Kimtools kimunits

.gitignore

@@ -1 +1,2 @@
 __pycache__
+kim-tools.log

docker/config/excerpts/compute.py

@@ -27,7 +27,7 @@
 import errno
 
 from . import util
-from . import kimunits
+from kim_tools import kimunits
 from . import kimobjects
 from . import config as cf
 

docker/config/excerpts/query_local/helper_functions.py

@@ -13,7 +13,7 @@
 
 from .. import kimquery
 from ..kimcodes import parse_kim_code
-from ..kimunits import convert_units, convert_list, UnitConversion
+from kim_tools.kimunits import convert_units, convert_list, UnitConversion
 
 RE_KIMID = r"^(?:([_a-zA-Z][_a-zA-Z0-9]*?)__)?([A-Z]{2})_([0-9]{12})(?:_([0-9]{3}))?$"
 RE_EXTENDED_ID = r"^[A-Za-z0-9_]+__[A-Z]{2}_[0-9]{12}_[0-9]{3}$"

docker/config/excerpts/query_local/queryapi.py

@@ -64,7 +64,7 @@
 from bson.code import Code
 from bson.json_util import dumps, loads
 
-from ..kimunits import convert_units, convert_list
+from kim_tools.kimunits import convert_units, convert_list
 from . import helper_functions as helpers
 
 

docker/config/excerpts/template.py

@@ -36,7 +36,7 @@
 from . import kimobjects
 from . import config as cf
 from . import util
-from .kimunits import convert
+from kim_tools.kimunits import convert
 
 
 # -----------------------------------------

test/run_all.sh

@@ -1,2 +1,2 @@
-DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && cp -r custom_kimitems/* ~ && bash set_up_and_run_$2.sh && export PYTHONPATH=\$PYTHONPATH:/pipeline/ && python compare_dbs.py $2 && bash compare_vcs.sh $2"
+DOCKER_COMMAND="echo openkim | sudo -S chown -R openkim test_scripts_and_data && cd /home/openkim/test_scripts_and_data && cp -r custom_kimitems/* ~ && bash set_up_and_run_$2.sh && export PYTHONPATH=\$PYTHONPATH:/pipeline/ && python compare_dbs.py $2 && bash compare_vcs.sh $2"
 docker run --rm --mount type=bind,src=$PWD/test/test_scripts_and_data,target=/home/openkim/test_scripts_and_data $1 /bin/bash -c "$DOCKER_COMMAND"

test/run_cg_example.sh

@@ -1,2 +1,2 @@
 DOCKER_COMMAND="cd /home/openkim/test-drivers/ && git clone https://github.com/openkim-hackathons/CrystalGenomeASEExample__TD_000000654321_000.git && cd CrystalGenomeASEExample__TD_000000654321_000 && git checkout 09d8cc8a74f83bdf8ad96329fb456e4815800337 && tail -n1 < test_generator.json > test_generator.json_ && mv test_generator.json_ test_generator.json && kimgenie tests --test-driver CrystalGenomeASEExample__TD_000000654321_000 --add-random-kimnums && kimitems install -D LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 && pipeline-run-matches LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 -v && if [[ \$(ls /home/openkim/test-results | wc -l) != "1" ]]; then exit 1; fi"
-docker run --rm --mount type=bind,src=$PWD/test/test_scripts_and_data,target=/home/openkim/test_scripts_and_data $1 /bin/bash -c "$DOCKER_COMMAND"
+docker run --rm $1 /bin/bash -c "$DOCKER_COMMAND"