From 72b3885524fd94aa838b4e85642db9a28bba5dff Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 09:04:09 -0400 Subject: [PATCH 01/26] Monkeypatch versioneer.py - Python 3.12 doesn't like SafeConfigParser - Python 2.7 doesn't like versioneer > 0.18 --- versioneer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/versioneer.py b/versioneer.py index 64fea1c892..3aa5da3720 100644 --- a/versioneer.py +++ b/versioneer.py @@ -339,9 +339,9 @@ def get_config_from_root(root): # configparser.NoOptionError (if it lacks "VCS="). See the docstring at # the top of versioneer.py for instructions on writing your setup.cfg . setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() + parser = configparser.ConfigParser() with open(setup_cfg, "r") as f: - parser.readfp(f) + parser.read_file(f) VCS = parser.get("versioneer", "VCS") # mandatory def get(parser, name): From 2c7136dd73b1848792db219bbe33044b877a61c6 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 10:24:26 -0400 Subject: [PATCH 02/26] Replace obj2sctype --- fipy/tools/dimensions/physicalField.py | 9 ++++----- fipy/variables/cellVariable.py | 2 +- fipy/variables/coupledCellVariable.py | 6 ++---- fipy/variables/meshVariable.py | 18 ++++++++++++++---- fipy/variables/variable.py | 10 +++++----- 5 files changed, 26 insertions(+), 19 deletions(-) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index 3f5e9a4c65..fdaf1874fd 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -864,18 +864,17 @@ def getsctype(self, default=None): Returns the NumPy sctype of the underlying array. - >>> PhysicalField(1, 'm').getsctype() == numerix.NUMERIX.obj2sctype(numerix.array(1)) + >>> PhysicalField(1, 'm').getsctype() == numerix.array(1).dtype True - >>> PhysicalField(1., 'm').getsctype() == numerix.NUMERIX.obj2sctype(numerix.array(1.)) + >>> PhysicalField(1., 'm').getsctype() == numerix.array(1.).dtype True - >>> PhysicalField((1, 1.), 'm').getsctype() == numerix.NUMERIX.obj2sctype(numerix.array((1., 1.))) + >>> PhysicalField((1, 1.), 'm').getsctype() == numerix.array((1., 1.)).dtype True """ if not hasattr(self, 'typecode'): - self.typecode = numerix.obj2sctype(rep=numerix.array(self.numericValue), - default=default) + self.typecode = numerix.asarray(self.numericValue).dtype return self.typecode diff --git a/fipy/variables/cellVariable.py b/fipy/variables/cellVariable.py index 89d6f10bae..38a99106fc 100644 --- a/fipy/variables/cellVariable.py +++ b/fipy/variables/cellVariable.py @@ -56,7 +56,7 @@ def _OperatorVariableClass(self, baseClass=None): >>> print(b) [2] >>> from builtins import str - >>> print(str(b.getsctype()) == str(numerix.NUMERIX.obj2sctype(numerix.array(1)))) + >>> print(str(b.getsctype()) == str(numerix.array(1).dtype) True replacing with the same thing is no problem diff --git a/fipy/variables/coupledCellVariable.py b/fipy/variables/coupledCellVariable.py index 641936c2ef..19ce232520 100644 --- a/fipy/variables/coupledCellVariable.py +++ b/fipy/variables/coupledCellVariable.py @@ -80,7 +80,7 @@ def __array__(self, t=None): [6 7] >>> print(v2) [8 9] - >>> v.getsctype() == numerix.NUMERIX.obj2sctype(numerix.array(1)) + >>> v.getsctype() == numerix.array(1).dtype True """ @@ -96,9 +96,7 @@ def __iter__(self): return iter(self.value) def getsctype(self, default=None): - if not hasattr(self, 'typecode'): - self.typecode = numerix.obj2sctype(rep=self.numericValue, default=default) - return self.typecode + return self.numericValue.dtype def ravel(self): return self.value.ravel() diff --git a/fipy/variables/meshVariable.py b/fipy/variables/meshVariable.py index 2bc4eab88e..93dbdf36d3 100644 --- a/fipy/variables/meshVariable.py +++ b/fipy/variables/meshVariable.py @@ -91,9 +91,9 @@ def __init__(self, mesh, name='', value=0., rank=None, elementshape=None, if not "array" in locals(): if numerix._isPhysical(value): - dtype = numerix.obj2sctype(value.value) + dtype = value.value.dtype else: - dtype = numerix.obj2sctype(value) + dtype = value.dtype #print "meshvariable elshape: ",self.elementshape #print "meshvariable _getShapeFromMesh: ",self._getShapeFromMesh(mesh) array = numerix.zeros(self.elementshape @@ -128,7 +128,7 @@ def _getGlobalValue(self, localIDs, globalIDs): globalIDs = numerix.concatenate(self.mesh.communicator.allgather(globalIDs)) globalValue = numerix.empty(localValue.shape[:-1] + (max(globalIDs) + 1,), - dtype=numerix.obj2sctype(localValue)) + dtype=localValue.dtype) globalValue[..., globalIDs] = numerix.concatenate(self.mesh.communicator.allgather(localValue), axis=-1) return globalValue @@ -600,9 +600,19 @@ def _getitemClass(self, index): else: index = (index,) indexshape = numerix._indexShape(index=index, arrayShape=self.shape) + + def _isbool(item): + if hasattr(item, "dtype"): + # This ridiculosity because numpy 2.0.0 removed obj2sctype + # and isinstance(dtype, np.dtype) doesn't work the way + # they say it does + return item.dtype is numerix.dtype(bool) + else: + return type(item) is bool + if (len(indexshape) > 0 and indexshape[-1] == self.shape[-1] - and numerix.obj2sctype(index[-1]) != numerix.obj2sctype(bool)): + and not _isbool(index[-1])): return self._OperatorVariableClass() else: return Variable._OperatorVariableClass(self, baseClass=Variable) diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 4718aa4789..fccfb8c4e7 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -772,17 +772,17 @@ def getsctype(self, default=None): Returns the Numpy `sctype` of the underlying array. - >>> Variable(1).getsctype() == numerix.NUMERIX.obj2sctype(numerix.array(1)) + >>> Variable(1).getsctype() == numerix.array(1).dtype True - >>> Variable(1.).getsctype() == numerix.NUMERIX.obj2sctype(numerix.array(1.)) + >>> Variable(1.).getsctype() == numerix.array(1.).dtype True - >>> Variable((1, 1.)).getsctype() == numerix.NUMERIX.obj2sctype(numerix.array((1., 1.))) + >>> Variable((1, 1.)).getsctype() == numerix.array((1., 1.))) True """ if not hasattr(self, 'typecode'): - self.typecode = numerix.obj2sctype(rep=self.numericValue, default=default) + self.typecode = numerix.asarray(self.numericValue).dtypes return self.typecode @@ -923,7 +923,7 @@ def _execInline(self, comment=None): self.canInline = False argDict['result'] = self.value self.canInline = True - self.typecode = numerix.obj2sctype(argDict['result']) + self.typecode = argDict['result'].dtype else: if self._value is None: if self.getsctype() == numerix.bool_: From 2eed4180e3a3a8d7b0899d708844be1ab0ee9b07 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 11:05:38 -0400 Subject: [PATCH 03/26] Replace `.getsctype()` with `.dtype` --- fipy/terms/unaryTerm.py | 2 +- fipy/tools/dimensions/physicalField.py | 15 ++++++-------- fipy/variables/cellVariable.py | 3 +-- fipy/variables/coupledCellVariable.py | 5 +++-- fipy/variables/operatorVariable.py | 6 +++--- fipy/variables/variable.py | 27 ++++++++++++-------------- 6 files changed, 26 insertions(+), 32 deletions(-) diff --git a/fipy/terms/unaryTerm.py b/fipy/terms/unaryTerm.py index 5412a26371..e0434c50a5 100644 --- a/fipy/terms/unaryTerm.py +++ b/fipy/terms/unaryTerm.py @@ -106,7 +106,7 @@ def _getDefaultSolver(self, var, solver, *args, **kwargs): def _checkVar(self, var): if ((var is not None) - and (numerix.sctype2char(var.getsctype()) not in numerix.typecodes['Float'])): + and issubclass(var.dtype.type, numerix.floating)): import warnings warnings.warn("""sweep() or solve() are likely to produce erroneous results when `var` does not contain floats.""", UserWarning, stacklevel=4) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index fdaf1874fd..e3645a305a 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -859,24 +859,21 @@ def inUnitsOf(self, *units): unit = units[i] return tuple(result) - def getsctype(self, default=None): + @property + def dtype(self): """ Returns the NumPy sctype of the underlying array. - >>> PhysicalField(1, 'm').getsctype() == numerix.array(1).dtype + >>> issubclass(PhysicalField(1, 'm').dtype.type, numerix.integer) True - >>> PhysicalField(1., 'm').getsctype() == numerix.array(1.).dtype + >>> issubclass(PhysicalField(1., 'm').dtype.type, numerix.floating) True - >>> PhysicalField((1, 1.), 'm').getsctype() == numerix.array((1., 1.)).dtype + >>> issubclass(PhysicalField((1, 1.), 'm').dtype.type, numerix.floating) True """ - - if not hasattr(self, 'typecode'): - self.typecode = numerix.asarray(self.numericValue).dtype - - return self.typecode + return numerix.asarray(self.numericValue).dtype def _getUnit(self): """ diff --git a/fipy/variables/cellVariable.py b/fipy/variables/cellVariable.py index 38a99106fc..19bff5558f 100644 --- a/fipy/variables/cellVariable.py +++ b/fipy/variables/cellVariable.py @@ -55,8 +55,7 @@ def _OperatorVariableClass(self, baseClass=None): >>> b = c.old + 3 >>> print(b) [2] - >>> from builtins import str - >>> print(str(b.getsctype()) == str(numerix.array(1).dtype) + >>> issubclass(b.dtype.type, numerix.integer) True replacing with the same thing is no problem diff --git a/fipy/variables/coupledCellVariable.py b/fipy/variables/coupledCellVariable.py index 19ce232520..b2326131fd 100644 --- a/fipy/variables/coupledCellVariable.py +++ b/fipy/variables/coupledCellVariable.py @@ -80,7 +80,7 @@ def __array__(self, t=None): [6 7] >>> print(v2) [8 9] - >>> v.getsctype() == numerix.array(1).dtype + >>> issubclass(v.dtype.type, numerix.integer) True """ @@ -95,7 +95,8 @@ def __abs__(self): def __iter__(self): return iter(self.value) - def getsctype(self, default=None): + @property + def dtype(self): return self.numericValue.dtype def ravel(self): diff --git a/fipy/variables/operatorVariable.py b/fipy/variables/operatorVariable.py index a93dfb7043..0024e19747 100644 --- a/fipy/variables/operatorVariable.py +++ b/fipy/variables/operatorVariable.py @@ -386,11 +386,11 @@ def _testBinOp(self): >>> a = -(numerix.sin(Variable() * Variable())) - Check that `getTypeCode()` works as expected. + Check that `dtype` works as expected. >>> a = Variable(1.) * Variable(1) - >>> print(a.getsctype() == numerix.float64) - 1 + >>> issubclass(a.dtype.type, numerix.floating) + True The following test is to correct an `--inline` bug that was being thrown by the Cahn-Hilliard example. The fix for this diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index fccfb8c4e7..d506ad6d0d 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -703,7 +703,7 @@ def setValue(self, value, unit=None, where=None): """ if where is not None: - tmp = numerix.empty(numerix.getShape(where), self.getsctype()) + tmp = numerix.empty(numerix.getShape(where), self.dtype) tmp[:] = value tmp = numerix.where(where, tmp, self.value) else: @@ -767,24 +767,21 @@ def _getShape(self): shape = property(_getShape) - def getsctype(self, default=None): + @property + def dtype(self): """ - Returns the Numpy `sctype` of the underlying array. + Returns the Numpy `dtype` of the underlying array. - >>> Variable(1).getsctype() == numerix.array(1).dtype + >>> issubclass(Variable(1).dtype.type, numerix.integer) True - >>> Variable(1.).getsctype() == numerix.array(1.).dtype + >>> issubclass(Variable(1.).dtype.type, numerix.floating) True - >>> Variable((1, 1.)).getsctype() == numerix.array((1., 1.))) + >>> issubclass(Variable((1, 1.)).dtype.type, numerix.floating) True """ - - if not hasattr(self, 'typecode'): - self.typecode = numerix.asarray(self.numericValue).dtypes - - return self.typecode + return numerix.asarray(self.numericValue).dtype @property def itemsize(self): @@ -926,10 +923,10 @@ def _execInline(self, comment=None): self.typecode = argDict['result'].dtype else: if self._value is None: - if self.getsctype() == numerix.bool_: + if self.dtype is numerix.dtype(bool): argDict['result'] = numerix.empty(dim, numerix.int8) else: - argDict['result'] = numerix.empty(dim, self.getsctype()) + argDict['result'] = numerix.empty(dim, self.dtype) else: argDict['result'] = self._value @@ -943,8 +940,8 @@ def _execInline(self, comment=None): if resultShape == (): argDict['result'] = numerix.reshape(argDict['result'], resultShape) - if self.getsctype() == numerix.bool_: - argDict['result'] = numerix.asarray(argDict['result'], dtype=self.getsctype()) + if issubclass(self.dtype.type, numerix.bool): + argDict['result'] = numerix.asarray(argDict['result'], dtype=self.dtype) return argDict['result'] From 62bd0ff9bf0fb3a79c1b0b0d34f7f202bdc87bb1 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 11:12:42 -0400 Subject: [PATCH 04/26] Replace `NUMERIX.issubclass_()` with `issubclass()` --- fipy/tools/numerix.py | 8 ++++---- fipy/variables/meshVariable.py | 5 +---- fipy/variables/variable.py | 2 +- 3 files changed, 6 insertions(+), 9 deletions(-) diff --git a/fipy/tools/numerix.py b/fipy/tools/numerix.py index b406357060..0c66882ffc 100644 --- a/fipy/tools/numerix.py +++ b/fipy/tools/numerix.py @@ -257,15 +257,15 @@ def sum(arr, axis=0): def _isFloat(arr): if isinstance(arr, NUMERIX.ndarray): - return NUMERIX.issubclass_(arr.dtype.type, NUMERIX.floating) + return issubclass(arr.dtype.type, NUMERIX.floating) else: - return NUMERIX.issubclass_(arr.