Reorganization to Core Structure - Phase 1

conda.recipe/meta.yaml

@@ -9,7 +9,7 @@ build:
   number: {{ environ.get('GIT_DESCRIBE_NUMBER', 0) }}
   detect_binary_files_with_prefix: true
   entry_points:
-    - hexrd = hexrd.cli.main:main
+    - hexrd = hexrd.hedm.cli.main:main
 
 requirements:
   build:

docs/source/conf.py

@@ -13,7 +13,7 @@
 import os
 import sys
 
-from hexrd.constants import __version__ as version
+from hexrd.core.constants import __version__ as version
 
 sys.path.insert(0, os.path.abspath('../..'))
 

hexrd/__init__.py

@@ -1,13 +1,15 @@
 import importlib
+import importlib.abc
+import importlib.machinery
 import sys
 
-from .material import crystallography
-from .material import jcpds
-from .material import mksupport
-from .material import spacegroup
-from .material import symbols
-from .material import symmetry
-from .material import unitcell
+from .core.material import crystallography
+from .core.material import jcpds
+from .core.material import mksupport
+from .core.material import spacegroup
+from .core.material import symbols
+from .core.material import symmetry
+from .core.material import unitcell
 
 # These are aliases for import paths, so we don't break old HEXRD scripts.
 # We will verify the alias files *do not* exist, to avoid confusion.
@@ -30,3 +32,16 @@
         raise Exception(f'"{alias}" is an alias path and should not exist')
 
     sys.modules[alias] = module
+
+
+from . import module_map
+
+
+def __getattr__(name):
+    # __getattr__ is only called if the attribute doesn't exist
+    module = module_map.get("hexrd." + name)
+    if module is not None:
+        if isinstance(module, str):
+            return importlib.import_module(module)
+        return module
+    raise AttributeError(f"Module `hexrd` has no attribute {name}")

hexrd/copyright.py

@@ -1,24 +1,24 @@
 # ============================================================
-# Copyright (c) 2012, Lawrence Livermore National Security, LLC. 
-# Produced at the Lawrence Livermore National Laboratory. 
-# Written by Joel Bernier <[email protected]> and others. 
-# LLNL-CODE-529294. 
+# Copyright (c) 2012, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+# Written by Joel Bernier <[email protected]> and others.
+# LLNL-CODE-529294.
 # All rights reserved.
-# 
+#
 # This file is part of HEXRD. For details on dowloading the source,
 # see the file COPYING.
-# 
+#
 # Please also see the file LICENSE.
-# 
+#
 # This program is free software; you can redistribute it and/or modify it under the
 # terms of the GNU Lesser General Public License (as published by the Free Software
 # Foundation) version 2.1 dated February 1999.
-# 
+#
 # This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY 
-# or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the 
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the terms and conditions of the
 # GNU General Public License for more details.
-# 
+#
 # You should have received a copy of the GNU Lesser General Public
 # License along with this program (see file LICENSE); if not, write to
 # the Free Software Foundation, Inc., 59 Temple Place, Suite 330,
@@ -36,4 +36,4 @@
 
 COPYRIGHT_FILE = 'COPYING'
 with open(os.path.join(os.path.dirname(__file__), COPYRIGHT_FILE), 'r') as f:
-     COPYRIGHT_TEXT = f.read()
+    COPYRIGHT_TEXT = f.read()

hexrd/config/beam.py → hexrd/core/config/beam.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from .config import Config
-from hexrd import imageseries
+from hexrd.core import imageseries
 
 
 class Beam(Config):

hexrd/config/config.py → hexrd/core/config/config.py

@@ -7,6 +7,7 @@
 
 logger = logging.getLogger('hexrd.config')
 
