Merge pull request #38 from ctlee/scratch

- Fix for Dolfin XML write out bug - Improved functionality for curvature calculations (requires matplotlib in Blender) - Added vertex valency constraint
ctlee · Jul 25, 2019 · b137dc9 · b137dc9
2 parents 93a89e4 + 71a737f
commit b137dc9
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Showing 28 changed files with 1,342 additions and 485 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -108,6 +108,15 @@ option(GAMER_DOCS "Download and configure documentation?" OFF)
 
 option(GAMER_CMAKE_VERBOSE "Print out information for debugging CMake configuration?")
 
+option (FORCE_COLORED_OUTPUT "Always produce ANSI-colored output (GNU/Clang only)." OFF)
+if (FORCE_COLORED_OUTPUT)
+    if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+       add_compile_options (-fdiagnostics-color=always)
+    elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+       add_compile_options (-fcolor-diagnostics)
+    endif ()
+endif ()
+
 #####################################################################
 # Configuration
 #####################################################################
@@ -177,8 +186,6 @@ target_include_directories(gamer_objlib PUBLIC
         $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
     )
 target_link_libraries(gamer_objlib PUBLIC casc tetstatic eigen)
-# target_compile_options(gamer_objlib PRIVATE -Werror -Wall -Weverything -Wextra -pedantic-errors -Wconversion -Wsign-conversion -ferror-limit=3 -Wno-c++17-extensions)
-# -ferror-limit=3 -Wno-unused-variable -Wno-unused-parameter)
 
 # SHARED LIBRARY
 add_library(gamershared SHARED $<TARGET_OBJECTS:gamer_objlib>)

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.0.2
+2.0.3
diff --git a/cmake-modules/FindBlender.cmake b/cmake-modules/FindBlender.cmake
@@ -35,7 +35,7 @@ find_program(BLENDER_EXECUTABLE blender)
 
 if(BLENDER_EXECUTABLE)
     # Get the python path and version from blender
-    execute_process(COMMAND ${BLENDER_EXECUTABLE} -b --factory-startup --python-expr
+    execute_process(COMMAND ${BLENDER_EXECUTABLE} -b -noaudio --factory-startup --python-expr
         "import sys;import struct;import bpy;
 print(str(bpy.app.version[0]) + '.' + str(bpy.app.version[1]) + '.' + str(bpy.app.version[2]))
 print(bpy.utils.script_path_user())

diff --git a/docs/conf.py.in b/docs/conf.py.in
@@ -40,7 +40,7 @@ extensions = [
     'sphinx.ext.intersphinx',
     'sphinx_issues',
     'nbsphinx',
-    'jupyter_sphinx.embed_widgets',
+    'jupyter_sphinx.execute',
 ]
 
 # Github repo
@@ -86,67 +86,6 @@ exhale_args = {
 autosummary_generate = True
 # autodoc_default_flags = ['members', 'inherited-members']
 
-# try to exclude deprecated
-# def skip_deprecated(app, what, name, obj, skip, options):
-#     if hasattr(obj, "func_dict") and "__deprecated__" in obj.func_dict:
-#         print("skipping " + name)
-#         return True
-#     return skip or False
-
-# def setup(app):
-#     app.connect('autodoc-skip-member', skip_deprecated)
-#     try:
-#         from sphinx.ext.autosummary import Autosummary
-#         from sphinx.ext.autosummary import get_documenter
-#         from docutils.parsers.rst import directives
-#         from sphinx.util.inspect import safe_getattr
-#         import re
-
-#         class AutoAutoSummary(Autosummary):
-
-#             option_spec = {
-#                 'methods': directives.unchanged,
-#                 'attributes': directives.unchanged
-#             }
-
-#             required_arguments = 1
-
-#             @staticmethod
-#             def get_members(obj, typ, include_public=None):
-#                 if not include_public:
-#                     include_public = []
-#                 items = []
-#                 for name in dir(obj):
-#                     try:
-#                         documenter = get_documenter(app, safe_getattr(obj, name), obj)
-#                     except AttributeError:
-#                         continue
-#                     if documenter.objtype == typ:
-#                         items.append(name)
-#                 public = [x for x in items if x in include_public or not x.startswith('_')]
-#                 return public, items
-
-#             def run(self):
-#                 clazz = self.arguments[0]
-#                 try:
-#                     (module_name, class_name) = clazz.rsplit('.', 1)
-#                     m = __import__(module_name, globals(), locals(), [class_name])
-#                     c = getattr(m, class_name)
-#                     if 'methods' in self.options:
-#                         _, methods = self.get_members(c, 'method', ['__init__'])
-
-#                         self.content = ["~%s.%s" % (clazz, method) for method in methods if not method.startswith('_')]
-#                     if 'attributes' in self.options:
-#                         _, attribs = self.get_members(c, 'attribute')
-#                         self.content = ["~%s.%s" % (clazz, attrib) for attrib in attribs if not attrib.startswith('_')]
-#                 finally:
-#                     return super(AutoAutoSummary, self).run()
-
-#         app.add_directive('autoautosummary', AutoAutoSummary)
-#     except BaseException as e:
-#         raise e
-
-
 ##############################
 # Napoleon Settings
 ##############################
@@ -178,7 +117,6 @@ templates_path = ['@CMAKE_CURRENT_SOURCE_DIR@/src/_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '_templates', '**.ipynb_checkpoints']
 
