fixes bugs for CI

.github/workflows/test_linux_build.yaml

@@ -21,7 +21,7 @@ jobs:
         run: pip install -v .
 
       - name: run example
-        run: mpiexec -n 4 python -u example/main.py
+        run: mpiexec --oversubscribe -n 4 python -u example/main.py
 
       - name: Setup tmate session
         if: ${{ failure() }}

example/config.py

@@ -34,9 +34,9 @@
 
 ### Filepath ###
 # path to initial ensemble, the filename is formatted for different time step
-init_ens_path:str = os.path.join('/home/ia923171/software/PDAF_V2.2.1/tutorial/inputs_online', 'ens_{i}.txt')
+init_ens_path:str = os.path.join('/home/runner/work/pyPDAF/pyPDAF/inputs_online', 'ens_{i}.txt')
 # path to initial truth
-init_truth_path:str = os.path.join('/home/ia923171/software/PDAF_V2.2.1/tutorial/inputs_online', 'true_initial.txt')
+init_truth_path:str = os.path.join('/home/runner/work/pyPDAF/pyPDAF/inputs_online', 'true_initial.txt')
 
 
 #### Model configurations ####

example/config_obsA.py

@@ -27,13 +27,13 @@
 # name of the observation
 obs_name = 'A'
 # path to the observation files
-obs_path:str = os.path.join('/home/ia923171/software/PDAF_V2.2.1/tutorial/inputs_online', 'obs_step{i}.txt')
+obs_path:str = os.path.join('/home/runner/work/pyPDAF/pyPDAF/inputs_online', 'obs_step{i}.txt')
 # time steps between observations / assimilation frequency
 dtobs:int = 2
 # Observation error standard deviation
 rms_obs:float = 0.5
 # Switch for assimilating observation type A
-assim:bool = False
+assim:bool = True
 # Type of distance computation to use for localization
 # It is mandatory for OMI even if we don't use localisation
 # 0=Cartesian 1=Cartesian periodic

example/config_obsB.py

@@ -27,13 +27,13 @@
 # name of the observation
 obs_name = 'B'
 # path to the observation files
-obs_path:str = os.path.join('/home/ia923171/software/PDAF_V2.2.1/tutorial/inputs_online', 'obsB_step{i}.txt')
+obs_path:str = os.path.join('/home/runner/work/pyPDAF/pyPDAF/inputs_online', 'obsB_step{i}.txt')
 # time steps between observations / assimilation frequency
 dtobs:int = 2
 # Observation error standard deviation
 rms_obs:float = 0.5
 # Switch for assimilating observation type A
-assim:bool = True
+assim:bool = False
 # Type of distance computation to use for localization
 # It is mandatory for OMI even if we don't use localisation
 # 0=Cartesian 1=Cartesian periodic

setup.cfg

@@ -8,7 +8,7 @@ install_requires =
 [pyPDAF]
 pwd = /home/runner/work/pyPDAF/pyPDAF
 PDAF_dir = PDAF_V2.2.1
-cmake_config_path = /home/runner/work/pyPDAF/pyPDAF/linux_gfortran_openmpi_pypdaf.cmake
+cmake_config_path = /home/runner/work/pyPDAF/pyPDAF/PDAFBuild/linux_gfortran_openmpi_pypdaf.cmake
 CC = mpicc
 condaBuild = False
 # if MKL is used, give the path to the static MKL library