mapFolding 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- mapFolding/__init__.py +2 -2
- mapFolding/babbage.py +2 -2
- mapFolding/beDRY.py +60 -40
- mapFolding/lovelace.py +194 -122
- mapFolding/oeis.py +37 -35
- mapFolding/reference/flattened.py +376 -0
- mapFolding/reference/hunterNumba.py +44 -44
- mapFolding/reference/lunnan.py +5 -5
- mapFolding/reference/lunnanNumpy.py +4 -4
- mapFolding/reference/lunnanWhile.py +5 -5
- mapFolding/reference/rotatedEntryPoint.py +68 -68
- mapFolding/reference/total_countPlus1vsPlusN.py +211 -0
- mapFolding/startHere.py +12 -12
- mapFolding/theSSOT.py +8 -3
- {mapFolding-0.2.1.dist-info → mapFolding-0.2.3.dist-info}/METADATA +4 -4
- mapFolding-0.2.3.dist-info/RECORD +30 -0
- tests/__init__.py +1 -1
- tests/conftest.py +111 -35
- tests/pythons_idiotic_namespace.py +1 -0
- tests/test_oeis.py +25 -26
- tests/test_other.py +135 -5
- tests/test_tasks.py +11 -1
- mapFolding/importPackages.py +0 -5
- mapFolding-0.2.1.dist-info/RECORD +0 -28
- {mapFolding-0.2.1.dist-info → mapFolding-0.2.3.dist-info}/WHEEL +0 -0
- {mapFolding-0.2.1.dist-info → mapFolding-0.2.3.dist-info}/entry_points.txt +0 -0
- {mapFolding-0.2.1.dist-info → mapFolding-0.2.3.dist-info}/top_level.txt +0 -0
mapFolding/__init__.py
CHANGED
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@@ -1,6 +1,6 @@
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from .theSSOT import *
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-
from
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from .beDRY import
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from Z0Z_tools import defineConcurrencyLimit, intInnit, oopsieKwargsie
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from .beDRY import getFilenameFoldsTotal, outfitCountFolds
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from .startHere import countFolds
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from .oeis import oeisIDfor_n, getOEISids, clearOEIScache
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mapFolding/babbage.py
CHANGED
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@@ -6,7 +6,7 @@ import numba
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import numpy
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@numba.jit(cache=True)
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def _countFolds(connectionGraph: NDArray[integer[Any]],
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def _countFolds(connectionGraph: NDArray[integer[Any]], foldsSubTotals: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], mapShape: Tuple[int, ...], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
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"""
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What in tarnation is this stupid module and function?
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@@ -27,4 +27,4 @@ def _countFolds(connectionGraph: NDArray[integer[Any]], foldsTotal: NDArray[inte
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"""
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# TODO learn if I really must change this jitted function to get the super jit to recompile
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# print('babbage')
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-
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countFoldsCompiled(connectionGraph=connectionGraph, foldsSubTotals=foldsSubTotals, gapsWhere=gapsWhere, my=my, the=the, track=track)
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mapFolding/beDRY.py
CHANGED
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@@ -1,13 +1,17 @@
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"""A relatively stable API for oft-needed functionality."""
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from mapFolding
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from mapFolding import dtypeDefault, dtypeLarge
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from mapFolding import indexMy, indexThe, indexTrack, computationState
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from mapFolding import intInnit, defineConcurrencyLimit, oopsieKwargsie
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from numpy import integer
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from numpy.typing import NDArray
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from typing import Any, List, Optional, Sequence, Type, Union
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import numpy
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import numba
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from numpy import integer
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import numpy
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import sys
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def getFilenameFoldsTotal(listDimensions: Sequence[int]) -> str:
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return str(sorted(listDimensions)).replace(' ', '') + '.foldsTotal'
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def getLeavesTotal(listDimensions: Sequence[int]) -> int:
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"""
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How many leaves are in the map.
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@@ -32,7 +36,7 @@ def getLeavesTotal(listDimensions: Sequence[int]) -> int:
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return productDimensions
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def getTaskDivisions(computationDivisions: Optional[Union[int, str]], concurrencyLimit: int,
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def getTaskDivisions(computationDivisions: Optional[Union[int, str]], concurrencyLimit: int, CPUlimit: Optional[Union[bool, float, int]], listDimensions: Sequence[int]):
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"""
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Determines whether or how to divide the computation into tasks.
