Initial implementation of TOML file

Makefile.Forthon

@@ -13,7 +13,7 @@ all: mppl2f90 $(BUILDDIR)/compydep $(BUILDDIR)/grdpydep $(BUILDDIR)/flxpydep $(B
 	rm -f uedgeC.so
 
 mppl2f90:
-	(export PYTHONPATH=.:./pyscripts; $(MYPYTHON) convertor)
+	(export PYTHONPATH=.:./buildscripts; $(MYPYTHON) convertor)
 
 $(BUILDDIR)/compydep: com/blasext.F com/brent.F com/comutil.F com/misc.F com/mnbrak.F com/dsum.f com/dummy_py.f com/error.f com/getmsg.f com/ssum.f com/$(PETSC-COM) com/com.v
 	$(FORTHON) -a $(INSTALLARGS) -a $(FCOMP) $(DEBUG) --interfacefile com/com.v -f com/blasext.F com com/brent.F com/comutil.F com/misc.F com/mnbrak.F com/dsum.f com/dummy_py.f com/error.f com/getmsg.f com/ssum.f $(PETSC-COM)

pyproject.toml

@@ -0,0 +1,75 @@
+[build-system]
+requires = ["setuptools >= 61.0", "forthon", "numpy"]
+build-backend = "setuptools.build_meta:__legacy__"
+
+[project]
+#dynamic = ["version"]
+version = "8.1.0-beta.0"
+name = "uedge"
+dependencies = [
+    "forthon",
+    "numpy",
+]
+requires-python = ">= 3.5" # TODO: verify
+authors = [
+  {name = "Tom Rognlien"}
+]
+maintainers = [
+  {name = "Bill Meyer", email = "[email protected]"},
+  {name = "Andreas Holm", email = "[email protected]"}
+]
+description = "2D Fluid simulation of plasma and neutrals in magnetic fusion devices"
+readme = "README.md"
+keywords = [
+    "plasma",
+    "fusion",
+    "tokamak",
+    "edge-plasma",
+    "scrape-off layer",
+    "multi-fluid"
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)",
+    "Operating System :: Unix",
+    "Operating System :: MacOS :: MacOS X",
+    "Programming Language :: Fortran",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+
+[project.urls]
+Homepage = "https://github.com/LLNL/UEDGE/"
+#Documentation = "https://readthedocs.org"
+Repository = "https://github.com/LLNL/UEDGE.git"
+Issues = "https://github.com/LLNL/UEDGE/issues"
+#Changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
+
+
+
+
+[project.optional-dependencies]
+ueplot = [
+    "matplotlib",
+    "scipy",
+    "scikit-image"
+]
+
+# TODO: rewrite scripts to be importable
+#[project.scripts]
+#spam-cli = "spam:main_cli"
+
+#[tool.setuptools]
+#script-files = [
+#    "pyscripts/pdb2hdf5",
+#    "pyscripts/bas2py",
+#    "pyscripts/hdf52pdb"
+#]
+#packages = ["uedge"]
+#package-dir = {"" = "pyscripts"}
+
+
+
+#[tool.setuptools.dynamic]
+#version = {attr = "uedge.__version__"}

setup.py

@@ -10,29 +10,21 @@
 from Forthon.compilers import FCompiler
 import getopt
 import logging
+from subprocess import call
+import numpy
+from setuptools import Extension, setup, Distribution
+from setuptools.command.build import build
+from setuptools.command.develop import develop
+from setuptools.command.egg_info import egg_info
+os.environ['PATH'] += os.pathsep + site.USER_BASE + '/bin'
 
-version='8.1.0-beta.0'
-
-try:
-    os.environ['PATH'] += os.pathsep + site.USER_BASE + '/bin'
-    import setuptools
-    import distutils
-    from distutils.core import setup
-    from distutils.core import Extension
-    from distutils.dist import Distribution
-    from distutils.command.build import build
-    from distutils.command.install import install
-    from subprocess import call
-    import numpy
-except:
-    raise SystemExit("Distutils problem")
-
-optlist, args = getopt.getopt(sys.argv[1:], 'gt:F:', ['parallel', 'petsc', 'omp'])
+
+optlist, args = getopt.getopt(sys.argv[1:], 'gt:F:', ['parallel', 'omp'])
 machine = sys.platform
 debug = 0
 fcomp = None
 parallel = 0
-petsc = 0
+#petsc = 0
 
 for o in optlist:
     if o[0] == '-g':
@@ -43,19 +35,19 @@
         fcomp = o[1]
     elif o[0] == '--parallel':
         parallel = 1
-    elif o[0] == '--petsc':
-        petsc = 1
+#    elif o[0] == '--petsc':
+#        petsc = 1
     elif o[0] == '--omp':
         os.putenv("OMP","1")
 
 
 
