CI: add compound lib

This enables tests that depend on the compound lib.

Squashed commit of the following:

commit b5bbb445
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 494222f9.

commit 494222f9
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 7d06d517
Author: Xavier Robin <xavier.robin@unibas.ch>
Date:   Wed Feb 14 15:27:45 2024 +0100

    CI: download compounds after first build

commit 89edc43d
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 4f94f46d
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 5d16d160
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 1e9803eb
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

@@ -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."