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@@ -46,15 +50,12 @@ def getTaskDivisions(computationDivisions: Optional[Union[int, str]], concurrenc
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- "cpu": limits the divisions to the number of available CPUs, i.e. `concurrencyLimit`
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concurrencyLimit:
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Maximum number of concurrent tasks allowed
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the:
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Array of settings, including `leavesTotal`
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CPUlimit: for error reporting
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listDimensions: for error reporting
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CPUlimit: for error reporting
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Returns
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-------
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-
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Updated settings, including for `taskDivisions`
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taskDivisions:
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Raises
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------
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@@ -65,26 +66,27 @@ def getTaskDivisions(computationDivisions: Optional[Union[int, str]], concurrenc
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-----
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Task divisions cannot exceed total leaves to prevent duplicate counting of folds.
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"""
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if not computationDivisions:
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return 0
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else:
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leavesTotal = getLeavesTotal(listDimensions)
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if isinstance(computationDivisions, int):
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taskDivisions = computationDivisions
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elif isinstance(computationDivisions, str):
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computationDivisions = computationDivisions.lower()
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if computationDivisions == "maximum":
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taskDivisions = leavesTotal
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elif computationDivisions == "cpu":
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-
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taskDivisions = min(concurrencyLimit, leavesTotal)
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else:
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raise ValueError(f"I received {computationDivisions} for the parameter, `computationDivisions`, but the so-called programmer didn't implement code for that.")
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if
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raise ValueError(f"Problem: `taskDivisions`, ({
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if taskDivisions > leavesTotal:
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raise ValueError(f"Problem: `taskDivisions`, ({taskDivisions}), is greater than `leavesTotal`, ({leavesTotal}), which will cause duplicate counting of the folds.\n\nChallenge: you cannot directly set `taskDivisions` or `leavesTotal`. They are derived from parameters that may or may not still be named `computationDivisions`, `CPUlimit` , and `listDimensions` and from dubious-quality Python code.\n\nFor those parameters, I received {computationDivisions=}, {CPUlimit=}, and {listDimensions=}.\n\nPotential solutions: get a different hobby or set `computationDivisions` to a different value.")
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return
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return taskDivisions
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def makeConnectionGraph(listDimensions: Sequence[int],
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def makeConnectionGraph(listDimensions: Sequence[int], **keywordArguments: Optional[Type]) -> NDArray[integer[Any]]:
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"""
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Constructs a multi-dimensional connection graph representing the connections between the leaves of a map with the given dimensions.
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Also called a Cartesian product decomposition or dimensional product mapping.
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@@ -94,16 +96,17 @@ def makeConnectionGraph(listDimensions: Sequence[int], dtype: Optional[Type] = n
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Returns:
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connectionGraph: A 3D numpy array with shape of (dimensionsTotal + 1, leavesTotal + 1, leavesTotal + 1).
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"""
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datatype = keywordArguments.get('datatype', dtypeDefault)
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mapShape = validateListDimensions(listDimensions)
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leavesTotal = getLeavesTotal(mapShape)
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arrayDimensions = numpy.array(mapShape, dtype=
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arrayDimensions = numpy.array(mapShape, dtype=datatype)
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dimensionsTotal = len(arrayDimensions)
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# Step 1: find the cumulative product of the map's dimensions
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cumulativeProduct = numpy.multiply.accumulate([1] + mapShape, dtype=
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cumulativeProduct = numpy.multiply.accumulate([1] + mapShape, dtype=datatype)
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# Step 2: create a coordinate system
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coordinateSystem = numpy.zeros((dimensionsTotal + 1, leavesTotal + 1), dtype=
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coordinateSystem = numpy.zeros((dimensionsTotal + 1, leavesTotal + 1), dtype=datatype)
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for dimension1ndex in range(1, dimensionsTotal + 1):
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for leaf1ndex in range(1, leavesTotal + 1):
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@@ -113,7 +116,7 @@ def makeConnectionGraph(listDimensions: Sequence[int], dtype: Optional[Type] = n
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)
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# Step 3: create and fill the connection graph
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connectionGraph = numpy.zeros((dimensionsTotal + 1, leavesTotal + 1, leavesTotal + 1), dtype=
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connectionGraph = numpy.zeros((dimensionsTotal + 1, leavesTotal + 1, leavesTotal + 1), dtype=datatype)
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for dimension1ndex in range(1, dimensionsTotal + 1):
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for activeLeaf1ndex in range(1, leavesTotal + 1):
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return connectionGraph
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def
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def makeDataContainer(shape, datatype: Optional[Type] = None):
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"""Create a container, probably numpy.ndarray, with the given shape and datatype."""
