Upgrade pyPDAF to be compatible with PDAF V2.2.1 (#4)

* adding new interface functions; improved documentation; improved file parser; adding array annotation in Cython; PDAF compilation with CMake in Linux * fixes bugs in C interface code; fixes issues with installation; add CMake configurations; uses single precision integer in examples for compatibility with Fortran and Cython declaration. * update the pointer to submodule update the pointer to submodule * add missed subroutine interface c__pdafomi_localize_covar_noniso work out build process and CI for Linux and Mac; cleaned compile pyPDAF on windows; hopefully improved stability using intel-fortran-rt and mpi when new conda version is published; cannot workout a windows build CI as it seems very difficult to set up Intel Fortran with Visual studio in github runner but it is useful to keep the compiler environment variable options. * separate model ensemble and model integrator * improved robustness of conda installation; allowing conda packaging from github runner for mac and linux
yumengch · Oct 10, 2024 · 89c610c · 89c610c
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diff --git a/.github/workflows/condaBuildMac.yaml → .github/workflows/conda_build_linux.yaml b/.github/workflows/condaBuildMac.yaml → .github/workflows/conda_build_linux.yaml
@@ -1,23 +1,31 @@
-name: condaBuild
+name: conda_build_linux
 on: [workflow_dispatch]
 jobs:
-  check_mac_installation:
-    runs-on: macos-latest
+  upload_conda_linux:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: 'true'
-          ref: intelMacConda
+          ref: upgrade2.2.1
 
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-activate-base: true
           auto-update-conda: true
+          activate-environment: ""
 
