Moved examples/ to src/microstructpy/examples

CHANGELOG.rst

@@ -6,6 +6,12 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog`_,
 and this project adheres to `Semantic Versioning`_.
 
+`1.1.2`_ - 2019-11-07
+---------------------
+Fixed
+'''''
+- Paths to demo files in CLI, moved into source directory.
+
 `1.1.1`_ - 2019-11-05
 ---------------------
 Added
@@ -51,7 +57,8 @@ Added
 
 .. LINKS
 
-.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.1.1...HEAD
+.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.1.2...HEAD
+.. _`1.1.2`: https://github.com/kip-hart/MicroStructPy/compare/v1.1.1...v1.1.2
 .. _`1.1.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.1.0...v1.1.1
 .. _`1.1.0`: https://github.com/kip-hart/MicroStructPy/compare/v1.0.1...v1.1.0
 .. _`1.0.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.0.0...v1.0.1

MANIFEST.in

@@ -1,5 +1,4 @@
 graft docs
-graft examples
 graft src
 graft tests
 
@@ -16,12 +15,13 @@ include requirements.txt
 
 prune docs/source/auto_examples
 prune docs/build*
+prune src/*/examples/*
 prune tests/tmp_out
-prune examples/*
 prune *.yml
 
 exclude examples/*.png
 include examples/aluminum_micro.png
 exclude examples/*.txt
+exclude src/*/examples/.gitignore
 
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.log Icon*

docs/source/cli/introduction.rst

@@ -60,7 +60,7 @@ The three fields of the input file that MicroStructPy looks for are:
 ``<material>``, ``<domain>``, and ``<settings>`` (optional).
 For example:
 
-.. literalinclude:: ../../../examples/minimal_paired.xml
+.. literalinclude:: ../../../src/microstructpy/examples/minimal_paired.xml
     :language: xml
 
 

docs/source/cli/material.rst

@@ -8,7 +8,7 @@ Single Material
 MicroStructPy supports an arbitrary number of materials, including just one.
 For example:
 
-.. literalinclude:: ../../../examples/minimal.xml
+.. literalinclude:: ../../../src/microstructpy/examples/minimal.xml
     :language: xml
 
 This input file will produce a microstructure with nearly circular grains

docs/source/examples/cli/basalt.rst

@@ -14,7 +14,7 @@ The file can be run using this command::
 
 The full text of the file is:
 
-.. literalinclude:: ../../../../examples/basalt_circle.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/basalt_circle.xml
     :language: xml
 
 
@@ -72,19 +72,19 @@ These three plots are shown in
 :numref:`f_ex_basalt_seeds` - :numref:`f_ex_basalt_tri`.
 
 .. _f_ex_basalt_seeds:
-.. figure:: ../../../../examples/basalt_circle/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/basalt_circle/seeds.png
     :alt: Seed geometries.
 
     Picritic basalt example - seed geometries
 
 .. _f_ex_basalt_poly:
-.. figure:: ../../../../examples/basalt_circle/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/basalt_circle/polymesh.png
     :alt: Polygonal mesh.
 
     Picritic basalt example - polygonal mesh
 
 .. _f_ex_basalt_tri:
-.. figure:: ../../../../examples/basalt_circle/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/basalt_circle/trimesh.png
     :alt: Triangular mesh.
 
     Picritic basalt example - triangular mesh
@@ -94,7 +94,7 @@ generated by MicroStructPy.
 The grain size distribution comparison is given in :numref:`f_ex_basalt_verif`.
 
 .. _f_ex_basalt_verif:
-.. figure:: ../../../../examples/basalt_circle/verification/size_cdf.png
+.. figure:: ../../../../src/microstructpy/examples/basalt_circle/verification/size_cdf.png
     :alt: Comparing input and output CSDs.
 
     Picritic basalt example - input and output crystal size

docs/source/examples/cli/colormap.rst

@@ -17,7 +17,7 @@ The file can be run using this command::
 
 The full text of the script is:
 
-.. literalinclude:: ../../../../examples/colormap.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/colormap.xml
     :language: xml
 
 
@@ -63,19 +63,19 @@ These three plots are shown in :numref:`f_ex_colormap_seeds` -
 :numref:`f_ex_colormap_tri`.
 
 .. _f_ex_colormap_seeds:
-.. figure:: ../../../../examples/colormap/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/colormap/seeds.png
     :alt: Seed geometries.
 
     Colormap example - seed geometries.
 
 .. _f_ex_colormap_poly:
-.. figure:: ../../../../examples/colormap/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/colormap/polymesh.png
     :alt: Polygonal mesh.
 
     Colormap example - polygonal mesh.
 