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if datatype is None:
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datatype = dtypeDefault
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return numpy.zeros(shape, dtype=datatype)
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def outfitCountFolds(listDimensions: Sequence[int], computationDivisions: Optional[Union[int, str]] = None, CPUlimit: Optional[Union[bool, float, int]] = None, **keywordArguments: Optional[Type]) -> computationState:
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"""
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Initializes and configures the computation state for map folding computations.
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listDimensions:
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The dimensions of the map to be folded
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computationDivisions (None):
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Specifies how to divide
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Specifies how to divide computations:
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- None: no division of the computation into tasks; sets task divisions to 0
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- int: direct set the number of task divisions; cannot exceed the map's total leaves
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- "maximum": divides into `leavesTotal`-many `taskDivisions`
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- "cpu": limits the divisions to the number of available CPUs, i.e. `concurrencyLimit`
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CPUlimit (None):
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dtypeDefault (numpy.int64):
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The default numpy dtype to use for arrays
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dtypeLarge (numpy.int64):
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The numpy dtype to use for larger arrays
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Whether and how to limit the CPU usage. See notes for details.
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Returns
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-------
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computationState
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An initialized computation state containing:
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- connectionGraph: Graph representing connections in the map
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- foldsSubTotals: Array tracking total folds
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- mapShape: Validated and sorted dimensions of the map
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- my: Array for internal state tracking
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- gapsWhere: Array tracking gap positions
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- the:
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- the: Static settings and metadata
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- track: Array for tracking computation progress
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Limits on CPU usage `CPUlimit`:
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- `False`, `None`, or `0`: No limits on CPU usage; uses all available CPUs. All other values will potentially limit CPU usage.
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- `True`: Yes, limit the CPU usage; limits to 1 CPU.
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- Integer `>= 1`: Limits usage to the specified number of CPUs.
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- Decimal value (`float`) between 0 and 1: Fraction of total CPUs to use.
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- Decimal value (`float`) between -1 and 0: Fraction of CPUs to *not* use.
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- Integer `<= -1`: Subtract the absolute value from total CPUs.
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"""
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datatypeDefault = keywordArguments.get('datatypeDefault', dtypeDefault)
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datatypeLarge = keywordArguments.get('datatypeLarge', dtypeLarge)