 
-
 ##############################
 # HTML Output Settings
 ##############################
@@ -207,4 +145,4 @@ html_context = {
 ##############################
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/3/': None}
diff --git a/docs/rtd-requirements.txt b/docs/rtd-requirements.txt
@@ -18,4 +18,4 @@ nbsphinx
 jupyter_sphinx
 
 # Visualization in docs
-threevis
+threevis
diff --git a/docs/src/_templates/autosummary/class.rst b/docs/src/_templates/autosummary/class.rst
@@ -5,6 +5,7 @@
 
 .. autoclass:: {{ objname }}
 
+{% block methods %}
 {% if methods %}
    .. rubric:: Methods
 
@@ -14,7 +15,10 @@
       {{ name }}.{{ item }}
    {% endfor %}
 {% endif %}
+{% endblock %}
 
+
+{% block attributes %}
 {% if attributes %}
    .. rubric:: Attributes
 
@@ -24,3 +28,4 @@
       {{ name }}.{{ item }}
    {% endfor %}
 {% endif %}
+{% endblock %}
diff --git a/docs/src/_templates/autosummary/module.rst b/docs/src/_templates/autosummary/module.rst
@@ -2,26 +2,28 @@
 
 .. rubric:: Description
 
-.. currentmodule:: {{ fullname }}
+.. automodule:: {{ fullname }}
 
+{% block classes %}
 {% if classes %}
-.. rubric:: Classes
-
-.. autosummary::
-    :toctree: .
-    {% for class in classes %}
-    {{ class }}
-    {% endfor %}
+   .. rubric:: Classes
 
+   .. autosummary::
+      :toctree: .
+      {% for class in classes %}
+      {{ class }}
+      {% endfor %}
 {% endif %}
+{% endblock %}
 
+{% block functions %}
 {% if functions %}
-.. rubric:: Functions
-
-.. autosummary::
-    :toctree: .
-    {% for function in functions %}
-    {{ function }}
-    {% endfor %}
+   .. rubric:: Functions
 
-{% endif %}
+   .. autosummary::
+      :toctree: .
+      {% for function in functions %}
+      {{ function }}
+      {% endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -12,7 +12,7 @@
 
 # Add the local lib to path if desired
 # import sys
-# sys.path.insert(0, os.path.abspath('/Users/ctlee/gamer/gamer/_skbuild/macosx-10.14-x86_64-3.7/cmake-build/lib/'))
+# sys.path.insert(0, os.path.abspath('/home/ctlee/gamer/gamer/buildpy37/lib/'))
 
 import os
 import pygamer
@@ -25,8 +25,8 @@
 copyright = '2019, Christopher T. Lee'
 author = 'Christopher T. Lee'
 
-version = '2.0.2'
-release = 'v2.0.2-dev-16-g721d135.dirty'
+version = '2.0.3'
+release = 'v2.0.3-dev-21-g2ecdc88.dirty'
 
 # -- General configuration ---------------------------------------------------
 
@@ -40,7 +40,7 @@
     'sphinx.ext.intersphinx',
     'sphinx_issues',
     'nbsphinx',
-    'jupyter_sphinx.embed_widgets',
+    'jupyter_sphinx.execute',
 ]
 
