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Merge pull request #167935 from wd15/fipy-fix-build

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python3Packages.fipy: fix broken build
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Artturi 2022-04-09 12:57:40 +03:00 committed by GitHub
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8
pkgs/development/python-modules/fipy/default.nix
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@ -39,6 +39,14 @@ buildPythonPackage rec {
] ++ lib.optionals isPy27 [ pysparse ]
++ lib.optionals (!stdenv.isDarwin) [ gmsh ];
# Reading version string from Gmsh is broken in latest release of FiPy
# This issue is repaired on master branch of FiPy
# Fixed with: https://github.com/usnistgov/fipy/pull/848/files
# Remove patch with next release.
patches = [ ./gmsh.patch ];
checkInputs = lib.optionals (!stdenv.isDarwin) [ gmsh ];
checkPhase = ''
export OMPI_MCA_plm_rsh_agent=${openssh}/bin/ssh
${python.interpreter} setup.py test --modules

182
pkgs/development/python-modules/fipy/gmsh.patch Normal file
View file

@ -0,0 +1,182 @@
diff --git a/fipy/meshes/gmshMesh.py b/fipy/meshes/gmshMesh.py
index fc3ff6c8..d529d532 100755
--- a/fipy/meshes/gmshMesh.py
+++ b/fipy/meshes/gmshMesh.py
@@ -13,11 +13,11 @@ import sys
import tempfile
from textwrap import dedent
import warnings
-from distutils.version import StrictVersion
from fipy.tools import numerix as nx
from fipy.tools import parallelComm
from fipy.tools import serialComm
+from fipy.tools.version import Version, parse_version
from fipy.tests.doctestPlus import register_skipper
from fipy.meshes.mesh import Mesh
@@ -38,7 +38,7 @@ def _checkForGmsh():
hasGmsh = True
try:
version = _gmshVersion(communicator=parallelComm)
- hasGmsh = version >= StrictVersion("2.0")
+ hasGmsh = version >= Version("2.0")
except Exception:
hasGmsh = False
return hasGmsh
@@ -68,6 +68,7 @@ def gmshVersion(communicator=parallelComm):
while True:
try:
# gmsh returns version in stderr (Why?!?)
+ # (newer versions of gmsh return the version in stdout)
# spyder on Windows throws
# OSError: [WinError 6] The handle is invalid
# if we don't PIPE stdout, too
@@ -77,8 +78,11 @@ def gmshVersion(communicator=parallelComm):
break
try:
- out, verStr = p.communicate()
- verStr = verStr.decode('ascii').strip()
+ out, err = p.communicate()
+ verStr = err.decode('ascii').strip()
+ if not verStr:
+ # newer versions of gmsh return the version in stdout
+ verStr = out.decode('ascii').strip()
break
except IOError:
# some weird conflict with things like PyQT can cause
@@ -93,12 +97,12 @@ def gmshVersion(communicator=parallelComm):
def _gmshVersion(communicator=parallelComm):
version = gmshVersion(communicator) or "0.0"
try:
- version = StrictVersion(version)
+ version = parse_version(version)
except ValueError:
# gmsh returns the version string in stderr,
# which means it's often unparsable due to irrelevant warnings
# assume it's OK and move on
- version = StrictVersion("3.0")
+ version = Version("3.0")
return version
@@ -133,7 +137,7 @@ def openMSHFile(name, dimensions=None, coordDimensions=None, communicator=parall
# Enforce gmsh version to be either >= 2 or 2.5, based on Nproc.
version = _gmshVersion(communicator=communicator)
- if version < StrictVersion("2.0"):
+ if version < Version("2.0"):
raise EnvironmentError("Gmsh version must be >= 2.0.")
# If we're being passed a .msh file, leave it be. Otherwise,
@@ -176,9 +180,11 @@ def openMSHFile(name, dimensions=None, coordDimensions=None, communicator=parall
gmshFlags = ["-%d" % dimensions, "-nopopup"]
if communicator.Nproc > 1:
