test_ligand_scoring.py_run. If it fails it means the compound lib is
properly setup.
commit 7d06d517d9679c80f0918de58bcbae99b25766db
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 15:27:45 2024 +0100
CI: download compounds after first build
commit 89edc43dd9c36b01f323fca400d9ee8a2eedfedb
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 15:18:25 2024 +0100
CI: use make as documented in the wiki
commit 4f94f46d892e38a4cc3cc6beece91f815d72bfb4
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 15:03:45 2024 +0100
CI: try to download and build a compound lib
commit 5d16d160b0b882ccf7fc4f9c25c419cccc0c71a7
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 14:55:55 2024 +0100
CI: try to link the compound lib differently
commit 1e9803eba5a8368ff79a7274da100e496f9a0c89
Author: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed Feb 14 14:31:07 2024 +0100
CI: try to use the group compound lib
This is likely to fail if we don't have the right mounts...
---
.gitlab-ci.yml | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 35d978d02..c24946cd1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,6 +26,7 @@ test:centos7.3:
- source /export/soft/lua_lmod/centos7/lmod/lmod/init/bash
- module use /scicore/soft/modules/all
- module load foss/2021a
+ - module load wget/1.21.1-GCCcore-10.3.0
- module load CMake/3.23.1-GCCcore-10.3.0
- module load Python/3.9.5-GCCcore-10.3.0
- module load Eigen/3.4.0-GCCcore-10.3.0
@@ -74,9 +75,20 @@ test:centos7.3:
-DCMAKE_C_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
-DCMAKE_CXX_FLAGS='-L${EBROOTLIBPNG}/lib/ -L${EBROOTLIBTIFF}/lib/ -L${EBROOTZLIB}/lib/ -isystem ${EBROOTBOOST}/include -isystem ${EBROOTOPENMM}/include'
-DCMAKE_EXE_LINKER_FLAGS=" -pthread"
- - make -j 2
+ - make -j 2 chemdict_tool
- echo " ... done building OST."
- - echo " Running unit tests for OST..."
+ - echo " Downloading chemical compounds..."
+ - wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
+ - echo " ... done downloading compounds"
+ - echo " Building a compound library..."
+ - stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb -i
+ - stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm
+ - echo " ... done building the compound lib."
+ - echo " Building OST with the compound lib..."
+ - cmake .. -DCOMPOUND_LIB=compounds.chemlib
+ - make -j 2
+ - echo " ... done building OST with the compound library..."
+ - echo " Running unit tests for OST..."
- make check
- echo " ... done running unit tests for OST..."
- echo "... done testing on CentOS 7."
--
GitLab