matplotlib 3.4 hotfix (#89)

.github/workflows/codeql-analysis.yml

@@ -16,7 +16,7 @@ jobs:
 
  steps:
  - name: Checkout repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
  with:
  # We must fetch at least the immediate parents so that if this is
  # a pull request then we can checkout the head.

.github/workflows/documentation.yaml

@@ -12,9 +12,10 @@ jobs:
 
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - name: Checkout
+ uses: actions/checkout@v3
  - name: Set up Python
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v4
  with:
  python-version: '3.10'
  - name: Setup Linux Environment
@@ -36,17 +37,26 @@ jobs:
  if [ "${{ matrix.doc-type }}" = html ]; then echo "art_path=docs/build-html" >> $GITHUB_ENV; fi
  if [ "${{ matrix.doc-type }}" = latex ]; then echo "art_path=docs/build-latex/MicroStructPy.pdf" >> $GITHUB_ENV; fi
  if [ "${{ matrix.doc-type }}" = epub ]; then echo "art_path=docs/build-epub/MicroStructPy.epub" >> $GITHUB_ENV; fi
+
+ - name: Build PDF (latex only)
+ if: matrix.doc-type == 'latex'
+ run: |
+ # Update apt
+ sudo apt-get update
  
- # Build PDF 
- if [ "${{ matrix.doc-type }}" = latex ]; then sudo apt install texlive-fonts-recommended; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then sudo apt install texlive-latex-recommended; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then sudo apt install texlive-lang-english; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then sudo apt install texlive-xetex; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then sudo apt install latexmk; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then cd docs/build-latex; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then make; fi
- if [ "${{ matrix.doc-type }}" = latex ]; then cd -; fi
- 
+ # Install LaTeX packages
+ # Recommended by Sphinx on their docs page:
+ # https://www.sphinx-doc.org/en/master/usage/builders/index.html#sphinx.builders.latex.LaTeXBuilder
+ sudo apt install texlive-latex-recommended
+ sudo apt install texlive-fonts-recommended
+ sudo apt install tex-gyre # (if latex_engine left to default)
+ sudo apt install texlive-latex-extra
+ sudo apt install latexmk
+
+ # Make
+ cd docs/build-latex
+ make
+ cd -
  
  - name: Upload artifact
  uses: actions/upload-artifact@v3

.github/workflows/ossar-analysis.yml

@@ -16,7 +16,7 @@ jobs:
  steps:
  # Checkout your code repository to scan
  - name: Checkout repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
  with:
  # We must fetch at least the immediate parents so that if this is
  # a pull request then we can checkout the head.

.github/workflows/python_package.yaml

@@ -13,9 +13,9 @@ jobs:
  os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
 
@@ -56,9 +56,9 @@ jobs:
 
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - name: Set up Python
- uses: actions/setup-python@v2
+ uses: actions/setup-python@v4
  with:
  python-version: '3.x'
  - name: Cache pip

.github/workflows/python_publish.yaml

@@ -17,7 +17,7 @@ jobs:
  steps:
  - uses: actions/checkout@v3
  - name: Set up Python
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v4
  with:
  python-version: '3.x'
  - name: Install dependencies

.readthedocs.yaml

@@ -0,0 +1,28 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+formats: all
+
+# Set the OS, Python version and other tools you might need
+build:
+ os: ubuntu-22.04
+ tools:
+ python: "3.8"
+ apt_packages:
+ - freeglut3-dev
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+ configuration: docs/source/conf.py
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+ install:
+ - requirements: docs/requirements.txt
+ - method: pip
+ path: .

CHANGELOG.rst

@@ -6,6 +6,14 @@ 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`_.
 
+`1.5.7`_ - 2023-08-06
+--------------------------
+Fixed
+'''''''
+- Errors associated with using keyword arguments in ``plt.gca()`` deprecated in matplotlib 3.4.
+- 3D plots now use matplotlib standard for setting equal aspect ratios.
+
+
 `1.5.6`_ - 2022-09-01
 --------------------------
 Fixed
@@ -292,7 +300,8 @@ Added
 
 .. LINKS
 
-.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.6...HEAD
+.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.7...HEAD
+.. _`1.5.7`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.6...v1.5.7
 .. _`1.5.6`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.5...v1.5.6
 .. _`1.5.5`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.4...v1.5.5
 .. _`1.5.4`: https://github.com/kip-hart/MicroStructPy/compare/v1.5.3...v1.5.4

MANIFEST.in

@@ -7,7 +7,7 @@ include .bumpversion.cfg
 include .coveragerc
 include .editorconfig
 include .pyup.yml
-include .readthedocs.yml
+include .readthedocs.yaml
 
 include CHANGELOG.rst
 include LICENSE.rst

docs/requirements.txt

@@ -1,6 +1,6 @@
-gmsh==4.10.5
-matplotlib==3.5.1
-numpy==1.22.0
+gmsh==4.11.1
+matplotlib==3.7.2
+numpy==1.24.4
 pybind11==2.4.3
 sphinx==4.2.0
 sphinx-gallery==0.8.1

docs/source/conf.py

@@ -15,17 +15,15 @@
 import os
 import sys
 sys.path.insert(0, os.path.abspath('../../src/'))
-sys.path.insert(0, os.path.abspath('../../src/MicroStructPy/'))
-
+sys.path.insert(0, os.path.abspath('../../src/microstructpy/'))
 import sphinx_gallery
-
 import microstructpy
 
