Fix installation

MANIFEST.in

@@ -1 +1 @@
-global-include  cLIBFMS/lib/libcFMS.*
+graft pyfms/lib

README.md

@@ -1 +1,46 @@
-# fms2py
+# **`fms2py`**
+
+## **Installation**
+pyFMS requires a compiled `cFMS` library and the pyFMS repository contains
+cFMS as a submodule.  If `cFMS` is not installed on the user's
+local system, the library can be installed with
+
+```
+1.  git clone --recursive https://github.com/NOAA-GFDL/pyFMS.git
+2.  cd pyFMS
+3.  emacs ./compile.py (see Section compile.py)
+4.  python ./compile.py
+```
+
+The script `compile.py` will first compile and install the FMS library (which is
+a submodule in cFMS) to `pyfms/lib/FMS`.   Then, compile.py will compile the cFMS library
+linking to FMS in `pyfms/lib/FMS`.  cFMS will be installed to `pyfms/lib/cFMS`.
+
+Upon `import pyfms`, pyFMS will automatically load the cFMS library
+in `pyfms/lib/cFMS`.  If the cFMS library does not exist, or if users wish to load a
+diferent instance of cFMS, the following should be set in the program before invoking
+any pyFMS methods:
+
+```
+import pyfms
+
+pyfms.cfms.init(libpath=path_to_cfms/libcFMS.so)
+```
+
+## compile.py
+To compile cFMS with the script `compile.py`, users will need to specify the following
+fields:
+
+1.  Fortran and C compilers, for example, as shown below:
+
+```
+FC = "mpif90"
+CC = "mpicc"
+```
+
+2.  Path to the libyaml and netCDF installations, for example, as shown below:
+
+```
+yaml = "/opt/libyaml/0.2.5/GNU/14.2.0/"
+netcdf = "/opt/netcdf/4.9.3/GNU/14.2.0/"
+```

compile.py

@@ -0,0 +1,100 @@
+import os
+import subprocess
+
+
+# path to the installed yaml library
+yaml = "/opt/libyaml/0.2.5/GNU/14.2.0/"
+
+# path to the installed netcdf library
+netcdf = "/opt/netcdf/4.9.3/GNU/14.2.0/"
+
+# Fortran compiler
+FC = "mpif90"
+
+# C compiler
+CC = "mpicc"
+
+# default Fortran compiler flags
+FMS_FCFLAGS = f"-I{yaml}/include -I{netcdf}/include -fPIC"
+
+# default C compiler flags
+FMS_CFLAGS = f"-I{yaml}/include -I{netcdf}/include -fPIC"
+
+# library flags
+FMS_LDFLAGS = f"-L{yaml}/lib -L{netcdf}/lib -lnetcdf"
+
+cFMS_FCFLAGS = "-fPIC"
+cFMS_CFLAGS = "-fPIC"
+cFMS_LDFLAGS = ""
+
+# current directory
+currdir = os.path.dirname(__file__)
+
+# absolute path to cFMS submodule
+cFMS = f"{currdir}/cFMS"
+
+# absolute path to FMS submodule
+FMS = f"{cFMS}/FMS"
+
+# absolue path to install libraries
+cFMS_install = f"{currdir}/pyfms/lib/cFMS"
+FMS_install = f"{currdir}/pyfms/lib/FMS"
+
+
+def compile_FMS():
+
+    """
+    Install FMS to FMS_install
+    """
+
+    currdir = os.path.dirname(__file__)
+    os.chdir(FMS)
+
+    subprocess.run(["autoreconf", "-iv"])
+    subprocess.run(
+        [
+            "./configure",
+            "--enable-portable-kinds",
+            "--with-yaml",
+            f"FC={FC}",
+            f"CC={CC}",
+            f"FCFLAGS={FMS_FCFLAGS}",
+            f"CFLAGS={FMS_CFLAGS}",
+            f"LDFLAGS={FMS_LDFLAGS}",
+            f"--prefix={FMS_install}",
+        ]
+    )
+    subprocess.run(["make", "install"])
+
+    os.chdir(currdir)
+
+
+def compile_cFMS():
+
+    """
+    Install cFMS to cFMS_install
+    """
+    currdir = os.path.dirname(__file__)
+    os.chdir(cFMS)
+
+    subprocess.run(["autoreconf", "-iv"])
+    subprocess.run(
+        [
+            "./configure",
+            f"--with-fms={FMS_install}",
+            f"FC={FC}",
+            f"CC={CC}",
+            f"FCFLAGS={cFMS_FCFLAGS}",
+            f"CFLAGS={cFMS_CFLAGS}",
+            f"LDFLAGS={cFMS_LDFLAGS}",
+            f"--prefix={cFMS_install}",
+        ]
+    )
+    subprocess.run(["make", "install"])
+
+    os.chdir(currdir)
+
+
+# compile
+compile_FMS()
+compile_cFMS()

