Retry activate EDGAR interpolation in CI

.gitlab-ci.yml

@@ -126,7 +126,7 @@ article:
     name: pycif/pycif-ubuntu:0.1
     entrypoint: [""]
   before_script:
-    - apt-get update
+#    - apt-get update
     - pip freeze
   script:
     - tox -e py38 -e coverage -- -m "(dummy and article and inversion and not adjtltest and not uncertainties) or (fwd and ref_config)"
@@ -152,7 +152,7 @@ article_uncertainties:
     name: pycif/pycif-ubuntu:0.1
     entrypoint: [""]
   before_script:
-    - apt-get update
+#    - apt-get update
     - pip freeze
   script:
     - tox -e py38 -e coverage -- -m "(dummy and article and inversion and not adjtltest and uncertainties) or (fwd and ref_config)"
@@ -179,10 +179,10 @@ tests_dummy:
     name: pycif/pycif-ubuntu:0.1
     entrypoint: [""]
   before_script:
-    - apt-get update
+#    - apt-get update
     - pip freeze
   script:
-    - tox -e py38 -e coverage -- -m "test_in_ci and dummy"
+    - tox -e py39 -e coverage -- -m "test_in_ci and dummy"
   after_script:
     - mkdir -p coverage
     - xmlstarlet sel -t -v "//coverage/@line-rate" reports/coverage.xml > coverage/.current_coverage
@@ -203,16 +203,16 @@ tests_chimere:
     name: pycif/pycif-ubuntu:0.1
     entrypoint: [""]
   before_script:
-    - apt-get update
+    #- apt-get update
     - pip freeze
     - rm -rf /tmp/PYCIF_DATA_TEST/
     - mkdir -p /tmp/PYCIF_DATA_TEST/
-    - wget https://sharebox.lsce.ipsl.fr/index.php/s/zUpoUXODKFLZJrf/download -O CHIMERE.tar
+    - wget https://sharebox.lsce.ipsl.fr/index.php/s/zUpoUXODKFLZJrf/download -O CHIMERE.tar  > /dev/null 2>&1
     - tar -xf CHIMERE.tar -C /tmp/PYCIF_DATA_TEST/
-    - wget https://sharebox.lsce.ipsl.fr/index.php/s/GgTDXL8peF4BOuV/download -O RAW.tar
+    - wget https://sharebox.lsce.ipsl.fr/index.php/s/GgTDXL8peF4BOuV/download -O RAW.tar  > /dev/null 2>&1
     - tar -xf RAW.tar -C /tmp/PYCIF_DATA_TEST/
   script:
-    - tox -e py38 -e coverage -- -m "test_in_ci and chimere"
+    - tox -e py39 -e coverage -- -m "test_in_ci and chimere"
   after_script:
     - mkdir -p coverage
     - xmlstarlet sel -t -v "//coverage/@line-rate" reports/coverage.xml > coverage/.current_coverage
@@ -241,7 +241,7 @@ tests_chimere:
 #    - tar -xf download -C /tmp/PYCIF_DATA_TEST/
 #    - ls -R /tmp/PYCIF_DATA_TEST/
 #  script:
-#    - tox -e py38 -e coverage -- -m "test_in_ci and flexpart"
+#    - tox -e py39 -e coverage -- -m "test_in_ci and flexpart"
 #  after_script:
 #    - mkdir -p coverage
 #    - xmlstarlet sel -t -v "//coverage/@line-rate" reports/coverage.xml > coverage/.current_coverage

MANIFEST.in

 # Include the Fortran file
-include pycif/plugins/models/flexpart/utils/mod_flexpart.f90
+# include pycif/plugins/models/flexpart/utils/mod_flexpart.f90

bin/docker_debug.sh

@@ -3,6 +3,7 @@
 # Provide local path to your yaml configuration file
 config_file=$1
 pycif_root_dir=`pwd`/../
+extra_volumns=$2
 
 # Convert to absolute paths
 config_file=`echo "$(cd "$(dirname "$config_file")"; pwd)/$(basename "$config_file")"`
@@ -16,16 +17,13 @@ with open('$config_file', 'r') as f:
 
 print(config['workdir']); "`
 
-echo $workdir
-exit
-
-
 mkdir -p $workdir
 
 # Run the configuration into the container and writing outputs to workdir
 docker run -v $config_file:/config/config.yml \
     -v $pycif_root_dir:/tmp/CIF/ \
     -v $workdir:/workdir/ \
+    $extra_volumns \
     -it pycif/pycif-ubuntu:0.1
 
 

bin/docker_entrypoint.sh

 #!/usr/bin/env bash
 
+# Clean the local configuration file and working directory
+rm -f /config/config_local.yml
+rm -rf /workdir/*
+
 # Modify the original workdir from host to a local container workdir
 python3 -c \
-"import yaml;
-with open('/config/config.yml', 'r') as f: config = yaml.load(f, Loader=yaml.SafeLoader);
+"from pycif.utils.yml import ordered_load, ordered_dump;
+with open('/config/config.yml', 'r') as f: config = ordered_load(f);
 config['workdir']='/workdir/';
-with open('/config/config_local.yml', 'w') as f: yaml.dump(config, f);
+with open('/config/config_local.yml', 'w') as f: ordered_dump(f, config);
 "
 
 # Run pycif on the local yaml

examples/chimere/config_fwd_setup_edgar.yml

 rootdir: &rootdir /tmp/CIF/
-outdir: !join [*rootdir, /.tox/py38/tmp]
-verbose: 2
+outdir: &outdir !join [*rootdir, /.tox/py38/tmp]
+verbose: 1
 logfile: pycif.logtest
 workdir: !join [*outdir, /fwd_setup_edgar/]
 datei: 2011-03-22 00:00:00

examples/chimere/config_fwd_setup_melchior.yml

 rootdir: &rootdir /tmp/CIF/
-outdir: !join [*rootdir, /.tox/py38/tmp]
-verbose: 2
+outdir: &outdir !join [*rootdir, /debug/melchior/]
+verbose: 1
 logfile: pycif.logtest
 workdir: !join [*outdir, /fwd_setup_melchior/]
 datei: 2011-03-22 00:00:00
@@ -93,6 +93,24 @@ datavect:
             version: AEMISSIONS
           tresol: 1H
           vresol: vpixels
+        NO2:
+          dir: /tmp/PYCIF_DATA_TEST//RAW//EMISSIONS/EDGARV5/TOTAL/
+          file: v50_N2O_%Y.0.1x0.1.nc
+          plugin:
+            name: EDGAR
+            type: fluxes
+            version: v5
+          regrid:
+            method: mass-conservation
+          time_interpolation:
+            method: linear
+          unit_conversion:
+            scale: 1.368e+21
+          varname: emi_n2o
+          vertical_interpolation:
+            fill_nans: false
+            fill_nans_value: 0
+            method: closest
       plugin:
         name: CHIMERE
         type: fluxes

tox.ini

@@ -18,8 +18,8 @@ deps=
 [testenv:py36]
 basepython=python3.6
 
-[testenv:py38]
-basepython=python3.8
+[testenv:py39]
+basepython=python3.9
 
 [testenv:coverage]
 skip_install=true