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the =
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the = makeDataContainer(len(indexThe), datatypeDefault)
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mapShape = tuple(sorted(validateListDimensions(listDimensions)))
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the[indexThe.leavesTotal] = getLeavesTotal(mapShape)
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the[indexThe.dimensionsTotal] = len(mapShape)
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concurrencyLimit = setCPUlimit(CPUlimit)
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the[indexThe.taskDivisions] = getTaskDivisions(computationDivisions, concurrencyLimit, CPUlimit, listDimensions)
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stateInitialized = computationState(
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connectionGraph = makeConnectionGraph(mapShape,
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connectionGraph = makeConnectionGraph(mapShape, datatype=datatypeDefault),
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foldsSubTotals = makeDataContainer(the[indexThe.leavesTotal], datatypeLarge),
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mapShape = mapShape,
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my =
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gapsWhere =
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the =
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track =
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my = makeDataContainer(len(indexMy), datatypeLarge),
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gapsWhere = makeDataContainer(int(the[indexThe.leavesTotal]) * int(the[indexThe.leavesTotal]) + 1, datatypeDefault),
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the = the,
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track = makeDataContainer((len(indexTrack), the[indexThe.leavesTotal] + 1), datatypeLarge)
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)
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stateInitialized['my'][indexMy.leaf1ndex.value] = 1
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mapFolding/lovelace.py
CHANGED
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from mapFolding import indexMy, indexThe, indexTrack
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from numpy import integer
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from numpy.typing import NDArray
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from typing import Any
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import numba
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import numpy
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def activeGapIncrement(my: NDArray[integer[Any]]):
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my[indexMy.gap1ndex.value] += 1
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def activeLeafGreaterThan0Condition(my: NDArray[integer[Any]]):
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return my[indexMy.leaf1ndex.value] > 0
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def activeLeafGreaterThanLeavesTotalCondition(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
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return my[indexMy.leaf1ndex.value] > the[indexThe.leavesTotal.value]
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def activeLeafIsTheFirstLeafCondition(my: NDArray[integer[Any]]):
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return my[indexMy.leaf1ndex.value] <= 1
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def activeLeafNotEqualToTaskDivisionsCondition(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
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return my[indexMy.leaf1ndex.value] != the[indexThe.taskDivisions.value]
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(
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from mapFolding import indexMy, indexThe, indexTrack
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from numpy import integer
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from numpy.typing import NDArray
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from typing import Any, Tuple, Optional
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import numba
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import numpy
