Add spectra calculation features

.gitignore

@@ -11,3 +11,6 @@ example/bar2vtk/result/*
 
 # testing
 .coverage
+
+# Documentation
+docs/_build/*

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api/requirements.txt

@@ -0,0 +1,2 @@
+sphinx-rtd-theme
+autodocsumm

docs/api/vtkpytools.barfiletools.rst

@@ -0,0 +1,20 @@
+Bar File tools (:mod:`barfiletools`)
+================================================
+
+Creating VTM files (:mod:`barfiletools.bar2vtk`)
+-------------------------------------------------------------
+
+.. automodule:: vtkpytools.barfiletools.bar2vtk
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:
+
+Post-Processing VTM files (:mod:`barfiletools.data`)
+-----------------------------------------------------------
+
+.. automodule:: vtkpytools.barfiletools.data
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:

docs/api/vtkpytools.bl.rst

@@ -0,0 +1,9 @@
+Boundary Layer tools (:mod:`bl`)
+=============================================================
+
+.. automodule:: vtkpytools.bl
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:
+

docs/api/vtkpytools.common.rst

@@ -0,0 +1,7 @@
+Common Utilities module (:mod:`common`)
+=========================================
+
+.. automodule:: vtkpytools.common
+   :members:
+   :autosummary:
+   :autosummary-nosignatures:

docs/api/vtkpytools.gridtools2d.rst

@@ -0,0 +1,9 @@
+Tools for 2D Grids (:mod:`gridtools2d`)
+===========================================
+
+.. automodule:: vtkpytools.gridtools2d.core
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:
+   :show-inheritance:

docs/api/vtkpytools.gridtools3d.rst

@@ -0,0 +1,9 @@
+Tools for 3D Grids (:mod:`gridtools3d`)
+=========================================
+
+.. automodule:: vtkpytools.gridtools3d.core
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:
+   :show-inheritance:

docs/api/vtkpytools.numtools.rst

@@ -0,0 +1,8 @@
+Numerical Tools (:mod:`numtools`)
+==================================
+
+.. automodule:: vtkpytools.numtools
+   :members:
+   :undoc-members:
+   :autosummary:
+   :autosummary-nosignatures:

docs/conf.py

@@ -0,0 +1,66 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import sphinx_rtd_theme
+sys.path.insert(0, os.path.abspath('../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'vtkpytools'
+copyright = '2021, James Wright'
+author = 'James Wright'
+
+# The full version, including alpha/beta/rc tags
+release = '1.1.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'autodocsumm',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.mathjax',
+    'sphinx_rtd_theme',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_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']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# 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 = ['_static']
+
+autodoc_member_order = 'bysource'
+
+default_role = 'autolink'

docs/index.rst

@@ -0,0 +1,29 @@
+Welcome to vtkpytools's documentation!
+======================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   api/vtkpytools.barfiletools
+   api/vtkpytools.gridtools2d
+   api/vtkpytools.gridtools3d
+
+Modules
+--------------------
+
+.. toctree::
+   :maxdepth: 4
+
+   api/vtkpytools.bl
+   api/vtkpytools.common
+   api/vtkpytools.numtools
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx-rtd-theme
+autodocsumm

tests/test_numtools.py

@@ -31,19 +31,71 @@ def test_calcStrainRate(twoFullTensors):
     assert np.allclose(strainrate, solution)
     assert strainrate.shape[0] == twoFullTensors.shape[0]
 
+class Test_symmetric2FullTensor():
 
-def test_symmetric2FullTensor(symAndFullTensor):
-    (full, sym) = symAndFullTensor
+    @staticmethod
+    def test_func2d(symAndFullTensor):
+        full, sym = symAndFullTensor
 
-    full_test = vpt.symmetric2FullTensor(sym)
-    assert np.allclose(full_test, full)
+        full_test = vpt.symmetric2FullTensor(sym)
+        assert np.allclose(full_test, full)
 
+    @staticmethod
+    def test_func_Nd(symAndFullTensor):
+        """Test (n,m,6) -> (n,m,3,3)"""
+        full, sym = symAndFullTensor
 
-def test_full2SymmetricTensor(symAndFullTensor):
-    (full, sym) = symAndFullTensor
+        sym = sym.reshape((1,-1,6))
+        full = full.reshape((1,-1,3,3))
+        full_test = vpt.symmetric2FullTensor(sym)
+        assert full_test.shape == full.shape
+        assert np.allclose(full_test, full)
 
-    sym_test = vpt.full2SymmetricTensor(full)
-    assert np.allclose(sym_test, sym)
+        sym = sym.reshape((-1,1,6))
+        full = full.reshape((-1,1,3,3))
+        full_test = vpt.symmetric2FullTensor(sym)
+        assert full_test.shape == full.shape
+        assert np.allclose(full_test, full)
+
+    @staticmethod
+    def test_inputCheck():
+        array = np.empty((6,4))
+        with pytest.raises(Exception):
+            vpt.symmetric2FullTensor(array)
+
+
+class Test_full2SymmetricTensor():
+
+    @staticmethod
+    def test_func3d(symAndFullTensor):
+        full, sym = symAndFullTensor
+
+        sym_test = vpt.full2SymmetricTensor(full)
+        assert sym_test.shape == sym.shape
+        assert np.allclose(sym_test, sym)
+
+    @staticmethod
+    def test_func_Nd(symAndFullTensor):
+        """Test (n,m,3,3) -> (n,m,6)"""
+        full, sym = symAndFullTensor
+
+        sym = sym.reshape((1,-1,6))
+        full = full.reshape((1,-1,3,3))
+        sym_test = vpt.full2SymmetricTensor(full)
+        assert sym_test.shape == sym.shape
+        assert np.allclose(sym_test, sym)
+
+        sym = sym.reshape((-1,1,6))
+        full = full.reshape((-1,1,3,3))
+        sym_test = vpt.full2SymmetricTensor(full)
+        assert sym_test.shape == sym.shape
+        assert np.allclose(sym_test, sym)
+
+    @staticmethod
+    def test_inputCheck():
+        array = np.empty((3,3,4))
+        with pytest.raises(Exception):
+            vpt.full2SymmetricTensor(array)
 
 
 @pytest.mark.parametrize('offset,expected', [(1, [0, 1] ),
@@ -53,7 +105,7 @@ def test_pwlinRoots(offset, expected):
     y = np.array([-1,   1, -1])
 
     roots = vpt.pwlinRoots(x, y + offset)
-    assert(np.allclose(roots, expected))
+    assert np.allclose(roots, expected)
 
 
 @pytest.mark.parametrize('kwargs,expected', [({'dx': 2.4}, [0, 1, 2, 4, 6.4, 8]),
@@ -63,8 +115,8 @@ def test_seriesDiffLimiter(kwargs, expected):
     series = np.array([0, 1, 2, 4, 8])
 
     result = vpt.seriesDiffLimiter(series, **kwargs)
-    assert(result.size == len(expected))
-    assert(np.allclose(result, expected))
+    assert result.size == len(expected)
+    assert np.allclose(result, expected)
 
 @pytest.mark.parametrize('kwargs', [{},
                                     {'dx': 2.0, 'magnitude': 4.0}])

vtkpytools/__init__.py

@@ -1,3 +1,4 @@
+from ._version import __version__
 from .barfiletools import *
 from .gridtools3d import *
 from .gridtools2d import *
@@ -8,3 +9,4 @@
                        pwlinRoots, seriesDiffLimiter)
 from .bl import (integratedVortBLThickness, sampleAlongVectors, delta_vortInt, delta_velInt, delta_percent)
 
+from .misc import *