-if petsc == 1 and os.getenv('PETSC_DIR') == None:
-    raise SystemExit("PETSc requested but PETSC_DIR not set")
-if os.getenv('PETSC_DIR') != None:
-    petsc = 1
-if petsc == 1 and os.getenv('PETSC_ARCH') == None:
-    raise SystemExit("PETSc requested but PETSC_ARCH not set")
+#if petsc == 1 and os.getenv('PETSC_DIR') == None:
+#    raise SystemExit("PETSc requested but PETSC_DIR not set")
+#if os.getenv('PETSC_DIR') != None:
+#    petsc = 1
+#if petsc == 1 and os.getenv('PETSC_ARCH') == None:
+#    raise SystemExit("PETSc requested but PETSC_ARCH not set")
 
 
 sys.argv = ['setup2.py']+args
@@ -64,36 +56,53 @@
                       fcompname=fcomp)
 
 
-class uedgeInstall(build):
-    def run(self):
-       install.run(self)
-       logging.basicConfig(stream=sys.stderr,level=logging.INFO)
-       log = logging.getLogger()
-       log.info("test")
+#class uedgeInstall(build):
+#    def run(self):
+#       install.run(self)
+#       logging.basicConfig(stream=sys.stderr,level=logging.INFO)
+#       log = logging.getLogger()
+#       log.info("test")
+
 class uedgeBuild(build):
     def run(self):
+        print("Building UEDGE...")
         # with python2 everything is put into a single uedgeC.so file
         if sys.hexversion < 0x03000000:
             raise SystemExit("Python versions < 3 not supported")
         else:
-            if petsc == 0:
-                status = call(['make', '-f','Makefile.Forthon'])
-            else:
-                status = call(['make', '-f', 'Makefile.PETSc'])
-            if status != 0: raise SystemExit("Build failure")
+#            if petsc == 0:
+            status = call(['make', '-f','Makefile.Forthon'])
+#            else:
+#                status = call(['make', '-f', 'Makefile.PETSc'])
+            if status != 0: 
+                raise SystemExit("Build failure")
             build.run(self)
 
 
 class uedgeClean(build):
     def run(self):
+        print("Cleaning UEDGE")
         if sys.hexversion < 0x03000000:
             raise SystemExit("Python versions < 3 not supported")
         else:
-            if petsc == 0:
-                status = call(['make', '-f', 'Makefile.Forthon', 'clean'])
-            else:
-                status = call(['make', '-f', 'Makefile.PETSc', 'clean'])
-            if status != 0: raise SystemExit("Clean failure")
+#            if petsc == 0:
+            status = call(['make', '-f', 'Makefile.Forthon', 'clean'])
+#            else:
+#                status = call(['make', '-f', 'Makefile.PETSc', 'clean'])
+            if status != 0: 
+                raise SystemExit("Clean failure")
+
+
+class CustomDevelopCommand(develop):
+    def run(self):
+        print("Develop called")
+        develop.run(self)
+
+
+class CustomEggInfoCommand(egg_info):
+    def run(self):
+        print("EggInfo called")
+        egg_info.run(self)
 
 uedgepkgs = ['aph', 'api', 'bbb', 'com', 'flx', 'grd', 'svr', 'wdf', 'ncl']
 
@@ -126,27 +135,27 @@ def makeobjects(pkg):
     library_dirs = fcompiler.libdirs
     libraries = fcompiler.libs
 
-if petsc:
+#if petsc:
     # PETSC_DIR = '/homes/mccomic/petsc-uedge'
     # PETSC_ARCH = 'linux-uedge'
-    PETSC_DIR = os.getenv('PETSC_DIR')
-    PETSC_ARCH = os.getenv('PETSC_ARCH')
-    library_dirs = fcompiler.libdirs + \
-        [os.path.join(PETSC_DIR, PETSC_ARCH, 'lib')]
-    libraries = ['petscts', 'petscsnes', 'petscksp', 'petscdm', 'petscmat',
-                 'petscvec', 'petsc', 'HYPRE', 'mpich', 'lapack', 'blas', 'X11',
-                 'pthread', 'rt', 'stdc++', 'm'] + fcompiler.libs
-    libraries = ['petsc'] + fcompiler.libs
+#    PETSC_DIR = os.getenv('PETSC_DIR')
+#    PETSC_ARCH = os.getenv('PETSC_ARCH')
+#    library_dirs = fcompiler.libdirs + \
+#        [os.path.join(PETSC_DIR, PETSC_ARCH, 'lib')]
+#    libraries = ['petscts', 'petscsnes', 'petscksp', 'petscdm', 'petscmat',
+#                 'petscvec', 'petsc', 'HYPRE', 'mpich', 'lapack', 'blas', 'X11',
+#                 'pthread', 'rt', 'stdc++', 'm'] + fcompiler.libs
+#    libraries = ['petsc'] + fcompiler.libs
 
 if parallel:
     library_dirs = fcompiler.libdirs + ['/usr/lpp/ppe.poe/lib']
     libraries = fcompiler.libs + ['mpi']
     # uedgeobjects = uedgeobjects + ['/usr/local/mpi/ifc_farg.o']
 