__class__, float) + return issubclass(arr.__class__, float) def _isInt(arr): if isinstance(arr, NUMERIX.ndarray): - return NUMERIX.issubclass_(arr.dtype.type, NUMERIX.integer) + return issubclass(arr.dtype.type, NUMERIX.integer) else: - return NUMERIX.issubclass_(arr.__class__, int) + return issubclass(arr.__class__, int) def tostring(arr, max_line_width=75, precision=8, suppress_small=False, separator=' ', array_output=0): r""" diff --git a/fipy/variables/meshVariable.py b/fipy/variables/meshVariable.py index 93dbdf36d3..b1bcf91d92 100644 --- a/fipy/variables/meshVariable.py +++ b/fipy/variables/meshVariable.py @@ -603,10 +603,7 @@ def _getitemClass(self, index): def _isbool(item): if hasattr(item, "dtype"): - # This ridiculosity because numpy 2.0.0 removed obj2sctype - # and isinstance(dtype, np.dtype) doesn't work the way - # they say it does - return item.dtype is numerix.dtype(bool) + return numerix.issubdtype(item.dtype, bool) else: return type(item) is bool diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index d506ad6d0d..914dc70d2c 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -940,7 +940,7 @@ def _execInline(self, comment=None): if resultShape == (): argDict['result'] = numerix.reshape(argDict['result'], resultShape) - if issubclass(self.dtype.type, numerix.bool): + if numerix.issubdtype(item.dtype, bool): argDict['result'] = numerix.asarray(argDict['result'], dtype=self.dtype) return argDict['result'] From 4e7923a69aebe5e27dd0fd68302181f389b0ba86 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 12:03:15 -0400 Subject: [PATCH 05/26] Replace `itemset()` with indexing --- fipy/tools/dimensions/physicalField.py | 30 -------------------------- fipy/variables/variable.py | 11 +--------- 2 files changed, 1 insertion(+), 40 deletions(-) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index e3645a305a..69485e77a5 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -520,36 +520,6 @@ def __setitem__(self, index, value): value = self._inMyUnits(value).value self.value[index] = value - def itemset(self, value): - """ - Assign the value of a scalar array, performing appropriate - conversions. - - >>> a = PhysicalField(4., "m") - >>> a.itemset(PhysicalField("6 ft")) - >>> print(a.allclose("1.8288 m")) - 1 - >>> a = PhysicalField(((3., 4.), (5., 6.)), "m") - >>> try: #doctest: +IGNORE_EXCEPTION_DETAIL - ... a.itemset(PhysicalField("6 ft")) - ... except IndexError: - ... # NumPy 1.7 has changed the exception type - ... raise ValueError("can only place a scalar for an array of size 1") - Traceback (most recent call last): - ... - ValueError: can only convert an array of size 1 to a Python scalar - >>> a.itemset(PhysicalField("2 min")) - Traceback (most recent call last): - ... - TypeError: Incompatible units - """ - if isinstance(value, string_types): - value = PhysicalField(value) - if isinstance(value, PhysicalField) or _isVariable(value): - value = self._inMyUnits(value).value - self.value.itemset(value) - - ## __array_priority__ and __array_wrap__ are required to override ## the default behavior of numpy. If a numpy array and a Variable ## are in a binary operation and numpy is first, then numpy will, diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 914dc70d2c..b69fccb330 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -447,12 +447,6 @@ def __setitem__(self, index, value): self._value[index] = value self._markFresh() - def itemset(self, value): - if self._value is None: - self._getValue() - self._value.itemset(value) - self._markFresh() - def put(self, indices, value): if self._value is None: self._getValue() @@ -714,10 +708,7 @@ def setValue(self, value, unit=None, where=None): value = self._makeValue(value=tmp, unit=unit, array=None) - if numerix.getShape(self._value) == (): - self._value.itemset(value) - else: - self._value[:] = value + self._value[...] = value self._markFresh() From 9921bf8f4bbb0a366fef0545074f03fe334d5956 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 12:08:11 -0400 Subject: [PATCH 06/26] Fix obsolete name for infinity --- fipy/meshes/abstractMesh.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/fipy/meshes/abstractMesh.py b/fipy/meshes/abstractMesh.py index 68a430ecbb..69f12cec2b 100644 --- a/fipy/meshes/abstractMesh.py +++ b/fipy/meshes/abstractMesh.py @@ -1229,7 +1229,7 @@ def _minmin(self, x): """return minimum of all the minima on all processors """ if len(x) == 0: - minx = numerix.infty + minx = numerix.inf else: minx = min(x) @@ -1239,7 +1239,7 @@ def _maxmax(self, x): """return maximum of all the maxima on all processors """ if len(x) == 0: - maxx = -numerix.infty + maxx = -numerix.inf else: maxx = max(x) From 55f78f326bfd80425585dfc21debfce3e47154f6 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Tue, 18 Jun 2024 12:28:47 -0400 Subject: [PATCH 07/26] Fix comparison operator representation --- fipy/variables/operatorVariable.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fipy/variables/operatorVariable.py b/fipy/variables/operatorVariable.py index 0024e19747..1b0ef37481 100644 --- a/fipy/variables/operatorVariable.py +++ b/fipy/variables/operatorVariable.py @@ -221,7 +221,7 @@ def _py3kInstructions(self, op, style, argDict, id, freshen): # LOAD_METHOD new in Python 3.7 stack.append(stack.pop() + "." + ins.argval) elif ins.opname == 'COMPARE_OP': - stack.append(stack.pop(-2) + " " + dis.cmp_op[ins.arg] + " " + stack.pop()) + stack.append(stack.pop(-2) + " " + ins.argrepr + " " + stack.pop()) elif ins.opname == 'LOAD_GLOBAL': # Changed in Python 3.11 stack.append(ins.argval) From 0b14cedc76ab4bc6362ad7edf3a4499c5be37838 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 22 Feb 2024 10:34:06 -0500 Subject: [PATCH 08/26] Use `ins.argrepr` for representation of operator variables --- fipy/variables/operatorVariable.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/fipy/variables/operatorVariable.py b/fipy/variables/operatorVariable.py index 1b0ef37481..cef10b0269 100644 --- a/fipy/variables/operatorVariable.py +++ b/fipy/variables/operatorVariable.py @@ -138,12 +138,6 @@ def __var(self, i, style, argDict, id, freshen): 62: "<<", 63: ">>", 64: "&", 65: "^", 66: "|", 106: "==" } - # introduced in Python 3.11 - _binary_op = { - 0: "+", 1: "&", 2: "//", 3: "<<", 4: "@", 5: "*", 6: "%", 7: "|", - 8: "**", 9: ">>", 10: "-", 11: "/", 12: "^" - } - def _py2kInstructions(self, bytecodes, style, argDict, id, freshen): def _popIndex(): return bytecodes.pop(0) + bytecodes.pop(0) * 256 @@ -249,7 +243,7 @@ def _py3kInstructions(self, op, style, argDict, id, freshen): pass elif ins.opname == 'BINARY_OP': # New in Python 3.11 - stack.append(stack.pop(-2) + " " + self._binary_op[ins.argval] + " " + stack.pop()) + stack.append(stack.pop(-2) + " " + ins.argrepr + " " + stack.pop()) elif ins.opname == 'PRECALL': # New in Python 3.11 pass From 08124c240913d9a245920ca59ba113f0b1238f42 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 22 Feb 2024 09:14:35 -0500 Subject: [PATCH 09/26] Remove future.standard_library This library no longer exists in Python 3.12 It looks like it isn't even needed in Python 2.7 to use pickle and redirecting_html.py should go away (but fixed it anyway). --- docs/source/sphinxext/redirecting_html.py | 10 +++++----- fipy/tools/dump.py | 2 -- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/docs/source/sphinxext/redirecting_html.py b/docs/source/sphinxext/redirecting_html.py index 7b779ed24b..0f8280c91d 100644 --- a/docs/source/sphinxext/redirecting_html.py +++ b/docs/source/sphinxext/redirecting_html.py @@ -1,9 +1,9 @@ from __future__ import unicode_literals -from future import standard_library -standard_library.install_aliases() from docutils import nodes -import urllib.parse - +try: + from urllib.parse import urlparse +except ImportError: + from urlparse import urlparse from sphinx.builders.html import StandaloneHTMLBuilder class RedirectingHTMLBuilder(StandaloneHTMLBuilder): @@ -17,7 +17,7 @@ def write_doc(self, docname, doctree): for node in doctree.traverse(nodes.reference): try: uri = node['refuri'] - uri = urllib.parse.urlparse(uri) + uri = urlparse(uri) if uri.scheme in ["http", "https"]: if not uri.netloc.endswith("nist.gov"): node['refuri'] = "/cgi-bin/redirect.py?url=" + uri.geturl() diff --git a/fipy/tools/dump.py b/fipy/tools/dump.py index b2398c0df7..a7f0b2c199 100644 --- a/fipy/tools/dump.py +++ b/fipy/tools/dump.py @@ -1,6 +1,4 @@ from __future__ import unicode_literals -from future import standard_library -standard_library.install_aliases() __docformat__ = 'restructuredtext' import io From d91ccdc929c945fd63743350e3c5d9468c63a455 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 09:20:02 -0400 Subject: [PATCH 10/26] Update locks --- environments/locks/conda-petsc-linux-64.lock | 335 +- environments/locks/conda-petsc-lock.yml | 6125 +++++++++------ environments/locks/conda-petsc-osx-64.lock | 322 +- environments/locks/conda-petsc-osx-arm64.lock | 322 +- .../locks/conda-pysparse-linux-64.lock | 99 +- environments/locks/conda-pysparse-lock.yml | 706 +- environments/locks/conda-pysparse-osx-64.lock | 125 +- environments/locks/conda-scipy-linux-64.lock | 304 +- environments/locks/conda-scipy-lock.yml | 6645 ++++++++++------- environments/locks/conda-scipy-osx-64.lock | 291 +- environments/locks/conda-scipy-osx-arm64.lock | 291 +- environments/locks/conda-scipy-win-64.lock | 206 +- .../locks/conda-trilinos-linux-64.lock | 119 +- environments/locks/conda-trilinos-lock.yml | 1203 +-- environments/locks/conda-trilinos-osx-64.lock | 203 +- 15 files changed, 10282 insertions(+), 7014 deletions(-) diff --git a/environments/locks/conda-petsc-linux-64.lock b/environments/locks/conda-petsc-linux-64.lock index