+
 class Config(object):
     """Access a level of the YAML configuration file
 
@@ -15,6 +16,7 @@ class Config(object):
     cfg: Config instance or a (pyyaml) YAMLObject
        config representings a level of the YAML input
     """
+
     _dirty = False
 
     def __init__(self, cfg):
@@ -41,14 +43,12 @@ def get(self, key, default=null):
             res = temp[item]
         except KeyError:
             if default is not null:
-                logger.info(
-                    '%s not specified, defaulting to %s', key, default
-                    )
+                logger.info('%s not specified, defaulting to %s', key, default)
                 res = temp.get(item, default)
             else:
                 raise RuntimeError(
                     '%s must be specified in configuration file' % key
-                    )
+                )
         return res
 
     def set(self, key, val):
@@ -80,12 +80,10 @@ def check_filename(fname, wdir):
 
         If fname is an absolute path, use that; otherwise take it as a path
         relative to the working directory.
-"""
+        """
         temp = fname
         if not os.path.isabs(fname):
             temp = os.path.join(wdir, temp)
         if os.path.exists(temp):
             return temp
-        raise IOError(
-            'file: "%s" not found' % temp
-            )
+        raise IOError('file: "%s" not found' % temp)

hexrd/config/dumper.py → hexrd/core/config/dumper.py

@@ -8,7 +8,7 @@ def _dict_path_by_id(d, value, path=()):
         return path
     elif isinstance(d, dict):
         for k, v in d.items():
-            p = _dict_path_by_id(v, value, path + (k, ))
+            p = _dict_path_by_id(v, value, path + (k,))
             if p is not None:
                 return p
     elif isinstance(d, list):
@@ -32,6 +32,7 @@ class NumPyIncludeDumper(yaml.Dumper):
     The ndarray would be saved in foo/bar.npy.
 
     """
+
     def __init__(self, stream, **kwargs):
         super().__init__(stream, **kwargs)
 
@@ -58,5 +59,6 @@ def represent(self, data):
         return super().represent(data)
 
 
-NumPyIncludeDumper.add_representer(np.ndarray,
-                                   NumPyIncludeDumper.ndarray_representer)
+NumPyIncludeDumper.add_representer(
+    np.ndarray, NumPyIncludeDumper.ndarray_representer
+)

hexrd/config/imageseries.py → hexrd/core/config/imageseries.py

@@ -1,7 +1,7 @@
 from .config import Config
-from hexrd import imageseries
+from hexrd.core import imageseries
 
-from hexrd.constants import shared_ims_key
+from hexrd.core.constants import shared_ims_key
 
 
 class ImageSeries(Config):
@@ -34,7 +34,7 @@ def imageseries(self):
                         panel = '_'.join(panel)
                     elif panel is None:
                         panel = shared_ims_key
-                except(KeyError):
+                except KeyError:
                     panel = shared_ims_key
                 self._image_dict[panel] = oms
 

hexrd/config/instrument.py → hexrd/core/config/instrument.py

@@ -4,7 +4,7 @@
 from .config import Config
 from .loader import NumPyIncludeLoader
 
-from hexrd import instrument
+from hexrd.core import instrument
 
 
 class Instrument(Config):
@@ -31,7 +31,7 @@ def hedm(self):
 
             try:
                 icfg = h5py.File(self.configuration, 'r')
-            except(OSError):
+            except OSError:
                 with open(self.configuration, 'r') as f:
                     icfg = yaml.load(f, Loader=NumPyIncludeLoader)
 
