(updated) Make pickleable and allow data_array to be retrieved and set

MANIFEST.in

@@ -1,6 +1,6 @@
 include CHANGELOG
 include LICENSE
 include AUTHORS
-include README.markdown
+include README.md
 recursive-include src *
 recursive-include tests *

README.markdown → README.md

@@ -10,20 +10,19 @@ The goal of `pybloomfiltermmap3` is simple: to provide a fast, simple, scalable,
 [![PyPI](https://img.shields.io/pypi/dw/pybloomfiltermmap3.svg)](https://pypi.python.org/pypi/pybloomfiltermmap3)
 [![PyPI](https://img.shields.io/pypi/pyversions/pybloomfiltermmap3.svg)](https://pypi.python.org/pypi/pybloomfiltermmap3)
 
-
 ## Why pybloomfiltermmap3?
 
 There are a couple reasons to use this module:
 
-* It natively uses [mmaped files](http://en.wikipedia.org/wiki/Mmap).
-* It is fast (see [benchmarks](http://axiak.github.io/pybloomfiltermmap/#benchmarks)).
-* It natively does the set things you want a Bloom filter to do.
-
+- It natively uses [mmapped files](http://en.wikipedia.org/wiki/Mmap).
+- It is fast (see [benchmarks](http://axiak.github.io/pybloomfiltermmap/#benchmarks)).
+- It natively does the set things you want a Bloom filter to do.
 
 ## Quickstart
 
 After you install, the interface to use is a cross between a file
 interface and an ste interface. As an example:
+
 ```python
     >>> import pybloomfilter
     >>> fruit = pybloomfilter.BloomFilter(100000, 0.1, '/tmp/words.bloom')
@@ -37,23 +36,36 @@ interface and an ste interface. As an example:
 ```
 
 To create an in-memory filter, simply omit the file location:
+
+```python
+    >>> fruit = pybloomfilter.BloomFilter(10000, 0.1)
+    >>> fruit.add('apple')
+    >>> 'apple' in fruit
+    True
+```
+
+These in-memory filters can be pickled and reloaded:
+
 ```python
-    >>> cakes = pybloomfilter.BloomFilter(10000, 0.1)
+    >>> import pickle
+    >>> pickled_fruit = pickle.dumps(fruit)
+    >>> unpickled_fruit = pickle.loads(pickled_fruit)
+    >>> 'apple' in unpickled_fruit
+    True
 ```
-*Caveat*: it is currently not possible to persist this filter later.
 
+_Caveat_: it is currently not possible to persist this filter later as an mmap file.
 
 ## Docs
 
 Current docs are available at [pybloomfiltermmap3.rtfd.io](https://pybloomfiltermmap3.readthedocs.io/en/latest).
 
-
 ## Install
 
 To install:
 
