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| author | CoprDistGit <infra@openeuler.org> | 2023-05-05 15:22:44 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-05 15:22:44 +0000 |
| commit | f88963705c762f56e5f38609ecb1febbca209dce (patch) | |
| tree | 4e9121f152729ab1270af9d3efc5a7c510074a82 | |
| parent | 8f8af3c81465ef2f445df5752cfa8db13a517d95 (diff) | |
automatic import of python-cykhashopeneuler20.03
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-cykhash.spec | 993 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 995 insertions, 0 deletions
@@ -0,0 +1 @@ +/cykhash-2.0.1.tar.gz diff --git a/python-cykhash.spec b/python-cykhash.spec new file mode 100644 index 0000000..cedec8d --- /dev/null +++ b/python-cykhash.spec @@ -0,0 +1,993 @@ +%global _empty_manifest_terminate_build 0 +Name: python-cykhash +Version: 2.0.1 +Release: 1 +Summary: cython wrapper for khash-sets/maps, efficient implementation of isin and unique +License: MIT +URL: https://github.com/realead/cykhash +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/a5/24/bc570e0f3bb769ebdc178dce52b5be3575ced0c8135a32f0299dff2c138e/cykhash-2.0.1.tar.gz +BuildArch: noarch + + +%description +# cykhash + +cython wrapper for khash-sets/maps, efficient implementation of `isin` and `unique` + +## About: + + * Brings functionality of khash (https://github.com/attractivechaos/klib/blob/master/khash.h) to Python and Cython and can be used seamlessly in numpy or pandas. + + * Numpy's world is lacking the concept of a (hash-)set. This shortcoming is fixed and efficient (memory- and speedwise compared to pandas') `unique` and `isin` are implemented. + + * Python-set/dict have big memory-footprint. For some datatypes the overhead can be reduced by using khash by factor 4-8. + +## Installation: + +The recommended way to install the library is via `conda` package manager using the `conda-forge` channel: + + conda install -c conda-forge cykhash + +You can also install the library using `pip`. To install the latest release: + + pip install cykhash + +To install the most recent version of the module: + + pip install https://github.com/realead/cykhash/zipball/master + +Attention: On Linux/Mac `python-dev` should be installed for that (see also https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory) and MSVC on Windows. + +## Dependencies: + +To build the library from source, Cython>=0.28 is required as well as a c-build tool chain. + +See (https://github.com/realead/cykhash/blob/master/doc/README4DEVELOPER.md) for dependencies needed for development. + +## Quick start + +#### Hash set and isin + +Creating a hashset and using it in `isin`: + + # prepare data: + >>> import numpy as np + >>> a = np.arange(42, dtype=np.int64) + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + # actually usage + >>> from cykhash import Int64Set_from_buffer, isin_int64 + + >>> lookup = Int64Set_from_buffer(a) # create a hashset + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> isin_int64(b, lookup, result) # lookup is reused and not recreated + + +### `unique` + +Finding `unique` in `O(n)` (compared to numpy's `np.unique` - `O(n*logn)`) and smaller memory-footprint than pandas' `pd.unique`: + + # prepare input + >>> import numpy as np + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + + # actual usage: + >>> from cykhash import unique_int64 + >>> unique_buffer = unique_int64(a) # unique element are exposed via buffer-protocol + + # can be converted to a numpy-array without copying via + >>> unique_array = np.ctypeslib.as_array(unique_buffer) + >>> unique_array.shape + (3,) + + +### Hash map + +Maps and sets handle `nan`-correctly (try it out with Python's dict/set): + + >>> from cykhash import Float64toInt64Map + >>> my_map = Float64toInt64Map() # values are 64bit integers + >>> my_map[float("nan")] = 1 + >>> my_map[float("nan")] + 1 + + + +## Functionality overview + +### Hash sets + +`Int64Set`, `Int32Set`, `Float64Set`, `Float32Set` ( and `PyObjectSet`) are implemented. They are more or less drop-in replacements for Python's `set`. Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + + +The biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-sets and are somewhat faster for integers or floats. + +As `PyObjectSet` is somewhat slower than the usual `set` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +The most efficient way to create such sets is to use `XXXXSet_from_buffer(...)`, e.g. `Int64Set_from_buffer`, if the data container at hand supports buffer protocol (e.g. numpy-arrays, `array.array` or `ctypes`-arrays). Or `XXXXSet_from(...)` for any iterator. + + +### Hash maps + +`Int64toInt64Map`, `Int32toInt32Map`, `Float64toInt64Map`, `Float32toInt32Map` ( and `PyObjectMap`) are implemented. They are more or less drop-in replacements for Python's `dict` (however, not every piece of `dict`'s functionality makes sense, for example `setdefault(x, default)` without `default`-argument, because `None` cannot be inserted, also the khash-maps don't preserve the insertion order, so there is also no `reversed`). Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + +Biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-dictionaries and are somewhat faster for integers or floats. + + +As `PyObjectMap` is somewhat slower than the usual `dict` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +### isin + + * implemented are `isin_int64`, `isin_int32`, `isin_float64`, `isin_float32` + * using hash set instead of arrays in `isin` function has the advantage, that the look-up data structure doesn't have to be reconstructed for every call, thus reducing the running time from `O(n+m)`to `O(n)`, where `n` is the number of queries and `m`-number of elements in the look up array. + * Thus cykash's `isin` can be order of magnitude faster than the numpy's or pandas' versions. + +#### all, none, any, and count_if + + * siblings functions of `isin_XXX` are: + * `all_XXX`/`all_XXX_from_iterator` which return `True` if all elements of the query array can be found in the set. + * `any_XXX`/`any_XXX_from_iterator` which return `True` if at least one element of the query array can be found in the set. + * `none_XXX`/`none_XXX_from_iterator` which return `True` if none of elements from the query array can be found in the set. + * `count_if_XXX`/`count_if_XXX_from_iterator` which return the number of elements from the query array can be found in the set. + * `all_XXX`, `any_XXX`, `none_XXX` and `count_if_XXX` are faster than using `isin_XXX` and applying numpy's versions of these function on the resulting array. + * `from_iterator` version works with any iterable, but the version for buffers are more efficient. + +### unique + + * implemented are `unique_int64`, `unique_int32`, `unique_float64`, `unique_float32` + * returns an object which implements the buffer protocol, so `np.ctypeslib.as_array` (recommended) or `np.frombuffer` (less safe, as memory can get reinterpreted) can be used to create numpy arrays. + * differently as pandas, the returned uniques aren't in the order of the appearance. If order of appearence is important use `unique_stable_xxx`-versions, which needs somewhat more memory. + * the signature is `unique_xxx(buffer, size_hint=0.0)` the initial memory-consumption of the hash-set will be `len(buffer)*size_hint` unless `size_hint<=0.0`, in this case it will be ensured, that no rehashing is needed even if all elements are unique in the buffer. + +As pandas uses maps instead of sets internally for `unique`, it needs about 4 times more peak memory and is 1.6-3 times slower. + + +### Floating-point numbers as keys + +There is a problem with floating-point sets or maps, i.e. `Float64Set`, `Float32Set`, `Float64toInt64Map` and `Float32toInt32Map`: The standard definition of "equal" and hash-function based on the bit representation don't define a meaningful or desired behavior for the hash set: + + * `NAN != NAN` and thus it is not equivalence relation + * `-0.0 == 0.0` but `hash(-0.0)!=hash(0.0)`, but `x==y => hash(x)==hash(y)` is neccessary for set to work properly. + +This problem is resolved through following special case handling: + + * `hash(-0.0):=hash(0.0)` + * `hash(x):=hash(NAN)` for any not a number `x`. + * `x is equal y <=> x==y || (x!=x && y!=y)` + +A consequence of the above rule, that the equivalence classes of `{0.0, -0.0}` and `e{x | x is not a number}` have more than one element. In the set these classes are represented by the first seen element from the class. + +The above holds also for `PyObjectSet` (this behavior is not the same as fro Python-`set` which shows a different behavior for nans). + +### Examples: + +#### Hash sets + +Python: Creates a set from a numpy-array and looks up whether an element is in the resulting set: + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer + >>> a = np.arange(42, dtype=np.int64) + >>> my_set = Int64Set_from_buffer(a) # no reallocation will be needed + >>> 41 in my_set + True + >>> 42 not in my_set + True + +Python: Create a set from an iterable and looks up whether an element is in the resulting set: + + >>> from cykhash import Int64Set_from + >>> my_set = Int64Set_from(range(42)) # no reallocation will be needed + >>> assert 41 in my_set and 42 not in my_set + +Cython: Create a set and put some values into it: + + from cykhash.khashsets cimport Int64Set + my_set = Int64Set(number_of_elements_hint=12) # reserve place for at least 12 integers + cdef Py_ssize_t i + for i in range(12): + my_set.add(i) + assert 11 in my_set and 12 not in my_set + +#### Hash maps + +Python: Creating `int64->float64` map using `Int64toFloat64Map_from_buffers`: + + >>> import numpy as np + >>> from cykhash import Int64toFloat64Map_from_buffers + >>> keys = np.array([1, 2, 3, 4], dtype=np.int64) + >>> vals = np.array([5, 6, 7, 8], dtype=np.float64) + >>> my_map = Int64toFloat64Map_from_buffers(keys, vals) # there will be no reallocation + >>> assert my_map[4] == 8.0 + +Python: Creating `int64->int64` map from scratch: + + >>> import numpy as np + >>> from cykhash import Int64toInt64Map + + # my_map will not need reallocation for at least 12 elements + >>> my_map = Int64toInt64Map(number_of_elements_hint=12) + >>> for i in range(12): my_map[i] = i+1 + >>> assert my_map[5] == 6 + + +#### isin + +Python: Creating look-up data structure from a numpy-array, performing `isin`-query + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer, isin_int64 + >>> a = np.arange(42, dtype=np.int64) + >>> lookup = Int64Set_from_buffer(a) + + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> assert np.sum(result.astype(np.int_)) == 42 + + +#### unique + +Python: using `unique_int64`: + + >>> import numpy as np + >>> from cykhash import unique_int64 + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_int64(a)) # there will be no reallocation + >>> assert set(u) == {1,2,3} + +Python: using `unique_stable_int64`: + + >>> import numpy as np + >>> from cykhash import unique_stable_int64 + >>> a = np.array([3,2,1,1,2,3], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_stable_int64(a)) # there