Added py-lxml, measures

README.md

@@ -55,3 +55,16 @@ make -C gnucxx11_opt/ -j
 The `configure.sh` file loads all the environment modules that are required to build the COBALT software. It also applies the following workarounds:
 1) The libraries of the host compiler (GCC 12) need to be added to the `LIBRARY_PATH`.
 2) `tParset` is broken, disable it in the build.
+
+## Notes: futher patches needed to run tests
+The following patches are needed to get the COBALT tests and code to run on the COBALT cluster:
+1) The path to libnvrtc-builtins.so (provided by Spack) needs to be added to LD_LIBRARY_PATH. Not doing so raises the error NVRTC_ERROR_BUILTIN_OPERATION_FAILURE.
+2) The casacore measures need to be installed:
+```bash
+wget ftp://ftp.astron.nl:21/outgoing/Measures/WSRT_Measures.ztar
+tar xfz WSRT_Measures.ztar
+mkdir ~/measures
+mv geodetic ephemerides ~/measures
+echo 'measures.directory: $HOME/measures' > ~/.casarc
+```
+3) make sure `ssh localhost` works without password

configure.sh

@@ -19,6 +19,7 @@ module load python
 module load numactl
 module load unittest-cpp
 module load hdf5
+module load py-lxml
 
 # tParset is broken, disable it
 sed -i '/lofar_add_test(tParset/s/^/#/' CoInterface/test/CMakeLists.txt

environment.yaml

@@ -12,6 +12,7 @@ spack:
   - log4cplus
   - py-kombu
   - py-casacore
+  - py-lxml
   - readline
   - ncurses
   - postgresql