Revert "Revert "Move 'dorie' wrapper into Python package.""

This reverts commit 79a3cb0d.

.gitignore

@@ -2,8 +2,10 @@
 build-cmake/
 
 # Exclude generated files
+python/dorie/wrapper/dorie
 python/dorie/wrapper/pf_from_file.py
 python/dorie/wrapper/test_dorie.py
+python/dorie/cli/cmds.py
 
 # Ignore temporary and auto-generated files #
 *~

CMakeLists.txt

@@ -41,7 +41,6 @@ dune_enable_all_packages()
 dune_require_cxx_standard(MODULE "dorie" VERSION 14)
 
 # add subdirectories
-add_subdirectory("bin")
 add_subdirectory("m4")
 add_subdirectory("cmake/modules")
 add_subdirectory("python")

bin/CMakeLists.txt

-configure_file(dorie.in ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/dorie @ONLY)
-# copy the temporary file into the final destination, setting the permissions
-file(COPY ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/dorie
-  DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
-  FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ
-  GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/dorie DESTINATION ${CMAKE_INSTALL_BINDIR} PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ
-  GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)

python/CMakeLists.txt

@@ -3,6 +3,7 @@ set(DUNE_PYTHON_INSTALL_EDITABLE TRUE)
 
 # install Python package
 add_subdirectory(dorie/wrapper)
+add_subdirectory(dorie/dorie/cli)
 dune_python_install_package(PATH dorie)
 
 # set cache variable

python/dorie/dorie/cli/CMakeLists.txt

+configure_file(cmds.py.in ${CMAKE_CURRENT_SOURCE_DIR}/cmds.py)
\ No newline at end of file

python/dorie/dorie/cli/cmds.py

+import os
+import sys
+import shutil
+import subprocess
+
+try: # Python 2.x compatibility
+    input = raw_input
+except NameError:
+    pass
+
+# paths set by cmake
+DORIEDIR = "/Users/lriedel/dune/dorie/build-cmake"
+MPIEXEC = "/usr/local/bin/mpiexec"
+MPIEXEC_NUMPROC_FLAG = "-n"
+MPIEXEC_PREFLAG = ""
+MPIEXEC_POSTFLAGS = ""
+
+# set some paths
+DORIE_EXECUTABLE = os.path.join(DORIEDIR, "dune/dorie/dorie")
+PARAMETERDIR = os.path.join(DORIEDIR, "doc/default_files")
+def MPIRUN(nproc,exe,*args,**kwargs):
+    mpi_flags = kwargs.get("mpi_flags") or []
+    return [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc)] \
+                        + mpi_flags + [MPIEXEC_PREFLAG,str(exe),
+                        MPIEXEC_POSTFLAGS] + list(args) if k]
+
+def run(args):
+    if not os.path.isfile(args["config"]):
+        raise IOError("Configuration file {} not found".format(args["config"]))
+    try:
+        if args["parallel"] == 1:
+            subprocess.check_call([DORIE_EXECUTABLE, args["config"]])
+        else:
+            subprocess.check_call(MPIRUN(args["parallel"], DORIE_EXECUTABLE,
+                                         args["config"], mpi_flags=args["mpi_flags"]))
+    except subprocess.CalledProcessError:
+        print("Error while running DORiE")
+        sys.exit(1)
+
+def create(args):
+    for f in ("config.ini", "parfield.ini", "2d_infiltr.bcdat", "3d_infiltr.bcdat"):
+        newfile = os.path.join(os.getcwd(),f)
+        if os.path.exists(newfile) and not args["force"]:
+            override = (input("File {} exists. Override? [Y/n] ".format(f)) or "Y") in ["Y","y"]
+            if not override:
+                continue
+        shutil.copyfile(os.path.join(PARAMETERDIR, f), newfile)
+    print("Folder initialized")
+
+def pfg(args):
+    if not os.path.isfile(args["config"]):
+        raise IOError("Configuration file {} not found".format(args["config"]))
+    try:
+        if args["parallel"] == 1:
+            subprocess.check_call(["pf_from_file.py", args["config"]])
+        else:
+            if args["mpi_flags"]:
+                mpi_flags = ["--mpi-flags=" + f for f in args["mpi_flags"]]
+            else:
+                mpi_flags = []
+            subprocess.check_call(["pf_from_file.py", args["config"],
+                                  "--parallel", str(args["parallel"])] + mpi_flags)
+    except subprocess.CalledProcessError:
+        print("Error while running DORiE")
+        sys.exit(1)
+
+def plot(args):
+    if not os.path.isfile(args["vtk"]):
+        raise IOError("File {} not found".format(args["vtk"]))
+    try:
+        if args["var"]:
+            subprocess.check_call(["plot_vtk.py", "-f", args["vtk"], "--var", args["var"]])
+        else:
+            subprocess.check_call(["plot_vtk.py", "-f", args["vtk"]])
+    except subprocess.CalledProcessError:
+        print("Error while running DORiE")
+        sys.exit(1)