 # Github repo
@@ -52,7 +52,7 @@
 ##############################
 # Breathe Settings
 ##############################
-breathe_projects = { "gamer_project": "/Users/ctlee/gamer/gamer/docs/src/_doxyoutput/xml" }
+breathe_projects = { "gamer_project": "/home/ctlee/gamer/gamer/docs/src/_doxyoutput/xml" }
 breathe_default_project = "gamer_project"
 
 ##############################
@@ -61,17 +61,17 @@
 
 doxystdin = \
 """
-INPUT = /Users/ctlee/gamer/gamer/include
+INPUT = /home/ctlee/gamer/gamer/include
 OPTIMIZE_OUTPUT_FOR_C  = YES
 EXTRACT_ALL            = YES
 """
 # ENABLED_SECTIONS       = detail
 
 exhale_args = {
-    "containmentFolder":     "/Users/ctlee/gamer/gamer/docs/src/_cppapi",
+    "containmentFolder":     "/home/ctlee/gamer/gamer/docs/src/_cppapi",
     "rootFileName":          "root.rst",
     "rootFileTitle":         "C++ API Reference",
-    "doxygenStripFromPath":  "/Users/ctlee/gamer/gamer",
+    "doxygenStripFromPath":  "/home/ctlee/gamer/gamer",
     # "pageLevelConfigMeta":   ":github_url: https://github.com/ctlee/gamer",
     "createTreeView":        True,
     "exhaleExecutesDoxygen": True,
@@ -86,67 +86,6 @@
 autosummary_generate = True
 # autodoc_default_flags = ['members', 'inherited-members']
 
-# try to exclude deprecated
-# def skip_deprecated(app, what, name, obj, skip, options):
-#     if hasattr(obj, "func_dict") and "__deprecated__" in obj.func_dict:
-#         print("skipping " + name)
-#         return True
-#     return skip or False
-
-# def setup(app):
-#     app.connect('autodoc-skip-member', skip_deprecated)
-#     try:
-#         from sphinx.ext.autosummary import Autosummary
-#         from sphinx.ext.autosummary import get_documenter
-#         from docutils.parsers.rst import directives
-#         from sphinx.util.inspect import safe_getattr
-#         import re
-
-#         class AutoAutoSummary(Autosummary):
-
-#             option_spec = {
-#                 'methods': directives.unchanged,
-#                 'attributes': directives.unchanged
-#             }
-
-#             required_arguments = 1
-
-#             @staticmethod
-#             def get_members(obj, typ, include_public=None):
-#                 if not include_public:
-#                     include_public = []
-#                 items = []
-#                 for name in dir(obj):
-#                     try:
-#                         documenter = get_documenter(app, safe_getattr(obj, name), obj)
-#                     except AttributeError:
-#                         continue
-#                     if documenter.objtype == typ:
-#                         items.append(name)
-#                 public = [x for x in items if x in include_public or not x.startswith('_')]
-#                 return public, items
-
-#             def run(self):
-#                 clazz = self.arguments[0]
-#                 try:
-#                     (module_name, class_name) = clazz.rsplit('.', 1)
-#                     m = __import__(module_name, globals(), locals(), [class_name])
-#                     c = getattr(m, class_name)
-#                     if 'methods' in self.options:
-#                         _, methods = self.get_members(c, 'method', ['__init__'])
-
-#                         self.content = ["~%s.%s" % (clazz, method) for method in methods if not method.startswith('_')]
-#                     if 'attributes' in self.options:
-#                         _, attribs = self.get_members(c, 'attribute')
-#                         self.content = ["~%s.%s" % (clazz, attrib) for attrib in attribs if not attrib.startswith('_')]
-#                 finally:
-#                     return super(AutoAutoSummary, self).run()
-
-#         app.add_directive('autoautosummary', AutoAutoSummary)
-#     except BaseException as e:
-#         raise e
-
-
 ##############################
 # Napoleon Settings
 ##############################
@@ -170,15 +109,14 @@
 show_authors = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['/Users/ctlee/gamer/gamer/docs/src/_templates']
+templates_path = ['/home/ctlee/gamer/gamer/docs/src/_templates']
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '_templates', '**.ipynb_checkpoints']
 
 
-
 ##############################
 # HTML Output Settings
 ##############################
@@ -194,7 +132,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['/Users/ctlee/gamer/gamer/docs/src/_static']
+html_static_path = ['/home/ctlee/gamer/gamer/docs/src/_static']
 
 html_context = {
     'css_files': [
@@ -207,4 +145,4 @@
 ##############################
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/3/': None}