 .. _f_ex_colormap_tri:
-.. figure:: ../../../../examples/colormap/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/colormap/trimesh.png
     :alt: Triangular mesh.
 
     Colormap example - triangular mesh.

docs/source/examples/cli/elliptical_grains.rst

@@ -14,7 +14,7 @@ The file can be run using this command::
 
 The full text of the file is:
 
-.. literalinclude:: ../../../../examples/elliptical_grains.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/elliptical_grains.xml
     :language: xml
 
 
@@ -73,19 +73,19 @@ These three plots are shown in :numref:`f_ex_ell_seeds` -
 :numref:`f_ex_ell_tri`.
 
 .. _f_ex_ell_seeds:
-.. figure:: ../../../../examples/elliptical_grains/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/elliptical_grains/seeds.png
     :alt: Seed geometries.
 
     Elliptical grain example - seed geometries.
 
 .. _f_ex_ell_poly:    
-.. figure:: ../../../../examples/elliptical_grains/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/elliptical_grains/polymesh.png
     :alt: Polygonal mesh.
 
     Elliptical grain example - polygonal mesh.
 
 .. _f_ex_ell_tri:
-.. figure:: ../../../../examples/elliptical_grains/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/elliptical_grains/trimesh.png
     :alt: Triangular mesh.
 
     Elliptical grain example - triangular mesh.

docs/source/examples/cli/minimal.rst

@@ -14,7 +14,7 @@ The file can be run using this command::
 
 The full text of the file is:
 
-.. literalinclude:: ../../../../examples/minimal_paired.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/minimal_paired.xml
     :language: xml
 
 
@@ -55,19 +55,19 @@ These three plots are shown in :numref:`f_ex_min_seeds` -
 :numref:`f_ex_min_tri`.
 
 .. _f_ex_min_seeds:
-.. figure:: ../../../../examples/minimal/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/minimal/seeds.png
     :alt: Seed geometries.
 
     Minimal example - seed geometries.
 
 .. _f_ex_min_poly:
-.. figure:: ../../../../examples/minimal/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/minimal/polymesh.png
     :alt: Polygonal mesh.
 
     Minimal example - polygonal mesh.
 
 .. _f_ex_min_tri:
-.. figure:: ../../../../examples/minimal/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/minimal/trimesh.png
     :alt: Triangular mesh.
 
     Minimal example - triangular mesh.

docs/source/examples/cli/two_phase_3d.rst

@@ -14,7 +14,7 @@ The file can be run using this command::
 
 The full text of the file is:
 
-.. literalinclude:: ../../../../examples/two_phase_3D.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/two_phase_3D.xml
     :language: xml
 
 
@@ -54,19 +54,19 @@ These three plots are shown in :numref:`f_ex_2p3d_seeds` -
 :numref:`f_ex_2p3d_tri`.
 
 .. _f_ex_2p3d_seeds:
-.. figure:: ../../../../examples/two_phase_3D/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/two_phase_3D/seeds.png
     :alt: Seed geometries.
 
     Two phase 3D example - seed geometries.
 
 .. _f_ex_2p3d_poly:
-.. figure:: ../../../../examples/two_phase_3D/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/two_phase_3D/polymesh.png
     :alt: Polygonal mesh.
 
     Two phase 3D example - polygonal mesh.
 
 .. _f_ex_2p3d_tri:
-.. figure:: ../../../../examples/two_phase_3D/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/two_phase_3D/trimesh.png
     :alt: Triangular mesh.
 
     Two phase 3D example - triangular mesh.

docs/source/examples/index.rst

@@ -26,37 +26,37 @@ Input File Introduction
 
 .. only:: html
 
-  .. image:: ../../../examples/intro_1_basic/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_1_basic/trimesh.png
     :alt: Triangular mesh from first intro example.
     :width: 32%
     :target: intro/intro_1.html
 
 
-  .. image:: ../../../examples/intro_2_quality/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_2_quality/trimesh.png
     :alt: Triangular mesh from second intro example.
     :width: 32%
     :target: intro/intro_2.html
 
 
-  .. image:: ../../../examples/intro_3_size_shape/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_3_size_shape/trimesh.png
     :alt: Triangular mesh from third intro example.
     :width: 32%
     :target: intro/intro_3.html
 
 
-  .. image:: ../../../examples/intro_4_oriented/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_4_oriented/trimesh.png
     :alt: Triangular mesh from fourth intro example.
     :width: 32%
     :target: intro/intro_4.html
 
 
-  .. image:: ../../../examples/intro_5_plotting/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_5_plotting/trimesh.png
     :alt: Triangular mesh from fifth intro example.
     :width: 32%
     :target: intro/intro_5.html
 
