Fix pyrichdem to import all cpp source files correctly

Clean up pyrichdem setup.py
Add .log files to .gitignore

Author: r-barnes

.gitignore

@@ -9,3 +9,4 @@ a.out
 travis.log
 build/
 .vscode/
+.log

CHANGELOG.md

@@ -1,3 +1,10 @@
+2022-02-11 (2.3.1)
+==================
+
+Fix pyrichdem to import all cpp source files correctly
+Clean up pyrichdem setup.py
+Add .log files to .gitignore
+
 2022-02-09 (2.3.0)
 ==================
 

wrappers/pyrichdem/lib/richdem

@@ -1 +1 @@
-../../../include/richdem
+../../../

wrappers/pyrichdem/richdem/__init__.py

@@ -1,12 +1,13 @@
-import pkg_resources
-import datetime
 import copy
+import datetime
 import numpy as np
+import pkg_resources
 
 try:
   import _richdem
-except ImportError:
+except ImportError as e:
   print('COULD NOT LOAD RichDEM ENGINE! NOTHING WILL WORK!')
+  raise e
 
 try:
   from osgeo import gdal
@@ -90,7 +91,7 @@ def rdShow(rda, ignore_colours=[], show=True, axes=True, cmap='gray', vmin=None,
 
   if all_zoom:
     axins = inset_axes(ax, width=2, height=2, loc=zloc, borderpad=0) #, bbox_to_anchor=(0.9, -0.05, 1, 1), bbox_transform=ax.transAxes, borderpad=0)
-    axins.set_xlim(xmin=zxmin,xmax=zxmax) 
+    axins.set_xlim(xmin=zxmin,xmax=zxmax)
     axins.set_ylim(ymin=zymin,ymax=zymax)
     plt.setp(axins.get_xticklabels(), visible=False)
     plt.setp(axins.get_yticklabels(), visible=False)
@@ -116,8 +117,8 @@ def rdShow(rda, ignore_colours=[], show=True, axes=True, cmap='gray', vmin=None,
 
 class rdarray(np.ndarray):
   def __new__(cls, array, meta_obj=None, no_data=None, dtype=None, order=None, **kwargs):
-    obj = np.asarray(array, dtype=dtype, order=order).view(cls) 
-    
+    obj = np.asarray(array, dtype=dtype, order=order).view(cls)
+
     if meta_obj is not None:
       obj.metadata     = copy.deepcopy(getattr(meta_obj, 'metadata',     dict()))
       obj.no_data      = copy.deepcopy(getattr(meta_obj, 'no_data',      None  ))
@@ -155,7 +156,7 @@ def wrap(self):
     dtype = str(self.dtype)
     if not dtype in richdem_arrs:
       raise Exception("No equivalent RichDEM datatype.")
-    
+
     rda = richdem_arrs[dtype](self)
 
     if self.no_data is None:
@@ -170,7 +171,7 @@ def wrap(self):
       print("Warning! No geotransform defined. Choosing a standard one! (Top left cell's top let corner at <0,0>; cells are 1x1.)")
       rda.geotransform = np.array([0,1,0,0,0,-1], dtype='float64')
 
-    return rda 
+    return rda
 
   def copyFromWrapped(self, wrapped):
     self.no_data   = wrapped.noData()
@@ -181,8 +182,8 @@ def copyFromWrapped(self, wrapped):
 
 class rd3array(np.ndarray):
   def __new__(cls, array, meta_obj=None, no_data=None, order=None, **kwargs):
-    obj = np.asarray(array, dtype=np.float32, order=order).view(cls) 
-    
+    obj = np.asarray(array, dtype=np.float32, order=order).view(cls)
+
     if meta_obj is not None:
       obj.metadata     = copy.deepcopy(getattr(meta_obj, 'metadata',     dict()))
       obj.no_data      = copy.deepcopy(getattr(meta_obj, 'no_data',      None  ))
@@ -211,7 +212,7 @@ def wrap(self):
     dtype = str(self.dtype)
     if not dtype in richdem_arrs:
       raise Exception("No equivalent RichDEM datatype.")
-    
+
     rda = richdem_arrs[dtype](self)
 
     if self.no_data is None:
@@ -226,7 +227,7 @@ def wrap(self):
       print("Warning! No geotransform defined. Choosing a standard one! (Top left cell's top let corner at <0,0>; cells are 1x1.)")
       rda.geotransform = np.array([0,1,0,0,0,-1], dtype='float64')
 
-    return rda 
+    return rda
 
   def copyFromWrapped(self, wrapped):
     self.no_data   = wrapped.noData()
@@ -250,7 +251,7 @@ def LoadGDAL(filename, no_data=None):
 
      Returns:
          A RichDEM array
-  """  
+  """
   if not GDAL_AVAILABLE:
     raise Exception("richdem.LoadGDAL() requires GDAL.")
 