pyfms/cfms.py

@@ -4,8 +4,8 @@
 import pyfms
 
 
-_libpath: str = os.path.dirname(__file__) + "/cLIBFMS/lib/libcFMS.so"
-_lib: type[ctypes.CDLL] = ctypes.cdll.LoadLibrary(_libpath)
+_libpath = None
+_lib = None
 
 
 def init(libpath: str = None):
@@ -21,7 +21,17 @@ def init(libpath: str = None):
 
     global _libpath, _lib
 
-    if libpath is not None:
+    if libpath is None:
+        _libpath = os.path.dirname(__file__) + "/lib/cFMS/lib/libcFMS.so"
+        try:
+            _lib = ctypes.cdll.LoadLibrary(_libpath)
+        except OSError:
+            print(
+                f"{_libpath} does not exist.  Please compile cFMS with ./compile.py\
+                or provide a path to cFMS with pyfms.cfms.init(libpath=path_to_cfms"
+            )
+            return
+    else:
         _libpath = libpath
         _lib = ctypes.cdll.LoadLibrary(_libpath)
 

run_tests.sh

@@ -14,8 +14,6 @@ function run_test() {
     eval $1
     if [ $? -ne 0 ] ; then exit 1 ; fi                                                                                           }
 
-run_test "python -m pytest tests/test_build.py"
-
 test="tests/test_fms.py"
 create_input $test
 run_test "python -m pytest -m parallel $test"

setup.py

@@ -1,34 +1,22 @@
-import subprocess
-from typing import List
-
 from setuptools import find_namespace_packages, setup
-from setuptools.command.build import build
-
-
-class CustomBuild(build):
-    def run(self):
-        with open("install.log", "w") as f:
-            subprocess.run(["./compile_c_libs.sh"], stdout=f)
-        build.run(self)
 
 
-test_requirements = ["pytest", "pytest-subtests", "coverage"]
+test_requirements = [
+    "pytest",
+    "pytest-subtests",
+    "coverage",
+    "xarray",
+    "netCDF4",
+    "h5netcdf",
+]
 develop_requirements = test_requirements + ["pre-commit"]
 
 extras_requires = {
     "test": test_requirements,
     "develop": develop_requirements,
 }
 
-requirements: List[str] = [
-    "dacite",
-    "h5netcdf",
-    "numpy",
-    "pyyaml",
-    "mpi4py",
-    "xarray",
-    "netcdf4",
-]
+requirements = ["dacite", "numpy", "pyyaml", "mpi4py"]
 
 setup(
     author="NOAA/GFDL",
@@ -45,9 +33,8 @@ def run(self):
     name="pyfms",
     license="",
     packages=find_namespace_packages(include=["pyfms", "pyfms.*"]),
-    cmdclass={"build": CustomBuild},
     include_package_data=True,
-    url="https://github.com/fmalatino/pyFMS.git",
-    version="2024.02.0",
+    url="https://github.com/NOAA-GFDL/pyFMS.git",
+    version="2024.12.0",
     zip_safe=False,
 )

tests/test_init.py

@@ -1,25 +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_library_loaded():
 
+    """
+    Test to ensure library loaded automatically
+    """
 
-def test_write_module():
-    myfile = open("module1.py", "w")
-    myfile.write(
-        """
-import pyfms
-class Module1Class():
-    module1_lib_id = id(pyfms.cfms.lib())
-        """
-    )
-    myfile.close()
+    assert pyfms.cfms._lib is not None
 
 
 def test_share_same_library():
@@ -32,20 +22,6 @@ def test_share_same_library():
     assert id(pyfms.cfms._lib) == id(pyfms.mpp_domains._lib)
 
 
-def test_load_library_same_object():
-    sys.path.append(par_dir)
-
-    """
-    Test to ensure the ctypes CDLL Library object
-    is instantiated only once
-    """
-
-    import module1
-
-    myclass = module1.Module1Class()
-    assert id(pyfms.cfms.lib()) == myclass.module1_lib_id
-
-
 @pytest.mark.xfail
 def test_library_load_fail():
 
@@ -55,11 +31,3 @@ def test_library_load_fail():
     """
 
     pyfms.cfms.changelib(libpath="do_not_exist")
-
-
-def test_remove_module():
-    os.remove("module1.py")
-
-
-if __name__ == "__main__":
-    test_write_module()