 
 # -- Project information -----------------------------------------------------
 
 project = 'MicroStructPy'
-copyright = '2019-2022, Georgia Tech Research Corporation'
+copyright = '2019-2023, Georgia Tech Research Corporation'
 author = 'Kenneth Hart'
 
 # The short X.Y version
@@ -138,7 +136,7 @@
  'logo_name': True,
  'sidebar_width': '230px',
  'description': 'Microstructure modeling, mesh generation, analysis, and visualization.',
- 'analytics_id': 'UA-147258715-1',
+ 'analytics_id': 'G-TK7PBETHC0',
  'code_font_size': '12.5px',
 }
 

docs/source/sphinx_gallery/geometry/plot_ellipse.py

@@ -20,7 +20,7 @@ def breakdown():
  b = 1
  x1 = 0.7
 
- plt.figure(figsize=(14, 6))
+ fig = plt.figure(figsize=(14, 6))
  ellipse = msp.geometry.Ellipse(a=a, b=b)
  approx = ellipse.approximate(x1)
  ellipse.plot(edgecolor='k', facecolor='none', lw=3)
@@ -34,8 +34,9 @@ def breakdown():
  plt.gca().set_xticklabels([str(round(float(label), 1)) for label in xticks])
  plt.axis('scaled')
  plt.grid(True, linestyle=':')
+ plt.tight_layout()
 
 
 if __name__ == '__main__':
- plt.rc('savefig', dpi=300, bbox='tight', pad_inches=0)
+ plt.rc('savefig', dpi=300, pad_inches=0)
  main()

docs/source/sphinx_gallery/geometry/plot_rectangle.py

@@ -20,7 +20,7 @@ def breakdown(length, width, x1, figsize):
  approx = r.approximate(x1=x1)
 
  # Plot rectangle
- plt.figure(figsize=figsize)
+ fig = plt.figure(figsize=figsize)
  r.plot(edgecolor='k', facecolor='none', lw=3)
 
  # Plot breakdown
@@ -38,8 +38,9 @@ def breakdown(length, width, x1, figsize):
 
  plt.axis('scaled')
  plt.grid(True, linestyle=':')
+ plt.tight_layout()
 
 
 if __name__ == '__main__':
- plt.rc('savefig', dpi=300, bbox='tight', pad_inches=0)
+ plt.rc('savefig', dpi=300, pad_inches=0)
  main()

docs/source/sphinx_gallery/plot_demos.py

@@ -70,7 +70,8 @@ def create_welcome():
 
  sub_fname = 'welcome_examples.png'
  sub_filename = os.path.join(example_dir, sub_fname)
- plt.savefig(sub_filename, pad_inches=0, bbox_inches='tight', dpi=200)
+ plt.tight_layout()
+ plt.savefig(sub_filename, pad_inches=0, dpi=200)
  plt.close('all')
 
 
@@ -92,7 +93,8 @@ def seed_poly_tri(filepath):
 
  sub_fname = 'joined.png'
  sub_filename = os.path.join(ex_path, sub_fname)
- plt.savefig(sub_filename, pad_inches=0, bbox_inches='tight', dpi=300)
+ plt.tight_layout()
+ plt.savefig(sub_filename, pad_inches=0, dpi=300)
  plt.close('all')
 
 

requirements.txt

@@ -1,12 +1,12 @@
 aabbtree==2.5.0
-matplotlib==3.5.3
+matplotlib==3.7.2
 pybind11==2.4.3
-pygmsh==7.0.2
+pygmsh==7.1.17
 MeshPy==2018.2.1
-numpy==1.23.2
+numpy==1.24.4
 pyquaternion==0.9.5
 pyvoro-mmalahe==1.3.3
-scipy==1.9.1
+scipy==1.10.1
 xmltodict==0.12.0
 tox==3.14.0
 lsq-ellipse==2.0.1

setup.py

@@ -79,7 +79,7 @@ def find_version(*fname):
  'aabbtree>=2.5.0',
  'pybind11', # must come before meshpy for successful install
  'lsq-ellipse',
- 'matplotlib>=3.3.0',
+ 'matplotlib>=3.4.0',
  'meshpy>=2018.2.1',
  'numpy>=1.13.0',
  'pygmsh>=7.0.2',

src/microstructpy/__init__.py

@@ -4,4 +4,4 @@
 import microstructpy.seeding
 import microstructpy.verification
 
-__version__ = '1.5.6'
+__version__ = '1.5.7'

src/microstructpy/_misc.py

@@ -156,14 +156,7 @@ def tangent_sphere(points, radii=None, simplices=None):
 
 
 def axisEqual3D(ax):
- '''From stackoverflow: https://stackoverflow.com/a/19248731'''
- extents = np.array([getattr(ax, 'get_{}lim'.format(d))() for d in 'xyz'])
- sz = extents[:, 1] - extents[:, 0]
- centers = np.mean(extents, axis=1)
- maxsize = max(abs(sz))
- r = maxsize/2
- for ctr, dim in zip(centers, 'xyz'):
- getattr(ax, 'set_{}lim'.format(dim))(ctr - r, ctr + r)
+ ax.set_aspect('equal')
 
 
 def ax_objects(ax):