exdown -> pytest-codeblocks (#213)

* exdown -> pytest-codeblocks

* updates for new black linter

Co-authored-by: Keith Roberts <krober@usp.edu>

Author: Keith Roberts

README.md

@@ -201,7 +201,7 @@ size.**
 
 ![Above shows the mesh in ParaView that results from running the code below.](https://user-images.githubusercontent.com/18619644/103445790-52cd8b00-4c57-11eb-8bd4-4af8f24d4c88.jpg)
 
-<!--exdown-skip-->
+<!--pytest-codeblocks:skip-->
 ```python
 from mpi4py import MPI
 import zipfile
@@ -819,13 +819,16 @@ Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## Unreleased
+## Unrelease
+- None
+## [3.6.1]-2021-05-22
 ### Added
 - Smoothed sets (e.g., intersections, differences, and unions)
 - Conversion of velocity data from feet-second to meters-second
 - Support for fixed points in iterative Laplacian mesh smoother.
 ### Improved
 - Simplified pybind11 build system.
+- Now using pytest-codeblocks instead of exdown
 
 ## [3.5.0]-2021-03-09
 ### Added

SeismicMesh/generation/mesh_generator.py

@@ -899,7 +899,7 @@ def _select_cgal_dim(dim):
 
 
 def _get_topology(dt):
-    """ Get points and entities from :clas:`CGAL:DelaunayTriangulation2/3` object"""
+    """Get points and entities from :clas:`CGAL:DelaunayTriangulation2/3` object"""
     p = dt.get_finite_vertices()
     t = dt.get_finite_cells()
     return p, t

SeismicMesh/migration/migration.py

@@ -53,7 +53,7 @@ def localize_sizing_function(fh, h0, bbox, dim, axis, comm):
 
 
 def localize_points(blocks, extents, comm, dim):
-    """ Distribute points to local subdomains """
+    """Distribute points to local subdomains"""
     rank = comm.Get_rank()
     size = comm.Get_size()
     for local in range(1, size):

SeismicMesh/sizing/mesh_size_function.py

@@ -435,7 +435,7 @@ def _enforce_courant_sizing(vp, cell_size, cr_max, dt, space_order):
 
 
 def _enforce_gradation_sizing(cell_size, grade, elen):
-    """Call-back to the cpp gradient limiter code """
+    """Call-back to the cpp gradient limiter code"""
     if grade == 0.0:
         warnings.warn(
             "Mesh size gradient is deactiavted. This may compromise mesh quality"

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = SeismicMesh
-version = 3.6.0
+version = 3.6.1
 url = https://github.com/krober10nd/SeismicMesh
 author = Keith Roberts
 email = keithrbt0@gmail.com
@@ -36,6 +36,7 @@ install_requires =
         mpi4py
         pybind11 >= 2.6
         pyamg == 4.0.0
+        pytest_codeblocks
 python_requires = >=3.0
 
 [options.extras_require]

tests/test_README.py

@@ -1,22 +1,16 @@
+import os
 import gzip
 import pathlib
 import shutil
 
-import exdown
 import pytest
 import requests
 
 this_dir = pathlib.Path(__file__).resolve().parent
 
 
 @pytest.mark.serial
-@pytest.mark.parametrize(
-    "string,lineno",
-    exdown.extract(
-        this_dir.parent / "README.md", syntax_filter="python", max_num_lines=100000
-    ),
-)
-def test_readme(string, lineno):
+def test_readme():
 
     # download
     url = "http://s3.amazonaws.com/open.source.geoscience/open_data/bpvelanal2004/vel_z6.25m_x12.5m_exact.segy.gz"
@@ -31,9 +25,4 @@ def test_readme(string, lineno):
     ) as f_out:
         shutil.copyfileobj(f_in, f_out)
 
-    try:
-        # https://stackoverflow.com/a/62851176/353337
-        exec(string, {"__MODULE__": "__main__"})
-    except Exception:
-        print(f"README.md (line {lineno}):\n```\n{string}```")
-        raise
+    os.system(f"pytest --codeblocks {this_dir.parent}/README.md")

tox.ini

@@ -1,21 +1,21 @@
-[tox]
-envlist = py36, py37, py38, py39
-isolated_build = True
-
-[mpi]
-mpiexec = {env:MPIEXEC:mpiexec}
-
-[testenv]
-setenv =
-    MPLBACKEND = agg
-deps =
-    exdown
-    requests
-    pytest
-    pytest-cov
-    mpi4py
-whitelist_externals = {[mpi]mpiexec}
-commands =
-    {[mpi]mpiexec} -n 2 -mca btl ^openib pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 -m "parallel2"
-    {[mpi]mpiexec} -n 2 -mca btl ^openib pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 --cov-append -m "parallel3"
-    pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 --cov-append  -m "serial"
+[tox]
+envlist = py36, py37, py38, py39
+isolated_build = True
+
+[mpi]
+mpiexec = {env:MPIEXEC:mpiexec}
+
+[testenv]
+setenv =
+    MPLBACKEND = agg
+deps =
+    pytest-codeblocks
+    requests
+    pytest
+    pytest-cov
+    mpi4py
+whitelist_externals = {[mpi]mpiexec}
+commands =
+    {[mpi]mpiexec} -n 2 -mca btl ^openib pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 -m "parallel2"
+    {[mpi]mpiexec} -n 2 -mca btl ^openib pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 --cov-append -m "parallel3"
+    pytest --cov {envsitepackagesdir}/SeismicMesh --cov-report xml --cov-report term --ignore=pybind11 --cov-append  -m "serial"