test condition in gitlab CI

.gitlab-ci.yml

@@ -172,27 +172,27 @@ article:
   image:
     name: pycif/pycif-ubuntu:0.1
     entrypoint: [""]
-#  before_script:
-##    - apt-get update
-#    - pip freeze
+  before_script:
+#    - apt-get update
+    - pip freeze
   script:
-    - echo AAAAAAAAAAAAAAAAAAAAAAAAaaa
-    - echo ${CI_COMMIT_BRANCH}
-    - echo AAAAAAAAAAAAAAAAAAAAAAAAaaa
-    - echo ${CI_MERGE_REQUEST_TARGET_BRANCH_NAME}
-    - echo AAAAAAAAAAAAAAAAAAAAAAAAaaa
-    - if [ ${CI_COMMIT_BRANCH} == "new_classes" ]; then echo "TTTTTTTTTTTTTTTTTTTTTTTTT"; fi;
-
-    #- tox -e py38 -e coverage -- -m "(dummy and article and inversion and not adjtltest and not uncertainties) or (fwd and ref_config)"
-#  after_script:
-#    - mkdir -p coverage
-#    - xmlstarlet sel -t -v "//coverage/@line-rate" reports/coverage.xml > coverage/.current_coverage
-#    - calc() { awk "BEGIN{print $*}"; }
-#    - percent_coverage=`cat coverage/.current_coverage`
-#    - tot_coverage=`calc ${percent_coverage}*100`
-#    - echo 'TOTAL COVERAGE:'" ${tot_coverage}%"
-#    - mv coverage_raw/coverage/.coverage coverage_raw/.coverage.article
-#  coverage: '/^TOTAL COVERAGE: ([0-9\.]+\%)$/'
+    - |
+      if [ ${CI_COMMIT_BRANCH} == "LSCE" ]; then
+        tox -e py38 -e coverage -- -m "(dummy and article and inversion and not adjtltest and not uncertainties)
+                                       or (fwd and ref_config) or (allsimulations)";
+      else
+        tox -e py38 -e coverage -- -m "(dummy and article and inversion and not adjtltest and not uncertainties)
+                                       or (fwd and ref_config)";
+      fi;
+  after_script:
+    - mkdir -p coverage
+    - xmlstarlet sel -t -v "//coverage/@line-rate" reports/coverage.xml > coverage/.current_coverage
+    - calc() { awk "BEGIN{print $*}"; }
+    - percent_coverage=`cat coverage/.current_coverage`
+    - tot_coverage=`calc ${percent_coverage}*100`
+    - echo 'TOTAL COVERAGE:'" ${tot_coverage}%"
+    - mv coverage_raw/coverage/.coverage coverage_raw/.coverage.article
+  coverage: '/^TOTAL COVERAGE: ([0-9\.]+\%)$/'
   artifacts:
     when: always
     paths:

bin/pycif_test.sh

@@ -16,10 +16,10 @@ export PYCIF_DATATEST=/home/chimereges/PYCIF_TEST_DATA/
 export PYCIF_PLATFORM=LSCE
 ###
 # select a subset of tests to run by using the tags ("mark")
-#mark="(dummy and article and inversion and not adjtltest and not uncertainties) or (fwd and ref_config)"
+mark="(dummy and article and inversion and not adjtltest and not uncertainties) or (fwd and ref_config) or (toto)"
 #mark="(dummy and article and inversion and not adjtltest and uncertainties) or (fwd and ref_config)"
 #mark="(fwd and ref_config)"
-mark="test_in_ci and dummy"
+#mark="test_in_ci and dummy"
 #mark="test_in_ci and chimere"
 #mark="chimere and argfrsd and fwd"
 #mark="tm5 and test_in_ci and fwd"

pycif/plugins/modes/analytic/build_H.py

@@ -44,7 +44,7 @@ def build_H(controlvect, obsvect, base_dir):
                     "{}/obsvect_{:04d}/{}/{}/monitor.nc"\
                         .format(base_dir, idim, comp, trcr)
                 data = read_datastore(monitor_file)
-                hloc.loc[:, idim] = data.loc[:, "sim"].values
+                hloc.loc[:, idim] = data.loc[:, ("maindata", "sim")].values
                 
             jacobian[(comp, trcr)] = hloc
             harray[tracer.ypointer: tracer.ypointer + tracer.dim, :] = \

pycif/plugins/modes/ensrf/build_H.py

@@ -40,7 +40,7 @@ def build_Hx(obsvect, ensemble_dir, x_sample):
                     "{}/H_matrix/obsvect_{:04d}/{}/{}/monitor.nc"\
                         .format(ensemble_dir, isample, comp, trcr)
                 data = read_datastore(monitor_file)
-                hloc.loc[:, isample] = data.loc[:, "sim"].values
+                hloc.loc[:, isample] = data.loc[:, ("maindata", "sim")].values
                 
             jacobian[(comp, trcr)] = hloc
             harray[tracer.ypointer: tracer.ypointer + tracer.dim, :] = \

tests/dummy/test_integration_3inversions.py

@@ -39,11 +39,20 @@ def test_integration_inversion(dummy_config_inversion, settings, pytestconfig):
     # from forward to make computation faster
     config["model"]["reload_H"] = "{}/../H_matrix.pickle".format(tmpdir)
     
-    # Changing mode
+    # Update number of simulations depending on pytests options
+    marker = pytestconfig.getoption('-m')
     nsimmax = 10
+    montecarlo = settings.get("montecarlo", 10)
+    nsample = settings.get("nsample", 5)
+    if "allsimulations" not in marker:
+        nsimmax = 4
+        montecarlo = 4
+        nsample = 1
+        
+    # Changing mode
     if config["datavect"]["components"]["flux"]\
             ["parameters"]["CH4"]["hresol"] == "hpixels":
-        nsimmax = 25
+        nsimmax = int(2.5 * nsimmax)
     
     elif config["datavect"]["components"]["flux"]\
             ["parameters"]["CH4"]["hresol"] == "global" \