Remove pypardiso as a hard dependency

Author: ma-sadeghi

.github/workflows/examples.yml

@@ -36,6 +36,7 @@ jobs:
           pip install \
             -r requirements.txt \
             -r requirements/tests.txt
+          pip install pypardiso
 
       - name: Running tests
         run:

.github/workflows/gh-pages.yml

@@ -36,6 +36,7 @@ jobs:
         run: |
           pip install -r requirements.txt
           pip install -r requirements/docs.txt
+          pip install pypardiso
 
       - name: Build the documentation
         run: |

.github/workflows/nightly.yml

@@ -49,6 +49,11 @@ jobs:
             -r requirements.txt \
             -r requirements/tests.txt
 
+      - name: Install pypardiso on non-macOS
+        if: (matrix.os != 'macos-latest')
+        run: |
+          pip install pypardiso            
+
       - name: Running tests
         run:
           pytest . --color=yes

.github/workflows/tests.yml

@@ -46,6 +46,11 @@ jobs:
             -r requirements.txt \
             -r requirements/tests.txt
 
+      - name: Install pypardiso on non-macOS
+        if: (matrix.os != 'macos-latest')
+        run: |
+          pip install pypardiso
+
       - name: Disable numba JIT for codecov to include jitted methods
         if: (matrix.python-version == 3.9) && (matrix.os == 'ubuntu-latest')
         run: |

openpnm/__init__.py

@@ -8,25 +8,34 @@
 
 """
 
-from . import _skgraph
-from . import utils
-from . import core
-from . import models
-from . import topotools
-from . import network
-from . import phase
-from . import algorithms
-from . import solvers
-from . import integrators
-from . import io
-from . import contrib
-from . import visualization
-
-from .utils import Workspace, Project
+import logging
+
+from rich.logging import RichHandler
+
+FORMAT = "%(message)s"
+logging.basicConfig(
+    format=FORMAT, datefmt="[%X]", handlers=[RichHandler(rich_tracebacks=True)]
+)
 
 import numpy as _np
+
+from . import (
+    _skgraph,
+    algorithms,
+    contrib,
+    core,
+    integrators,
+    io,
+    models,
+    network,
+    phase,
+    solvers,
+    topotools,
+    utils,
+    visualization,
+)
+from .utils import Project, Workspace
+
 _np.seterr(divide='ignore', invalid='ignore')
 
 __version__ = utils._get_version()
-
-utils._setup_logger_rich()

openpnm/solvers/_pardiso.py

@@ -1,15 +1,17 @@
-from pypardiso import spsolve
+from scipy.sparse import csc_matrix, csr_matrix
+
 from openpnm.solvers import DirectSolver
-from scipy.sparse import csr_matrix, csc_matrix
 
 __all__ = ['PardisoSpsolve']
 
 
 class PardisoSpsolve(DirectSolver):
     """Solves a linear system using ``pypardiso.spsolve``."""
-
+   
     def solve(self, A, b, **kwargs):
         """Solves the given linear system of equations Ax=b."""
+        from pypardiso import spsolve
+        
         if not isinstance(A, (csr_matrix, csc_matrix)):
             A = A.tocsr()
         return (spsolve(A, b), 0)

openpnm/utils/_workspace.py

@@ -1,6 +1,7 @@
 import logging
 import pickle
 import re
+import sys
 from datetime import datetime
 from uuid import uuid4
 
@@ -39,7 +40,16 @@ class WorkspaceSettings(SettingsAttr):
                 may be unable to continue running.
         ======= ==============================================================
     """
-    default_solver = 'PardisoSpsolve'
+    # Pardiso requires MKL, which is not available on new Apple chips
+    if sys.platform == 'darwin':
+        default_solver = 'ScipySpsolve'
+    else:
+        try:
+            import pypardiso
+            default_solver = 'PardisoSpsolve'
+        except ImportError:
+            default_solver = 'ScipySpsolve'
+            logger.error('Pardiso not installed, run `pip install pypardiso`')
 
     @property
     def loglevel(self):

setup.py

@@ -1,9 +1,10 @@
-import os
-import sys
 import codecs
+import os
 import os.path
+import sys
 from distutils.util import convert_path
-from setuptools import setup, find_packages
+
+from setuptools import find_packages, setup
 
 sys.path.append(os.getcwd())
 ver_path = convert_path('openpnm/__version__.py')
@@ -59,7 +60,6 @@ def get_version(rel_path):
         'numpy',
         'pandas',
         'pyamg',
-        'pypardiso',
         'rich',
         'scikit-image',
         'scipy',

tests/unit/algorithms/SolversTest.py

@@ -1,5 +1,9 @@
+import sys
+
 import numpy as np
 import numpy.testing as nt
+import pytest
+
 import openpnm as op
 
 
@@ -25,6 +29,7 @@ def test_scipy_spsolve(self):
         x = self.alg['pore.x']
         nt.assert_allclose(x.mean(), 0.624134, rtol=1e-5)
 
+    @pytest.mark.skipif(sys.platform == 'darwin', reason="Pardiso not available on arm64")
     def test_pardiso_spsolve(self):
         solver = op.solvers.PardisoSpsolve()
         self.alg.run(solver=solver)

tests/unit/algorithms/TransientMultiPhysicsTest.py

@@ -1,5 +1,6 @@
 import numpy as np
 import numpy.testing as nt
+
 import openpnm as op
 import openpnm.models.geometry.diffusive_size_factors as gd
 import openpnm.models.physics as pm
@@ -48,7 +49,6 @@ def setup_class(self):
             "cache_A": False,
             "cache_b": False
         }
-        self.pardiso = op.solvers.PardisoSpsolve()
         self.rk45 = op.integrators.ScipyRK45(verbose=True)
 
         # First algorithm, transient fourier conduction