fb37f05aa4..93a19b9a09 100644 --- a/environments/locks/conda-petsc-linux-64.lock +++ b/environments/locks/conda-petsc-linux-64.lock @@ -3,77 +3,60 @@ # input_hash: 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category: main optional: false - name: ca-certificates - version: 2023.11.17 + version: 2024.6.2 manager: conda platform: linux-64 dependencies: {} - url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.11.17-hbcca054_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda hash: - md5: 01ffc8d36f9eba0ce0b3c1955fa780ee - sha256: fb4b9f4b7d885002db0b93e22f44b5b03791ef3d4efdc9d0662185a0faafd6b6 + md5: 847c3c2905cc467cea52c24f9cfa8080 + sha256: 979af0932b2a5a26112044891a2d79e402e5ae8166f50fa48b8ebae47c0a2d65 category: main optional: false - name: ca-certificates - version: 2023.11.17 + version: 2024.6.2 manager: conda platform: osx-64 dependencies: {} - url: https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2023.11.17-h8857fd0_0.conda + url: https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.6.2-h8857fd0_0.conda hash: - md5: c687e9d14c49e3d3946d50a413cdbf16 - sha256: 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https://conda.anaconda.org/conda-forge/linux-64/curl-7.86.0-h7bff187_1.tar.bz2 hash: @@ -426,7 +426,7 @@ package: krb5: '>=1.20.1,<1.21.0a0' libcurl: 8.1.2 libssh2: '>=1.10.0,<2.0a0' - libzlib: '>=1.2.13,<1.3.0a0' + libzlib: '>=1.2.13,<2.0.0a0' openssl: '>=3.1.0,<4.0a0' zstd: '>=1.5.2,<1.6.0a0' url: https://conda.anaconda.org/conda-forge/osx-64/curl-8.1.2-hbee3ae8_0.conda @@ -552,28 +552,28 @@ package: category: main optional: false - name: expat - version: 2.5.0 + version: 2.6.2 manager: conda platform: linux-64 dependencies: - libexpat: 2.5.0 + libexpat: 2.6.2 libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda + url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda hash: - md5: 8b9b5aca60558d02ddaa09d599e55920 - sha256: 36dfeb4375059b3bba75ce9b38c29c69fd257342a79e6cf20e9f25c1523f785f + md5: 53fb86322bdb89496d7579fe3f02fd61 + sha256: 89916c536ae5b85bb8bf0cfa27d751e274ea0911f04e4a928744735c14ef5155 category: main optional: false - name: expat - version: 2.5.0 + version: 2.6.2 manager: conda platform: osx-64 dependencies: - libexpat: 2.5.0 - url: https://conda.anaconda.org/conda-forge/osx-64/expat-2.5.0-hf0c8a7f_1.conda + libexpat: 2.6.2 + url: https://conda.anaconda.org/conda-forge/osx-64/expat-2.6.2-h73e2aa4_0.conda hash: - md5: e12630038077877cbb6c7851e139c17c - sha256: 15c04a5a690b337b50fb7550cce057d843cf94dd0109d576ec9bc3448a8571d0 + md5: dc0882915da2ec74696ad87aa2350f27 + sha256: 0fd1befb18d9d937358a90d5b8f97ac2402761e9d4295779cbad9d7adfb47976 category: main optional: false - name: ffmpeg @@ -588,7 +588,7 @@ package: lame: '>=3.100,<3.101.0a0' libgcc-ng: '>=10.3.0' libstdcxx-ng: '>=10.3.0' - libzlib: '>=1.2.11,<1.3.0a0' + libzlib: '>=1.2.11,<2.0.0a0' openh264: '>=2.1.1,<2.2.0a0' x264: '>=1!161.3030,<1!162' url: https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-4.3.2-h37c90e5_3.tar.bz2 @@ -613,8 +613,8 @@ package: libcxx: '>=14.0.6' libiconv: '>=1.17,<2.0a0' libvpx: 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font-ttf-ubuntu @@ -759,10 +759,10 @@ package: manager: conda platform: osx-64 dependencies: {} - url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda + url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda hash: - md5: 6185f640c43843e5ad6fd1c5372c3f80 - sha256: 056c85b482d58faab5fd4670b6c1f5df0986314cca3bc831d458b22e4ef2c792 + md5: cbbe59391138ea5ad3658c76912e147f + sha256: c940f6e969143e13a3a9660abb3c7e7e23b8319efb29dbdd5dee0b9939236e13 category: main optional: false - name: fontconfig @@ -774,7 +774,7 @@ package: freetype: '>=2.12.1,<3.0a0' libgcc-ng: '>=12' libuuid: '>=2.32.1,<3.0a0' - libzlib: '>=1.2.13,<1.3.0a0' + libzlib: '>=1.2.13,<2.0.0a0' url: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda hash: md5: 0f69b688f52ff6da70bccb7ff7001d1d @@ -788,7 +788,7 @@ package: dependencies: expat: '>=2.5.0,<3.0a0' freetype: '>=2.12.1,<3.0a0' - libzlib: '>=1.2.13,<1.3.0a0' + libzlib: 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+ url: https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda + hash: + md5: 02e41ab5834dcdcc8590cf29d9526f50 + sha256: 99d26d272a8203d30b3efbe734a99c823499884d7759b4291674438137c4b5ca + category: main + optional: false +- name: libasprintf-devel + version: 0.22.5 + manager: conda + platform: osx-64 + dependencies: + libasprintf: 0.22.5 + url: https://conda.anaconda.org/conda-forge/osx-64/libasprintf-devel-0.22.5-h5ff76d1_2.conda + hash: + md5: c7182eda3bc727384e2f98f4d680fa7d + sha256: 39fa757378b49993142013c1f69dd56248cc3703c2f04c5bcf4cc4acdc644ae3 + category: main + optional: false - name: libblas version: 3.9.0 manager: conda @@ -1869,10 +1954,10 @@ package: dependencies: libcxx: '>=16.0.6' libllvm13: '>=13.0.1,<13.1.0a0' - url: https://conda.anaconda.org/conda-forge/osx-64/libclang-13.0.1-root_63002_h09a4f16_5.conda + url: https://conda.anaconda.org/conda-forge/osx-64/libclang-13.0.1-default_h255f2f3_6.conda hash: - md5: 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'' lz4-c: '>=1.9.3,<1.9.4.0a0' proj: '>=8.2.0,<8.2.1.0a0' @@ -4854,8 +5021,8 @@ package: libpng: '>=1.6.37,<1.7.0a0' libtheora: '>=1.1.1,<1.2.0a0' libtiff: '>=4.4.0,<4.5.0a0' - libxml2: '>=2.9.14,<2.11.0a0' - libzlib: '>=1.2.12,<1.3.0a0' + libxml2: '>=2.9.14,<3.0.0a0' + libzlib: '>=1.2.12,<2.0.0a0' loguru: '' lz4-c: '>=1.9.3,<1.10.0a0' proj: '>=9.0.1,<9.0.2.0a0' @@ -4888,15 +5055,15 @@ package: category: main optional: false - name: wheel - version: 0.42.0 + version: 0.43.0 manager: conda platform: osx-64 dependencies: - python: '>=3.7' - url: https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda + python: '>=3.8' + url: https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda hash: - md5: 1cdea58981c5cbc17b51973bcaddcea7 - sha256: 80be0ccc815ce22f80c141013302839b0ed938a2edb50b846cf48d8a8c1cfa01 + md5: 0b5293a157c2b5cd513dd1b03d8d3aae + sha256: cb318f066afd6fd64619f14c030569faf3f53e6f50abf743b4c865e7d95b96bc category: main optional: false - name: x264 @@ -5032,19 +5199,19 @@ package: category: main optional: false - name: xorg-libx11 - version: 1.8.7 + version: 1.8.9 manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' - libxcb: '>=1.15,<1.16.0a0' + libxcb: '>=1.16,<1.17.0a0' xorg-kbproto: '' xorg-xextproto: '>=7.3.0,<8.0a0' xorg-xproto: '' - url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.7-h8ee46fc_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.conda hash: - md5: 49e482d882669206653b095f5206c05b - sha256: 7a02a7beac472ae2759498550b5fc5261bf5be7a9a2b4648a3f67818a7bfefcf + md5: 4a6d410296d7e39f00bacdee7df046e9 + sha256: 66eabe62b66c1597c4a755dcd3f4ce2c78adaf7b32e25dfee45504d67d7735c1 category: main optional: false - name: xorg-libx11 @@ -5167,14 +5334,14 @@ package: manager: conda platform: linux-64 dependencies: - libgcc-ng: '>=9.3.0' - xorg-libx11: '>=1.7.0,<2.0a0' - xorg-libxext: 1.3.* - xorg-libxt: '>=1.2.1,<2.0a0' - url: 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+https://conda.anaconda.org/conda-forge/osx-64/gst-plugins-base-1.22.9-h3fb38fc_1.conda#7bc7cdc3d7e58558c3986108d5840645 https://conda.anaconda.org/conda-forge/osx-64/numpy-1.24.4-py38h9a4a08f_0.conda#85debc55a30068d6bb76a6deaf599afa https://conda.anaconda.org/conda-forge/osx-64/occt-7.7.2-novtk_h0a0d97a_101.conda#8a337666ac2b42fff1325f55f4f210a2 -https://conda.anaconda.org/conda-forge/osx-64/pyqt5-sip-12.12.2-py38h45c2d83_5.conda#122cd3be133d87d04a6030a9dbf9dd91 -https://conda.anaconda.org/conda-forge/noarch/requests-2.31.0-pyhd8ed1ab_0.conda#a30144e4156cdbb236f99ebb49828f8b +https://conda.anaconda.org/conda-forge/noarch/pooch-1.8.2-pyhd8ed1ab_0.conda#8dab97d8a9616e07d779782995710aed https://conda.anaconda.org/conda-forge/osx-64/suitesparse-5.10.1-h0a40b7c_2.conda#31ae28651c3e544afa792b37e00deccd https://conda.anaconda.org/conda-forge/osx-64/contourpy-1.1.1-py38h15a1a5b_1.conda#1c702bb95106dbed8ddb262ad4041432 https://conda.anaconda.org/conda-forge/osx-64/gmsh-4.11.1-h0adee99_3.conda#cee0efa9fc71ab991575aea2f072efb1 -https://conda.anaconda.org/conda-forge/noarch/pooch-1.8.0-pyhd8ed1ab_0.conda#134b2b57b7865d2316a7cce1915a51ed https://conda.anaconda.org/conda-forge/osx-64/qt-main-5.15.8-h1d3b3f8_6.conda#5d816352174169f7ab45fb54a0fba4ed +https://conda.anaconda.org/conda-forge/osx-64/scipy-1.10.1-py38h9cf86d3_3.conda#5e20c77455e815704b008ab8f42f6169 https://conda.anaconda.org/conda-forge/osx-64/matplotlib-base-3.7.3-py38hcd1b199_0.conda#7e17b15addb42d41728f580757e3f528 https://conda.anaconda.org/conda-forge/osx-64/pyqt-5.15.9-py38he1c912d_5.conda#8d3d0247189e802e3b157275cf5acd2c -https://conda.anaconda.org/conda-forge/osx-64/scipy-1.10.1-py38h9cf86d3_3.conda#5e20c77455e815704b008ab8f42f6169 +https://conda.anaconda.org/conda-forge/osx-64/scikit-umfpack-0.3.3-py38h5a9ab09_1.conda#b38f638ea54a9791c0fa5def3adcea3c https://conda.anaconda.org/conda-forge/osx-64/vtk-9.1.0-qt_py38hf4ddb89_211.tar.bz2#c6b03542ca636798129f9860913604db https://conda.anaconda.org/conda-forge/noarch/pyface-8.0.0-pyhd8ed1ab_0.conda#53751c009f36a67406d321a991d78a0e -https://conda.anaconda.org/conda-forge/osx-64/scikit-umfpack-0.3.3-py38h5a9ab09_1.conda#b38f638ea54a9791c0fa5def3adcea3c https://conda.anaconda.org/conda-forge/osx-64/pytrilinos-12.18.1-py38hf6ca725_5.tar.bz2#16122b86dd347ff2181a38719a176aff https://conda.anaconda.org/conda-forge/noarch/traitsui-8.0.0-pyhd8ed1ab_0.conda#230a8da760e3037989d8d9ec8a370368 https://conda.anaconda.org/conda-forge/noarch/apptools-5.1.0-pyh44b312d_0.tar.bz2#67f86126bb65837378ddd31caff9f420 From 29047eedfe7fef5982729a961cf55dc19a392a6b Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 11:59:58 -0400 Subject: [PATCH 11/26] Add `return_scalar` to `__array_wrap__` for NumPy 2.0 --- fipy/tools/dimensions/physicalField.py | 6 +++++- fipy/variables/variable.py | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index 69485e77a5..70bdbe183d 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -531,7 +531,7 @@ def __setitem__(self, index, value): __array_priority__ = 100.0 - def __array_wrap__(self, arr, context=None): + def __array_wrap__(self, arr, context=None, return_scalar=False): """ Required to prevent numpy not calling the reverse binary operations. Both the following tests are examples ufuncs. @@ -561,6 +561,10 @@ def __makePhysical(v): if meth is not None and callable(meth): result = meth(*args[1:]) + if return_scalar: + # NumPy 2.0 compatibility + result = result[()] + return result def __array__(self, t = None): diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index b69fccb330..771f606839 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -106,7 +106,7 @@ def __init__(self, value=0., unit=None, array=None, name='', cached=1): __array_priority__ = 100.0 - def __array_wrap__(self, arr, context=None): + def __array_wrap__(self, arr, context=None, return_scalar=False): """ Required to prevent numpy not calling the reverse binary operations. Both the following tests are examples ufuncs. @@ -138,6 +138,10 @@ def __makeVariable(v): else: result = NotImplemented + if return_scalar and result != NotImplemented: + # NumPy 2.0 compatibility + result = result[()] + return result def __array__(self, t=None): From 69a4e241c9dc088525aa1d482f66309d2da4e449 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 14:56:07 -0400 Subject: [PATCH 12/26] Add `copy=` argument to `__array__` for NumPy 2.0 --- fipy/tools/dimensions/physicalField.py | 4 ++-- fipy/variables/coupledCellVariable.py | 4 ++-- fipy/variables/variable.