-with open('pyscripts/__version__.py','w') as ff:
-    ff.write("__version__ = '%s'\n"%version)
-with open('pyscripts/__src__.py','w') as ff:
-    ff.write("__src__ = '%s'\n"%os.getcwd())
+#with open('pyscripts/__version__.py','w') as ff:
+#    ff.write("__version__ = '%s'\n"%version)
+#with open('pyscripts/__src__.py','w') as ff:
+#    ff.write("__src__ = '%s'\n"%os.getcwd())
 
 define_macros=[("WITH_NUMERIC", "0"),
                ("FORTHON_PKGNAME", '\"uedgeC\"'),
@@ -161,37 +170,25 @@ def makeobjects(pkg):
    libraries = ['readline'] + libraries
 
 
-setup(name="uedge",
-      version=version,
-      author='Tom Rognlien',
-      author_email="[email protected]",
-      maintainer='Bill Meyer',
-      maintainer_email='[email protected]',
-      description="2D Fluid simulation of plasma and neutrals in magnetic fusion devices",
-      platforms="Unix, Windows (cygwin), Mac OSX",
-      packages=['uedge'],
-      package_dir={'uedge': 'pyscripts'},
-      # include_package_data=True,
-      scripts=['pyscripts/pdb2hdf5', 'pyscripts/bas2py', 'pyscripts/hdf52pdb'],
-      ext_modules=[Extension('uedge.uedgeC',
-                             ['uedgeC_Forthon.c',
-                              os.path.join(builddir, 'Forthon.c'),
-                              'com/handlers.c', 'com/vector.c','bbb/exmain.c'],
-                             include_dirs=[builddir, numpy.get_include()],
-                             library_dirs=library_dirs,
-                             libraries=libraries,
-                             define_macros=define_macros,
-                             extra_objects=uedgeobjects,
-                             extra_link_args=['-g','-DFORTHON'] +
-                             fcompiler.extra_link_args,
-                             extra_compile_args=fcompiler.extra_compile_args
-                             )],
-
-      cmdclass={'build': uedgeBuild, 'clean': uedgeClean},
-      test_suite="pytests",
-      install_requires=['forthon'],
-      # note that include_dirs may have to be expanded in the line above
-      classifiers=['Programming Language :: Python',
-                   'Programming Language :: Python :: 3']
-
-      )
+setup(
+        ext_modules=[Extension('uedge.uedgeC',
+                            ['uedgeC_Forthon.c',
+                            os.path.join(builddir, 'Forthon.c'),
+                            'com/handlers.c', 'com/vector.c','bbb/exmain.c'],
+                            include_dirs=[builddir, numpy.get_include()],
+                            library_dirs=library_dirs,
+                            libraries=libraries,
+                            define_macros=define_macros,
+                            extra_objects=uedgeobjects,
+                            extra_link_args=['-g','-DFORTHON'] +
+                            fcompiler.extra_link_args,
+                            extra_compile_args=fcompiler.extra_compile_args
+                    )],
+        cmdclass={
+            'build': uedgeBuild, 
+            'clean': uedgeClean,
+            'develop': CustomDevelopCommand,
+            'egg_info': CustomEggInfoCommand,
+        },
+#      test_suite="pytests",
+)

pyscripts/__init__.py → src/uedge/__init__.py

@@ -1,19 +1,12 @@
 from .uedge import *
 from os import path
 from pathlib import Path
-try:
-    from uedge.__version__ import __version__
-    from uedge.__src__ import __src__
-    import uedge.checkver
-except:
-    try:
-        from __version__ import __version__
-        from __src__ import __src__
-        import checkver
-    except:
-        __version__ = 'unknown'
-        __src__ = 'unknown'
+import uedge.checkver
+from uedge._version import version
 
+__version__ = version()
+with open('test.txt', 'w') as f:
+    f.write("kakka")
 #
 # Load the startup file .uedgerc.py from cwd or home.
 #

src/uedge/__src__.py

@@ -0,0 +1 @@
+__src__ = '/Users/holm10/Documents/fusion/uedge/src/master'

src/uedge/_version.py

@@ -0,0 +1,2 @@
+def version():
+    return "8.1.0-beta.0"

src/uedge/filelists.py

@@ -0,0 +1,17 @@
+# Methods to create a list of files in a directory, and a sub-list containing sspecified suffixes.
+
+import os
+import string
+def filelist(path):
+   return os.listdir(path)
+
+def filesublist(path,suffix):
+   sublist = []
+   biglist = filelist(path)
+   for filename in biglist:
+       filesplit = filename.split(".")
+       if filesplit[-1] == suffix:
+           sublist.append(filename)
+   return sublist
+
+