will be no reallocation + >>> assert list(u) == [3,2,1] + + + +## API + +See (https://github.com/realead/cykhash/blob/master/doc/README_API.md) for a more detailed API description. + +## Performance + +See (https://github.com/realead/cykhash/blob/master/doc/README_PERFORMANCE.md) for results of performance tests. + +## Trivia + +* This project was inspired by the following stackoverflow question: https://stackoverflow.com/questions/50779617/pandas-pd-series-isin-performance-with-set-versus-array. + +* pandas also uses `khash` (and thus was a source of inspiration), but wraps only maps and doesn't wrap sets. Thus, pandas' `unique` needs more memory as it should. Those maps are also never exposed, so there is no way to reuse the look-up structure for multiple calls to `isin`. + +* `khash` is a good choice, but there are other alternatives, e.g. https://github.com/sparsehash/sparsehash. See also https://stackoverflow.com/questions/48129713/fastest-way-to-find-all-unique-elements-in-an-array-with-cython/48142655#48142655 for a comparison for different `unique` implementations. + +* A similar approach for sets/maps in pure Cython: https://github.com/realead/tighthash, which is quite slower than khash. + +* There is no dependency on `numpy`: this library uses buffer protocol, thus it works for `array.array`, `numpy.ndarray`, `ctypes`-arrays and anything else. However, some interfaces are somewhat cumbersome (which type should be created as answer?) and for convenient usage it might be a good idea to wrap the functionality so objects of right types are created. + +## Compatibility between cykhash-versions: + +There are different levels of compatibility: + + * for code using only pure python interface + * for code using cython/cdef-interface and built against a particular cykash version + +Ther rules are as follows: + + * there is no warranty for major versions mismatch: i.e. code written with cykhash `1.x.y` might not run with cykhash `2.z.w` and vice versa. + * if only pure python interface is used, code for the same major version will ran for version with higher minor version, i.e. code for cykhash `2.0.x` will run with cykhash `2.1.y` (but not the other way around: that means new functions could be added to pure python interface) + * if cython's `cdef` interface is used, i.e. a cython-extension was build using pxi-files from cykhash, then versions are compartible only if the the minor versions are the same, e.g. `2.0.x` could be replaced by `2.0.y` in the installation, but when replacing with `2.1.z` the dependent cython-extension must be rebuilt. + +## History: +### Release 2.0.1 (05.02.2022): + + * Tests work for Python 3.11 + * Tests work for numpy 1.24 + * Drops support for Python 3.6 and Python 3.7 + +#### Release 2.0.0 (09.11.2021): + + * Implementation of `any`, `all`, `none` and `count_if` + * Hash-sets are now (almost) drop-in replacements of Python's sets + * Breaking change: iterator from maps doesn't no longer returns items but only keys. However there are following new methods `keys()`, `values()` and `items()`which return so called mapvies, which correspond more or less to dictviews (but for mapsview doesn't hold that "Dictionary order is guaranteed to be insertion order."). + * Hash-Maps are now (almost) drop-in replacements of Python's dicts. Differences: insertion order isn't preserved, thus there is also no `reversed()`-method, `setdefault(key, default)` isn't possible without `default` because `None` cannot be inserted in the map + * Better hash-functions for float64, float32, int64 and int32 (gh-issue #4). + * Breaking change: different names/signatures for maps + * supports tracemalloc for Py3.6+ + * supports Python 3.10 + +#### Release 1.0.2 (30.05.2020): + + * can be installed via conda-forge to all operating systems + * can be installed via pip in a clean environment (Cython>=0.28 is now fetched automatically) + +#### Release 1.0.1 (27.05.2020): + + * released on PyPi + +#### Older: + + * 0.4.0: uniques_stable, preparing for release + * 0.3.0: PyObjectSet, Maps for Int64/32 and also Float64/32, unique-versions + * 0.2.0: Int32Set, Float64Set, Float32Set + * 0.1.0: Int64Set + + + + + +%package -n python3-cykhash +Summary: cython wrapper for khash-sets/maps, efficient implementation of isin and unique +Provides: python-cykhash +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-cykhash +# cykhash + +cython wrapper for khash-sets/maps, efficient implementation of `isin` and `unique` + +## About: + + * Brings functionality of khash (https://github.com/attractivechaos/klib/blob/master/khash.h) to Python and Cython and can be used seamlessly in numpy or pandas. + + * Numpy's world is lacking the concept of a (hash-)set. This shortcoming is fixed and efficient (memory- and speedwise compared to pandas') `unique` and `isin` are implemented. + + * Python-set/dict have big memory-footprint. For some datatypes the overhead can be reduced by using khash by factor 4-8. + +## Installation: + +The recommended way to install the library is via `conda` package manager using the `conda-forge` channel: + + conda install -c conda-forge cykhash + +You can also install the library using `pip`. To install the latest release: + + pip install cykhash + +To install the most recent version of the module: + + pip install https://github.com/realead/cykhash/zipball/master + +Attention: On Linux/Mac `python-dev` should be installed for that (see also https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory) and MSVC on