update gitlab CI to make sure changes are pulled.

.gitlab-ci.yml

@@ -30,7 +30,8 @@ before_script:
   - cd phasexmlparser
   - pip install .
   - cd ../
-  - if [[ ! -d 'phasexmlcreator' ]]; then git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/phasexmlcreator.git; fi
+  - if [[ -d 'phasexmlcreator' ]]; then rm -r phasexmlcraetor; fi
+  - git clone https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.developers.cam.ac.uk/ch/hunter/ssiptools/ssimpleapps/phasexmlcreator.git
   - cd phasexmlcreator
   - pip install .
   - cd ../

phasecalculator/runners/phasetransferrunner.py

@@ -165,7 +165,7 @@ def run_calculation(arg_list):
         result of system call.
 
     """
-    return subprocess.run(arg_list)
+    return subprocess.run(arg_list,capture_output=True)
 
 
 def generate_vle_calc_args(jar_path, phase_filename, output_filename, **kwargs):