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index 70bdbe183d..04da68651d 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -567,7 +567,7 @@ def __makePhysical(v): return result - def __array__(self, t = None): + def __array__(self, dtype=None, copy=None): """ Return a dimensionless `PhysicalField` as a Numeric_ ``array``. @@ -597,7 +597,7 @@ def __array__(self, t = None): else: value = self.inSIUnits().value - return numerix.array(value, t) + return numerix.array(value, dtype=dtype, copy=copy) # if self.unit.isDimensionlessOrAngle(): # value = self.numericValue diff --git a/fipy/variables/coupledCellVariable.py b/fipy/variables/coupledCellVariable.py index b2326131fd..9d6b9f4340 100644 --- a/fipy/variables/coupledCellVariable.py +++ b/fipy/variables/coupledCellVariable.py @@ -64,7 +64,7 @@ def unit(self): from fipy.tools.dimensions import physicalField return physicalField._unity - def __array__(self, t=None): + def __array__(self, dtype=None, copy=None): """ Attempt to convert the `_CoupledCellVariable` to a numerix `array` object @@ -84,7 +84,7 @@ def __array__(self, t=None): True """ - return numerix.array(self.value, t) + return numerix.array(self.value, dtype=dtype, copy=copy) def __neg__(self): return _CoupledCellVariable([-var for var in self.vars]) diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 771f606839..68db11f8ee 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -144,7 +144,7 @@ def __makeVariable(v): return result - def __array__(self, t=None): + def __array__(self, dtype=None, copy=None): """ Attempt to convert the `Variable` to a numerix `array` object @@ -159,7 +159,7 @@ def __array__(self, t=None): array([ 0.002, 0.003]) """ - return numerix.array(self.value, t) + return numerix.array(self.value, dtype=dtype, copy=copy) ## def _get_array_interface(self): ## return self._array.__array_interface__ From 908825deb275b1b4cef7cfca6c9bb14e5ba47103 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 15:31:20 -0400 Subject: [PATCH 13/26] Address `copy=None` for NumPy < 2.0 Based on https://github.com/scipy/scipy/pull/20172/files as suggested by https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword --- fipy/tools/dimensions/physicalField.py | 3 +++ fipy/tools/numerix.py | 20 ++++++++++++++++++++ fipy/variables/coupledCellVariable.py | 3 +++ fipy/variables/variable.py | 2 ++ 4 files changed, 28 insertions(+) diff --git a/fipy/tools/dimensions/physicalField.py b/fipy/tools/dimensions/physicalField.py index 04da68651d..786f6b1660 100755 --- a/fipy/tools/dimensions/physicalField.py +++ b/fipy/tools/dimensions/physicalField.py @@ -597,6 +597,9 @@ def __array__(self, dtype=None, copy=None): else: value = self.inSIUnits().value + if not copy: + copy = numerix.copy_if_needed + return numerix.array(value, dtype=dtype, copy=copy) # if self.unit.isDimensionlessOrAngle(): diff --git a/fipy/tools/numerix.py b/fipy/tools/numerix.py index 0c66882ffc..85e056b86f 100644 --- a/fipy/tools/numerix.py +++ b/fipy/tools/numerix.py @@ -77,6 +77,26 @@ from fipy.tools import inline +# --------------------- + +# Lifted from https://github.com/scipy/scipy/pull/20172/files +# Copyright (c) 2001-2002 Enthought, Inc. 2003-2024, SciPy Developers +# BSD 3-Clause "New" or "Revised" License +# +# as suggested by https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword +if NUMERIX.lib.NumpyVersion(NUMERIX.__version__) >= "2.0.0": + copy_if_needed = None +elif NUMERIX.lib.NumpyVersion(NUMERIX.__version__) < "1.28.0": + copy_if_needed = False +else: + # 2.0.0 dev versions, handle cases where copy may or may not exist + try: + NUMERIX.array([1]).__array__(copy=None) # type: ignore[call-overload] + copy_if_needed = None + except TypeError: + copy_if_needed = False +# --------------------- + # we want NumPy's __all__, with adjustments import sys __all__ = list(sys.modules['numpy'].__dict__.setdefault('__all__', [])) diff --git a/fipy/variables/coupledCellVariable.py b/fipy/variables/coupledCellVariable.py index 9d6b9f4340..cb0305bc0d 100644 --- a/fipy/variables/coupledCellVariable.py +++ b/fipy/variables/coupledCellVariable.py @@ -84,6 +84,9 @@ def __array__(self, dtype=None, copy=None): True """ + if not copy: + copy = numerix.copy_if_needed + return numerix.array(self.value, dtype=dtype, copy=copy) def __neg__(self): diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 68db11f8ee..21dcf0b910 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -158,6 +158,8 @@ def __array__(self, dtype=None, copy=None): >>> numerix.array(v) array([ 0.002, 0.003]) """ + if not copy: + copy = numerix.copy_if_needed return numerix.array(self.value, dtype=dtype, copy=copy) From 6e6c68e11f800df8ebf864ead520490917e353a6 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 15:37:29 -0400 Subject: [PATCH 14/26] Defer return_scalar for OperatorVariables --- fipy/variables/binaryOperatorVariable.py | 6 +++++- fipy/variables/operatorVariable.py | 3 ++- fipy/variables/unaryOperatorVariable.py | 6 +++++- fipy/variables/variable.py | 23 +++++++++++++---------- 4 files changed, 25 insertions(+), 13 deletions(-) diff --git a/fipy/variables/binaryOperatorVariable.py b/fipy/variables/binaryOperatorVariable.py index 7fc70f19c5..70fad7bf32 100644 --- a/fipy/variables/binaryOperatorVariable.py +++ b/fipy/variables/binaryOperatorVariable.py @@ -45,7 +45,11 @@ def _calcValue_(self): self.var[1] = physicalField.PhysicalField(value=self.var[1]) val1 = self.var[1] - return self.op(self.var[0].value, val1) + value = self.op(self.var[0].value, val1) + if self.return_scalar: + value = value[()] + + return value @property def unit(self): diff --git a/fipy/variables/operatorVariable.py b/fipy/variables/operatorVariable.py index cef10b0269..bf30f0bf9c 100644 --- a/fipy/variables/operatorVariable.py +++ b/fipy/variables/operatorVariable.py @@ -14,7 +14,7 @@ def _OperatorVariableClass(baseClass=object): class _OperatorVariable(baseClass): - def __init__(self, op, var, opShape=(), canInline=True, unit=None, inlineComment=None, valueMattersForUnit=None, *args, **kwargs): + def __init__(self, op, var, opShape=(), canInline=True, unit=None, inlineComment=None, valueMattersForUnit=None, return_scalar=False, *args, **kwargs): self.op = op self.var = var self.opShape = opShape @@ -23,6 +23,7 @@ def __init__(self, op, var, opShape=(), canInline=True, unit=None, inlineComment self.valueMattersForUnit = [False for v in var] else: self.valueMattersForUnit = valueMattersForUnit + self.return_scalar = return_scalar self.canInline = canInline #allows for certain functions to opt out of --inline baseClass.__init__(self, value=None, *args, **kwargs) self.name = '' diff --git a/fipy/variables/unaryOperatorVariable.py b/fipy/variables/unaryOperatorVariable.py index 0b4725dc98..5bdafd17d9 100644 --- a/fipy/variables/unaryOperatorVariable.py +++ b/fipy/variables/unaryOperatorVariable.py @@ -33,7 +33,11 @@ def _UnaryOperatorVariable(operatorClass=None): class unOp(operatorClass): def _calcValue_(self): - return self.op(self.var[0].value) + value = self.op(self.var[0].value) + if self.return_scalar: + value = value[()] + + return value @property def unit(self): diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 21dcf0b910..3cf73a2ac2 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -132,16 +132,12 @@ def __makeVariable(v): cannotInline = ["expi", "logical_and", "logical_or", "logical_not", "logical_xor", "sign", "conjugate", "dot", "allclose", "allequal"] if len(args) == 1: - result = args[0]._UnaryOperatorVariable(op=func, opShape=arr.shape, canInline=func.__name__ not in cannotInline) + result = args[0]._UnaryOperatorVariable(op=func, opShape=arr.shape, canInline=func.__name__ not in cannotInline, return_scalar=return_scalar) elif len(args) == 2: - result = args[0]._BinaryOperatorVariable(op=func, other=args[1], opShape=arr.shape, canInline=func.__name__ not in cannotInline) + result = args[0]._BinaryOperatorVariable(op=func, other=args[1], opShape=arr.shape, canInline=func.__name__ not in cannotInline, return_scalar=return_scalar) else: result = NotImplemented - if return_scalar and result != NotImplemented: - # NumPy 2.0 compatibility - result = result[()] - return result def __array__(self, dtype=None, copy=None): @@ -989,7 +985,7 @@ def _OperatorVariableClass(self, baseClass=None): return operatorVariable._OperatorVariableClass(baseClass=baseClass) def _UnaryOperatorVariable(self, op, operatorClass=None, opShape=None, canInline=True, unit=None, - valueMattersForUnit=False): + valueMattersForUnit=False, return_scalar=False): """ Check that unit works for `unOp` @@ -1008,6 +1004,9 @@ def _UnaryOperatorVariable(self, op, operatorClass=None, opShape=None, canInline valueMattersForUnit : bool Whether value of `self` should be used when determining unit, e.g., ??? + return_scalar : bool + Whether to reduce returned zero rank array to a scalar + # Introduced in NumPy 2.0 """ operatorClass = operatorClass or self._OperatorVariableClass() from fipy.variables import unaryOperatorVariable @@ -1026,7 +1025,7 @@ def _UnaryOperatorVariable(self, op, operatorClass=None, opShape=None, canInline return unOp(op=op, var=[self], opShape=opShape, canInline=canInline, unit=unit, inlineComment=inline._operatorVariableComment(canInline=canInline), - valueMattersForUnit=[valueMattersForUnit]) + valueMattersForUnit=[valueMattersForUnit], return_scalar=return_scalar) def _shapeClassAndOther(self, opShape, operatorClass, other): """ @@ -1047,7 +1046,7 @@ def _shapeClassAndOther(self, opShape, operatorClass, other): return (opShape, baseClass, other) def _BinaryOperatorVariable(self, op, other, operatorClass=None, opShape=None, canInline=True, unit=None, - value0mattersForUnit=False, value1mattersForUnit=False): + value0mattersForUnit=False, value1mattersForUnit=False, return_scalar=False): """ Parameters ---------- @@ -1066,6 +1065,9 @@ def _BinaryOperatorVariable(self, op, other, operatorClass=None, opShape=None, c value1MattersForUnit : bool Whether value of `self` should be used when determining unit, e.g., `__pow__` + return_scalar : bool + Whether to reduce returned zero rank array to a scalar + # Introduced in NumPy 2.0 """ if not isinstance(other, Variable): from fipy.variables.constant import _Constant @@ -1087,7 +1089,8 @@ def _BinaryOperatorVariable(self, op, other, operatorClass=None, opShape=None, c return binOp(op=op, var=[self, other], opShape=opShape, canInline=canInline, unit=unit, inlineComment=inline._operatorVariableComment(canInline=canInline), - valueMattersForUnit=[value0mattersForUnit, value1mattersForUnit]) + valueMattersForUnit=[value0mattersForUnit, value1mattersForUnit], + return_scalar=return_scalar) def __add__(self, other): from fipy.terms.term import Term From 729e2c5952e556149544dc2ff68fca529166a1a3 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 15:47:00 -0400 Subject: [PATCH 15/26] Fix polarity of floating CellVariable check Broken in 2eed418 --- fipy/terms/unaryTerm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fipy/terms/unaryTerm.py b/fipy/terms/unaryTerm.py index e0434c50a5..b5013f98e5 100644 --- a/fipy/terms/unaryTerm.py +++ b/fipy/terms/unaryTerm.py @@ -106,7 +106,7 @@ def _getDefaultSolver(self, var, solver, *args, **kwargs): def _checkVar(self, var): if ((var is not None) - and issubclass(var.dtype.type, numerix.floating)): + and not issubclass(var.dtype.type, numerix.floating)): import warnings warnings.warn("""sweep() or solve() are likely to produce erroneous results when `var` does not contain floats.""", UserWarning, stacklevel=4) From 130983ffa34aa5cfe69c21e252afbbcf97cca506 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 16:16:53 -0400 Subject: [PATCH 16/26] Replace deprecated `numpy.in1d` with `numpy.isin` --- fipy/matrices/sparseMatrix.py | 4 +- fipy/meshes/abstractMesh.py | 8 +- fipy/meshes/topologies/abstractTopology.py | 8 +- fipy/tools/numerix.py | 130 +-------------------- 4 files changed, 11 insertions(+), 139 deletions(-) diff --git a/fipy/matrices/sparseMatrix.py b/fipy/matrices/sparseMatrix.py index 69ea15a2cf..e5797bfd29 100644 --- a/fipy/matrices/sparseMatrix.py +++ b/fipy/matrices/sparseMatrix.py @@ -239,7 +239,7 @@ def _getStencil_(self, id1, id2, if overlapping: mask = numerix.ones(id1.shape, dtype=bool) else: - mask = numerix.in1d(id1, globalNonOverlappihgIDs) + mask = numerix.isin(id1, globalNonOverlappihgIDs) id1 = self.matrix()._mesh2matrix(id1[mask]) id2 = numerix.asarray(id2)[mask] @@ -275,7 +275,7 @@ def globalVectorAndIDs(self, vector, id1, id2, overlapping=False): @property def bodies(self): if self._bodies is None: - self._bodies = numerix.in1d(self.mesh._globalOverlappingCellIDs, + self._bodies = numerix.isin(self.mesh._globalOverlappingCellIDs, self.mesh._globalNonOverlappingCellIDs) return self._bodies diff --git a/fipy/meshes/abstractMesh.py b/fipy/meshes/abstractMesh.py index 69f12cec2b..c212149054 100644 --- a/fipy/meshes/abstractMesh.py +++ b/fipy/meshes/abstractMesh.py @@ -387,11 +387,11 @@ def _getAddedMeshValues(self, other, resolution=1e-2): self_faceVertexIDs = MA.masked_values(self_faceVertexIDs, -1) # want self's Faces for which all faceVertexIDs are in vertexCorrelates - self_matchingFaces = numerix.in1d(self_faceVertexIDs, + self_matchingFaces = numerix.isin(self_faceVertexIDs, vertexCorrelates[0]).reshape(self_faceVertexIDs.shape).all(axis=0).nonzero()[0] # want other's Faces for which all faceVertexIDs are in vertexCorrelates - other_matchingFaces = numerix.in1d(other_faceVertexIDs, + other_matchingFaces = numerix.isin(other_faceVertexIDs, vertexCorrelates[1]).reshape(other_faceVertexIDs.shape).all(axis=0).nonzero()[0] # map other's Vertex IDs to new Vertex IDs, @@ -429,9 +429,9 @@ def _getAddedMeshValues(self, other, resolution=1e-2): other_faceHash = other_faceHash[face_sort] other_matchingFaces = other_matchingFaces[face_sort] - self_matchingFaces = self_matchingFaces[numerix.in1d(self_faceHash, + self_matchingFaces = self_matchingFaces[numerix.isin(self_faceHash, other_faceHash)] - other_matchingFaces = other_matchingFaces[numerix.in1d(other_faceHash, + other_matchingFaces = other_matchingFaces[numerix.isin(other_faceHash, self_faceHash)] faceCorrelates = numerix.array((self_matchingFaces, diff --git a/fipy/meshes/topologies/abstractTopology.py b/fipy/meshes/topologies/abstractTopology.py index 97f91ddfff..9a64cf3eca 100644 --- a/fipy/meshes/topologies/abstractTopology.py +++ b/fipy/meshes/topologies/abstractTopology.py @@ -221,10 +221,10 @@ def _nonOverlappingFaces(self): || ``` """ - return (numerix._in1dMA(self.mesh.faceCellIDs[0], - self._localNonOverlappingCellIDs).filled(False) - | numerix._in1dMA(self.mesh.faceCellIDs[1], - self._localNonOverlappingCellIDs).filled(False)) + return (numerix.isin(self.mesh.faceCellIDs[0], + self._localNonOverlappingCellIDs).filled(False) + | numerix.isin(self.mesh.faceCellIDs[1], + self._localNonOverlappingCellIDs).filled(False)) @property def _localNonOverlappingFaceIDs(self): diff --git a/fipy/tools/numerix.py b/fipy/tools/numerix.py index 85e056b86f..12b73142d6 100644 --- a/fipy/tools/numerix.py +++ b/fipy/tools/numerix.py @@ -105,7 +105,7 @@ "rank", "sum", "tostring", "dot", "sqrtDot", "nearest", "allequal", "allclose", "all", "isclose", "take", "indices", "empty", "loadtxt", - "savetxt", "L1norm", "L2norm", "LINFnorm", "in1d"], + "savetxt", "L1norm", "L2norm", "LINFnorm"], key=str.lower)) from future.utils import text_to_native_str __all__ = [text_to_native_str(n) for n in __all__] @@ -960,134 +960,6 @@ def _broadcastShape(shape1, shape2): shape1, shape2, broadcastshape = _broadcastShapes(shape1, shape2) return broadcastshape -if not hasattr(NUMERIX, "in1d"): - # this handy function was introduced at some point (but it's not in 1.4.1) - # we define if necessary - - def in1d(ar1, ar2, assume_unique=False): - """ - Test whether each element of a 1D array is also present in a second array. - - Returns a Boolean array the same length as `ar1` that is True - where an element of `ar1` is in `ar2` and False otherwise. - - Parameters - ---------- - ar1 : array_like, shape (M,) - Input array. - ar2 : array_like - The values against which to test each value of `ar1`. - assume_unique : bool, optional - If True, the input arrays are both assumed to be unique, which - can speed up the calculation. Default is False. - - Returns - ------- - mask : ndarray of bools, shape(M,) - The values `ar1[mask]` are in `ar2`. - - See Also - -------- - numpy.lib.arraysetops : Module with a number of other functions for - performing set operations on arrays. - - Notes - ----- - `in1d` can be considered as an element-wise function version of the - python keyword `in`, for 1D sequences. ``in1d(a, b)`` is roughly - equivalent to ``np.array([item in b for item in a])``. - - .. versionadded:: NOT 1.4.0 !!!! - - Examples - -------- - >>> test = NUMERIX.array([0, 1, 2, 5, 0]) - >>> states = [0, 2] - >>> mask = in1d(test, states) - >>> mask - array([ True, False, True, False, True], dtype=bool) - >>> test[mask] - array([0, 2, 0]) - - """ - if not assume_unique: - - try: - ar1, rev_idx = NUMERIX.unique(ar1, return_inverse=True) - except TypeError: - ar1, rev_idx = NUMERIX.unique1d(ar1, return_inverse=True) - - ar2 = NUMERIX.unique(ar2) - - ar = NUMERIX.concatenate( (ar1, ar2) ) - # We need this to be a stable sort, so always use 'mergesort' - # here. The values from the first array should always come before - # the values from the second array. - order = ar.argsort(kind='mergesort') - sar = ar[order] - equal_adj = (sar[1:] == sar[:-1]) - flag = NUMERIX.concatenate( (equal_adj, [False] ) ) - indx = order.argsort(kind='mergesort')[:len( ar1 )] - - if assume_unique: - return flag[indx] - else: - return flag[indx][rev_idx] - -def _in1dMA(ar1, ar2, assume_unique=False, invert=False): - """ - Test whether each unmasked element of an array is also present and - unmasked in a second array. - The output is always a masked array. See `numpy.in1d` for more details. - We recommend using :func:`isin` instead of `in1d` for new code. - - Parameters - ---------- - ar1 : (M,) array_like - Input array. - ar2 : array_like - The values against which to test each value of `ar1`. - assume_unique : bool, optional - If True, the input arrays are both assumed to be unique, which - can speed up the calculation. Default is False. - invert : bool, optional - If True, the values in the returned array are inverted (that is, - False where an element of `ar1` is in `ar2` and True otherwise). - Default is False. ``np.in1d(a, b, invert=True)`` is equivalent - to (but is faster than) ``np.invert(in1d(a, b))``. - - Returns - ------- - in1d : (M,) ndarray, bool - The values `ar1[in1d]` are in `ar2`. - - See Also - -------- - isin : Version of this function that preserves the shape of ar1. - numpy.in1d : Equivalent function for ndarrays. - - Notes - ----- - .. versionadded:: 1.4.0 - - Replaces buggy `numpy.ma.in1d`, fixed in - https://github.com/numpy/numpy/pull/20011. - """ - ar1, ar2 = MA.asarray(ar1), MA.asarray(ar2) - m = MA.getmask(ar1) - res = MA.empty_like(ar1, dtype='bool') - if ar1.mask is not MA.nomask: - ar1 = ar1[~ar1.mask] - if ar2.mask is not MA.nomask: - ar2 = ar2[~ar2.mask] - out = NUMERIX.in1d(ar1, ar2, assume_unique=assume_unique, - invert=invert) - if m is not MA.nomask: - res[~m] = out - else: - res[:] = out - return res - def _invert_indices(arr, axis=-1): """Invert an index array From afd1697b33103b7b8a8e42382cda024d9a7a68f1 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 16:17:25 -0400 Subject: [PATCH 17/26] Replace deprecated `tol=` with `rtol=` to SciPy Krylov solvers --- fipy/solvers/scipy/scipyKrylovSolver.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fipy/solvers/scipy/scipyKrylovSolver.py b/fipy/solvers/scipy/scipyKrylovSolver.py index 97eb9191ee..b3fadd8a50 100644 --- a/fipy/solvers/scipy/scipyKrylovSolver.py +++ b/fipy/solvers/scipy/scipyKrylovSolver.py @@ -30,7 +30,7 @@ def _solve_(self, L, x, b): with Timer() as t: x, info = self.solveFnc(A, b, x, - tol=self.tolerance, + rtol=self.tolerance, maxiter=self.iterations, M=M, atol='legacy') From 43c143a20b05b79cf579b4a7066cfc612c8caba0 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 17:45:59 -0400 Subject: [PATCH 18/26] Replace deprecated `atol='legacy'` for SciPy Krylov solves --- fipy/solvers/scipy/scipyKrylovSolver.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fipy/solvers/scipy/scipyKrylovSolver.py b/fipy/solvers/scipy/scipyKrylovSolver.py index b3fadd8a50..7581d2a6b0 100644 --- a/fipy/solvers/scipy/scipyKrylovSolver.py +++ b/fipy/solvers/scipy/scipyKrylovSolver.py @@ -33,7 +33,7 @@ def _solve_(self, L, x, b): rtol=self.tolerance, maxiter=self.iterations, M=M, - atol='legacy') + atol=0.0) self._log.debug("END solve - {} ns".format(t.elapsed)) From 3a1e3169d8ed2a3a6eb4634d5ca23ecf06e9b89c Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 17:49:05 -0400 Subject: [PATCH 19/26] Remove internal implementation details of numpy.array2string --- fipy/tools/numerix.py | 32 +++++--------------------------- 1 file changed, 5 insertions(+), 27 deletions(-) diff --git a/fipy/tools/numerix.py b/fipy/tools/numerix.py index 12b73142d6..35fdb356ea 100644 --- a/fipy/tools/numerix.py +++ b/fipy/tools/numerix.py @@ -345,34 +345,12 @@ def tostring(arr, max_line_width=75, precision=8, suppress_small=False, separato max_line_width=max_line_width, suppress_small=suppress_small, separator=separator) - elif _isFloat(arr): - try: - ## this is for numpy 1.14 and above - ## why has the interface changed *again*? - from numpy.core.arrayprint import FloatingFormat - return FloatingFormat(data=NUMERIX.array((arr,)), precision=precision, - floatmode='maxprec', suppress_small=suppress_small, legacy=False)(arr).strip() - except ImportError: - try: - ## this is for numpy 1.0.4 and above - ## why has the interface changed again? - from numpy.core.arrayprint import FloatFormat - return FloatFormat(NUMERIX.array((arr,)), precision, suppress_small)(arr).strip() - except ImportError: - from numpy.core.arrayprint import _floatFormat, _formatFloat - return _formatFloat(arr, format='%%1.%df' % precision) - - elif _isInt(arr): - try: - ## this is for numpy 1.7 and above - ## why has the interface changed again? - from numpy.core.arrayprint import IntegerFormat - return IntegerFormat(NUMERIX.array((arr,)))(arr).strip() - except: - from numpy.core.arrayprint import _formatInteger - return _formatInteger(arr, format='%d') else: - raise TypeError('cannot convert ' + str(arr) + ' to string') + return NUMERIX.array2string(NUMERIX.asarray(arr), + precision=precision, + max_line_width=max_line_width, + suppress_small=suppress_small, + separator=separator) ######################### # # From 0ce2a4603065415f1e48956e8c66e46b3466c748 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Thu, 20 Jun 2024 22:23:02 -0400 Subject: [PATCH 20/26] Override legacy formatting set for tests --- fipy/tools/numerix.