Windows. + +## Dependencies: + +To build the library from source, Cython>=0.28 is required as well as a c-build tool chain. + +See (https://github.com/realead/cykhash/blob/master/doc/README4DEVELOPER.md) for dependencies needed for development. + +## Quick start + +#### Hash set and isin + +Creating a hashset and using it in `isin`: + + # prepare data: + >>> import numpy as np + >>> a = np.arange(42, dtype=np.int64) + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + # actually usage + >>> from cykhash import Int64Set_from_buffer, isin_int64 + + >>> lookup = Int64Set_from_buffer(a) # create a hashset + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> isin_int64(b, lookup, result) # lookup is reused and not recreated + + +### `unique` + +Finding `unique` in `O(n)` (compared to numpy's `np.unique` - `O(n*logn)`) and smaller memory-footprint than pandas' `pd.unique`: + + # prepare input + >>> import numpy as np + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + + # actual usage: + >>> from cykhash import unique_int64 + >>> unique_buffer = unique_int64(a) # unique element are exposed via buffer-protocol + + # can be converted to a numpy-array without copying via + >>> unique_array = np.ctypeslib.as_array(unique_buffer) + >>> unique_array.shape + (3,) + + +### Hash map + +Maps and sets handle `nan`-correctly (try it out with Python's dict/set): + + >>> from cykhash import Float64toInt64Map + >>> my_map = Float64toInt64Map() # values are 64bit integers + >>> my_map[float("nan")] = 1 + >>> my_map[float("nan")] + 1 + + + +## Functionality overview + +### Hash sets + +`Int64Set`, `Int32Set`, `Float64Set`, `Float32Set` ( and `PyObjectSet`) are implemented. They are more or less drop-in replacements for Python's `set`. Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + + +The biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-sets and are somewhat faster for integers or floats. + +As `PyObjectSet` is somewhat slower than the usual `set` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +The most efficient way to create such sets is to use `XXXXSet_from_buffer(...)`, e.g. `Int64Set_from_buffer`, if the data container at hand supports buffer protocol (e.g. numpy-arrays, `array.array` or `ctypes`-arrays). Or `XXXXSet_from(...)` for any iterator. + + +### Hash maps + +`Int64toInt64Map`, `Int32toInt32Map`, `Float64toInt64Map`, `Float32toInt32Map` ( and `PyObjectMap`) are implemented. They are more or less drop-in replacements for Python's `dict` (however, not every piece of `dict`'s functionality makes sense, for example `setdefault(x, default)` without `default`-argument, because `None` cannot be inserted, also the khash-maps don't preserve the insertion order, so there is also no `reversed`). Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + +Biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-dictionaries and are somewhat faster for integers or floats. + + +As `PyObjectMap` is somewhat slower than the usual `dict` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +### isin + + * implemented are `isin_int64`, `isin_int32`, `isin_float64`, `isin_float32` + * using hash set instead of arrays in `isin` function has the advantage, that the look-up data structure doesn't have to be reconstructed for every call, thus reducing the running time from `O(n+m)`to `O(n)`, where `n` is the number of queries and `m`-number of elements in the look up array. + * Thus cykash's `isin` can be order of magnitude faster than the numpy's or pandas' versions. + +#### all, none, any, and count_if + + * siblings functions of `isin_XXX` are: + * `all_XXX`/`all_XXX_from_iterator` which return `True` if all elements of the query array can be found in the set. + * `any_XXX`/`any_XXX_from_iterator` which return `True` if at least one element of the query array can be found in the set. + * `none_XXX`/`none_XXX_from_iterator` which return `True` if none of elements from the query array can be found in the set. + * `count_if_XXX`/`count_if_XXX_from_iterator` which return the number of elements from the query array can be found in the set. + * `all_XXX`, `any_XXX`, `none_XXX` and `count_if_XXX` are faster than using `isin_XXX` and applying numpy's versions of these function on the resulting array. + * `from_iterator` version works with any iterable, but the version for buffers are more efficient. + +### unique + + * implemented are `unique_int64`, `unique_int32`, `unique_float64`, `unique_float32` + * returns an object which implements the buffer protocol, so `np.ctypeslib.as_array` (recommended) or `np.frombuffer` (less safe, as memory can get reinterpreted) can be used to create numpy arrays. + * differently as pandas, the returned uniques aren't in the order of the appearance. If order of appearence is important use `unique_stable_xxx`-versions, which needs somewhat more memory. + * the signature is `unique_xxx(buffer, size_hint=0.0)` the initial memory-consumption of the hash-set will be `len(buffer)*size_hint` unless `size_hint<=0.0`, in this case it will be ensured, that no rehashing is needed even if all elements are unique in the buffer. + +As pandas uses maps instead of sets internally for `unique`, it needs about 4 times more peak memory and is 1.6-3 times slower. + + +### Floating-point numbers as keys + +There is a problem with floating-point sets or maps, i.e. `Float64Set`, `Float32Set`, `Float64toInt64Map` and `Float32toInt32Map`: The standard definition of "equal" and hash-function based on the bit representation don't define a meaningful or desired behavior for the hash set: + + * `NAN != NAN` and thus it is not equivalence relation + * `-0.0 == 0.0` but `hash(-0.0)!