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def allDimensionsAreUnconstrained(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
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return my[indexMy.dimensionsUnconstrained.value] == the[indexThe.dimensionsTotal.value]
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return my[indexMy.leaf1ndex.value] != the[indexThe.taskDivisions.value] or \
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(my[indexMy.leafConnectee.value] % the[indexThe.taskDivisions.value]) == my[indexMy.taskIndex.value]
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def backtrack(my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
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my[indexMy.leaf1ndex.value] -= 1
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track[indexTrack.leafBelow.value, track[indexTrack.leafAbove.value, my[indexMy.leaf1ndex.value]]] = track[indexTrack.leafBelow.value, my[indexMy.leaf1ndex.value]]
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29
|
+
track[indexTrack.leafAbove.value, track[indexTrack.leafBelow.value, my[indexMy.leaf1ndex.value]]] = track[indexTrack.leafAbove.value, my[indexMy.leaf1ndex.value]]
|
|
30
30
|
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
if initializeUnconstrainedLeaf:
|
|
34
|
-
return my[indexMy.dimensionsUnconstrained.value] == the[indexThe.dimensionsTotal.value]
|
|
35
|
-
else:
|
|
36
|
-
return False
|
|
31
|
+
def backtrackCondition(my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
32
|
+
return my[indexMy.leaf1ndex.value] > 0 and my[indexMy.gap1ndex.value] == track[indexTrack.gapRangeStart.value, my[indexMy.leaf1ndex.value] - 1]
|
|
37
33
|
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
if
|
|
41
|
-
|
|
42
|
-
|
|
34
|
+
def countGaps(gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
35
|
+
gapsWhere[my[indexMy.gap1ndexCeiling.value]] = my[indexMy.leafConnectee.value]
|
|
36
|
+
if track[indexTrack.countDimensionsGapped.value, my[indexMy.leafConnectee.value]] == 0:
|
|
37
|
+
gap1ndexCeilingIncrement(my=my)
|
|
38
|
+
track[indexTrack.countDimensionsGapped.value, my[indexMy.leafConnectee.value]] += 1
|
|
39
|
+
|
|
40
|
+
def dimension1ndexIncrement(my: NDArray[integer[Any]]):
|
|
41
|
+
my[indexMy.dimension1ndex.value] += 1
|
|
42
|
+
|
|
43
|
+
def dimensionsUnconstrainedCondition(connectionGraph: NDArray[integer[Any]], my: NDArray[integer[Any]]):
|
|
44
|
+
return connectionGraph[my[indexMy.dimension1ndex.value], my[indexMy.leaf1ndex.value], my[indexMy.leaf1ndex.value]] == my[indexMy.leaf1ndex.value]
|
|
45
|
+
|
|
46
|
+
def dimensionsUnconstrainedIncrement(my: NDArray[integer[Any]]):
|
|
47
|
+
my[indexMy.dimensionsUnconstrained.value] += 1
|
|
48
|
+
|
|
49
|
+
def filterCommonGaps(gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
50
|
+
gapsWhere[my[indexMy.gap1ndex.value]] = gapsWhere[my[indexMy.indexMiniGap.value]]
|
|
51
|
+
if track[indexTrack.countDimensionsGapped.value, gapsWhere[my[indexMy.indexMiniGap.value]]] == the[indexThe.dimensionsTotal.value] - my[indexMy.dimensionsUnconstrained.value]:
|
|
52
|
+
activeGapIncrement(my=my)
|
|
53
|
+
track[indexTrack.countDimensionsGapped.value, gapsWhere[my[indexMy.indexMiniGap.value]]] = 0
|
|
54
|
+
|
|
55
|
+
def findGapsInitializeVariables(my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
56
|
+
my[indexMy.dimensionsUnconstrained.value] = 0
|
|
57
|
+
my[indexMy.gap1ndexCeiling.value] = track[indexTrack.gapRangeStart.value, my[indexMy.leaf1ndex.value] - 1]
|
|
58
|
+
my[indexMy.dimension1ndex.value] = 1
|
|
59
|
+
|
|
60
|
+
def foldsSubTotalIncrement(foldsSubTotals: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
|
|
61
|
+
foldsSubTotals[my[indexMy.taskIndex.value]] += the[indexThe.leavesTotal.value]
|
|
62
|
+
|
|
63
|
+
def gap1ndexCeilingIncrement(my: NDArray[integer[Any]]):
|
|
64
|
+
my[indexMy.gap1ndexCeiling.value] += 1
|
|
65
|
+
|
|
66
|
+
def indexMiniGapIncrement(my: NDArray[integer[Any]]):
|
|
67
|
+
my[indexMy.indexMiniGap.value] += 1
|
|
68
|
+
|
|
69
|
+
def indexMiniGapInitialization(my: NDArray[integer[Any]]):
|
|
70
|
+
my[indexMy.indexMiniGap.value] = my[indexMy.gap1ndex.value]
|
|
71
|
+
|
|
72
|
+
def insertUnconstrainedLeaf(gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]]):
|
|
73
|
+
my[indexMy.indexLeaf.value] = 0
|
|
74
|
+