@@ -333,7 +334,7 @@ def FillDepressions(
          epsilon (float):   If True, an epsilon gradient is imposed to all flat regions.
                             This ensures that there is always a local gradient.
          in_place (bool):   If True, the DEM is modified in place and there is
-                            no return; otherwise, a new, altered DEM is returned.                                     
+                            no return; otherwise, a new, altered DEM is returned.
          topology (string): A topology indicator
 
      Returns:
@@ -380,7 +381,7 @@ def BreachDepressions(
      Args:
          dem     (rdarray): An elevation model
          in_place (bool):   If True, the DEM is modified in place and there is
-                            no return; otherwise, a new, altered DEM is returned.                                     
+                            no return; otherwise, a new, altered DEM is returned.
          topology (string): A topology indicator
 
      Returns:
@@ -420,7 +421,7 @@ def ResolveFlats(
      Args:
          dem          (rdarray):   An elevation model
          in_place (bool):   If True, the DEM is modified in place and there is
-                            no return; otherwise, a new, altered DEM is returned.         
+                            no return; otherwise, a new, altered DEM is returned.
 
      Returns:
          DEM modified such that all flats drain.
@@ -456,15 +457,15 @@ def FlowAccumulation(
      Args:
          dem      (rdarray): An elevation model
          method   (str):     Flow accumulation method to use. (See below.)
-         exponent (float):   Some methods require an exponent; refer to the 
+         exponent (float):   Some methods require an exponent; refer to the
                              relevant publications for details.
          weights  (rdarray): Flow accumulation weights to use. This is the
                              amount of flow generated by each cell. If this is
                              not provided, each cell will generate 1 unit of
                              flow.
          in_place (bool):    If True, then `weights` is modified in place. An
                              accumulation matrix is always returned, but it will
-                             just be a view of the modified data if `in_place` 
+                             just be a view of the modified data if `in_place`
                              is True.
 
      =================== ============================== ===========================
@@ -565,7 +566,7 @@ def FlowAccumFromProps(
                              flow.
          in_place (bool):    If True, then `weights` is modified in place. An
                              accumulation matrix is always returned, but it will
-                             just be a view of the modified data if `in_place` 
+                             just be a view of the modified data if `in_place`
                              is True.
 
      Returns:
@@ -612,7 +613,7 @@ def FlowProportions(
      Args:
          dem      (rdarray): An elevation model
          method   (str):     Flow accumulation method to use. (See below.)
-         exponent (float):   Some methods require an exponent; refer to the 
+         exponent (float):   Some methods require an exponent; refer to the
                              relevant publications for details.
 
      =================== ============================== ===========================
@@ -698,14 +699,14 @@ def TerrainAttribute(
      ======================= =========
      Method                  Reference
      ======================= =========
-     slope_riserun           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_ 
-     slope_percentage        `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_ 
-     slope_degrees           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_ 
-     slope_radians           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_ 
-     aspect                  `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_ 
-     curvature               `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_ 
-     planform_curvature      `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_ 
-     profile_curvature       `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_ 
+     slope_riserun           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_
+     slope_percentage        `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_
+     slope_degrees           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_
+     slope_radians           `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_
+     aspect                  `Horn (1981)                   doi: 10.1109/PROC.1981.11918 <http://dx.doi.org/10.1109/PROC.1981.11918>`_
+     curvature               `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_
+     planform_curvature      `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_
+     profile_curvature       `Zevenbergen and Thorne (1987) doi: 10.1002/esp.3290120107  <http://dx.doi.org/10.1002/esp.3290120107>`_
      ======================= =========
 
      Returns:

wrappers/pyrichdem/setup.py

@@ -1,15 +1,14 @@
-from collections import defaultdict
-import setuptools
-from setuptools.command.build_ext import build_ext as _build_ext
 import glob
-import datetime
-import subprocess
 import re
+import setuptools
+import subprocess
+from setuptools.command.build_ext import build_ext as _build_ext
+from typing import Optional
 
 from pybind11.setup_helpers import Pybind11Extension
 
-RICHDEM_COMPILE_TIME = None
-RICHDEM_GIT_HASH     = None
+richdem_compile_time: Optional[str] = None
+richdem_git_hash: Optional[str]     = None
 