=hash(0.0)`, but `x==y => hash(x)==hash(y)` is neccessary for set to work properly. + +This problem is resolved through following special case handling: + + * `hash(-0.0):=hash(0.0)` + * `hash(x):=hash(NAN)` for any not a number `x`. + * `x is equal y <=> x==y || (x!=x && y!=y)` + +A consequence of the above rule, that the equivalence classes of `{0.0, -0.0}` and `e{x | x is not a number}` have more than one element. In the set these classes are represented by the first seen element from the class. + +The above holds also for `PyObjectSet` (this behavior is not the same as fro Python-`set` which shows a different behavior for nans). + +### Examples: + +#### Hash sets + +Python: Creates a set from a numpy-array and looks up whether an element is in the resulting set: + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer + >>> a = np.arange(42, dtype=np.int64) + >>> my_set = Int64Set_from_buffer(a) # no reallocation will be needed + >>> 41 in my_set + True + >>> 42 not in my_set + True + +Python: Create a set from an iterable and looks up whether an element is in the resulting set: + + >>> from cykhash import Int64Set_from + >>> my_set = Int64Set_from(range(42)) # no reallocation will be needed + >>> assert 41 in my_set and 42 not in my_set + +Cython: Create a set and put some values into it: + + from cykhash.khashsets cimport Int64Set + my_set = Int64Set(number_of_elements_hint=12) # reserve place for at least 12 integers + cdef Py_ssize_t i + for i in range(12): + my_set.add(i) + assert 11 in my_set and 12 not in my_set + +#### Hash maps + +Python: Creating `int64->float64` map using `Int64toFloat64Map_from_buffers`: + + >>> import numpy as np + >>> from cykhash import Int64toFloat64Map_from_buffers + >>> keys = np.array([1, 2, 3, 4], dtype=np.int64) + >>> vals = np.array([5, 6, 7, 8], dtype=np.float64) + >>> my_map = Int64toFloat64Map_from_buffers(keys, vals) # there will be no reallocation + >>> assert my_map[4] == 8.0 + +Python: Creating `int64->int64` map from scratch: + + >>> import numpy as np + >>> from cykhash import Int64toInt64Map + + # my_map will not need reallocation for at least 12 elements + >>> my_map = Int64toInt64Map(number_of_elements_hint=12) + >>> for i in range(12): my_map[i] = i+1 + >>> assert my_map[5] == 6 + + +#### isin + +Python: Creating look-up data structure from a numpy-array, performing `isin`-query + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer, isin_int64 + >>> a = np.arange(42, dtype=np.int64) + >>> lookup = Int64Set_from_buffer(a) + + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> assert np.sum(result.astype(np.int_)) == 42 + + +#### unique + +Python: using `unique_int64`: + + >>> import numpy as np + >>> from cykhash import unique_int64 + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_int64(a)) # there will be no reallocation + >>> assert set(u) == {1,2,3} + +Python: using `unique_stable_int64`: + + >>> import numpy as np + >>> from cykhash import unique_stable_int64 + >>> a = np.array([3,2,1,1,2,3], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_stable_int64(a)) # there will be no reallocation + >>> assert list(u) == [3,2,1] + + + +## API + +See (https://github.com/realead/cykhash/blob/master/doc/README_API.md) for a more detailed API description. + +## Performance + +See (https://github.com/realead/cykhash/blob/master/doc/README_PERFORMANCE.md) for results of performance tests. + +## Trivia + +* This project was inspired by the following stackoverflow question: https://stackoverflow.com/questions/50779617/pandas-pd-series-isin-performance-with-set-versus-array. + +* pandas also uses `khash` (and thus was a source of inspiration), but wraps only maps and doesn't wrap sets. Thus, pandas' `unique` needs more memory as it should. Those maps are also never exposed, so there is no way to reuse the look-up structure for multiple calls to `isin`. + +* `khash` is a good choice, but there are other alternatives, e.g. https://github.com/sparsehash/sparsehash. See also https://stackoverflow.com/questions/48129713/fastest-way-to-find-all-unique-elements-in-an-array-with-cython/48142655#48142655 for a comparison for different `unique` implementations. + +* A similar approach for sets/maps in pure Cython: https://github.com/realead/tighthash, which is quite slower than khash. + +* There is no dependency on `numpy`: this library uses buffer protocol, thus it works for `array.array`, `numpy.ndarray`, `ctypes`-arrays and anything else. However, some interfaces are somewhat cumbersome (which type should be created as answer?) and for convenient usage it might be a good idea to wrap the functionality so objects of right types are created. + +## Compatibility between cykhash-versions: + +There are different levels of compatibility: + + * for code using only pure python interface + * for code using cython/cdef-interface and built against a particular cykash version + +Ther rules are as follows: + + * there is no warranty for major versions mismatch: i.e. code written with cykhash `1.x.y` might not run with cykhash `2.z.w` and vice versa. + * if only pure python interface is used, code for the same major version will ran for version with higher minor version, i.e. code for cykhash `2.0.x` will run with cykhash `2.1.y` (but not the other way around: that means new functions could be added to pure python interface) + * if cython's `cdef` interface is used, i.e. a