Resolved merging conflicts.

Author: StuntsPT

.travis.yml

@@ -15,3 +15,9 @@ script:
   - tests/structure_field_test.sh
   - tests/fastStructure_field_test.sh
   - tests/maverick_field_test.sh
+
+# Other stuff
+notifications:
+  email:
+    - [email protected]
+    - [email protected]

structure_threader/structure_threader.py

@@ -60,6 +60,11 @@ def runprogram(wrapped_prog, iterations):
                                    str(rep_num))
         cli = [arg.external_prog, "-K", str(K), "-i", arg.infile, "-o",
                output_file]
+        if arg.params is not None:
+            mainparams = arg.params
+            extraparams = os.path.join(os.path.dirname(arg.params),
+                                       "extraparams")
+            cli += ["-m", mainparams, "-e", extraparams]
 
     elif wrapped_prog == "maverick":  # Run MavericK
         # This will break on non-POSIX OSes, but maverick requires a trailing /
@@ -226,7 +231,7 @@ def maverick_merger(outdir, k_list, tests):
     """
     files_list = ["outputEvidence.csv", "outputEvidenceDetails.csv"]
     mrg_res_dir = os.path.join(outdir, "merged")
-    os.makedirs(mrg_res_dir)
+    os.makedirs(mrg_res_dir, exist_ok=True)
     log_evidence_ti = {}
 
     def _mav_output_parser(filename, get_header):
@@ -249,7 +254,7 @@ def _ti_test(outdir, log_evidence_ti):
         Write a bestK result based in TI results.
         """
         bestk_dir = os.path.join(outdir, "bestK")
-        os.makedirs(bestk_dir)
+        os.makedirs(bestk_dir, exist_ok=True)
         bestk = max(log_evidence_ti, key=log_evidence_ti.get).replace("K", "1")
         bestk_file = open(os.path.join(bestk_dir, "TI_integration.txt"), "w")
         output_text = ("MavericK's 'Thermodynamic Integration' test revealed "

tests/maverick_field_test.sh

@@ -15,7 +15,7 @@
 # You should have received a copy of the GNU General Public License
 # along with structure_threader. If not, see <http://www.gnu.org/licenses/>.
 
-# set -e
+set -e
 
 LightGreen='\033[1;32m'
 NoColor='\033[0m'

tests/structure_field_test.sh

@@ -25,6 +25,6 @@ echo "Runnig STRUCTURE 'field test'. This will simulate a full wrapped run on sm
 git_dir=`pwd`
 str_bin=`which structure`
 
-~/virtualenv/python3.5/bin/structure_threader -i ${git_dir}/tests/smalldata/Reduced_dataset.structure -o ~/results -st ${str_bin} -K 3 -t 4 -R 5
+~/virtualenv/python3.5/bin/structure_threader -i ${git_dir}/tests/smalldata/Reduced_dataset.structure -o ~/results -st ${str_bin} -K 3 -t 4 -R 5 --params ${git_dir}/tests/smalldata/mainparams
 
 echo -e "${LightGreen}STRUCTURE 'Field test' ran successfully. Yay!${NoColor}"