-```shell
-    $ pip install pybloomfiltermmap3
+```bash
+pip install pybloomfiltermmap3
 ```
 
 and you should be set.
@@ -62,7 +74,6 @@ and you should be set.
 
 This library is specifically meant for Python 3.5 and above. [As of 2020](https://www.python.org/doc/sunset-python-2/), we strongly advise you to switch to an actively maintained distribution of Python 3. If for any reason your current environment is restricted to Python 2, please see [pybloomfiltermmap](https://github.com/axiak/pybloomfiltermmap). Please note that the latter is not actively maintained and will lack bug fixes and new features.
 
-
 ## History and Future
 
 [pybloomfiltermmap](https://github.com/axiak/pybloomfiltermmap) is an excellent Bloom filter implementation for Python 2 by [@axiak](https://github.com/axiak) and contributors. I, [@prashnts](https://github.com/prashnts), made initial changes to add support for Python 3 sometime in 2016 as the current [pybloomfiltermmap3](https://pypi.org/project/pybloomfiltermmap3/) on `PyPI`. Since then, with the help of contributors, there have been incremental improvements and bug fixes while maintaining the API from versions `0.4.x` and below.
@@ -71,18 +82,47 @@ Some new features and changes were first introduced in version `0.5.0`. From thi
 
 Suggestions, bug reports, and / or patches are welcome!
 
-
 ## Contributions and development
 
 When contributing, you should set up an appropriate Python 3 environment and install the dependencies listed in `requirements-dev.txt`.
 Package installation depends on a generated `pybloomfilter.c` file, which requires Cython module to be in your current environment.
 
+### Environment setup
 
-## Maintainers
+```bash
+# Installs the venv and python3-dev packages
+sudo apt install python3.10-venv python3-dev
+
+# Creates a virtual env called "env"
+python -m venv env
+
+# Activates the created virtual env
+source ./env/bin/activate
+```
+
+### Dependencies
+
+```bash
+python -m pip install --upgrade pip
+pip install cython
+```
 
-* [Prashant Sinha](https://github.com/prashnts)
-* [Vytautas Mizgiris](https://github.com/vmizg)
+### Build
+
+```bash
+python setup.py develop
+```
+
+### Test
+
+```bash
+python setup.py test
+```
+
+## Maintainers
 
+- [Prashant Sinha](https://github.com/prashnts)
+- [Vytautas Mizgiris](https://github.com/vmizg)
 
 ## License
 

setup.py

@@ -9,7 +9,7 @@
 here = os.path.dirname(__file__)
 
 # Get the long description from the README file
-with open(os.path.join(here, "README.markdown"), encoding="utf-8") as fp:
+with open(os.path.join(here, "README.md"), encoding="utf-8") as fp:
     long_description = fp.read()
 
 setup_kwargs = {}

src/bloomfilter.c

@@ -9,7 +9,7 @@
 #include "bloomfilter.h"
 
 BloomFilter *bloomfilter_Create_Malloc(size_t max_num_elem, double error_rate,
-                                BTYPE num_bits, int *hash_seeds, int num_hashes)
+                                BTYPE num_bits, int *hash_seeds, int num_hashes, const char *data)
 {
     BloomFilter * bf = (BloomFilter *)malloc(sizeof(BloomFilter));
     MBArray * array;
@@ -35,6 +35,9 @@ BloomFilter *bloomfilter_Create_Malloc(size_t max_num_elem, double error_rate,
         bloomfilter_Destroy(bf);
         return NULL;
     }
+    if (data) {
+        memcpy(array->vector, data, num_bits / 8);
+    }
 
     bf->array = array;
 

src/bloomfilter.h

@@ -28,7 +28,7 @@ typedef struct _BloomFilter BloomFilter;
 
 /* Create a bloom filter without a memory-mapped file backing it */
 BloomFilter *bloomfilter_Create_Malloc(size_t max_num_elem, double error_rate,
-                                BTYPE num_bits, int *hash_seeds, int num_hashes);
+                                BTYPE num_bits, int *hash_seeds, int num_hashes, const char * data);
 
 /* Create a bloom filter with a memory-mapped file backing it */
 BloomFilter *bloomfilter_Create_Mmap(size_t max_num_elem, double error_rate,

src/cbloomfilter.pxd

@@ -48,7 +48,7 @@ cdef extern from "bloomfilter.h":
      BloomFilter * bloomfilter_Create_Malloc(long max_num_elem,
                                       double error_rate,
                                       long num_bits,
-                                      int * hash_seeds, int num_hashes)
+                                      int * hash_seeds, int num_hashes, char * data)
      void bloomfilter_Destroy(BloomFilter * bf)
      int bloomfilter_Add(BloomFilter * bf, Key * key)
      int bloomfilter_Test(BloomFilter * bf, Key * key)

src/pybloomfilter.pyx

@@ -5,7 +5,6 @@ AUTHOR = "Michael Axiak"
 
 __VERSION__ = VERSION
 
-
 cimport cbloomfilter
 cimport cpython
 
@@ -62,6 +61,9 @@ cdef class BloomFilter:
     :param list hash_seeds: optionally specify hash seeds to use for the
         hashing algorithm. Each hash seed must not exceed 32 bits. The number
         of hash seeds will determine the number of hashes performed.
+    :param bytes data_array: optionally specify the filter data array, same as
+        given by BloomFilter.data_array. Only valid for in-memory bloomfilters.
+        If provided, hash_seeds must be given too.
 