bin/dorie.in → python/dorie/dorie/cli/cmds.py.in

-#!/usr/bin/env python3
-
 import os
 import sys
 import shutil
-import argparse
-import warnings
 import subprocess
-import multiprocessing
 
 try: # Python 2.x compatibility
     input = raw_input
@@ -19,12 +14,10 @@ MPIEXEC = "@MPIEXEC@"
 MPIEXEC_NUMPROC_FLAG = "@MPIEXEC_NUMPROC_FLAG@"
 MPIEXEC_PREFLAG = "@MPIEXEC_PREFLAG@"
 MPIEXEC_POSTFLAGS = "@MPIEXEC_POSTFLAGS@"
-#
 
 # set some paths
 DORIE_EXECUTABLE = os.path.join(DORIEDIR, "dune/dorie/dorie")
 PARAMETERDIR = os.path.join(DORIEDIR, "doc/default_files")
-DORIE_PYTHON = os.path.join(DORIEDIR, "run-in-dune-env")
 def MPIRUN(nproc,exe,*args,**kwargs):
     mpi_flags = kwargs.get("mpi_flags") or []
     return [k for k in [MPIEXEC,MPIEXEC_NUMPROC_FLAG,str(nproc)] \
@@ -59,13 +52,13 @@ def pfg(args):
         raise IOError("Configuration file {} not found".format(args["config"]))
     try:
         if args["parallel"] == 1:
-            subprocess.check_call([DORIE_PYTHON, "pf_from_file.py", args["config"]])
+            subprocess.check_call(["pf_from_file.py", args["config"]])
         else:
             if args["mpi_flags"]:
                 mpi_flags = ["--mpi-flags=" + f for f in args["mpi_flags"]]
             else:
                 mpi_flags = []
-            subprocess.check_call([DORIE_PYTHON, "pf_from_file.py", args["config"],
+            subprocess.check_call(["pf_from_file.py", args["config"],
                                   "--parallel", str(args["parallel"])] + mpi_flags)
     except subprocess.CalledProcessError:
         print("Error while running DORiE")
@@ -76,69 +69,9 @@ def plot(args):
         raise IOError("File {} not found".format(args["vtk"]))
     try:
         if args["var"]:
-            subprocess.check_call([DORIE_PYTHON, "plot_vtk.py", "-f", args["vtk"], "--var", args["var"]])
+            subprocess.check_call(["plot_vtk.py", "-f", args["vtk"], "--var", args["var"]])
         else:
-            subprocess.check_call([DORIE_PYTHON, "plot_vtk.py", "-f", args["vtk"]])
+            subprocess.check_call(["plot_vtk.py", "-f", args["vtk"]])
     except subprocess.CalledProcessError:
         print("Error while running DORiE")
-        sys.exit(1)
-
-if __name__ == "__main__": # parse command line and call command handler
-    try:
-        with warnings.catch_warnings(record=True) as warn:
-            parser = argparse.ArgumentParser(description="DORiE command line interface",
-                                             epilog="For more information check our online documentation: "
-                                                    "http://dorie-docs.bitballoon.com (password: 'richards')."
-                                            )
-            subparsers = parser.add_subparsers(title="Commands",dest="command")
-            subparsers.required = True
-
-            parser_create = subparsers.add_parser('create',
-                                                  description="Copy example configuration to current folder.",
-                                                  help="Copy example configuration to current folder.")
-            parser_create.add_argument('-f','--force', help="Override existing files.", action="store_true")
