merge devel

.github/workflows/docker-publish-and-test.yml

@@ -238,13 +238,8 @@ jobs:
 
       - name: Test minimal image
         run: |
-          bash test/run_tests.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test pm_fast_tests
-          bash test/run_tests.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test sm_fast_tests
-          bash test/run_vcs.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test pm_fast_vcs
-          bash test/run_vcs.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test sm_fast_vcs
-          bash test/run_tests.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test equilibriumcrystalstructure
-          bash test/run_tests.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test sp_sm_test
-
+          bash test/run_all.sh ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:test all
+
       # Re-run the previous buildx action, except this time push the image if needed. Because of caching, this
       # does not rebuild the image.
       #

docker/config/excerpts/compute.py

@@ -18,6 +18,9 @@
 import time
 from contextlib import contextmanager
 
+import kim_edn
+import kim_property
+
 import pty
 import select
 import errno
@@ -188,6 +191,7 @@ def __init__(
         subject=None,
         result_code="",
         verbose=False,
+        verify=True,
     ):
         """
         A pipeline computation object that utilizes all of the pipeline
@@ -198,13 +202,17 @@ def __init__(
             * subject : A Model
             * result_code : if provided, the result will be moved
                 to the appropriate location
+            * verify : If True, the contents of results.edn will be verified to contain
+                valid KIM property instances when the output of the computation is
+                processed. 
         """
         self.runner = runner
         self.subject = subject
         self.runner_temp = runner
         self.runtime = -1
         self.result_code = result_code
         self.verbose = verbose
+        self.verify = verify
         self.info_dict = None
         self.uuid = None
         self.retcode = None
@@ -373,11 +381,21 @@ def process_output(self):
                     properties_reported.sort()
                     self.info_dict = {"properties": properties_reported}
             except Exception:
-                raise cf.PipelineRuntimeError(
+                raise cf.PipelineResultsError(
                     "The results file produced by "
                     "the Test or Verification Check ({}) is not valid "
                     "EDN".format(_result_file_path)
                 )
+
+            if self.verify:
+                # Check whether the entries in results file are valid
+                # property instances
+                valid, msg = test_result_valid(_result_file_path)
+                if not valid:
+                    raise cf.PipelineResultsError(
+                        "Test Result or Verification Result did not conform "
+                        "to property definition\n{}".format(msg)
+                    )
 
         with self.runner_temp.in_dir(), open(
             _result_file_path, "w", encoding="utf-8"
@@ -641,3 +659,23 @@ def append_newline(string):
     if len(string) > 0 and string[-1] != "\n":
         string += "\n"
     return string
+
+
+def test_result_valid(flname):
+    """
+    Uses the kim_property module to check whether all property instances
+    contained in file are valid w.r.t. the current KIM property
+    definitions.  See
+
+        https://github.com/openkim/kim-property
+    """
+    try:
+        kim_property.check_property_instances(fi=flname, fp_path=kim_property.get_properties())
+    except (kim_property.KIMPropertyError, kim_edn.KIMEDNDecodeError):
+        valid = False
+        msg = traceback.format_exc()
+    else:
+        valid = True
+        msg = None
+
+    return valid, msg

docker/git/Dockerfile

@@ -20,11 +20,11 @@ RUN git clone -q https://github.com/openkim/kim-python-utils -b master ${PACKAGE
   && git checkout e4e21b202264373a9f33dfc47b6e05c0af625950
 RUN git clone -q https://github.com/openkim/crystal-genome-util -b main ${PACKAGE_DIR}/crystal-genome-util \
   && cd ${PACKAGE_DIR}/crystal-genome-util \
-  && git checkout ee3b739636eb7e2562b8baa6799d213caea68019 
+  && git checkout e18a2d62fc3e391acbf9c98a28efaebca914b007
 RUN git clone -q https://github.com/lammps/lammps -b stable_2Aug2023_update1 ${PACKAGE_DIR}/lammps
 RUN git clone -q https://gitlab.com/openkim/ase -b user-species ${PACKAGE_DIR}/ase \
   && cd ${PACKAGE_DIR}/ase \
-  && git checkout e00c8da0f84fb3a726c411f7ef2792241434c9a3
+  && git checkout abe2d6c6e265f7ba6e79cc9b437ef1940731eccc
 RUN git clone -q https://gitlab.com/micronano_public/MDpp -b release ${PACKAGE_DIR}/MD++ \
   && cd ${PACKAGE_DIR}/MD++ \
   && git checkout f7d64a7720a4bc1602371a128c8db7779fcf8dcb

docker/install/Dockerfile

@@ -39,7 +39,7 @@ RUN ${PIP} install markupsafe==2.0.1
 RUN ${PIP} install Jinja2==2.11.3
 RUN ${PIP} install edn_format==0.7.5
 RUN ${PIP} install kim-edn==1.3.1
-RUN ${PIP} install kim-property==2.5.7
+RUN ${PIP} install kim-property==2.6.0
 RUN ${PIP} install kim-query==3.0.0
 RUN ${PIP} install simplejson==3.17.2
 RUN ${PIP} install numpy==1.19.5
@@ -160,7 +160,7 @@ RUN cd ${PACKAGE_DIR}/ase/ \
 #########################################
 RUN cd ${PACKAGE_DIR}/kim-python-utils \
  && ${PIP} install .
-
+ 
 #########################################
 ## crystal-genome-util
 #########################################

test/run_vcs.sh → test/run_all.sh

@@ -1,2 +1,2 @@
-DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && bash set_up_and_run_$2.sh && 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 --env LD_LIBRARY_PATH=:/usr/local/lib $1 /bin/bash -c "$DOCKER_COMMAND"
+DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && bash set_up_and_run_$2.sh && 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 --env LD_LIBRARY_PATH=:/usr/local/lib $1 /bin/bash -c "$DOCKER_COMMAND"

test/run_tests.sh

@@ -1,3 +1,2 @@
 DOCKER_COMMAND="cd /home/openkim/test_scripts_and_data && bash set_up_and_run_$2.sh && python compare_dbs.py $2"
-docker run --rm --mount type=bind,src=$PWD/test/test_scripts_and_data,target=/home/openkim/test_scripts_and_data --env LD_LIBRARY_PATH=:/usr/local/lib $1 /bin/bash -c "$DOCKER_COMMAND"
-
+docker run --rm --mount type=bind,src=$PWD/test/test_scripts_and_data,target=/home/openkim/test_scripts_and_data --env LD_LIBRARY_PATH=:/usr/local/lib $1 /bin/bash -c "$DOCKER_COMMAND"

test/test_scripts_and_data/all.grades

@@ -0,0 +1,13 @@
+P
+P
+P
+P
+P
+P
+P
+P
+N/A
+P
+P
+P
+P