while my[indexMy.indexLeaf.value] < my[indexMy.leaf1ndex.value]:
|
|
75
|
+
gapsWhere[my[indexMy.gap1ndexCeiling.value]] = my[indexMy.indexLeaf.value]
|
|
76
|
+
my[indexMy.gap1ndexCeiling.value] += 1
|
|
77
|
+
my[indexMy.indexLeaf.value] += 1
|
|
78
|
+
|
|
79
|
+
def leafBelowSentinelIs1Condition(track: NDArray[integer[Any]]):
|
|
80
|
+
return track[indexTrack.leafBelow.value, 0] == 1
|
|
81
|
+
|
|
82
|
+
def leafConnecteeInitialization(connectionGraph: NDArray[integer[Any]], my: NDArray[integer[Any]]):
|
|
83
|
+
my[indexMy.leafConnectee.value] = connectionGraph[my[indexMy.dimension1ndex.value], my[indexMy.leaf1ndex.value], my[indexMy.leaf1ndex.value]]
|
|
84
|
+
|
|
85
|
+
def leafConnecteeUpdate(connectionGraph: NDArray[integer[Any]], my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
86
|
+
my[indexMy.leafConnectee.value] = connectionGraph[my[indexMy.dimension1ndex.value], my[indexMy.leaf1ndex.value], track[indexTrack.leafBelow.value, my[indexMy.leafConnectee.value]]]
|
|
87
|
+
|
|
88
|
+
def loopingLeavesConnectedToActiveLeaf(my: NDArray[integer[Any]]):
|
|
89
|
+
return my[indexMy.leafConnectee.value] != my[indexMy.leaf1ndex.value]
|
|
90
|
+
|
|
91
|
+
def loopingTheDimensions(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
|
|
92
|
+
return my[indexMy.dimension1ndex.value] <= the[indexThe.dimensionsTotal.value]
|
|
93
|
+
|
|
94
|
+
def loopingToActiveGapCeiling(my: NDArray[integer[Any]]):
|
|
95
|
+
return my[indexMy.indexMiniGap.value] < my[indexMy.gap1ndexCeiling.value]
|
|
96
|
+
|
|
97
|
+
def placeLeaf(gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
98
|
+
my[indexMy.gap1ndex.value] -= 1
|
|
99
|
+
track[indexTrack.leafAbove.value, my[indexMy.leaf1ndex.value]] = gapsWhere[my[indexMy.gap1ndex.value]]
|
|
100
|
+
track[indexTrack.leafBelow.value, my[indexMy.leaf1ndex.value]] = track[indexTrack.leafBelow.value, track[indexTrack.leafAbove.value, my[indexMy.leaf1ndex.value]]]
|
|
101
|
+
track[indexTrack.leafBelow.value, track[indexTrack.leafAbove.value, my[indexMy.leaf1ndex.value]]] = my[indexMy.leaf1ndex.value]
|
|
102
|
+
track[indexTrack.leafAbove.value, track[indexTrack.leafBelow.value, my[indexMy.leaf1ndex.value]]] = my[indexMy.leaf1ndex.value]
|
|
103
|
+
track[indexTrack.gapRangeStart.value, my[indexMy.leaf1ndex.value]] = my[indexMy.gap1ndex.value]
|
|
104
|
+
my[indexMy.leaf1ndex.value] += 1
|
|
105
|
+
|
|
106
|
+
def placeLeafCondition(my: NDArray[integer[Any]]):
|
|
107
|
+
return my[indexMy.leaf1ndex.value] > 0
|
|
108
|
+
|
|
109
|
+
def taskIndexCondition(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
|
|
110
|
+
return my[indexMy.leafConnectee.value] % the[indexThe.taskDivisions.value] == my[indexMy.taskIndex.value]
|
|
111
|
+
|
|
112
|
+
def thereAreComputationDivisionsYouMightSkip(my: NDArray[integer[Any]], the: NDArray[integer[Any]]):
|
|
113
|
+
if activeLeafNotEqualToTaskDivisionsCondition(my=my, the=the):
|
|
114
|
+
return True
|
|
115
|
+
if taskIndexCondition(my=my, the=the):
|
|
116
|
+
return True
|
|
117
|
+
return False
|
|
118
|
+
|
|
119
|
+
def initialize(connectionGraph: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
120
|
+
while activeLeafGreaterThan0Condition(my=my):
|
|
121
|
+
if activeLeafIsTheFirstLeafCondition(my=my) or leafBelowSentinelIs1Condition(track=track):
|
|
122
|
+
findGapsInitializeVariables(my=my, track=track)
|
|
123
|
+
while loopingTheDimensions(my=my, the=the):
|
|
124
|
+
if dimensionsUnconstrainedCondition(connectionGraph=connectionGraph, my=my):
|
|
125
|
+
dimensionsUnconstrainedIncrement(my=my)
|
|
126
|
+
else:
|
|
127
|
+
leafConnecteeInitialization(connectionGraph=connectionGraph, my=my)
|
|
128
|
+
while loopingLeavesConnectedToActiveLeaf(my=my):
|
|
129
|
+
countGaps(gapsWhere=gapsWhere, my=my, track=track)
|
|
130
|
+
leafConnecteeUpdate(connectionGraph=connectionGraph, my=my, track=track)
|
|
131
|
+
dimension1ndexIncrement(my=my)
|
|
132
|
+
if allDimensionsAreUnconstrained(my=my, the=the):
|
|
133
|
+
insertUnconstrainedLeaf(gapsWhere=gapsWhere, my=my)
|
|
134
|
+
indexMiniGapInitialization(my=my)
|
|
135
|
+
while loopingToActiveGapCeiling(my=my):
|
|
136
|
+
filterCommonGaps(gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
137
|
+
indexMiniGapIncrement(my=my)
|
|
138
|
+
if placeLeafCondition(my=my):
|
|
139
|
+
placeLeaf(gapsWhere=gapsWhere, my=my, track=track)
|
|
43
140
|
if my[indexMy.gap1ndex.value] > 0:
