support for python 3.9 (#202)

* support for python 3.9 Co-authored-by: Keith Roberts <krober@usp.edu>
krober10nd · Mar 9, 2021 · cabf0ac · cabf0ac
1 parent 2a6d4ce
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -9,6 +9,25 @@ jobs:
       - run: pip install -U black flake8 --user
       - run: black --check .
       - run: flake8 .
+  build_3.9.0:
+    docker:
+      - image: circleci/python:3.9.0
+    steps:
+      - checkout
+      - run: python --version
+      - run: pip --version
+      - run: sudo apt install -y libopenmpi3 libopenmpi-dev openmpi-bin
+      - run: sudo apt-get update && sudo apt install -y cmake
+      - run: sudo apt-get install libboost-all-dev
+      - run: sudo apt-get install libmpfr-dev
+      - run: git clone https://github.com/CGAL/cgal.git && cd cgal/ && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && sudo make install
+      - run: sudo apt install -y libhdf5-dev
+      - run: sudo apt install -y python-pybind11
+      - run: pip install .[io] --user
+      - run:
+             pip install tox --user && tox -e py39
+      - run: bash <(curl -s https://codecov.io/bash)
+
   build_3.8.1:
     docker:
       - image: circleci/python:3.8.1
@@ -23,7 +42,7 @@ jobs:
       - run: git clone https://github.com/CGAL/cgal.git && cd cgal/ && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && sudo make install
       - run: sudo apt install -y libhdf5-dev
       - run: sudo apt install -y python-pybind11
-      - run: pip install . --user
+      - run: pip install .[io] --user
       - run:
              pip install tox --user && pip uninstall -y virtualenv && tox -e py38
       - run: bash <(curl -s https://codecov.io/bash)
@@ -41,7 +60,7 @@ jobs:
       - run: git clone https://github.com/CGAL/cgal.git && cd cgal/ && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && sudo make install
       - run: sudo apt install -y libhdf5-dev
       - run: sudo apt install -y python-pybind11
-      - run: pip install . --user
+      - run: pip install .[io] --user
       - run:
              pip install tox --user && tox -e py37
       - run: bash <(curl -s https://codecov.io/bash)
@@ -59,7 +78,7 @@ jobs:
       - run: git clone https://github.com/CGAL/cgal.git && cd cgal/ && git checkout 6f8f790 && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && sudo make install
       - run: sudo apt install -y libhdf5-dev
       - run: pip install pytest --user && git clone https://github.com/pybind/pybind11.git && cd pybind11 && mkdir build && cd build && cmake .. && sudo make install
-      - run: pip install . --user
+      - run: pip install .[io] --user
       - run:
              pip install tox --user && /home/circleci/.local/bin/tox -e py36
       - run: bash <(curl -s https://codecov.io/bash)
@@ -72,3 +91,4 @@ workflows:
       - build_3.6.5
       - build_3.7.4
       - build_3.8.1
+      - build_3.9.0
diff --git a/README.md b/README.md
@@ -57,9 +57,6 @@ Table of contents
 Installation
 ============
 
-**Nov. 21, 2020 our software is not yet compatible with Python 3.9 because of the `segyio` package dependency which doesn't build yet with this version of Python. Until this is fixed, please use a Python version prior to 3.9 to run your scripts with this package.**
-
-
 For installation, SeismicMesh needs [CGAL](https://www.cgal.org/) and
 [pybind11](https://github.com/pybind/pybind11):
 
@@ -68,7 +65,7 @@ For installation, SeismicMesh needs [CGAL](https://www.cgal.org/) and
 After that, SeismicMesh can be installed from the Python Package Index
 ([pypi](https://pypi.org/project/SeismicMesh/)), so with:
 
-    pip install -U SeismicMesh
+    pip install -U SeismicMesh[io]
 
 For more detailed information about installation and requirements see:
 
@@ -827,6 +824,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Rotations for all geometric primitives
 - Stretching for all geometric primitives
 - Visuzlization of signed distance functions
+### Fixed
+- Support for Python 3.9
 