     **Note that we do not check capacity.** This is important, because
     we want to be able to support logical OR and AND (see :meth:`BloomFilter.union`
@@ -80,20 +82,35 @@ cdef class BloomFilter:
     cdef int _in_memory
     cdef int _oflags
 
-    def __cinit__(self, capacity, error_rate, filename=None, perm=0755, hash_seeds=None):
+    def __reduce__(self):
+        """Makes an in-memory BloomFilter pickleable."""
+        callable = BloomFilter
+        args = (self.capacity, self.error_rate, None, None, self.hash_seeds, self.data_array)
+        return (callable, args)
+
+
+    def __cinit__(self, capacity, error_rate, filename=None, perm=0755, hash_seeds=None, data_array=None):
         self._closed = 0
         self._in_memory = 0
         self._oflags = os.O_RDWR
 
         if capacity is NoConstruct:
             return
 
-        self._create(capacity, error_rate, filename, perm, hash_seeds)
+        self._create(capacity, error_rate, filename, perm, hash_seeds, data_array)
+
 
-    def _create(self, capacity, error_rate, filename=None, perm=0755, hash_seeds=None):
+    def _create(self, capacity, error_rate, filename=None, perm=0755, hash_seeds=None, data_array=None):
         cdef char * seeds
+        cdef char * data = NULL
         cdef long long num_bits
 
+        if data_array is not None:
+            if filename:
+                raise ValueError("data_array cannot be used for an mmapped filter.")
+            if hash_seeds is None:
+                raise ValueError("hash_seeds must be specified if a data_array is provided.")
+
         # Make sure that if the filename is defined, that the
         # file exists
         if filename and os.path.exists(filename):
@@ -135,6 +152,10 @@ cdef class BloomFilter:
         # Minimum bit vector of 128 bits
         num_bits = max(num_hashes * bits_per_hash,128)
 
+        # Override calculated capacity if we are provided a data array
+        if data_array is not None:
+            num_bits = 8 * len(data_array)
+
         # print("k = %d  m = %d  n = %d   p ~= %.8f" % (
         #     num_hashes, num_bits, capacity,
         #     (1.0 - math.exp(- float(num_hashes) * float(capacity) / num_bits))
@@ -153,18 +174,21 @@ cdef class BloomFilter:
                                                     num_hashes)
         else:
             self._in_memory = 1
+            if data_array is not None:
+                data = data_array
             self._bf = cbloomfilter.bloomfilter_Create_Malloc(capacity,
                                                     error_rate,
                                                     num_bits,
                                                     <int *>seeds,
-                                                    num_hashes)
+                                                    num_hashes, <const char *>data)
         if self._bf is NULL:
             if filename:
                 raise OSError(errno, '%s: %s' % (os.strerror(errno),
                                                     filename))
             else:
                 cpython.PyErr_NoMemory()
 
+
     def _open(self, filename, mode="rw"):
         # Should not overwrite
         mode = mode.replace("+", "")
@@ -202,6 +226,19 @@ cdef class BloomFilter:
         arr = (<char *>cbloomfilter.mbarray_CharData(self._bf.array))[start_pos:end_pos]
         return int.from_bytes(arr, byteorder="big", signed=False)
 
+    @property
+    def data_array(self):
+        """Bytes array of the Bloom filter contents.
+        """
+        self._assert_open()
+        start_pos = self._bf.array.preamblebytes
+        end_pos = start_pos + self._bf.array.bytes 
+        arr = array.array('B')
+        arr.frombytes(
+            (<char *>cbloomfilter.mbarray_CharData(self._bf.array))[start_pos:end_pos]
+        )
+        return bytes(arr)
+
     @property
     def hash_seeds(self):
         """Integer seeds used for the random hashing. Returns a list of integers."""
@@ -345,6 +382,7 @@ cdef class BloomFilter:
             key.shash = item
             key.nhash = len(item)
         else:
+            # Warning! Only works reliably for objects whose hash is based on value not memory address.
             item = item_
             key.shash = NULL
             key.nhash = hash(item)

tests/simpletest.py

@@ -2,6 +2,7 @@
 import string
 import unittest
 import tempfile
+import pickle
 from random import randint, choice, getrandbits
 
 import pybloomfilter
@@ -400,6 +401,19 @@ def test_approximate_size_after_union_called(self):
         intersection = len(bf1) + len(bf2) - len(union_bf)
         assert intersection == 11  # approximate size
 
+    def test_pickle(self):
+        bf = pybloomfilter.BloomFilter(100, 0.1)
+        bf.add('apple')
+        assert 'apple' in bf
+        assert 'hello' not in bf
+
+        pickled = pickle.dumps(bf)
+        unpickled = pickle.loads(pickled)
+        assert 'apple' in unpickled
+        assert 'hello' not in unpickled
+
+        # Expecting same hashing sequence
+        self.assertEqual(bf.bit_array, unpickled.bit_array)
 
 def suite():
     suite = unittest.TestSuite()