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
if my[indexMy.leaf1ndex.value] <= 1 or track[indexTrack.leafBelow.value, 0] == 1:
|
|
52
|
-
if my[indexMy.leaf1ndex.value] > the[indexThe.leavesTotal.value]:
|
|
53
|
-
foldsTotal[my[indexMy.taskIndex.value]] += the[indexThe.leavesTotal.value]
|
|
141
|
+
break
|
|
142
|
+
|
|
143
|
+
def countParallel(connectionGraph: NDArray[integer[Any]], foldsSubTotals: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
144
|
+
while activeLeafGreaterThan0Condition(my=my):
|
|
145
|
+
if activeLeafIsTheFirstLeafCondition(my=my) or leafBelowSentinelIs1Condition(track=track):
|
|
146
|
+
if activeLeafGreaterThanLeavesTotalCondition(my=my, the=the):
|
|
147
|
+
foldsSubTotalIncrement(foldsSubTotals=foldsSubTotals, my=my, the=the)
|
|
54
148
|
else:
|
|
55
|
-
my
|
|
56
|
-
my
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
if connectionGraph[my[indexMy.dimension1ndex.value], my[indexMy.leaf1ndex.value], my[indexMy.leaf1ndex.value]] == my[indexMy.leaf1ndex.value]:
|
|
60
|
-
my[indexMy.dimensionsUnconstrained.value] += 1
|
|
149
|
+
findGapsInitializeVariables(my=my, track=track)
|
|
150
|
+
while loopingTheDimensions(my=my, the=the):
|
|
151
|
+
if dimensionsUnconstrainedCondition(connectionGraph=connectionGraph, my=my):
|
|
152
|
+
dimensionsUnconstrainedIncrement(my=my)
|
|
61
153
|
else:
|
|
62
|
-
|
|
63
|
-
while my
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
my
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
if
|
|
100
|
-
|
|
101
|
-
return foldsTotal, my, gapsWhere, track
|
|
154
|
+
leafConnecteeInitialization(connectionGraph=connectionGraph, my=my)
|
|
155
|
+
while loopingLeavesConnectedToActiveLeaf(my=my):
|
|
156
|
+
if thereAreComputationDivisionsYouMightSkip(my=my, the=the):
|
|
157
|
+
countGaps(gapsWhere=gapsWhere, my=my, track=track)
|
|
158
|
+
leafConnecteeUpdate(connectionGraph=connectionGraph, my=my, track=track)
|
|
159
|
+
dimension1ndexIncrement(my=my)
|
|
160
|
+
indexMiniGapInitialization(my=my)
|
|
161
|
+
while loopingToActiveGapCeiling(my=my):
|
|
162
|
+
filterCommonGaps(gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
163
|
+
indexMiniGapIncrement(my=my)
|
|
164
|
+
while backtrackCondition(my=my, track=track):
|
|
165
|
+
backtrack(my=my, track=track)
|
|
166
|
+
if placeLeafCondition(my=my):
|
|
167
|
+
placeLeaf(gapsWhere=gapsWhere, my=my, track=track)
|
|
168
|
+
|
|
169
|
+
def countSequential(connectionGraph: NDArray[integer[Any]], foldsSubTotals: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
170
|
+
while activeLeafGreaterThan0Condition(my=my):
|
|
171
|
+
if activeLeafIsTheFirstLeafCondition(my=my) or leafBelowSentinelIs1Condition(track=track):
|
|
172
|
+
if activeLeafGreaterThanLeavesTotalCondition(my=my, the=the):
|
|
173
|
+
foldsSubTotalIncrement(foldsSubTotals=foldsSubTotals, my=my, the=the)
|
|
174
|
+
else:
|
|
175
|
+
findGapsInitializeVariables(my=my, track=track)
|
|
176
|
+
while loopingTheDimensions(my=my, the=the):
|
|
177
|
+
if dimensionsUnconstrainedCondition(connectionGraph=connectionGraph, my=my):
|
|
178
|
+
dimensionsUnconstrainedIncrement(my=my)
|
|
179
|
+
else:
|
|
180
|
+
leafConnecteeInitialization(connectionGraph=connectionGraph, my=my)
|
|
181
|
+
while loopingLeavesConnectedToActiveLeaf(my=my):
|
|
182
|
+
countGaps(gapsWhere=gapsWhere, my=my, track=track)
|
|
183
|
+
leafConnecteeUpdate(connectionGraph=connectionGraph, my=my, track=track)
|
|
184
|
+
dimension1ndexIncrement(my=my)
|
|
185
|
+
indexMiniGapInitialization(my=my)
|
|
186
|
+
while loopingToActiveGapCeiling(my=my):
|
|
187
|
+
filterCommonGaps(gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
188
|
+
indexMiniGapIncrement(my=my)
|
|
189
|
+
while backtrackCondition(my=my, track=track):
|
|
190
|
+
backtrack(my=my, track=track)
|
|
191
|
+
if placeLeafCondition(my=my):
|
|
192
|
+
placeLeaf(gapsWhere=gapsWhere, my=my, track=track)
|
|
102
193
|
|
|
103
194
|
@numba.jit(parallel=True, _nrt=True, boundscheck=False, error_model='numpy', fastmath=True, forceinline=True, looplift=False, no_cfunc_wrapper=True, no_cpython_wrapper=True, nogil=True, nopython=True)
|
|
104
|
-
def doTaskIndices(connectionGraph: NDArray[integer[Any]],
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
Run the counting algorithm but with conditional execution of a few lines of code, so each task has an incomplete count that does not overlap with other tasks."""