 ## [3.4.0]-2021-02-14
 ### Added

diff --git a/SeismicMesh/sizing/mesh_size_function.py b/SeismicMesh/sizing/mesh_size_function.py
@@ -17,7 +17,6 @@
 import h5py
 import matplotlib.pyplot as plt
 import numpy as np
-import segyio
 from mpi4py import MPI
 from scipy import ndimage
 from scipy.interpolate import RegularGridInterpolator
@@ -26,6 +25,7 @@
 
 from .cpp import limgrad
 
+
 __all__ = [
     "get_sizing_function_from_segy",
     "write_velocity_model",
@@ -51,7 +51,7 @@ def get_sizing_function_from_segy(filename, bbox, comm=None, **kwargs):
         * *hmax* (``float``) --
             Maximum edge length in the domain (default==10,000 m)
         * *wl* (``int``) --
-            Number of vertices per wavelength for a given 𝑓𝑚𝑎𝑥 (default==0 vertices)
+            Number of cells per wavelength for a given 𝑓𝑚𝑎𝑥 (default==0 cells)
         * *freq* (``float``) --
             𝑓𝑚𝑎𝑥 in hertz for which to estimate `wl` (default==2 Hertz)
         * *grad* (``float``) --
@@ -406,7 +406,8 @@ def _gradient_sizing(vp, grad, stencil_size):
     win_var = win_sqr_mean - win_mean ** 2
 
     # normalize variance to [0,1]
-    win_var /= np.amax(win_var)
+    win_var = np.divide(win_var, np.amax(win_var))
+    # win_var /= np.amax(win_var)
     win_var -= np.amin(win_var)
     return grad / (win_var + 0.10)
 
@@ -587,11 +588,16 @@ def _read_bin(filename, nz, nx, ny, byte_order, axes_order, axes_order_sort, dty
         else:
             raise ValueError("Please specify byte_order as either: little or big.")
         vp = vp.reshape(*axes, order=axes_order_sort)
-        return np.flipud(vp.transpose((*axes_order))), nz, nx, ny  # z, x and then y
+
+        vp = np.flipud(vp.transpose((*axes_order,)))
+
+        return vp, nz, nx, ny  # z, x and then y
 
 
 def _read_segy(filename):
     """Read a velocity model from a SEG-y file"""
+    import segyio
+
     with segyio.open(filename, ignore_geometry=True) as f:
         nz, nx = len(f.samples), len(f.trace)
         vp = np.zeros(shape=(nz, nx))

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = SeismicMesh
-version = 3.4.0
+version = 3.5.0
 url = https://github.com/krober10nd/SeismicMesh
 author = Keith Roberts
 email = keithrbt0@gmail.com
@@ -24,7 +24,7 @@ classifiers =
     Topic :: Scientific/Engineering :: Visualization
 [options]
 packages = find:
-setup_requires = pybind11 >= 2.2
+setup_requires = pybind11 >= 2.5
 install_requires =
         numpy
         segyio
@@ -33,6 +33,11 @@ install_requires =
         h5py
         matplotlib
         mpi4py
-        pybind11 >= 2.2
+        pybind11 >= 2.5
         pyamg
 python_requires = >=3.0
+
+[options.extras_require]
+benchmarking = meshplex; pygalmesh; pygmsh; meshio; termplotlib
+io = segyio
+all = segyio; meshplex; pygalmesh; pygmsh; meshio; termplotlib
diff --git a/setup.py b/setup.py
@@ -12,26 +12,6 @@
 except ImportError:
     print("Setuptools is required to build!")
 
-if sys.version_info < (3, 0):
-    print("Python 3.0 or higher required, please upgrade.")
-    sys.exit(1)
-
-if sys.version_info >= (3, 9, 0):
-    print(
-        "Python 3.9.0 or higher is not yet supported, please use an older Python version."
-    )
-    sys.exit(1)
-
-
-benchmarking = [
-    "meshplex == 0.13.3",
-    "pygalmesh == 0.8.2",
-    "pygmsh == 7.0.0",
-    "termplotlib == 0.3.2",
-    "meshio == 4.2.2",
-    "termplotlib == 0.3.2",
-]
-
 
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=""):
@@ -104,8 +84,4 @@ def build_extension(self, ext):
         CMakeExtension("SeismicMesh/geometry/cpp/fast_geometry"),
     ],
     cmdclass=dict(build_ext=CMakeBuild),
-    extras_require={
-        "benchmarking": benchmarking,
-    },
-    python_requires=">=3.0",
 )
diff --git a/tox.ini b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py36, py37, py38
+envlist = py36, py37, py38, py39
 isolated_build = True
 
 [mpi]