 #Compiler specific arguments
 BUILD_ARGS = {
@@ -22,40 +21,40 @@
 class build_ext_compiler_check(_build_ext):
   def build_extensions(self):
     compiler = self.compiler.compiler_type
-    print('COMPILER',compiler)
+    print(f'COMPILER {compiler}')
     args     = BUILD_ARGS[compiler]
     for ext in self.extensions:
         ext.extra_compile_args = args
-    print('COMPILER ARGUMENTS',ext.extra_compile_args)
+        print(f'COMPILER ARGUMENTS: {ext.extra_compile_args}')
     _build_ext.build_extensions(self)
 
-if RICHDEM_GIT_HASH is None:
+if richdem_git_hash is None:
   try:
     shash = subprocess.Popen(["git log --pretty=format:'%h' -n 1"], shell=True, stderr=subprocess.STDOUT, stdout=subprocess.PIPE).stdout.readlines()[0].decode('utf8').strip()
     sdate = subprocess.Popen(["git log -1 --pretty='%ci'"], shell=True, stderr=subprocess.STDOUT, stdout=subprocess.PIPE).stdout.readlines()[0].decode('utf8').strip()
     if re.match(r'^[0-9a-z]+$', shash) and re.match(r'^[0-9]{4}-[0-9]{2}-[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2}.*$', sdate):
-      RICHDEM_COMPILE_TIME = sdate
-      RICHDEM_GIT_HASH     = shash
+      richdem_compile_time = sdate
+      richdem_git_hash     = shash
   except:
     print("Warning! Could not find RichDEM version. Software will still work, but reproducibility will be compromised.")
     pass
 
-if RICHDEM_GIT_HASH is None:
-  RICHDEM_COMPILE_TIME = 'Unknown'
-  RICHDEM_GIT_HASH     = 'Unknown'
+if richdem_git_hash is None:
+  richdem_compile_time = 'Unknown'
+  richdem_git_hash     = 'Unknown'
 
-print("Using RichDEM hash={0}, time={1}".format(RICHDEM_GIT_HASH, RICHDEM_COMPILE_TIME))
+print("Using RichDEM hash={0}, time={1}".format(richdem_git_hash, richdem_compile_time))
 
 ext_modules = [
     Pybind11Extension(
       "_richdem",
-      glob.glob('src/*.cpp') + glob.glob('lib/richdem/*.cpp'),
-      include_dirs  = ['lib/'],
+      sorted(glob.glob('src/*.cpp') + glob.glob('lib/richdem/src/**/*.cpp', recursive=True)),
+      include_dirs  = ['lib/richdem/include/'],
       define_macros = [
-        ('DOCTEST_CONFIG_DISABLE', None                ),
-        ('RICHDEM_COMPILE_TIME',   '"\\"'+RICHDEM_COMPILE_TIME+'\\""'),
-        ('RICHDEM_GIT_HASH',       '"\\"'+RICHDEM_GIT_HASH+'\\""'    ),
-        ('RICHDEM_LOGGING',        None                ),
+        ('DOCTEST_CONFIG_DISABLE', None),
+        ('RICHDEM_COMPILE_TIME',   f'"\\"{richdem_compile_time}\\""'),
+        ('RICHDEM_GIT_HASH',       f'"\\"{richdem_git_hash}\\""'    ),
+        ('RICHDEM_LOGGING',        None),
         ('_USE_MATH_DEFINES',      None) #To ensure that `#include <cmath>` imports `M_PI` in MSVC
       ]
     ),
@@ -73,7 +72,7 @@ def build_extensions(self):
 #TODO: https://packaging.python.org/tutorials/distributing-packages/#configuring-your-project
 setuptools.setup(
   name              = 'richdem',
-  version           = '0.3.4',
+  version           = '0.4.0',
   description       = 'High-Performance Terrain Analysis',
   long_description  = long_description,
   url               = 'https://github.com/r-barnes/richdem',
@@ -93,20 +92,10 @@ def build_extensions(self):
   ext_modules      = ext_modules,
   cmdclass         = {'build_ext': build_ext_compiler_check},
   keywords         = 'GIS terrain hydrology geomorphology raster',
-  #packages        = find_packages(exclude=['contrib', 'docs', 'tests*']),
   install_requires = [
     "numpy>=1.7,<2; python_version > '3.4' or python_version < '3.0'",
     "numpy>=1.7,<1.12; python_version < '3.4' and python_version > '3.0'"
   ],
-  # extras_require    = {
-  #   ':python_version > "3.4"': [
-  #     'numpy>=1.7,<2'
-  #   ],
-  #   ':python_version < "3.4"': [
-  #     'numpy>=1.7,<1.12'
-  #   ]
-  # },
-  #python_requires  = ' >= 2.6, !=3.0.*, !=3.1.*, !=3.2.*, <4',
 
   #TODO: https://pypi.python.org/pypi?%3Aaction=list_classifiers
   classifiers      = [