|
|
108
|
-
stateFoldsSubTotal = foldsTotal.copy()
|
|
195
|
+
def doTaskIndices(connectionGraph: NDArray[integer[Any]], foldsSubTotals: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
196
|
+
|
|
197
|
+
stateGapsWhere = gapsWhere.copy()
|
|
109
198
|
stateMy = my.copy()
|
|
110
|
-
statePotentialGaps = gapsWhere.copy()
|
|
111
199
|
stateTrack = track.copy()
|
|
112
200
|
|
|
113
201
|
for indexSherpa in numba.prange(the[indexThe.taskDivisions.value]):
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
202
|
+
mySherpa = stateMy.copy()
|
|
203
|
+
mySherpa[indexMy.taskIndex.value] = indexSherpa
|
|
204
|
+
countParallel(connectionGraph=connectionGraph, foldsSubTotals=foldsSubTotals, gapsWhere=stateGapsWhere.copy(), my=mySherpa, the=the, track=stateTrack.copy())
|
|
117
205
|
|
|
118
|
-
|
|
206
|
+
return foldsSubTotals
|
|
119
207
|
|
|
120
|
-
|
|
208
|
+
def countFoldsCompiled(connectionGraph: NDArray[integer[Any]], foldsSubTotals: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], my: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]]):
|
|
121
209
|
|
|
122
|
-
|
|
123
|
-
def countFoldsCompileBranch(connectionGraph: NDArray[integer[Any]], foldsTotal: NDArray[integer[Any]], my: NDArray[integer[Any]], gapsWhere: NDArray[integer[Any]], the: NDArray[integer[Any]], track: NDArray[integer[Any]], obviousFlagForNumba: bool) -> NDArray[integer[Any]]:
|
|
124
|
-
"""Allegedly, `obviousFlagForNumba` allows Numba to compile two versions: one for parallel execution and one leaner version for sequential execution."""
|
|
125
|
-
if obviousFlagForNumba:
|
|
126
|
-
foldsTotal, _1, _2, _3 = doWhile(connectionGraph, foldsTotal, my, gapsWhere, the, track, initializeUnconstrainedLeaf=False)
|
|
127
|
-
else:
|
|
128
|
-
foldsTotal = doTaskIndices(connectionGraph, foldsTotal, my, gapsWhere, the, track)
|
|
210
|
+
initialize(connectionGraph=connectionGraph, gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
129
211
|
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
# ^ Receive the data structures.
|
|
135
|
-
|
|
136
|
-
# Initialize baseline values primarily to eliminate the need for the logic of `insertUnconstrainedLeaf`
|
|
137
|
-
_0, my, gapsWhere, track = doWhile(connectionGraph, foldsTotal, my, gapsWhere, the, track, initializeUnconstrainedLeaf=True)
|
|
138
|
-
|
|
139
|
-
obviousFlagForNumba = the[indexThe.taskDivisions.value] == int(False)
|
|
140
|
-
|
|
141
|
-
# Call the function that will branch to sequential or parallel counting
|
|
142
|
-
foldsTotal = countFoldsCompileBranch(connectionGraph, foldsTotal, my, gapsWhere, the, track, obviousFlagForNumba)
|
|
212
|
+
if the[indexThe.taskDivisions.value] > 0:
|
|
213
|
+
doTaskIndices(connectionGraph=connectionGraph, foldsSubTotals=foldsSubTotals, gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
214
|
+
else:
|
|
215
|
+
countSequential(connectionGraph=connectionGraph, foldsSubTotals=foldsSubTotals, gapsWhere=gapsWhere, my=my, the=the, track=track)
|
|
143
216
|
|
|
144
|
-
|
|
145
|
-
return numpy.sum(foldsTotal).item()
|
|
217
|
+
numba.jit_module(parallel=False, _nrt=True, boundscheck=False, error_model='numpy', fastmath=True, forceinline=True, looplift=False, no_cfunc_wrapper=True, no_cpython_wrapper=True, nogil=True, nopython=True)
|