       - name: install pyPDAF
         shell: bash -el {0}
         run: |
+          cp PDAFBuild/setup_conda_linux.cfg setup.cfg
           conda install python anaconda-client conda-build conda-verify
           anaconda login --username yumengch --password ${{ secrets.ANACONDA }}
           conda  config --set anaconda_upload yes
-          conda-build -c conda-forge -c intel conda.recipe/
+          conda-build -c conda-forge conda.recipe/
+          conda install -y -c conda-forge --use-local pypdaf
+          mpiexec -n 4 python -u example/main.py 
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/conda_build_mac_intel.yaml b/.github/workflows/conda_build_mac_intel.yaml
@@ -0,0 +1,37 @@
+name: conda_build_mac_intel
+on: [workflow_dispatch]
+jobs:
+  upload_conda_mac_intel:
+    runs-on: macos-13
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+          ref: upgrade2.2.1
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-activate-base: true
+          auto-update-conda: true
+          activate-environment: ""
+
+      - name: build pyPDAF
+        shell: bash -el {0}
+        run: |
+          cp PDAFBuild/setup_conda_intel_mac.cfg setup.cfg
+          conda install python anaconda-client conda-build conda-verify
+          anaconda login --username yumengch --password ${{ secrets.ANACONDA }}
+          conda  config --set anaconda_upload yes
+          conda-build -c conda-forge conda.recipe/
+
+      - name: install pyPDAF
+        shell: bash -el {0}
+        run: |
+          conda install -y -c conda-forge --use-local pypdaf
+          mv example/config_mac.py example/config.py
+          mv example/config_obsA_mac.py example/config_obsA.py
+          mpiexec -n 4 python -u example/main.py 
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/conda_build_mac_m1.yaml b/.github/workflows/conda_build_mac_m1.yaml
@@ -0,0 +1,37 @@
+name: conda_build_mac_m1
+on: [workflow_dispatch]
+jobs:
+  upload_conda_mac_m1:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+          ref: upgrade2.2.1
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-activate-base: true
+          auto-update-conda: true
+          activate-environment: ""
+
+      - name: build pyPDAF
+        shell: bash -el {0}
+        run: |
+          cp PDAFBuild/setup_conda_m1_mac.cfg setup.cfg
+          conda install python anaconda-client conda-build conda-verify
+          anaconda login --username yumengch --password ${{ secrets.ANACONDA }}
+          conda  config --set anaconda_upload yes
+          conda-build -c conda-forge conda.recipe/
+
+      - name: install pyPDAF
+        shell: bash -el {0}
+        run: |
+          conda install -y -c conda-forge --use-local pypdaf
+          mv example/config_mac.py example/config.py
+          mv example/config_obsA_mac.py example/config_obsA.py
+          mpiexec -n 4 python -u example/main.py 
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/test_build.yaml b/.github/workflows/test_build.yaml
diff --git a/.github/workflows/test_linux_build.yaml b/.github/workflows/test_linux_build.yaml
@@ -0,0 +1,28 @@
+name: test_linux_build
+on: [workflow_dispatch]
+
+jobs:
+  test_ubuntu_build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: check out code
+        uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+          ref: main
+
+      - name: installing dependent libraries
+        run: sudo apt install -y liblapack-dev libblas-dev libopenmpi-dev
+
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v5
+
+      - name: install pyPDAF
+        run: pip install -v .
+
+      - name: run example
+        run: mpiexec --oversubscribe -n 4 python -u example/main.py
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/test_mac_build.yaml b/.github/workflows/test_mac_build.yaml
@@ -0,0 +1,40 @@
+name: test_mac_build
+on: [workflow_dispatch]
+
+jobs:
+  test_mac_build:
+    runs-on: macos-latest
+    steps:
+      - name: check out code
+        uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+          ref: upgrade2.2.1
+
+      - name: Setup Fortran compiler
+        uses: fortran-lang/[email protected]
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 13
+
+      - name: install dependent Libaries
+        run: brew install openblas lapack open-mpi
+
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v5
+
+      - name: install pyPDAF
+        run: |
+          mv setup_mac.cfg setup.cfg
+          pip install -v .
+
+      - name: run example
+        run: |
+          mv example/config_mac.py example/config.py
+          mv example/config_obsA_mac.py example/config_obsA.py
+          mpiexec --oversubscribe -n 4 python -u example/main.py
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/test_win_build.yaml b/.github/workflows/test_win_build.yaml
@@ -0,0 +1,81 @@
+name: test_win_build
+on: [workflow_dispatch]
+
+env:
+  WINDOWS_BASEKIT_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/e83a8e64-04fc-45df-85c6-c2208d03bdb5/w_BaseKit_p_2024.2.0.635_offline.exe
+  WINDOWS_HPCKIT_URL: https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0d500705-397e-41b3-8b2b-2a3da1753fc2/w_HPCKit_p_2024.2.0.633_offline.exe
+  WINDOWS_FORTRAN_COMPONENTS: intel.oneapi.win.ifort-compiler
+  WINDOWS_DPCPP_COMPONENTS: intel.oneapi.win.mkl.devel:intel.oneapi.win.tbb.devel
+  CACHE_NUMBER: 5
+  COMPILER_VERSION: 2024.2.0
+  TBB_VERSION: 2021.13.0
+  VS_VER: vs2022
+
+jobs:
+  test_windows_build:
+    runs-on: windows-latest
+    steps:
+      - name: check out oneAPI code
+        uses: actions/checkout@v4
+        with:
+          repository: oneapi-src/oneapi-ci
+
+      - name: cache install fortran
+        id: cache-install-fortran
+        uses: actions/cache@v2
+        with:
+          path: |
+              C:\Program Files (x86)\Intel\oneAPI\setvars-vcvarsall.bat
+              C:\Program Files (x86)\Intel\oneAPI\compiler
+          key: install-${{ env.CACHE_NUMBER }}-${{ env.WINDOWS_HPCKIT_URL }}-${{ env.WINDOWS_FORTRAN_COMPONENTS }}-compiler-${{ hashFiles('**/scripts/cache_exclude_windows.sh') }}
+
+      - name: install fortran
+        if: steps.cache-install.outputs.cache-hit != 'true'
+        shell: bash
+        run: scripts/install_windows.bat $WINDOWS_HPCKIT_URL $WINDOWS_FORTRAN_COMPONENTS
+
+      - name: cache install mkl
+        id: cache-install-mkl
+        uses: actions/cache@v2
+        with:
+          path: |
+            C:\Program Files (x86)\Intel\oneAPI\setvars-vcvarsall.bat
+            C:\Program Files (x86)\Intel\oneAPI\compiler
+            C:\Program Files (x86)\Intel\oneAPI\tbb
+            C:\Windows\System32\OpenCL.dll
+          key: install-${{ env.CACHE_NUMBER }}-${{ env.WINDOWS_BASEKIT_URL }}-${{ env.WINDOWS_DPCPP_COMPONENTS }}-compiler-tbb-opencl-${{ hashFiles('**/scripts/cache_exclude_windows.sh') }}
+
+      - name: install mkl
+        if: steps.cache-install.outputs.cache-hit != 'true'
+        shell: bash
+        run: scripts/install_windows.bat $WINDOWS_BASEKIT_URL $WINDOWS_DPCPP_COMPONENTS
+
+      - name: restore registry on cache hit
+        if: steps.cache-install.outputs.cache-hit == 'true'
+        shell: bash
+        run: scripts/restore_registry.bat $COMPILER_VERSION $TBB_VERSION
+
+      - name: check out pyPDAF code
+        uses: actions/checkout@v4
+        with:
+          submodules: 'true'
+          ref: upgrade2.2.1
+
+      - name: install pyPDAF
+        run: |
+          cmd.exe /k "C:\Program Files\Microsoft Visual Studio\2022\Community\VC\Auxiliary\Build\vcvars64.bat"
+          cmd.exe /k "C:\Program Files (x86)\Intel\oneAPI\compiler\2024.2\env\vars.bat"
+          cmd.exe /k '"C:\Program Files (x86)\Intel\oneAPI\mkl\latest\env\vars.bat" && powershell'
+          cd D:\a\pyPDAF\pyPDAF
+          Move-Item -Path setup_win.cfg -Destination setup.cfg -Force
+          pip install -v .
+
+      - name: run example
+        run: |
+          Move-Item -Path example/config_win.py -Destination example/config.py -Force
+          Move-Item -Path example/config_obsA_win.py -Destination example/config_obsA.py -Force
+          mpiexec --oversubscribe -n 4 python -u example/main.py
+
+      - name: Setup tmate session
+        if: ${{ failure() }}
+        uses: mxschmitt/action-tmate@v3
diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
-[submodule "PDAF_V2.1"]
-	path = PDAF_V2.1
-	url = https://github.com/PDAF/PDAF/
-	branch = PDAF_V2.1
+[submodule "PDAF_V2.2.1"]
+	path = PDAF_V2.2.1
+	url = https://github.com/PDAF/PDAF.git
+	branch = PDAF_V2.2.1