Feature: CI

.github/workflows/lint.yaml

@@ -21,7 +21,7 @@ jobs:
             python-version: '3.11.7'
         - name: Install OpenMPI for gt4py
           run: |
-            sudo apt-get install libopenmpi-dev
+            sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
         - name: Install Python packages
           run: |
             python -m pip install --upgrade pip setuptools wheel

.github/workflows/unit_tests.yaml

@@ -0,0 +1,29 @@
+name: "pyfms unit tests"
+on: [push, pull_request]
+
+# cancel running jobs if theres a newer push
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pyfms_unit_tests:
+    runs-on: ubuntu-latest
+    steps:
+        - name: Checkout out hash that triggered CI
+          uses: actions/checkout@v4
+          with:
+            submodules: 'recursive'
+        - name: Step Python
+          uses: actions/setup-python@v4.6.0
+          with:
+            python-version: '3.11.7'
+        - name: Install OpenMPI for gt4py
+          run: |
+            sudo apt-get install libopenmpi-dev netcdf-bin libnetcdf-dev libnetcdff-dev nco libyaml-dev diffutils
+        - name: install packages
+          run: |
+            pip install .[test]
+        - name: run tests
+          run: |
+            ./run_tests.sh

MANIFEST.in

@@ -0,0 +1 @@
+global-include  cLIBFMS/lib/libcFMS.*

compile_c_libs.sh

@@ -1,15 +1,18 @@
 #!/bin/bash
 
-curr_dir=$PWD/cFMS
-install_fms=$curr_dir/FMS/LIBFMS
+set -xe
+
+pyfms_dir=$PWD/pyfms
+cfms_dir=$PWD/cFMS
+install_fms=$cfms_dir/FMS/LIBFMS
 
 export FC=mpif90
 export CC=mpicc
 
-cd $curr_dir/FMS
+cd $cfms_dir/FMS
 autoreconf -iv
-export FCFLAGS="$FCFLAGS -fPIC"
-export CFLAGS="$CFLAGS -fPIC"
+export FCFLAGS="$FCFLAGS `nf-config --fflags` -fPIC"
+export CFLAGS="$CFLAGS `nc-config --cflags` -fPIC"
 ./configure --enable-portable-kinds --with-yaml --prefix=$install_fms
 make install
 
@@ -21,5 +24,5 @@ export CFLAGS="$CFLAGS -I$install_fms/include"
 export LDFLAGS="$LDFLAGS -lFMS -L$install_fms/lib"
 
 autoreconf -iv
-./configure --prefix=$curr_dir/cLIBFMS
+./configure --with-fms=$install_fms --prefix=$pyfms_dir/cLIBFMS
 make install

pyfms/cfms.py

@@ -4,8 +4,8 @@
 import pyfms
 
 
-_libpath = os.path.dirname(__file__) + "/../cFMS/cLIBFMS/lib/libcFMS.so"
-_lib = ctypes.cdll.LoadLibrary(_libpath)
+_libpath: str = os.path.dirname(__file__) + "/cLIBFMS/lib/libcFMS.so"
+_lib: type[ctypes.CDLL] = ctypes.cdll.LoadLibrary(_libpath)
 
 
 def init(libpath: str = None):

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools >= 64"]
+build-backend = "setuptools.build_meta"

run_tests.sh

@@ -14,39 +14,39 @@ function run_test() {
     eval $1
     if [ $? -ne 0 ] ; then exit 1 ; fi                                                                                           }
 
-run_test "pytest tests/test_build.py"
+run_test "python -m pytest tests/test_build.py"
 
 test="tests/test_fms.py"
 create_input $test
-run_test "pytest -m parallel $test"
+run_test "python -m pytest -m parallel $test"
 remove_input $test
 
 test="tests/py_mpp/test_define_domains.py"
 create_input $test
-run_test "mpirun -n 8 python -m pytest -m 'parallel' $test"
+run_test "mpirun -n 8 --oversubscribe python -m pytest -m 'parallel' $test"
 remove_input $test
 
 test="tests/py_mpp/test_getset_domains.py"
 create_input $test
-run_test "mpirun -n 4 python -m pytest -m 'parallel' tests/py_mpp/test_getset_domains.py"
+run_test "mpirun -n 4 --oversubscribe python -m pytest -m 'parallel' tests/py_mpp/test_getset_domains.py"
 remove_input $test
 
 test="tests/py_mpp/test_update_domains.py"
 create_input $test
-run_test "mpirun -n 4 python -m pytest -m 'parallel' tests/py_mpp/test_update_domains.py"
+run_test "mpirun -n 4 --oversubscribe python -m pytest -m 'parallel' tests/py_mpp/test_update_domains.py"
 remove_input $test
 