-            parser_create.set_defaults(func=create)
-
-            parser_pfg = subparsers.add_parser('pfg', help="Start parameter field generator.",
-                                               description="Start parameter field generator.",
-                                               usage="%(prog)s <config> [-h] [-p [N]] [-m=MPI_FLAGS]")
-            parser_pfg.add_argument('config',
-                                    help="Configuration file for the parameter field generator. "
-                                         "Can be created with 'dorie create'.")
-            parser_pfg.add_argument('-p','--parallel', metavar='N', nargs='?', default=1,
-                                    const=multiprocessing.cpu_count(), type=int, required=False,
-                                    help="Run in parallel on N processes. "
-                                         "If N is not specified, run on all available CPU threads.")
-            parser_pfg.add_argument('-m','--mpi-flags', action="append", required=False,
-                                    help="Additional flags that are passed to mpirun when run in parallel. "
-                                         "May be specified multiple times.")
-            parser_pfg.set_defaults(func=pfg)
-
-            parser_run = subparsers.add_parser('run', help="Run DORiE.", description="Run DORiE.",
-                                               usage="%(prog)s <config> [-h] [-p [N]] [-m=MPI_FLAGS]")
-            parser_run.add_argument('config',help="DORiE configuration file. Can be created with 'dorie create'.")
-            parser_run.add_argument('-p','--parallel', metavar='N', nargs='?', default=1,
-                                    const=multiprocessing.cpu_count(), type=int, required=False,
-                                    help="Run in parallel on N processes. "
-                                         "If N is not specified, run on all available CPU threads.")
-            parser_run.add_argument('-m','--mpi-flags', action="append", required=False,
-                                    help="Additional flags that are passed to mpirun when run in parallel. "
-                                         "May be specified multiple times.")
-            parser_run.set_defaults(func=run)
-
-            parser_plot = subparsers.add_parser('plot', help="Plot a preview of a VTK file created by DORiE.",
-                                                description="Plot a preview of a VTK file created by DORiE.",
-                                                usage="%(prog)s <vtk> [-h] [--v [VAR [VAR ...]]]")
-            parser_plot.add_argument('vtk', help="Input VTK file.")
-            parser_plot.add_argument('-v','--var', nargs='*', required=False,
-                                     help="Plot only given variables. If not specified, all variables are plotted.")
-            parser_plot.set_defaults(func=plot)
-
-            try:
-                args = parser.parse_args()
-            except SystemExit:
-                sys.exit(1)
-            args.func(vars(args))
-    except Exception as e:
-        print("dorie failed with ({0}) warning(s) and ({1}) error(s)".format(len(warn),1))
-        raise
+        sys.exit(1)
\ No newline at end of file