 
-  .. image:: ../../../examples/intro_6_culmination/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/intro_6_culmination/trimesh.png
     :alt: Triangular mesh from sixth intro example.
     :width: 32%
     :target: intro/intro_6.html
@@ -78,27 +78,27 @@ CLI Examples
 
 .. only:: html
 
-  .. image:: ../../../examples/elliptical_grains/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/elliptical_grains/trimesh.png
     :alt: Triangular mesh with elliptical grains.
     :width: 64%
     :target: cli/elliptical_grains.html
 
-  .. image:: ../../../examples/minimal/polymesh.png
+  .. image:: ../../../src/microstructpy/examples/minimal/polymesh.png
     :alt: Polygonal mesh from minimal example.
     :width: 32%
     :target: cli/minimal.html
 
-  .. image:: ../../../examples/basalt_circle/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/basalt_circle/trimesh.png
     :alt: Triangular mesh from basalt example.
     :width: 32%
     :target: cli/basalt.html
 
-  .. image:: ../../../examples/two_phase_3D/polymesh.png
+  .. image:: ../../../src/microstructpy/examples/two_phase_3D/polymesh.png
     :alt: Polygonal mesh from 3D two phase example.
     :width: 32%
     :target: cli/two_phase_3d.html
 
-  .. image:: ../../../examples/colormap/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/colormap/trimesh.png
       :alt: Triangular mesh from 3D colormap example.
       :width: 32%
       :target: cli/colormap.html
@@ -123,36 +123,36 @@ Python Package Examples
 
 .. only:: html
 
-  .. image:: ../../../examples/standard_voronoi/voronoi_diagram.png
+  .. image:: ../../../src/microstructpy/examples/standard_voronoi/voronoi_diagram.png
     :alt: Standard Voronoi diagram.
     :height: 210px
     :target: package/standard_voronoi.html
 
-  .. image:: ../../../examples/uniform_seeding/voronoi_diagram.png
+  .. image:: ../../../src/microstructpy/examples/uniform_seeding/voronoi_diagram.png
     :alt: Voronoi diagram with uniformly-spaced seeds, colored by area.
     :height: 210px
     :target: package/uniform_seeding.html
 
-  .. image:: ../../../examples/foam/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/foam/trimesh.png
     :alt: Mesh of foam microstructure.
     :height: 210px
     :target: package/foam.html
 
-  .. image:: ../../../examples/logo/logo.png
+  .. image:: ../../../src/microstructpy/examples/logo/logo.png
     :alt: MicroStructPy logo.
     :height: 210px
     :target: package/logo.html
 
-  .. image:: ../../../examples/grain_neighborhoods/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/grain_neighborhoods/trimesh.png
     :alt: Triangular mesh of microstructure with seed neighborhoods.
     :height: 210px
     :target: package/grain_neighborhoods.html
 
-  .. image:: ../../../examples/from_image/trimesh.png
+  .. image:: ../../../src/microstructpy/examples/from_image/trimesh.png
     :alt: Triangular mesh of aluminum microstructure.
     :height: 210px
     :target: package/from_image.html
 
-  .. image:: ../../../examples/docs_banner/banner.png
+  .. image:: ../../../src/microstructpy/examples/docs_banner/banner.png
     :alt: Microstructure meshing process..
     :target: package/mesh_process.html

docs/source/examples/intro/intro_1.rst

@@ -14,7 +14,7 @@ The file can be run using this command::
 
 The full text of the file is:
 
-.. literalinclude:: ../../../../examples/intro_1_basic.xml
+.. literalinclude:: ../../../../src/microstructpy/examples/intro_1_basic.xml
     :language: xml
 
 
@@ -66,19 +66,19 @@ These three plots are shown in :numref:`f_ex_1_basic_seeds` -
 :numref:`f_ex_1_basic_tri`.
 
 .. _f_ex_1_basic_seeds:
-.. figure:: ../../../../examples/intro_1_basic/seeds.png
+.. figure:: ../../../../src/microstructpy/examples/intro_1_basic/seeds.png
     :alt: Seed geometries.
 
     Introduction 1 - seed geometries.
 
 .. _f_ex_1_basic_poly:
-.. figure:: ../../../../examples/intro_1_basic/polymesh.png
+.. figure:: ../../../../src/microstructpy/examples/intro_1_basic/polymesh.png
     :alt: Polygonal mesh.
 
     Introduction 1 - polygonal mesh.
 
 .. _f_ex_1_basic_tri:
-.. figure:: ../../../../examples/intro_1_basic/trimesh.png
+.. figure:: ../../../../src/microstructpy/examples/intro_1_basic/trimesh.png
     :alt: Triangular mesh.
 
     Introduction 1 - triangular mesh.