upgrade to compatible with PDAF-V2.0 with nearly full subroutine supp…

…ort with PDAF.
yumengch · May 10, 2022 · 52485d1 · 52485d1
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diff --git a/.github/workflows/test_build.yaml b/.github/workflows/test_build.yaml
@@ -8,10 +8,11 @@ jobs:
       - run: sudo apt install -y liblapack-dev libblas-dev libopenmpi-dev
       - name: get PDAF
         run: |
-            wget -O PDAF-D_V1.16.tar.gz "${{ env.PDAF_LINK }}"
-            tar -zxvf PDAF-D_V1.16.tar.gz
+            wget -O PDAF_V2.0.tar.gz "${{ env.PDAF_LINK }}"
+            gzip -d PDAF_V2.0.tar.gz
+            tar -xvf PDAF_V2.0.tar
         env:
-          PDAF_LINK: ${{ secrets.PDAF116_LINK }}
+          PDAF_LINK: ${{ secrets.PDAF_V2 }}
 
       - name: Set up Python 3.8
         uses: actions/setup-python@v2

diff --git a/README.md b/README.md
@@ -1,11 +1,11 @@
 # pyPDAF
-A (incomplete) Python interface to the Fortran-written data assimilation library - [PDAF](http://pdaf.awi.de/trac/wiki)
+A Python interface to the Fortran-written data assimilation library - [PDAF](http://pdaf.awi.de/trac/wiki)
 
 ![GitHub Workflow Status](https://img.shields.io/github/workflow/status/yumengch/pyPDAF/test_build)
 
 
 ## Prerequisite:
-- `PDAF-V1.16`
+- `PDAF-V2.0`
 - `Fortran compiler: e.g.:gfortran/intel fortran`
 - `a message passing interface (MPI) implementation: e.g. openMPI/MPICH`
 - `Python>=3.8`
@@ -17,16 +17,12 @@ A (incomplete) Python interface to the Fortran-written data assimilation library
 
 ## Run example:
 ```bash
-mpiexec -n 8 python -u example/main.py
+mpiexec -n 4 python -u example/main.py
 ```
 Will run the model with 4 ensemble members where each member uses 2 processes. 
 
 ## Note:
-Currently, it only interfaces with limited subroutines of ```PDAF-V1.16``` with an example for online coupling with PDAF using a simple model based on the [tutorial](http://pdaf.awi.de/trac/wiki/FirstSteps) from PDAF. Some interface in Python changes slightly due to different ways to handling return values in Python from Fortran. It is possible to check Python interface [here](https://yumengch.github.io/pyPDAF/index.html). More subroutines will be supported in future release. 
-
-## Development
-The interface between Fortran and Python relies on [Cython](https://cython.readthedocs.io/en/stable/index.html) and the feature of [iso_c_binding](https://gcc.gnu.org/onlinedocs/gfortran/ISO_005fC_005fBINDING.html) in Fortran. 
-
+Currently, it interfaces with subroutines of ```PDAF-V2.0``` with an example for online coupling with PDAF using a simple model based on the [tutorial](http://pdaf.awi.de/trac/wiki/FirstSteps) from PDAF. Some interface in Python changes slightly due to different ways to handling return values in Python from Fortran. Visit [here](https://yumengch.github.io/pyPDAF/index.html) to check more detailed documentation on installation, Python interface, and implementation guide on pyPDAF. The simplified interfaces in PDAF are not supported. 
 
 ## Contributors:
 Yumeng Chen, Lars Nerger

diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/PDAF/PDAFomi.html b/docs/PDAF/PDAFomi.html
diff --git a/docs/PDAF/index.html b/docs/PDAF/index.html
diff --git a/docs/UserFunc/c__PDAFomi.html b/docs/UserFunc/c__PDAFomi.html