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/fipy/tools/numerix.py b/fipy/tools/numerix.py index 35fdb356ea..5f8b5c055f 100644 --- a/fipy/tools/numerix.py +++ b/fipy/tools/numerix.py @@ -350,7 +350,8 @@ def tostring(arr, max_line_width=75, precision=8, suppress_small=False, separato precision=precision, max_line_width=max_line_width, suppress_small=suppress_small, - separator=separator) + separator=separator, + legacy=False) # override legacy formatting for tests ######################### # # From f7c0adacadc2d33403a10c7f857cc32ebf80d1fc Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Fri, 21 Jun 2024 15:26:11 -0400 Subject: [PATCH 21/26] Lock out petsc 3.21 petsc(4py) 3.21.2 crashes when running tests in parallel: ``` mesh2D (examples.cahnHilliard) Doctest: examples.cahnHilliard.mesh2D ... Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Internal error 2 in DMUMPS_LOAD_RECV_MSGS 1275068685 52 Internal error 1 in DMUMPS_LOAD_PROCESS_MESSAGE Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 1 (rank 1 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 1 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Abort(-99) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, -99) - process 0 Internal error 1 in DMUMPS_LOAD_PROCESS_MESSAGE Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Internal error 2 in DMUMPS_LOAD_RECV_MSGS 1275068685 52 Internal error 1 in DMUMPS_LOAD_PROCESS_MESSAGE Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Internal error 1 in DMUMPS_LOAD_PROCESS_MESSAGE Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 Internal error 2 in DMUMPS_LOAD_RECV_MSGS 1275068685 52 Internal error 1 in DMUMPS_LOAD_PROCESS_MESSAGE Internal error 1 in DMUMPS_LOAD_RECV_MSGS 1 ``` --- environments/locks/conda-petsc-linux-64.lock | 29 +- environments/locks/conda-petsc-lock.yml | 641 ++++++++---------- environments/locks/conda-petsc-osx-64.lock | 29 +- environments/locks/conda-petsc-osx-arm64.lock | 31 +- environments/petsc-environment.yml | 3 +- 5 files changed, 330 insertions(+), 403 deletions(-) diff --git a/environments/locks/conda-petsc-linux-64.lock b/environments/locks/conda-petsc-linux-64.lock index 93a19b9a09..a6296b8773 100644 --- a/environments/locks/conda-petsc-linux-64.lock +++ b/environments/locks/conda-petsc-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: d07a3e2e58642e501aa6458416b059e13ee67443d579035571fd1b49c4c2d551 +# input_hash: c19b310372b3e2c2b66681e74881e8f17bd8cb901c8a3de0b404f16f4d4882a1 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080 @@ -10,7 +10,7 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74 https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-mpich.tar.bz2#c1fcff3417b5a22bbc4cf6e8c23648cf -https://conda.anaconda.org/conda-forge/linux-64/mumps-include-5.7.2-ha770c72_0.conda#5cd4042ea914dd6234a98da967747ed8 +https://conda.anaconda.org/conda-forge/linux-64/mumps-include-5.2.1-ha770c72_11.tar.bz2#765196257c11b54dc52522d2fcafdd69 https://conda.anaconda.org/conda-forge/linux-64/nlohmann_json-3.11.3-h59595ed_0.conda#df9ae69b85e0cab9bde23eff1e87f183 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8 @@ -71,7 +71,7 @@ https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda#34672 https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.3.0-h59595ed_0.conda#c2f83a5ddadadcdb08fe05863295ee97 https://conda.anaconda.org/conda-forge/linux-64/eigen-3.4.0-h00ab1b0_0.conda#b1b879d6d093f55dd40d58b5eb2f0699 https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61 -https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-h59595ed_1.conda#e358c7c5f6824c272b5034b3816438a7 +https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda#c94a5994ef49749880a8139cf9afcbe1 https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda#bd77f8da987968ec3927990495dc22e4 https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff @@ -126,7 +126,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb5 https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-hf974151_0.conda#72724f6a78ecb15559396966226d5838 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155 https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-4.25.3-h08a7969_0.conda#6945825cebd2aeb16af4c69d97c32c13 -https://conda.anaconda.org/conda-forge/linux-64/libscotch-7.0.4-h3055ed5_5.conda#3fb10abc770864c88eb2f8921b11aee5 https://conda.anaconda.org/conda-forge/linux-64/libtheora-1.1.1-h7f98852_1005.tar.bz2#1a7c35f56343b7e9e8db20b296c7566c https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_1.conda#340278ded8b0dc3a73f3660bbb0adbc6 @@ -136,7 +135,7 @@ https://conda.anaconda.org/conda-forge/linux-64/mysql-libs-8.3.0-hca2cd23_4.cond https://conda.anaconda.org/conda-forge/linux-64/nss-3.100-hca3bf56_0.conda#949c4a82290ee58b3c970cef4bcfd4ad https://conda.anaconda.org/conda-forge/linux-64/openexr-3.2.2-haf962dd_1.conda#34e58e21fc28e404207d6ce4287da264 https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84 -https://conda.anaconda.org/conda-forge/linux-64/scotch-6.1.3-hfeb400c_0.tar.bz2#f1a2c68c2d5c4f530bc8577f44fb4b7e +https://conda.anaconda.org/conda-forge/linux-64/scotch-6.0.9-hb2e6521_2.tar.bz2#20eb1f0c247d10da95b1da761e7f4c10 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.46.0-h6d4b2fc_0.conda#77ea8dff5cf8550cc8f5629a6af56323 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.0-hd590300_1.conda#9bfac7ccd94d54fd21a0501296d60424 https://conda.anaconda.org/conda-forge/linux-64/xcb-util-keysyms-0.4.0-h8ee46fc_1.conda#632413adcd8bc16b515cab87a2932913 @@ -164,7 +163,6 @@ https://conda.anaconda.org/conda-forge/linux-64/libhwloc-2.10.0-default_h5622ce7 https://conda.anaconda.org/conda-forge/linux-64/libllvm15-15.0.7-hb3ce162_4.conda#8a35df3cbc0c8b12cc8af9473ae75eef https://conda.anaconda.org/conda-forge/linux-64/libllvm18-18.1.7-hb77312f_0.conda#bc0ea7e1f75a9b1c8467597fbbd9f86b https://conda.anaconda.org/conda-forge/linux-64/libpq-16.3-ha72fbe1_0.conda#bac737ae28b79cfbafd515258d97d29e -https://conda.anaconda.org/conda-forge/linux-64/libptscotch-7.0.4-h2376d02_5.conda#a4386e49cd4abdcba2be073096d6fa56 https://conda.anaconda.org/conda-forge/linux-64/loguru-0.7.2-py312h7900ff3_1.conda#507696b7c888a8b872b50f24ac860089 https://conda.anaconda.org/conda-forge/linux-64/mpi4py-3.1.6-py312h60e9011_1.conda#53d66537c3fdb11cad7283fed3439b20 https://conda.anaconda.org/conda-forge/linux-64/msgpack-python-1.0.8-py312h2492b07_0.conda#0df463266eaaa1b8a35f8fd26368c1a1 @@ -174,6 +172,7 @@ https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.2-h488ebb8_0.conda# https://conda.anaconda.org/conda-forge/noarch/packaging-24.1-pyhd8ed1ab_0.conda#cbe1bb1f21567018ce595d9c2be0f0db https://conda.anaconda.org/conda-forge/linux-64/parmetis-4.0.3-h583469f_1006.conda#7bf58fa5868ae3cf8895deb430cc0810 https://conda.anaconda.org/conda-forge/noarch/ply-3.11-pyhd8ed1ab_2.conda#18c6deb6f9602e32446398203c8f0e91 +https://conda.anaconda.org/conda-forge/linux-64/ptscotch-6.0.9-hb499603_2.tar.bz2#2bb2d071f5cb419e4ce0e1eb7372eb9b https://conda.anaconda.org/conda-forge/noarch/pygments-2.18.0-pyhd8ed1ab_0.conda#b7f5c092b8f9800150d998a71b76d5a1 https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.1.2-pyhd8ed1ab_0.conda#b9a4dacf97241704529131a0dfc0494f https://conda.anaconda.org/conda-forge/noarch/setuptools-70.1.0-pyhd8ed1ab_0.conda#258e66f95f814d51ada2a1fe9274039b @@ -195,7 +194,7 @@ https://conda.anaconda.org/conda-forge/noarch/configobj-5.0.8-pyhd8ed1ab_0.conda https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.53.0-py312h9a8786e_0.conda#8490346e9d5efd7a6869582aa0c95b25 https://conda.anaconda.org/conda-forge/linux-64/glib-2.80.2-hf974151_0.conda#d427988dc3dbd0a4c136f52db356cc6a https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.3-mpi_mpich_h0f54ddc_5.conda#f55c36b28c66cd668e0974367ec02dc9 -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda#0896606848b2dc5cebdf111b6543aa04 +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.2.0-pyha770c72_0.conda#e1d9f6dc77209defc283bdf61588e968 https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.0-pyhd8ed1ab_0.conda#c5d3907ad8bd7bf557521a1833cf7e6d https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda#4b31699e0ec5de64d5896e580389c9a1 https://conda.anaconda.org/conda-forge/linux-64/libclang-cpp15-15.0.7-default_h127d8a8_5.conda#d0a9633b53cdc319b8a1a532ae7822b8 @@ -225,8 +224,8 @@ https://conda.anaconda.org/conda-forge/linux-64/glew-2.1.0-h9c3ff4c_2.tar.bz2#fb https://conda.anaconda.org/conda-forge/linux-64/gnutls-3.7.9-hb077bed_0.conda#33eded89024f21659b1975886a4acf70 https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.24.4-haf2f30d_0.conda#926c2c7ee7a0b48d6d70783a33f7bc80 https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.5.0-hfac3d4d_0.conda#f5126317dd0ce0ba26945e411ecc6960 -https://conda.anaconda.org/conda-forge/linux-64/hypre-2.31.0-mpi_mpich_hd1da18f_1.conda#621c53b587caf1696dfc55c5fb128d13 -https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-7.1.0-hd8ed1ab_0.conda#6ef2b72d291b39e479d7694efa2b2b98 +https://conda.anaconda.org/conda-forge/linux-64/hypre-2.28.0-mpi_mpich_h716cb5e_0.conda#b41fa6129b3dad329dff734b935130ca +https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-7.2.0-hd8ed1ab_0.conda#3de0087b2b86443cfae650dea6ecec6f https://conda.anaconda.org/conda-forge/linux-64/libgcrypt-1.10.3-hd590300_0.conda#32d16ad533c59bb0a3c5ffaf16110829 https://conda.anaconda.org/conda-forge/linux-64/libnetcdf-4.9.2-nompi_h135f659_114.conda#a908e463c710bd6b10a9eaa89fdf003c https://conda.anaconda.org/conda-forge/linux-64/libopenvino-2024.1.0-h2da1b83_7.conda#692bb11510bfceb34723c5115045096e @@ -234,9 +233,9 @@ https://conda.anaconda.org/conda-forge/linux-64/libsndfile-1.2.2-hc60ed4a_1.cond https://conda.anaconda.org/conda-forge/linux-64/numpy-1.26.4-py312heda63a1_0.conda#d8285bea2a350f63fab23bf460221f3f https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.12.2-py312h30efb56_5.conda#8a2a122dc4fe14d8cff38f1cf426381f https://conda.anaconda.org/conda-forge/linux-64/scalapack-2.2.0-h417d24c_2.conda#e5e137423c99bce653ab68c2f30ed2c6 -https://conda.anaconda.org/conda-forge/linux-64/suitesparse-7.7.0-hf4753ba_1.conda#5937a97231967e642b1f865fc2181fee +https://conda.anaconda.org/conda-forge/linux-64/suitesparse-5.10.1-h5a4f163_3.conda#f363554b9084fb9d5e3366fbbc0d18e0 https://conda.anaconda.org/conda-forge/linux-64/superlu-5.2.2-h00795ac_0.tar.bz2#2fe6fcc1c7d6e2e8ea3f16ebd3306dbe -https://conda.anaconda.org/conda-forge/linux-64/superlu_dist-9.0.0-h3feb4ed_1.conda#347b03cd9d5a1f2e4c5bb20e25c3d169 +https://conda.anaconda.org/conda-forge/linux-64/superlu_dist-7.2.0-h25dcc4a_0.tar.bz2#fac36f70854e425ad3aaa30992d58c1b https://conda.anaconda.org/conda-forge/linux-64/tbb-devel-2021.12.0-h7c56ddd_1.conda#f896f49efc2e33ab5d4d3690bb4f32ef https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.2.1-py312h8572e83_0.conda#12c6a831ef734f0b2dd4caff514cbb7f https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.24.4-h9ad1361_0.conda#147cce520ec59367549fd0d96d404213 @@ -254,16 +253,16 @@ https://conda.anaconda.org/conda-forge/linux-64/libopenvino-pytorch-frontend-202 https://conda.anaconda.org/conda-forge/linux-64/libopenvino-tensorflow-frontend-2024.1.0-h39126c6_7.conda#d6aac92f4b03be8c86b09f40e1f5263a https://conda.anaconda.org/conda-forge/linux-64/libopenvino-tensorflow-lite-frontend-2024.1.0-he02047a_7.conda#f7a46aa4f5c53423bf3e036da8c1b632 https://conda.anaconda.org/conda-forge/linux-64/libsystemd0-255-h3516f8a_1.conda#3366af27f0b593544a6cd453c7932ac5 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libgfortran: 5.