cython-extension was build using pxi-files from cykhash, then versions are compartible only if the the minor versions are the same, e.g. `2.0.x` could be replaced by `2.0.y` in the installation, but when replacing with `2.1.z` the dependent cython-extension must be rebuilt. + +## History: +### Release 2.0.1 (05.02.2022): + + * Tests work for Python 3.11 + * Tests work for numpy 1.24 + * Drops support for Python 3.6 and Python 3.7 + +#### Release 2.0.0 (09.11.2021): + + * Implementation of `any`, `all`, `none` and `count_if` + * Hash-sets are now (almost) drop-in replacements of Python's sets + * Breaking change: iterator from maps doesn't no longer returns items but only keys. However there are following new methods `keys()`, `values()` and `items()`which return so called mapvies, which correspond more or less to dictviews (but for mapsview doesn't hold that "Dictionary order is guaranteed to be insertion order."). + * Hash-Maps are now (almost) drop-in replacements of Python's dicts. Differences: insertion order isn't preserved, thus there is also no `reversed()`-method, `setdefault(key, default)` isn't possible without `default` because `None` cannot be inserted in the map + * Better hash-functions for float64, float32, int64 and int32 (gh-issue #4). + * Breaking change: different names/signatures for maps + * supports tracemalloc for Py3.6+ + * supports Python 3.10 + +#### Release 1.0.2 (30.05.2020): + + * can be installed via conda-forge to all operating systems + * can be installed via pip in a clean environment (Cython>=0.28 is now fetched automatically) + +#### Release 1.0.1 (27.05.2020): + + * released on PyPi + +#### Older: + + * 0.4.0: uniques_stable, preparing for release + * 0.3.0: PyObjectSet, Maps for Int64/32 and also Float64/32, unique-versions + * 0.2.0: Int32Set, Float64Set, Float32Set + * 0.1.0: Int64Set + + + + + +%package help +Summary: Development documents and examples for cykhash +Provides: python3-cykhash-doc +%description help +# cykhash + +cython wrapper for khash-sets/maps, efficient implementation of `isin` and `unique` + +## About: + + * Brings functionality of khash (https://github.com/attractivechaos/klib/blob/master/khash.h) to Python and Cython and can be used seamlessly in numpy or pandas. + + * Numpy's world is lacking the concept of a (hash-)set. This shortcoming is fixed and efficient (memory- and speedwise compared to pandas') `unique` and `isin` are implemented. + + * Python-set/dict have big memory-footprint. For some datatypes the overhead can be reduced by using khash by factor 4-8. + +## Installation: + +The recommended way to install the library is via `conda` package manager using the `conda-forge` channel: + + conda install -c conda-forge cykhash + +You can also install the library using `pip`. To install the latest release: + + pip install cykhash + +To install the most recent version of the module: + + pip install https://github.com/realead/cykhash/zipball/master + +Attention: On Linux/Mac `python-dev` should be installed for that (see also https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory) and MSVC on Windows. + +## Dependencies: + +To build the library from source, Cython>=0.28 is required as well as a c-build tool chain. + +See (https://github.com/realead/cykhash/blob/master/doc/README4DEVELOPER.md) for dependencies needed for development. + +## Quick start + +#### Hash set and isin + +Creating a hashset and using it in `isin`: + + # prepare data: + >>> import numpy as np + >>> a = np.arange(42, dtype=np.int64) + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + # actually usage + >>> from cykhash import Int64Set_from_buffer, isin_int64 + + >>> lookup = Int64Set_from_buffer(a) # create a hashset + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> isin_int64(b, lookup, result) # lookup is reused and not recreated + + +### `unique` + +Finding `unique` in `O(n)` (compared to numpy's `np.unique` - `O(n*logn)`) and smaller memory-footprint than pandas' `pd.unique`: + + # prepare input + >>> import numpy as np + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + + # actual usage: + >>> from cykhash import unique_int64 + >>> unique_buffer = unique_int64(a) # unique element are exposed via buffer-protocol + + # can be converted to a numpy-array without copying via + >>> unique_array = np.ctypeslib.as_array(unique_buffer) + >>> unique_array.shape + (3,) + + +### Hash map + +Maps and sets handle `nan`-correctly (try it out with Python's dict/set): + + >>> from cykhash import Float64toInt64Map + >>> my_map = Float64toInt64Map() # values are 64bit integers + >>> my_map[float("nan")] = 1 + >>> my_map[float("nan")] + 1 + + + +## Functionality overview + +### Hash sets + +`Int64Set`, `Int32Set`, `Float64Set`, `Float32Set` ( and `PyObjectSet`) are implemented. They are more or less drop-in replacements for Python's `set`. Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + + +The biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-sets and are somewhat faster for integers or floats. + +As `PyObjectSet` is somewhat slower than the usual `set` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +The most efficient way to create such sets is to use `XXXXSet_from_buffer(...)`, e.g. `Int64Set_from_buffer`, if the data container at hand supports buffer protocol (e.g. numpy-arrays, `array.array` or `ctypes`-arrays). Or `XXXXSet_from(...)