Increase speed of Delta encoding using np.subtract

[ehgus]

This PR accelerated Delta encoding by replacing np.diff into np.subtract.
Using inplace operation of np.subtract reduce array creation time.

Here is a simple benchmark:

from numcodecs import Delta
from numcodecs.compat import ensure_ndarray
import numpy as np
import time

# new codec
class CustomDelta(Delta):
    def encode(self, buf):
        arr = ensure_ndarray(buf).view(self.dtype)
        arr = arr.reshape(-1, order='A')
        enc = np.empty_like(arr, dtype=self.astype)
        enc[0] = arr[0]

        # only difference from Delta!!
        np.subtract(arr[1:], arr[0:-1], out = enc[1:])

        return enc

data_length = int(1e9)
x = np.random.randint(0,10000,(data_length,),dtype='i4')

# benchmark
base_codec = Delta(dtype='i4')
new_codec = CustomDelta(dtype='i4')
for codec in (base_codec, new_codec):
    time_start = time.perf_counter()
    for _ in range(10):
        codec.encode(x)
    time_end = time.perf_counter()
    benchmark_time = (time_end-time_start)/10
    print(f'time of {str(codec)} = {benchmark_time:.6f}')
# time of Delta(dtype='<i4') = 1.510299
# time of CustomDelta(dtype='<i4') = 0.953429

assert np.all(base_codec.encode(x) == new_codec.encode(x)), 'They should be equal'

TODO:

• Unit tests and/or doctests in docstrings
• Tests pass locally
• Changes documented in docs/release.rst
• Docs build locally
• GitHub Actions CI passes
• Test coverage to 100% (Codecov passes)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.91%. Comparing base (e836f39) to head (61e4298).
Report is 62 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #584   +/-   ##
=======================================
  Coverage   99.91%   99.91%           
=======================================
  Files          59       59           
  Lines        2332     2332           
=======================================
  Hits         2330     2330           
  Misses          2        2           

Files with missing lines	Coverage Δ
numcodecs/delta.py	100.00% <100.00%> (ø)

[dstansby]

Looks good to me 👍 - could you just leave a comment above the line you changed explaining that you're using subtract for speed, otherwise someone might come along later and switch it back 🙈

[ehgus]

Sure! I will leave a comment.

[jakirkham]

Thanks Lee and David! 🙏

This is a good improvement. Always good to avoid unneeded array creation and copies 🙂

Noticed that bool needs a bit of extra handling. This wasn't tested previously. Idk to what extent it is used (maybe Delta + PackBits is effective in some cases?). Still it seems like a good idea to keep that case working given it is low effort. Made a small tweak to this effect with a test in PR: #595

[bnavigator]

Breaks zarr: #653