* - libgfortran5: '>=13.2.0' + libgfortran5: '>=11.0.1.dev0' liblapack: '>=3.9.0,<4.0a0' - llvm-openmp: '>=18.1.6' - metis: '>=5.1.0,<5.2.0a0' - mpich: '>=4.2.1,<5.0a0' + llvm-openmp: '>=12.0.1' + metis: '>=5.1.0,<5.1.1.0a0' + mpich: '>=3.4.2,<5.0a0' parmetis: '>=4.0.3,<4.1.0a0' - url: https://conda.anaconda.org/conda-forge/osx-arm64/superlu_dist-9.0.0-h2cb61f8_1.conda + url: https://conda.anaconda.org/conda-forge/osx-arm64/superlu_dist-7.2.0-h7df07b8_0.tar.bz2 hash: - md5: 2f5ac565026197408d272914d6a53e95 - sha256: 4bcd44809c18eb0fc6ff9dc3732df34d6e0e96d49e937f9e83c00a4df362b81e + md5: 0ff06c2b04381ff8d492b5fba96d9961 + sha256: 58a2dd80f6adde68e7276b0ab46356434fbb4fc7dcf33fe1b05b3ae966019a73 category: main optional: false - name: svt-av1 @@ -9983,45 +9912,45 @@ package: category: main optional: false - name: wslink - version: 2.1.0 + version: 2.1.1 manager: conda platform: linux-64 dependencies: aiohttp: <4 msgpack-python: '>=1,<2' python: '>=3.7' - url: 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optional: false - name: wslink - version: 2.1.0 + version: 2.1.1 manager: conda platform: osx-arm64 dependencies: python: '>=3.7' aiohttp: <4 msgpack-python: '>=1,<2' - url: https://conda.anaconda.org/conda-forge/noarch/wslink-2.1.0-pyhd8ed1ab_0.conda + url: https://conda.anaconda.org/conda-forge/noarch/wslink-2.1.1-pyhd8ed1ab_0.conda hash: - md5: 088c224d81a1828e283186e14a4db25f - sha256: e5edbda78cb21b696ce7f9f3cb2f4c0dbaf1bd90a715cedf12f5e879754eae8c + md5: 6b1aef9c878c58baa7bb9f0d44457174 + sha256: 446a1d5952f603c52c2083b224405e54a940c012dfef9d0642ffcfc1b29f0ab6 category: main optional: false - name: x264 diff --git a/environments/locks/conda-petsc-osx-64.lock b/environments/locks/conda-petsc-osx-64.lock index 02bd846dde..34920bd69f 100644 --- a/environments/locks/conda-petsc-osx-64.lock +++ b/environments/locks/conda-petsc-osx-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: osx-64 -# input_hash: 4663c99e3e572345ccf329abcbffbcf1d4cffd0baad31bdb658225a7fd1fe01e +# input_hash: 9cc0bf9a785c64453f36b969d235531b685c581d634a9a34bff955a9880c85ee @EXPLICIT https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h10d778d_5.conda#6097a6ca9ada32699b5fc4312dd6ef18 https://conda.anaconda.org/conda-forge/osx-64/c-ares-1.28.1-h10d778d_0.conda#d5eb7992227254c0e9a0ce71151f0079 @@ -29,7 +29,7 @@ https://conda.anaconda.org/conda-forge/osx-64/libunistring-0.9.10-h0d85af4_0.tar https://conda.anaconda.org/conda-forge/osx-64/libwebp-base-1.4.0-h10d778d_0.conda#b2c0047ea73819d992484faacbbe1c24 https://conda.anaconda.org/conda-forge/osx-64/metis-5.1.0-he965462_1007.conda#0c64ad59bbcae7772c16a55cbd353e25 https://conda.anaconda.org/conda-forge/osx-64/mpi-1.0-mpich.tar.bz2#7316a634ed27146b42d28433ec3bc227 -https://conda.anaconda.org/conda-forge/osx-64/mumps-include-5.7.2-h694c41f_0.conda#c1f8a609ee007e7a9115b987dee1046b +https://conda.anaconda.org/conda-forge/osx-64/mumps-include-5.2.1-h694c41f_11.tar.bz2#ed3d032dc307436df39ff27f34ab7ab8 https://conda.anaconda.org/conda-forge/osx-64/ncurses-6.5-h5846eda_0.conda#02a888433d165c99bf09784a7b14d900 https://conda.anaconda.org/conda-forge/osx-64/nettle-3.9.1-h8e11ae5_0.conda#400dffe5d2fbb9813b51948d3e9e9ab1 https://conda.anaconda.org/conda-forge/osx-64/nlohmann_json-3.11.3-h73e2aa4_0.conda#7e82f8ccb0f18ad05ef405369263937d @@ -70,7 +70,7 @@ https://conda.anaconda.org/conda-forge/osx-64/eigen-3.4.0-h1c7c39f_0.conda#5b2cf https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab https://conda.anaconda.org/conda-forge/osx-64/gettext-tools-0.22.5-h5ff76d1_2.conda#37e1cb0efeff4d4623a6357e37e0105d https://conda.anaconda.org/conda-forge/osx-64/glew-2.1.0-h046ec9c_2.tar.bz2#6b753c8c7e4c46a8eb17b6f1781f958a -https://conda.anaconda.org/conda-forge/osx-64/gmp-6.3.0-h73e2aa4_1.conda#92f8d748d95d97f92fc26cfac9bb5b6e +https://conda.anaconda.org/conda-forge/osx-64/gmp-6.3.0-hf036a51_2.conda#427101d13f19c4974552a4e5b072eef1 https://conda.anaconda.org/conda-forge/osx-64/graphite2-1.3.13-h73e2aa4_1003.conda#fc7124f86e1d359fc5d878accd9e814c https://conda.anaconda.org/conda-forge/osx-64/hdf4-4.2.15-h8138101_7.conda#7ce543bf38dbfae0de9af112ee178af2 https://conda.anaconda.org/conda-forge/osx-64/imath-3.1.11-h2d185b6_0.conda#39c1f288d263e971db74f8803e28dabd @@ -126,7 +126,7 @@ https://conda.anaconda.org/conda-forge/osx-64/mysql-libs-8.3.0-ha9146f8_4.conda# https://conda.anaconda.org/conda-forge/osx-64/nss-3.100-h6606ded_0.conda#614b1b9b0a0b1bfbfa9d04a10afa4240 https://conda.anaconda.org/conda-forge/osx-64/openexr-3.2.2-h3f0570e_1.conda#95bd8b6b83801d99b064c785585bd15d https://conda.anaconda.org/conda-forge/osx-64/python-3.12.3-h1411813_0_cpython.conda#df1448ec6cbf8eceb03d29003cf72ae6 -https://conda.anaconda.org/conda-forge/osx-64/scotch-6.1.3-h601ff3b_0.tar.bz2#bad3fcb3816c1b157d8123f98543fb75 +https://conda.anaconda.org/conda-forge/osx-64/scotch-6.0.9-h3da7401_2.tar.bz2#201a64c35a3b3ce59b56a33f08c7a70e https://conda.anaconda.org/conda-forge/osx-64/sqlite-3.46.0-h28673e1_0.conda#b76e50276ebb3131cb84aac8123ca75d https://conda.anaconda.org/conda-forge/osx-64/xorg-libxext-1.3.4-hb7f2c08_2.conda#0f98aff18e0455f0bdc4326c04f98883 https://conda.anaconda.org/conda-forge/osx-64/xorg-libxfixes-5.0.3-h0d85af4_1004.tar.bz2#6ecbef6618bb15e389a8bb5618e579f6 @@ -147,7 +147,6 @@ https://conda.anaconda.org/conda-forge/osx-64/libclang-cpp15-15.0.7-default_h715 https://conda.anaconda.org/conda-forge/osx-64/libclang-cpp16-16.0.6-default_h4c8afb6_8.conda#50f4e969d77f64fe7d53f192b4b1f23c https://conda.anaconda.org/conda-forge/osx-64/libclang13-18.1.7-default_h0449792_0.conda#be4f24df1938154adcb08673fbce71be https://conda.anaconda.org/conda-forge/osx-64/libopenblas-0.3.27-openmp_hfef2a42_0.conda#00237c9c7f2cb6725fe2960680a6e225 -https://conda.anaconda.org/conda-forge/osx-64/libscotch-7.0.4-hfcec5db_5.conda#f57a6f56faf3b877e01f7e77ad957151 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+https://conda.anaconda.org/conda-forge/osx-arm64/gmp-6.3.0-h7bae524_2.conda#eed7278dfbab727b56f2c0b64330814b https://conda.anaconda.org/conda-forge/osx-arm64/graphite2-1.3.13-hebf3989_1003.conda#339991336eeddb70076d8ca826dac625 https://conda.anaconda.org/conda-forge/osx-arm64/hdf4-4.2.15-h2ee6834_7.conda#ff5d749fd711dc7759e127db38005924 https://conda.anaconda.org/conda-forge/osx-arm64/imath-3.1.11-h1059232_0.conda#e95ef5164e69abc370842b41438065fa @@ -126,7 +126,7 @@ https://conda.anaconda.org/conda-forge/osx-arm64/mysql-libs-8.3.0-hf036fc4_4.con https://conda.anaconda.org/conda-forge/osx-arm64/nss-3.100-hc6e9f88_0.conda#5510f8855b43310ed7609395f8d777dd https://conda.anaconda.org/conda-forge/osx-arm64/openexr-3.2.2-h2c51e1d_1.conda#4ccfab8e79256a8480165969dd1d350c https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.3-h4a7b5fc_0_cpython.conda#8643ab37bece6ae8f112464068d9df9c -https://conda.anaconda.org/conda-forge/osx-arm64/scotch-6.1.3-hd898c4b_0.tar.bz2#b36afe3494ea25eeb0c46dfa100c4498 +https://conda.anaconda.org/conda-forge/osx-arm64/scotch-6.0.9-h7537618_2.tar.bz2#84c5fcd61737aa430b8d31bb6e2c011b https://conda.anaconda.org/conda-forge/osx-arm64/sqlite-3.46.0-h5838104_0.conda#05c5dc8cd793dcfc5849d0569da9b175 https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxext-1.3.4-h1a8c8d9_2.conda#0ea792d9a253b64752e9fcfaafe8d529 https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxfixes-5.0.3-h3422bc3_1004.tar.bz2#2f28b8528708008ff42d979c1fd2b196 @@ -147,7 +147,6 @@ https://conda.anaconda.org/conda-forge/osx-arm64/libclang-cpp15-15.0.7-default_h https://conda.anaconda.org/conda-forge/osx-arm64/libclang-cpp16-16.0.6-default_hb63da90_8.conda#076ad35c90bdd646e9e48af5cd2a08dc https://conda.anaconda.org/conda-forge/osx-arm64/libclang13-18.1.7-default_hb9c8b4a_0.conda#df9346ad9c343cf8ae933da34c092fa2 https://conda.anaconda.org/conda-forge/osx-arm64/libopenblas-0.3.27-openmp_h6c19121_0.conda#82eba59f4eca26a9fc904d584f8761c0 -https://conda.anaconda.org/conda-forge/osx-arm64/libscotch-7.0.4-h75850e6_5.conda#b50fab6e4a0aa6355ac685f5cde7c188 https://conda.anaconda.org/conda-forge/osx-arm64/loguru-0.7.2-py312h81bd7bf_1.conda#c3f8892c76329082e82916808654bd58 https://conda.anaconda.org/conda-forge/osx-arm64/mpich-4.2.1-h9ee2227_101.conda#06e88a9bd424c345767e0dac54e8cdb2 https://conda.anaconda.org/conda-forge/osx-arm64/msgpack-python-1.0.8-py312h157fec4_0.conda#b815836e3b798dff1d7a28095761658b @@ -174,17 +173,17 @@ https://conda.anaconda.org/conda-forge/osx-arm64/fftw-3.3.10-mpi_mpich_hd148bab_ https://conda.anaconda.org/conda-forge/osx-arm64/fonttools-4.53.0-py312h7e5086c_0.conda#498008567a4abf4cd2f61f112ff53648 https://conda.anaconda.org/conda-forge/osx-arm64/glib-2.80.2-h535f939_0.conda#9b69f620f2a8153ba4467fedc09e89f1 https://conda.anaconda.org/conda-forge/osx-arm64/hdf5-1.14.3-mpi_mpich_hb65fe4a_5.conda#73efeafc7528c76f9b8e62c4825d6dec -https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.1.0-pyha770c72_0.conda#0896606848b2dc5cebdf111b6543aa04 +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-7.2.0-pyha770c72_0.conda#e1d9f6dc77209defc283bdf61588e968 https://conda.anaconda.org/conda-forge/noarch/importlib_resources-6.4.0-pyhd8ed1ab_0.conda#c5d3907ad8bd7bf557521a1833cf7e6d https://conda.anaconda.org/conda-forge/osx-arm64/libblas-3.9.0-22_osxarm64_openblas.conda#aeaf35355ef0f37c7c1ba35b7b7db55f https://conda.anaconda.org/conda-forge/osx-arm64/libidn2-2.3.7-h93a5062_0.conda#6e4a21ef7a8e4c0cc65381854848e232 https://conda.anaconda.org/conda-forge/osx-arm64/libopenvino-2024.1.0-h5c9529b_7.conda#1087dc2e91d634ed72952e16328713c9 -https://conda.anaconda.org/conda-forge/osx-arm64/libptscotch-7.0.4-h44b462d_5.conda#19d28d7db4b7eab378d80025b96f6726 https://conda.anaconda.org/conda-forge/osx-arm64/libraw-0.21.1-h2ee6834_2.conda#339cc6b928bfb4d395f530d9b0c6857a https://conda.anaconda.org/conda-forge/osx-arm64/mpi4py-3.1.6-py312h66645bf_1.conda#13ab94fc85df2def429a3f9085c61dd6 https://conda.anaconda.org/conda-forge/osx-arm64/parmetis-4.0.3-hb315350_1006.conda#ec17768fe7a59cc802925bca75820206 https://conda.anaconda.org/conda-forge/osx-arm64/pillow-10.3.0-py312h8a801b1_0.conda#1d42544faaed27dce36268912b8dfedf https://conda.anaconda.org/conda-forge/noarch/pip-24.0-pyhd8ed1ab_0.conda#f586ac1e56c8638b64f9c8122a7b8a67 +https://conda.anaconda.org/conda-forge/osx-arm64/ptscotch-6.0.9-hd02db47_2.tar.bz2#192bba8a27718aa0dab53c1cdbb5db9d https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda#2cf4264fffb9e6eff6031c5b6884d61c https://conda.anaconda.org/conda-forge/osx-arm64/sip-6.8.3-py312h20a0b95_0.conda#498e79c9e8495f9b85bad956ddbaceb4 https://conda.anaconda.org/conda-forge/osx-arm64/tbb-devel-2021.12.0-h94f16c5_1.conda#36632e54f2864b82bf76b4d017f0c0ee @@ -194,7 +193,7 @@ https://conda.anaconda.org/conda-forge/osx-arm64/freeimage-3.18.0-hd0e3f39_20.co https://conda.anaconda.org/conda-forge/osx-arm64/gnutls-3.7.9-hd26332c_0.conda#64af58bb3f2a635471dfbe798a1b81f5 