@@ -47,7 +47,7 @@ def hedm(self, icfg_fname):
         """Set the HEDMInstrument class."""
         try:
             icfg = h5py.File(icfg_fname, 'r')
-        except(OSError):
+        except OSError:
             with open(icfg_fname, 'r') as f:
                 icfg = yaml.load(f, Loader=NumPyIncludeLoader)
 

hexrd/config/material.py → hexrd/core/config/material.py

@@ -2,16 +2,16 @@
 
 import numpy as np
 
-from hexrd import material
-from hexrd.constants import keVToAngstrom
-from hexrd.valunits import valWUnit
+from hexrd.core import material
+from hexrd.core.constants import keVToAngstrom
+from hexrd.core.valunits import valWUnit
 
 from .config import Config
 from .utils import get_exclusion_parameters
 
 
-DMIN_DFLT = 0.5    # angstrom
-TTHW_DFLT = 0.25   # degrees
+DMIN_DFLT = 0.5  # angstrom
+TTHW_DFLT = 0.25  # degrees
 
 
 class MaterialConfig(Config):
@@ -30,9 +30,7 @@ def definitions(self):
             temp = os.path.join(self._cfg.working_dir, temp)
         if os.path.exists(temp):
             return temp
-        raise IOError(
-            f'"material:definitions": "{temp}" does not exist'
-        )
+        raise IOError(f'"material:definitions": "{temp}" does not exist')
 
     @property
     def active(self):

hexrd/config/root.py → hexrd/core/config/root.py

@@ -3,13 +3,15 @@
 import logging
 import multiprocessing as mp
 
-from hexrd.constants import shared_ims_key
-from hexrd import imageseries
+from hexrd.core.constants import shared_ims_key
+from hexrd.core import imageseries
 
 from .config import Config
 from .instrument import Instrument
-from .findorientations import FindOrientationsConfig
-from .fitgrains import FitGrainsConfig
+
+# TODO: Resolve extra-core-dependency
+from hexrd.hedm.config.findorientations import FindOrientationsConfig
+from hexrd.hedm.config.fitgrains import FitGrainsConfig
 from .material import MaterialConfig
 
 logger = logging.getLogger('hexrd.config')
@@ -67,8 +69,10 @@ def analysis_dir(self):
     @property
     def analysis_id(self):
         return '_'.join(
-            [self.analysis_name.strip().replace(' ', '-'),
-             self.material.active.strip().replace(' ', '-')]
+            [
+                self.analysis_name.strip().replace(' ', '-'),
+                self.material.active.strip().replace(' ', '-'),
+            ]
         )
 
     @property
@@ -134,8 +138,9 @@ def multiprocessing(self):
                 if multiproc > ncpus:
                     logger.warning(
                         'Resuested %s processes, %d available',
-                        multiproc, ncpus
-                        )
+                        multiproc,
+                        ncpus,
+                    )
                     res = ncpus
                 else:
                     res = multiproc if multiproc else 1
@@ -144,17 +149,15 @@ def multiprocessing(self):
                 if temp < 1:
                     logger.warning(
                         'Cannot use less than 1 process, requested %d of %d',
-                        temp, ncpus
-                        )
+                        temp,
+                        ncpus,
+                    )
                     res = 1
                 else:
                     res = temp
         else:
             temp = ncpus - 1
-            logger.warning(
-                "Invalid value %s for multiprocessing",
-                multiproc
-                )
+            logger.warning("Invalid value %s for multiprocessing", multiproc)
             res = temp
         return res
 
@@ -163,13 +166,13 @@ def multiprocessing(self, val):
         isint = isinstance(val, int)
         if val in ('half', 'all', -1):
             self.set('multiprocessing', val)
-        elif (isint and val >= 0 and val <= mp.cpu_count()):
+        elif isint and val >= 0 and val <= mp.cpu_count():
             self.set('multiprocessing', int(val))
         else:
             raise RuntimeError(
                 '"multiprocessing": must be 1:%d, got %s'
                 % (mp.cpu_count(), val)
-                )
+            )
 
     @property
     def image_series(self):
@@ -189,10 +192,10 @@ def image_series(self):
                         panel = '_'.join(panel)
                     elif panel is None:
                         panel = shared_ims_key
-                except(KeyError):
+                except KeyError:
                     try:
                         panel = oms.metadata['panel']
-                    except(KeyError):
+                    except KeyError:
                         panel = shared_ims_key
                 self._image_dict[panel] = oms