-run_test "pytest tests/py_horiz_interp"
+run_test "python -m pytest tests/py_horiz_interp"
 
-run_test "pytest tests/py_data_override/test_generate_files.py"
-run_test "mpirun -n 6 python -m pytest -m 'parallel' tests/py_data_override/test_data_override.py"
+run_test "python -m pytest tests/py_data_override/test_generate_files.py"
+run_test "mpirun -n 6 --oversubscribe python -m pytest -m 'parallel' tests/py_data_override/test_data_override.py"
 remove_input "tests/py_data_override/test_data_override.py"
 
-run_test "pytest tests/py_diag_manager/test_generate_files.py"
+run_test "python -m pytest tests/py_diag_manager/test_generate_files.py"
 run_test "mpirun -n 1 python -m pytest tests/py_diag_manager/test_diag_manager.py"
 
-pytest tests/utils/test_constants.py
+run_test "python -m pytest tests/utils/test_constants.py"
 
-pytest tests/test_init.py
+run_test "python -m pytest tests/test_init.py"
 
 rm -rf INPUT *logfile* *warnfile*

setup.py

@@ -2,15 +2,14 @@
 from typing import List
 
 from setuptools import find_namespace_packages, setup
-from setuptools.command.install import install
+from setuptools.command.build import build
 
 
-class CustomInstall(install):
+class CustomBuild(build):
     def run(self):
-        # subprocess.run(["./compile_c_libs.sh"], capture_output=True, text=True)
         with open("install.log", "w") as f:
             subprocess.run(["./compile_c_libs.sh"], stdout=f)
-        install.run(self)
+        build.run(self)
 
 
 test_requirements = ["pytest", "pytest-subtests", "coverage"]
@@ -21,7 +20,15 @@ def run(self):
     "develop": develop_requirements,
 }
 
-requirements: List[str] = ["dacite", "h5netcdf", "numpy", "pyyaml", "mpi4py", "xarray"]
+requirements: List[str] = [
+    "dacite",
+    "h5netcdf",
+    "numpy",
+    "pyyaml",
+    "mpi4py",
+    "xarray",
+    "netcdf4",
+]
 
 setup(
     author="NOAA/GFDL",
@@ -38,9 +45,9 @@ def run(self):
     name="pyfms",
     license="",
     packages=find_namespace_packages(include=["pyfms", "pyfms.*"]),
-    cmdclass={"install": CustomInstall},
+    cmdclass={"build": CustomBuild},
     include_package_data=True,
     url="https://github.com/fmalatino/pyFMS.git",
-    version="2024.12.0",
+    version="2024.02.0",
     zip_safe=False,
 )

tests/test_build.py

@@ -2,4 +2,6 @@
 
 
 def test_shared_object_exists():
-    assert os.path.exists(os.path.dirname(__file__) + "/../cFMS/cLIBFMS/lib/libcFMS.so")
+    assert os.path.exists(
+        os.path.dirname(__file__) + "/../pyfms/cLIBFMS/lib/libcFMS.so"
+    )

tests/test_init.py

@@ -1,10 +1,15 @@
 import os
+import sys
 
 import pytest
 
 import pyfms
 
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+par_dir = os.path.dirname(curr_dir)
+
+
 def test_write_module():
     myfile = open("module1.py", "w")
     myfile.write(
@@ -28,6 +33,7 @@ def test_share_same_library():
 
 
 def test_load_library_same_object():
+    sys.path.append(par_dir)
 
     """
     Test to ensure the ctypes CDLL Library object