- if not (StrictVersion("2.5") < version <= StrictVersion("4.0")):
- warnstr = "Cannot partition with Gmsh version < 2.5 or >= 4.0. " \
- + "Reverting to serial."
+ if ((version < Version("2.5"))
+ or (Version("4.0") <= version < Version("4.5.2"))):
+ warnstr = ("Cannot partition with Gmsh version < 2.5 "
+ "or 4.0 <= version < 4.5.2. "
+ "Reverting to serial.")
warnings.warn(warnstr, RuntimeWarning, stacklevel=2)
communicator = serialComm
@@ -188,13 +194,13 @@ def openMSHFile(name, dimensions=None, coordDimensions=None, communicator=parall
raise ValueError("'dimensions' must be specified to generate a mesh from a geometry script")
else: # gmsh version is adequate for partitioning
gmshFlags += ["-part", "%d" % communicator.Nproc]
- if version >= StrictVersion("4.0"):
+ if version >= Version("4.0"):
# Gmsh 4.x needs to be told to generate ghost cells
- # Unfortunately, the ghosts are broken
+ # Unfortunately, the ghosts are broken in Gmsh 4.0--4.5.1
# https://gitlab.onelab.info/gmsh/gmsh/issues/733
gmshFlags += ["-part_ghosts"]
- gmshFlags += ["-format", "msh2"]
+ gmshFlags += ["-format", "msh2", "-smooth", "8"]
if background is not None:
if communicator.procID == 0:
@@ -1387,6 +1393,11 @@ class _GmshTopology(_MeshTopology):
class Gmsh2D(Mesh2D):
"""Construct a 2D Mesh using Gmsh
+ If called in parallel, the mesh will be partitioned based on the value
+ of `parallelComm.Nproc`. If an `MSH` file is supplied, it must have
+ been previously partitioned with the number of partitions matching
+ `parallelComm.Nproc`.
+
>>> radius = 5.
>>> side = 4.
>>> squaredCircle = Gmsh2D('''
@@ -1875,6 +1886,11 @@ class Gmsh2D(Mesh2D):
class Gmsh2DIn3DSpace(Gmsh2D):
"""Create a topologically 2D Mesh in 3D coordinates using Gmsh
+ If called in parallel, the mesh will be partitioned based on the value
+ of `parallelComm.Nproc`. If an `MSH` file is supplied, it must have
+ been previously partitioned with the number of partitions matching
+ `parallelComm.Nproc`.
+
Parameters
----------
arg : str
@@ -1959,6 +1975,11 @@ class Gmsh2DIn3DSpace(Gmsh2D):
class Gmsh3D(Mesh):
"""Create a 3D Mesh using Gmsh
+ If called in parallel, the mesh will be partitioned based on the value
+ of `parallelComm.Nproc`. If an `MSH` file is supplied, it must have
+ been previously partitioned with the number of partitions matching
+ `parallelComm.Nproc`.
+
Parameters
----------
arg : str
@@ -2225,7 +2246,7 @@ class GmshGrid2D(Gmsh2D):
width = nx * dx
numLayers = int(ny / float(dy))
- if _gmshVersion() < StrictVersion("2.7"):
+ if _gmshVersion() < Version("2.7"):
# kludge: must offset cellSize by `eps` to work properly
eps = float(dx)/(nx * 10)
else:
@@ -2299,7 +2320,7 @@ class GmshGrid3D(Gmsh3D):
width = nx * dx
depth = nz * dz
- if _gmshVersion() < StrictVersion("2.7"):
+ if _gmshVersion() < Version("2.7"):
# kludge: must offset cellSize by `eps` to work properly
eps = float(dx)/(nx * 10)
else:
diff --git a/fipy/tools/version.py b/fipy/tools/version.py
new file mode 100644
index 00000000..93d89c18
--- /dev/null
+++ b/fipy/tools/version.py
@@ -0,0 +1,18 @@
+"""Shim for version checking
+
+`distutils.version` is deprecated, but `packaging.version` is unavailable
+in Python 2.7
+"""
+from __future__ import unicode_literals
+
+__docformat__ = 'restructuredtext'
+
+
+__all__ = ["Version", "parse_version"]
+from future.utils import text_to_native_str
+__all__ = [text_to_native_str(n) for n in __all__]
+
+try:
+ from packaging.version import Version, parse as parse_version
+except ImportError:
+ from distutils.version import StrictVersion as Version, StrictVersion as parse_version