https://conda.anaconda.org/conda-forge/osx-arm64/gstreamer-1.24.4-h430e707_0.conda#73dec96255be4192c5de3b26e94ef995 https://conda.anaconda.org/conda-forge/osx-arm64/harfbuzz-8.5.0-h1836168_0.conda#aa22b942b980c17612d344adcd0f8798 -https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-7.1.0-hd8ed1ab_0.conda#6ef2b72d291b39e479d7694efa2b2b98 +https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-7.2.0-hd8ed1ab_0.conda#3de0087b2b86443cfae650dea6ecec6f https://conda.anaconda.org/conda-forge/osx-arm64/libcblas-3.9.0-22_osxarm64_openblas.conda#37b3682240a69874a22658dedbca37d9 https://conda.anaconda.org/conda-forge/osx-arm64/liblapack-3.9.0-22_osxarm64_openblas.conda#f2794950bc005e123b2c21f7fa3d7a6e https://conda.anaconda.org/conda-forge/osx-arm64/libnetcdf-4.9.2-nompi_he469be0_114.conda#8fd3ce6d910ed831c130c391c4364d3f @@ -210,27 +209,27 @@ https://conda.anaconda.org/conda-forge/osx-arm64/libopenvino-tensorflow-frontend https://conda.anaconda.org/conda-forge/osx-arm64/libopenvino-tensorflow-lite-frontend-2024.1.0-h00cdb27_7.conda#002043b46dbefc3404a6725fbaf64568 https://conda.anaconda.org/conda-forge/osx-arm64/pyqt5-sip-12.12.2-py312h9f69965_5.conda#d96792bb6923eb754ed7295e9926907d https://conda.anaconda.org/conda-forge/osx-arm64/gst-plugins-base-1.24.4-h8a8f8c8_0.conda#05d2fa13307d6e949f883b9de658e154 -https://conda.anaconda.org/conda-forge/osx-arm64/hypre-2.31.0-mpi_mpich_hbb1104e_1.conda#18bee803daae4bbe1acd69dec2a9c422 +https://conda.anaconda.org/conda-forge/osx-arm64/hypre-2.28.0-mpi_mpich_hd226f01_0.conda#e3a5c41b4f6fe1c003317e35ba63f6ff https://conda.anaconda.org/conda-forge/osx-arm64/libass-0.17.1-hf7da4fe_1.conda#53fff6fc379154382f5121325c5fe2f5 https://conda.anaconda.org/conda-forge/osx-arm64/numpy-1.26.4-py312h8442bc7_0.conda#d83fc83d589e2625a3451c9a7e21047c https://conda.anaconda.org/conda-forge/osx-arm64/occt-7.7.2-novtk_h5f4376a_101.conda#5d28db29700879ae6f1e86ad06c13d6e https://conda.anaconda.org/conda-forge/osx-arm64/scalapack-2.2.0-h908211e_2.conda#d495ae034d1379c2fbd42e84f109f06c -https://conda.anaconda.org/conda-forge/osx-arm64/suitesparse-7.7.0-hf6fcff2_1.conda#47112a1d681f75116124518210338225 +https://conda.anaconda.org/conda-forge/osx-arm64/suitesparse-5.10.1-h79486c6_3.conda#01db3ca43ae81129b959890c3aaaac43 https://conda.anaconda.org/conda-forge/osx-arm64/superlu-5.2.2-hc615359_0.tar.bz2#563c35f95395ad5b986dc66239a938a9 -https://conda.anaconda.org/conda-forge/osx-arm64/superlu_dist-9.0.0-h2cb61f8_1.conda#2f5ac565026197408d272914d6a53e95 -https://conda.anaconda.org/conda-forge/noarch/wslink-2.1.0-pyhd8ed1ab_0.conda#088c224d81a1828e283186e14a4db25f +https://conda.anaconda.org/conda-forge/osx-arm64/superlu_dist-7.2.0-h7df07b8_0.tar.bz2#0ff06c2b04381ff8d492b5fba96d9961 +https://conda.anaconda.org/conda-forge/noarch/wslink-2.1.1-pyhd8ed1ab_0.conda#6b1aef9c878c58baa7bb9f0d44457174 https://conda.anaconda.org/conda-forge/osx-arm64/contourpy-1.2.1-py312h0fef576_0.conda#f825cced50aa6ae9f6ae158a49ecb68c https://conda.anaconda.org/conda-forge/osx-arm64/ffmpeg-6.1.1-gpl_hc16618e_112.conda#4c170cbb2109cd40318db2f09724a031 https://conda.anaconda.org/conda-forge/osx-arm64/gmsh-4.12.2-hd427cfb_0.conda#72f01e6c242e38a1e0441500e22a4c75 -https://conda.anaconda.org/conda-forge/osx-arm64/mumps-mpi-5.7.2-hd0c33d2_0.conda#3c283e6a1373cb4226a8d04fc7c3eb21 +https://conda.anaconda.org/conda-forge/osx-arm64/mumps-mpi-5.2.1-hfd295ca_11.tar.bz2#67944dc05491af4d3c4702bca7b7a518 https://conda.anaconda.org/conda-forge/osx-arm64/qt-main-5.15.8-hf679f28_21.conda#715342108a6cc6336f489c36b85ba6f1 https://conda.anaconda.org/conda-forge/osx-arm64/qt6-main-6.7.1-h845717a_2.conda#9fac1875f08258e5476ab7ec18962668 https://conda.anaconda.org/conda-forge/osx-arm64/scipy-1.13.1-py312h14ffa8f_0.conda#0ef7359585e53bb3ff4539cf204f9c62 https://conda.anaconda.org/conda-forge/osx-arm64/matplotlib-base-3.8.4-py312h4479663_2.conda#e4c7e00cc31a921bb2541c10c3c58a8c -https://conda.anaconda.org/conda-forge/osx-arm64/petsc-3.21.2-real_hb21bb17_102.conda#69fbf45db2c2dd2a177eab384c2ec589 +https://conda.anaconda.org/conda-forge/osx-arm64/petsc-3.20.2-real_hfe62963_100.conda#e618cc0847fec2e1ed28f844dac11ce8 https://conda.anaconda.org/conda-forge/osx-arm64/pyqt-5.15.9-py312h550cae4_5.conda#e32e9f00bf2c00aa568fa1b0af31c800 https://conda.anaconda.org/conda-forge/osx-arm64/vtk-base-9.3.0-qt_py312h1234567_200.conda#5c5394e96300c37f9a97e660ff7d60ee -https://conda.anaconda.org/conda-forge/osx-arm64/petsc4py-3.21.2-py312h293dd43_1.conda#05fed76312b4daf23e084d180bfcecef +https://conda.anaconda.org/conda-forge/osx-arm64/petsc4py-3.20.2-real_hd567e68_100.conda#077dbb7929e2fb3b5482a2159416034b https://conda.anaconda.org/conda-forge/noarch/pyface-8.0.0-pyhd8ed1ab_0.conda#53751c009f36a67406d321a991d78a0e https://conda.anaconda.org/conda-forge/osx-arm64/vtk-io-ffmpeg-9.3.0-qt_py312h1234567_200.conda#20f1f8840b265c4b0d3c343ad03c98cc https://conda.anaconda.org/conda-forge/noarch/traitsui-8.0.0-pyhd8ed1ab_0.conda#230a8da760e3037989d8d9ec8a370368 diff --git a/environments/petsc-environment.yml b/environments/petsc-environment.yml index 62ecc7a1b4..dbe6b6e6d6 100644 --- a/environments/petsc-environment.yml +++ b/environments/petsc-environment.yml @@ -16,7 +16,8 @@ dependencies: # as a result of linking scotch 7.0.2 # https://github.com/conda-forge/petsc-feedstock/issues/180 - scotch <7 - - petsc4py + # petsc 3.21 has parallel failure when running tests + - petsc4py < 3.21 platforms: - linux-64 - osx-64 From b9f75b893ba9ac15bbec1bd95e0c02420a25c242 Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Fri, 21 Jun 2024 16:06:03 -0400 Subject: [PATCH 22/26] Make directory that already exists --- .azure/pipelines.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.azure/pipelines.yml b/.azure/pipelines.yml index a9a5c38032..d762be6731 100644 --- a/.azure/pipelines.yml +++ b/.azure/pipelines.yml @@ -220,7 +220,7 @@ stages: - bash: | conda create --quiet --name wheelEnvironment --channel conda-forge python=3.10 source activate wheelEnvironment - mkdir tmp + mkdir -p tmp cd tmp python -m pip install ../dist/*.whl FIPY_SOLVERS=scipy python -c "import fipy; fipy.test()" @@ -232,7 +232,7 @@ stages: - bash: | source activate myEnvironment FIPY_VERSION=`python setup.py --version` - mkdir tmp + mkdir -p tmp cd tmp cp ../dist/FiPy-${FIPY_VERSION}.tar.gz . tar zxvf FiPy-${FIPY_VERSION}.tar.gz @@ -248,7 +248,7 @@ stages: - bash: | source activate myEnvironment FIPY_VERSION=`python setup.py --version` - mkdir tmp + mkdir -p tmp cd tmp cp ../dist/FiPy-${FIPY_VERSION}.zip . unzip FiPy-${FIPY_VERSION}.zip From 4e30696c51d86e975ba54fdcacb7525a8289adcd Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Fri, 21 Jun 2024 16:25:08 -0400 Subject: [PATCH 23/26] Fix case of tarball --- .azure/pipelines.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.azure/pipelines.yml b/.azure/pipelines.yml index d762be6731..d249787976 100644 --- a/.azure/pipelines.yml +++ b/.azure/pipelines.yml @@ -234,9 +234,9 @@ stages: FIPY_VERSION=`python setup.py --version` mkdir -p tmp cd tmp - cp ../dist/FiPy-${FIPY_VERSION}.tar.gz . - tar zxvf FiPy-${FIPY_VERSION}.tar.gz - cd FiPy-${FIPY_VERSION} + cp ../dist/fipy-${FIPY_VERSION}.tar.gz . + tar zxvf fipy-${FIPY_VERSION}.tar.gz + cd fipy-${FIPY_VERSION} python setup.py install cd .. python -c "import fipy; fipy.test()" From 1e411d48b27855a543f097a048efc9a35ed31dff Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Fri, 21 Jun 2024 16:28:50 -0400 Subject: [PATCH 24/26] Fix type of int Variable for Windows --- fipy/variables/variable.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index 3cf73a2ac2..37360e5fa3 100644 --- a/fipy/variables/variable.py +++ b/fipy/variables/variable.py @@ -59,7 +59,8 @@ def __init__(self, value=0., unit=None, array=None, name='', cached=1): Variable(value=array(3)) >>> Variable(value=3, unit="m") Variable(value=PhysicalField(3,'m')) - >>> Variable(value=3, unit="m", array=numerix.zeros((3, 2), 'l')) + >>> Variable(value=3, unit="m", array=numerix.zeros((3, 2), + ... dtype=int)) Variable(value=PhysicalField(array([[3, 3], [3, 3], [3, 3]]),'m')) From 21bc31e329dec30db140c44a5c7b221f23d4a1b6 Mon Sep 17 00:00:00 2001 From: Daniel Wheeler Date: Tue, 25 Jun 2024 13:00:05 -0400 Subject: [PATCH 25/26] build(nix): update to python 3.12 and nixos 24.05 Update Nix build to use Python 3.12, NixOS 24.05. Also, include aarch4-darwin as a possible build. Currently, there is a single test failure in fipy.matrices.scipyMatrix._ScipyMatrix. --- flake.lock | 14 +++++++------- flake.nix | 6 +++--- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/flake.lock b/flake.lock index 4be15d1e0b..4bab270cb8 100644 --- a/flake.lock +++ b/flake.lock @@ -2,16 +2,16 @@ "nodes": { "nixpkgs": { "locked": { - "lastModified": 1704732714, - "narHash": "sha256-ABqK/HggMYA/jMUXgYyqVAcQ8QjeMyr1jcXfTpSHmps=", + "lastModified": 1719145550, + "narHash": "sha256-K0i/coxxTEl30tgt4oALaylQfxqbotTSNb1/+g+mKMQ=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "6723fa4e4f1a30d42a633bef5eb01caeb281adc3", + "rev": "e4509b3a560c87a8d4cb6f9992b8915abf9e36d8", "type": "github" }, "original": { "owner": "NixOS", - "ref": "nixos-23.11", + "ref": "nixos-24.05", "repo": "nixpkgs", "type": "github" } @@ -42,11 +42,11 @@ "systems": "systems" }, "locked": { - "lastModified": 1701680307, - "narHash": "sha256-kAuep2h5ajznlPMD9rnQyffWG8EM/C73lejGofXvdM8=", + "lastModified": 1710146030, + "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", "owner": "numtide", "repo": "flake-utils", - "rev": "4022d587cbbfd70fe950c1e2083a02621806a725", + "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", "type": "github" }, "original": { diff --git a/flake.nix b/flake.nix index 9cc7041126..6238ddbb1a 100644 --- a/flake.nix +++ b/flake.nix @@ -2,14 +2,14 @@ description = "Python environment for fipy"; inputs = { - nixpkgs.url = "github:NixOS/nixpkgs/nixos-23.11"; + nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05"; utils.url = "github:numtide/flake-utils"; }; - outputs = { self, nixpkgs, utils}: (utils.lib.eachSystem ["x86_64-linux" "x86_64-darwin" ] (system: + outputs = { self, nixpkgs, utils}: (utils.lib.eachSystem [ "x86_64-linux" "x86_64-darwin" "aarch64-darwin" ] (system: let pkgs = nixpkgs.legacyPackages.${system}; - pypkgs = pkgs.python310Packages; + pypkgs = pkgs.python312Packages; env = (pypkgs.fipy.overridePythonAttrs (old: rec { From e25c210ecbb96f88a62afb650d51f7d1f8d1d94c Mon Sep 17 00:00:00 2001 From: Daniel Wheeler Date: Tue, 25 Jun 2024 13:04:05 -0400 Subject: [PATCH 26/26] ci(actions): generate egg_info Generate the egg_info before executing the tests otherwise setup.py doesn't register the correct version of the test suite, but possibly the older version already available in nixpkgs. --- .github/workflows/nix.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/nix.yml b/.github/workflows/nix.yml index f593eae2da..18533ebb7f 100644 --- a/.github/workflows/nix.yml +++ b/.github/workflows/nix.yml @@ -23,6 +23,7 @@ jobs: with: path: /run/user/${{ env.UID }}/http_cache.sqlite key: ${{ runner.os }}-http_cache.sqlite + - run: nix develop --command bash -c "python setup.py egg_info" - run: nix develop --command bash -c "python setup.py test" - run: nix develop --command bash -c "py.test --nbval --nbval-sanitize-with examples/sanitize.cfg examples/index.ipynb" - uses: actions/cache/save@v3