` for any iterator. + + +### Hash maps + +`Int64toInt64Map`, `Int32toInt32Map`, `Float64toInt64Map`, `Float32toInt32Map` ( and `PyObjectMap`) are implemented. They are more or less drop-in replacements for Python's `dict` (however, not every piece of `dict`'s functionality makes sense, for example `setdefault(x, default)` without `default`-argument, because `None` cannot be inserted, also the khash-maps don't preserve the insertion order, so there is also no `reversed`). Furthermore, given the Cython-interface, efficient extensions of functionality are easily done. + +Biggest advantage of these sets is that they need about 4-8 times less memory than the usual Python-dictionaries and are somewhat faster for integers or floats. + + +As `PyObjectMap` is somewhat slower than the usual `dict` and needs about the same amount of memory, it should be used only if all `nan`s should be treated as equivalent. + +### isin + + * implemented are `isin_int64`, `isin_int32`, `isin_float64`, `isin_float32` + * using hash set instead of arrays in `isin` function has the advantage, that the look-up data structure doesn't have to be reconstructed for every call, thus reducing the running time from `O(n+m)`to `O(n)`, where `n` is the number of queries and `m`-number of elements in the look up array. + * Thus cykash's `isin` can be order of magnitude faster than the numpy's or pandas' versions. + +#### all, none, any, and count_if + + * siblings functions of `isin_XXX` are: + * `all_XXX`/`all_XXX_from_iterator` which return `True` if all elements of the query array can be found in the set. + * `any_XXX`/`any_XXX_from_iterator` which return `True` if at least one element of the query array can be found in the set. + * `none_XXX`/`none_XXX_from_iterator` which return `True` if none of elements from the query array can be found in the set. + * `count_if_XXX`/`count_if_XXX_from_iterator` which return the number of elements from the query array can be found in the set. + * `all_XXX`, `any_XXX`, `none_XXX` and `count_if_XXX` are faster than using `isin_XXX` and applying numpy's versions of these function on the resulting array. + * `from_iterator` version works with any iterable, but the version for buffers are more efficient. + +### unique + + * implemented are `unique_int64`, `unique_int32`, `unique_float64`, `unique_float32` + * returns an object which implements the buffer protocol, so `np.ctypeslib.as_array` (recommended) or `np.frombuffer` (less safe, as memory can get reinterpreted) can be used to create numpy arrays. + * differently as pandas, the returned uniques aren't in the order of the appearance. If order of appearence is important use `unique_stable_xxx`-versions, which needs somewhat more memory. + * the signature is `unique_xxx(buffer, size_hint=0.0)` the initial memory-consumption of the hash-set will be `len(buffer)*size_hint` unless `size_hint<=0.0`, in this case it will be ensured, that no rehashing is needed even if all elements are unique in the buffer. + +As pandas uses maps instead of sets internally for `unique`, it needs about 4 times more peak memory and is 1.6-3 times slower. + + +### Floating-point numbers as keys + +There is a problem with floating-point sets or maps, i.e. `Float64Set`, `Float32Set`, `Float64toInt64Map` and `Float32toInt32Map`: The standard definition of "equal" and hash-function based on the bit representation don't define a meaningful or desired behavior for the hash set: + + * `NAN != NAN` and thus it is not equivalence relation + * `-0.0 == 0.0` but `hash(-0.0)!=hash(0.0)`, but `x==y => hash(x)==hash(y)` is neccessary for set to work properly. + +This problem is resolved through following special case handling: + + * `hash(-0.0):=hash(0.0)` + * `hash(x):=hash(NAN)` for any not a number `x`. + * `x is equal y <=> x==y || (x!=x && y!=y)` + +A consequence of the above rule, that the equivalence classes of `{0.0, -0.0}` and `e{x | x is not a number}` have more than one element. In the set these classes are represented by the first seen element from the class. + +The above holds also for `PyObjectSet` (this behavior is not the same as fro Python-`set` which shows a different behavior for nans). + +### Examples: + +#### Hash sets + +Python: Creates a set from a numpy-array and looks up whether an element is in the resulting set: + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer + >>> a = np.arange(42, dtype=np.int64) + >>> my_set = Int64Set_from_buffer(a) # no reallocation will be needed + >>> 41 in my_set + True + >>> 42 not in my_set + True + +Python: Create a set from an iterable and looks up whether an element is in the resulting set: + + >>> from cykhash import Int64Set_from + >>> my_set = Int64Set_from(range(42)) # no reallocation will be needed + >>> assert 41 in my_set and 42 not in my_set + +Cython: Create a set and put some values into it: + + from cykhash.khashsets cimport Int64Set + my_set = Int64Set(number_of_elements_hint=12) # reserve place for at least 12 integers + cdef Py_ssize_t i + for i in range(12): + my_set.add(i) + assert 11 in my_set and 12 not in my_set + +#### Hash maps + +Python: Creating `int64->float64` map using `Int64toFloat64Map_from_buffers`: + + >>> import numpy as np + >>> from cykhash import Int64toFloat64Map_from_buffers + >>> keys = np.array([1, 2, 3, 4], dtype=np.int64) + >>> vals = np.array([5, 6, 7, 8], dtype=np.float64) + >>> my_map = Int64toFloat64Map_from_buffers(keys, vals) # there will be no reallocation + >>> assert my_map[4] == 8.0 + +Python: Creating `int64->int64` map from scratch: + + >>> import numpy as np + >>> from cykhash import Int64toInt64Map + + # my_map will not need reallocation for at least 12 elements + >>> my_map = Int64toInt64Map(number_of_elements_hint=12) + >>> for i in range(12): my_map[i] = i+1 + >>> assert my_map[5] == 6 + + +#### isin + +Python: Creating look-up data structure from a numpy-array, performing `isin`-query + + >>> import numpy as np + >>> from cykhash import Int64Set_from_buffer, isin_int64 + >>> a = np.arange(42, dtype=np.int64) + >>> lookup = Int64Set_from_buffer(a) + + >>> b = np.arange(84, dtype=np.int64) + >>> result = np.empty(b.size, dtype=np.bool_) + + >>> isin_int64(b, lookup, result) # running time O(b.size) + >>> assert np.sum(result.astype(np.int_)) == 42 + + +#### unique + +Python: using `unique_int64`: + + >>> import numpy as np + >>> from cykhash import unique_int64 + >>> a = np.array([1,2,3,3,2,1], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_int64(a)) # there will be no reallocation + >>> assert set(u) == {1,2,3} + +Python: using `unique_stable_int64`: + + >>> import numpy as np + >>> from cykhash import unique_stable_int64 + >>> a = np.array([3,2,1,1,2,3], dtype=np.int64) + >>> u = np.ctypeslib.as_array(unique_stable_int64(a)) # there will be no reallocation + >>> assert list(u) == [3,2,1] + + + +## API + +See (https://github.com/realead/cykhash/blob/master/doc/README_API.md) for a more detailed API description. + +## Performance + +See (https://github.com/realead/cykhash/blob/master/doc/README_PERFORMANCE.md) for results of performance tests. + +## Trivia + +* This project was inspired by the following stackoverflow question: https://stackoverflow.com/questions/50779617/pandas-pd-series-isin-performance-with-set-versus-array. + +* pandas also uses `khash` (and thus was a source of inspiration), but wraps only maps and doesn't wrap sets. Thus, pandas' `unique` needs more memory as it should. Those maps are also never exposed, so there is no way to reuse the look-up structure for multiple calls to `isin`. + +* `khash` is a good choice, but there are other alternatives, e.g. https://github.com/sparsehash/sparsehash. See also https://stackoverflow.com/questions/48129713/fastest-way-to-find-all-unique-elements-in-an-array-with-cython/48142655#48142655 for a comparison for different `unique` implementations. + +* A similar approach for sets/maps in pure Cython: https://github.com/realead/tighthash, which is quite slower than khash. + +* There is no dependency on `numpy`: this library uses buffer protocol, thus it works for `array.array`, `numpy.ndarray`, `ctypes`-arrays and anything else. However, some interfaces are somewhat cumbersome (which type should be created as answer?) and for convenient usage it might be a good idea to wrap the functionality so objects of right types are created. + +## Compatibility between cykhash-versions: + +There are different levels of compatibility: + + * for code using only pure python interface + * for code using cython/cdef-interface and built against a particular cykash version + +Ther rules are as follows: + + * there is no warranty for major versions mismatch: i.e. code written with cykhash `1.x.y` might not run with cykhash `2.z.w` and vice versa. + * if only pure python interface is used, code for the same major version will ran for version with higher minor version, i.e. code for cykhash `2.0.x` will run with cykhash `2.1.y` (but not the other way around: that means new functions could be added to pure python interface) + * if cython's `cdef` interface is used, i.e. a cython-extension was build using pxi-files from cykhash, then versions are compartible only if the the minor versions are the same, e.g. `2.0.x` could be replaced by `2.0.y` in the installation, but when replacing with `2.1.z` the dependent cython-extension must be rebuilt. + +## History: +### Release 2.0.1 (05.02.2022): + + * Tests work for Python 3.11 + * Tests work for numpy 1.24 + * Drops support for Python 3.6 and Python 3.7 + +#### Release 2.0.0 (09.11.2021): + + * Implementation of `any`, `all`, `none` and `count_if` + * Hash-sets are now (almost) drop-in replacements of Python's sets + * Breaking change: iterator from maps doesn't no longer returns items but only keys. However there are following new methods `keys()`, `values()` and `items()`which return so called mapvies, which correspond more or less to dictviews (but for mapsview doesn't hold that "Dictionary order is guaranteed to be insertion order."). + * Hash-Maps are now (almost) drop-in replacements of Python's dicts. Differences: insertion order isn't preserved, thus there is also no `reversed()`-method, `setdefault(key, default)` isn't possible without `default` because `None` cannot be inserted in the map + * Better hash-functions for float64, float32, int64 and int32 (gh-issue #4). + * Breaking change: different names/signatures for maps + * supports tracemalloc for Py3.6+ + * supports Python 3.10 + +#### Release 1.0.2 (30.05.2020): + + * can be installed via conda-forge to all operating systems + * can be installed via pip in a clean environment (Cython>=0.28 is now fetched automatically) + +#### Release 1.0.1 (27.05.2020): + + * released on PyPi + +#### Older: + + * 0.4.0: uniques_stable, preparing for release + * 0.3.0: PyObjectSet, Maps for Int64/32 and also Float64/32, unique-versions + * 0.2.0: Int32Set, Float64Set, Float32Set + * 0.1.0: Int64Set + + + + + +%prep +%autosetup -n cykhash-2.0.1 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-cykhash -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 2.0.1-1 +- Package Spec generated @@ -0,0 +1 @@ +6ad6a480531dc3cf1083cbc45b8ddd35 cykhash-2.0.1.tar.gz |
