docs: renaming cython to _cython so its not included in docs

LoopStructural/interpolators/_discrete_fold_interpolator.py

@@ -11,7 +11,7 @@
 
 logger = getLogger(__name__)
 
-from .cython.dsi_helper import fold_cg
+from ._cython.dsi_helper import fold_cg
 
 
 class DiscreteFoldInterpolator(PiecewiseLinearInterpolator):

LoopStructural/interpolators/piecewiselinear_interpolator.py

@@ -2,7 +2,7 @@
 Piecewise linear interpolator
 """
 import numpy as np
-from LoopStructural.interpolators.cython.dsi_helper import cg, fold_cg
+from LoopStructural.interpolators._cython.dsi_helper import cg, fold_cg
 
 from LoopStructural.interpolators import DiscreteInterpolator
 from LoopStructural.interpolators import InterpolatorType

docs/Dockerfile

@@ -0,0 +1,20 @@
+FROM continuumio/miniconda3
+LABEL maintainer="lachlan.grose@monash.edu"
+#This docker image has been adapted from the lavavu dockerfile
+# install things
+
+RUN apt-get update -qq && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
+    gcc \
+    g++ \
+    libc-dev \
+    make
+RUN conda install -c conda-forge theano cython numpy pandas imageio scipy matplotlib  sphinx sphinx-gallery sphinxcontrib-bibtex sphinx_rtd_theme myst-parser scikit-learn scikit-image pyamg flake8 pytest networkx -y
+RUN pip install lavavu-osmesa 
+COPY . LoopStructural
+#RUN git clone https://github.com/Loop3D/LoopStructural.git 
+WORKDIR LoopStructural
+RUN pip install .
+WORKDIR docs
+RUN conda install -c conda-forge pydata-sphinx-theme 
+RUN make html

setup.py

@@ -1,25 +1,23 @@
-#setup cython code
+# setup cython code
 import sys
+
 try:
-	from setuptools import setup, find_packages
+    from setuptools import setup, find_packages
 except:
-	raise RuntimeError("Cannot import setuptools \n"\
-	     "python -m pip install setuptools")
-	sys.exit(1)
+    raise RuntimeError("Cannot import setuptools \n" "python -m pip install setuptools")
+    sys.exit(1)
 
 try:
-	from Cython.Build import cythonize
+    from Cython.Build import cythonize
 except:
-	raise RuntimeError("Cannot import cython \n"\
-	     "python -m pip install cython")
-	sys.exit(1)
+    raise RuntimeError("Cannot import cython \n" "python -m pip install cython")
+    sys.exit(1)
 try:
-	import numpy
+    import numpy
 except:
-	raise RuntimeError("Cannot import numpy \n"\
-	     "python -m pip install numpy")
-	sys.exit(1)	 
-
+    raise RuntimeError("Cannot import numpy \n" "python -m pip install numpy")
+    sys.exit(1)
+
 import numpy
 import os
 import codecs
@@ -32,44 +30,53 @@
 version = version["__version__"]
 
 setup(
-	name="LoopStructural",
-	install_requires=[
-	'numpy>=1.18', #need to fix numpy to 1.18 because we build against it
-	'pandas',
-	'scipy',
-	'scikit-image',
-	'scikit-learn',
-	'tqdm',
-	'numba',
-	'geostatspy',
-	'statsmodels',
-	'scikit-fmm'
-	],
-	description="Open source 3D structural geology modelling",
-          long_description=codecs.open("README.md", "r", "utf-8").read(),
-          author="Lachlan Grose",
-          author_email="lachlan.grose@monash.edu",
-          license=("MIT"),
-          url="https://loop3d.github.io/LoopStructural/",
-          classifiers=[
-              "Development Status :: 4 - Beta",
-              "Intended Audience :: Developers",
-              "Intended Audience :: Other Audience",
-              "Intended Audience :: Science/Research",
-              "License :: OSI Approved :: MIT License",
-              "License :: Free for non-commercial use",
-              "Natural Language :: English",
-              "Programming Language :: Python",
-              "Programming Language :: Python :: 3",
-              "Topic :: Multimedia :: Graphics :: 3D Modeling",
-              "Topic :: Scientific/Engineering",
-              "Topic :: Scientific/Engineering :: GIS",
-              ],
-	version=version,
+    name="LoopStructural",
+    install_requires=[
+        "numpy>=1.18",  # need to fix numpy to 1.18 because we build against it
+        "pandas",
+        "scipy",
+        "scikit-image",
+        "scikit-learn",
+        "tqdm",
+        "numba",
+        "geostatspy",
+        "statsmodels",
+        "scikit-fmm",
+    ],
+    description="Open source 3D structural geology modelling",
+    long_description=codecs.open("README.md", "r", "utf-8").read(),
+    author="Lachlan Grose",
+    author_email="lachlan.grose@monash.edu",
+    license=("MIT"),
+    url="https://loop3d.github.io/LoopStructural/",
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Other Audience",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "License :: Free for non-commercial use",
+        "Natural Language :: English",
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Topic :: Multimedia :: Graphics :: 3D Modeling",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Scientific/Engineering :: GIS",
+    ],
+    version=version,
     packages=find_packages(),
-	ext_modules=cythonize("LoopStructural/interpolators/cython/*.pyx",compiler_directives={"language_level": "3"}),
-	include_dirs=[numpy.get_include()],
-	include_package_data=True,
-	package_data={'LoopStructural':['datasets/data/*.csv','datasets/data/*.txt']},
-	keywords=['earth sciences','geology', '3-D modelling', 'structural geology', 'uncertainty']
-	)
+    ext_modules=cythonize(
+        "LoopStructural/interpolators/_cython/*.pyx",
+        compiler_directives={"language_level": "3"},
+    ),
+    include_dirs=[numpy.get_include()],
+    include_package_data=True,
+    package_data={"LoopStructural": ["datasets/data/*.csv", "datasets/data/*.txt"]},
+    keywords=[
+        "earth sciences",
+        "geology",
+        "3-D modelling",
+        "structural geology",
+        "uncertainty",
+    ],
+)