python/dorie/dorie/cli/parser.py

+import argparse
+import multiprocessing
+
+# import all commands
+from .cmds import *
+
+def create_cl_parser():
+    """Create the command line parser for the DORiE CLI.
+
+    Returns:
+        ArgumentParser object for parsing the command line.
+    """
+    parser = argparse.ArgumentParser(description="DORiE Command Line Interface",
+                                     epilog="For more information check our online documentation: "
+                                            "http://dorie-doc.netlify.com."
+                                    )
+    subparsers = parser.add_subparsers(title="Commands", dest="command")
+    subparsers.required = True
+
+    parser_create = subparsers.add_parser('create',
+                                            description="Copy example configuration to current folder.",
+                                            help="Copy example configuration to current folder.")
+    parser_create.add_argument('-f','--force',
+                               action="store_true",
+                               help="Override existing files.")
+    parser_create.set_defaults(func=create)
+
+    parser_pfg = subparsers.add_parser('pfg', help="Start parameter field generator.",
+                                        description="Start parameter field generator.")
+    parser_pfg.add_argument('config',
+                            help="Configuration file for the parameter field generator. "
+                                 "A default version can be created with 'dorie create'.")
+    parser_pfg.add_argument('-p','--parallel',
+                            metavar='N',
+                            nargs='?',
+                            default=1,
+                            const=multiprocessing.cpu_count(),
+                            type=int,
+                            required=False,
+                            help="Run in parallel on N processes. "
+                                    "If N is not specified, run on all available CPU threads.")
+    parser_pfg.add_argument('-m','--mpi-flags',
+                            action="append",
+                            required=False,
+                            help="Additional flags that are passed to mpirun when run in parallel. "
+                                    "May be specified multiple times.")
+    parser_pfg.set_defaults(func=pfg)
+
+    parser_run = subparsers.add_parser('run', help="Run DORiE.", description="Run DORiE.")
+    parser_run.add_argument('config',
+                            help="DORiE configuration file. "
+                                 "A default version can be created with 'dorie create'.")
+    parser_run.add_argument('-p','--parallel', metavar='N',
+                            nargs='?',
+                            default=1,
+                            const=multiprocessing.cpu_count(),
+                            type=int,
+                            required=False,
+                            help="Run in parallel on N processes. "
+                                 "If N is not specified, run on all available CPU threads.")
+    parser_run.add_argument('-m','--mpi-flags',
+                            action="append",
+                            required=False,
+                            help="Additional flags that are passed to mpirun when run in parallel. "
+                                    "May be specified multiple times.")
+    parser_run.set_defaults(func=run)
+
+    parser_plot = subparsers.add_parser('plot', help="Plot a preview of a VTK file created by DORiE.",
+                                        description="Plot a preview of a VTK file created by DORiE.")
+    parser_plot.add_argument('vtk',
+                             help="Input VTK file.")
+    parser_plot.add_argument('-v','--var',
+                             nargs='*',
+                             help="Plot only given variables. If not specified, all variables are plotted.")
+    parser_plot.set_defaults(func=plot)
+
+    return parser
\ No newline at end of file

python/dorie/setup.py

@@ -24,6 +24,7 @@ setup(name='dorie',
                     'wheel'
     ],
     scripts=[
+        'wrapper/dorie',
         'wrapper/pf_from_file.py',
         'wrapper/plot_vtk.py',
         'wrapper/scrape_folder.py',

python/dorie/wrapper/CMakeLists.txt

+configure_file(dorie.in ${CMAKE_CURRENT_SOURCE_DIR}/dorie)
 configure_file(pf_from_file.py.in ${CMAKE_CURRENT_SOURCE_DIR}/pf_from_file.py)
 configure_file(test_dorie.py.in ${CMAKE_CURRENT_SOURCE_DIR}/test_dorie.py)
\ No newline at end of file

python/dorie/wrapper/dorie.in

+#!/usr/bin/env python3
+
+import sys
+import warnings
+
+from dorie.cli.parser import create_cl_parser
+
+if __name__ == "__main__": # parse command line and call command handler
+    try:
+        with warnings.catch_warnings(record=True) as warn:
+            try:
+                parser = create_cl_parser()
+                args = parser.parse_args()
+            except SystemExit:
+                sys.exit(1)
+            args.func(vars(args))
+    except Exception as e:
+        print("dorie failed with ({0}) warning(s) and ({1}) error(s)".format(len(warn),1))
+        raise

python/dorie/wrapper/test_dorie.py.in

@@ -9,14 +9,10 @@ from dune.testtools.wrapper.argumentparser import get_args
 from dune.testtools.parser import parse_ini_file
 from dorie.testtools.wrapper import test_dorie
 
-# paths set by cmake
-DORIEDIR = "@CMAKE_BINARY_DIR@"
-#
-
-DORIE_WRAPPER = os.path.join(DORIEDIR, "bin/dorie")
+DORIE_WRAPPER = "dorie"
 
 if __name__ == "__main__":
     args = get_args()
     iniargument = args["ini"]
     iniinfo = parse_ini_file(args["ini"])
-    sys.exit(test_dorie.test_dorie(iniinfo,iniargument,DORIE_WRAPPER))
+    sys.exit(test_dorie.test_dorie(iniinfo, iniargument, DORIE_WRAPPER))