Use new ByteRequest syntax and raise NotImplementedError on pickling

.github/workflows/gpu_test.yml

@@ -55,7 +55,7 @@ jobs:
         cache: 'pip'
     - name: Install Hatch and CuPy
       run: |
-        python -m pip install --upgrade pip 
+        python -m pip install --upgrade pip
         pip install hatch
     - name: Set Up Hatch Env
       run: |

.github/workflows/releases.yml

@@ -23,7 +23,7 @@ jobs:
 
       - name: Install PyBuild
         run: |
-          python -m pip install --upgrade pip 
+          python -m pip install --upgrade pip
           pip install hatch
       - name: Build wheel and sdist
         run: hatch build
@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/[email protected].2
+      - uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/test.yml

@@ -52,15 +52,20 @@ jobs:
         cache: 'pip'
     - name: Install Hatch
       run: |
-        python -m pip install --upgrade pip 
+        python -m pip install --upgrade pip
         pip install hatch
     - name: Set Up Hatch Env
       run: |
         hatch env create test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }}
         hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run
+        hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage
+    - name: Upload coverage
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true # optional (default = false)
 
   test-upstream-and-min-deps:
     name: py=${{ matrix.python-version }}-${{ matrix.dependency-set }}
@@ -84,7 +89,7 @@ jobs:
         cache: 'pip'
     - name: Install Hatch
       run: |
-        python -m pip install --upgrade pip 
+        python -m pip install --upgrade pip
         pip install hatch
     - name: Set Up Hatch Env
       run: |
@@ -93,3 +98,47 @@ jobs:
     - name: Run Tests
       run: |
         hatch env run --env ${{ matrix.dependency-set }} run
+
+  doctests:
+    name: doctests
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.13'
+        cache: 'pip'
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Set Up Hatch Env
+      run: |
+        hatch env create doctest
+        hatch env run -e doctest list-env
+    - name: Run Tests
+      run: |
+        hatch env run --env doctest run
+
+  test-complete:
+    name: Test complete
+
+    needs:
+      [
+        test,
+        test-upstream-and-min-deps,
+        doctests
+      ]
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check failure
+        if: |
+          contains(needs.*.result, 'failure') ||
+          contains(needs.*.result, 'cancelled')
+        run: exit 1
+      - name: Success
+        run: echo Success!

.gitignore

@@ -51,7 +51,10 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
-docs/_autoapi
+docs/api
+docs/data
+data
+data.zip
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -1,13 +1,12 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autoupdate_schedule: "monthly"
   autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
 default_stages: [pre-commit, pre-push]
-default_language_version:
-  python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.8.6
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -16,23 +15,23 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-        args: ["-L", "ba,ihs,kake,nd,noe,nwo,te,fo,zar", "-S", "fixture"]
+        args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-      - id: check-yaml
+    - id: check-yaml
+    - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         files: src|tests
         additional_dependencies:
           # Package dependencies
-          - asciitree
-          - crc32c
+          - packaging
           - donfig
-          - numcodecs
-          - numpy
+          - numcodecs[crc32c]
+          - numpy==2.1  # until https://github.com/numpy/numpy/issues/28034 is resolved
           - typing_extensions
           - universal-pathlib
           - obstore==0.3.0-beta.8

bench/compress_normal.txt

@@ -19,7 +19,7 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
 ==============================================================
    137                                           def compress(source, char* cname, int clevel, int shuffle):
    138                                               """Compress data in a numpy array.
-   139                                           
+   139
    140                                               Parameters
    141                                               ----------
    142                                               source : array-like
@@ -30,33 +30,33 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
    147                                                   Compression level.
    148                                               shuffle : int
    149                                                   Shuffle filter.
-   150                                           
+   150
    151                                               Returns
    152                                               -------
    153                                               dest : bytes-like
    154                                                   Compressed data.
-   155                                           
+   155
    156                                               """
-   157                                           
+   157
    158                                               cdef:
    159                                                   char *source_ptr
    160                                                   char *dest_ptr
    161                                                   Py_buffer source_buffer
    162                                                   size_t nbytes, cbytes, itemsize
    163       200          506      2.5      0.2          array.array char_array_template = array.array('b', [])
    164                                                   array.array dest
-   165                                           
+   165
    166                                               # setup source buffer
    167       200          458      2.3      0.2      PyObject_GetBuffer(source, &source_buffer, PyBUF_ANY_CONTIGUOUS)
    168       200          119      0.6      0.0      source_ptr = <char *> source_buffer.buf
-   169                                           
+   169
    170                                               # setup destination
    171       200          239      1.2      0.1      nbytes = source_buffer.len
    172       200          103      0.5      0.0      itemsize = source_buffer.itemsize
    173       200         2286     11.4      0.8      dest = array.clone(char_array_template, nbytes + BLOSC_MAX_OVERHEAD,
    174                                                                  zero=False)
    175       200          129      0.6      0.0      dest_ptr = <char *> dest.data.as_voidptr
-   176                                           
+   176
    177                                               # perform compression
    178       200         1734      8.7      0.6      if _get_use_threads():
    179                                                   # allow blosc to use threads internally
@@ -67,24 +67,24 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
    184                                                       cbytes = blosc_compress(clevel, shuffle, itemsize, nbytes,
    185                                                                               source_ptr, dest_ptr,
    186                                                                               nbytes + BLOSC_MAX_OVERHEAD)
-   187                                           
+   187
    188                                               else:
    189                                                   with nogil:
    190                                                       cbytes = blosc_compress_ctx(clevel, shuffle, itemsize, nbytes,
    191                                                                                   source_ptr, dest_ptr,
    192                                                                                   nbytes + BLOSC_MAX_OVERHEAD, cname,
    193                                                                                   0, 1)
-   194                                           
+   194
    195                                               # release source buffer
    196       200          616      3.1      0.2      PyBuffer_Release(&source_buffer)
-   197                                           
+   197
    198                                               # check compression was successful
    199       200          120      0.6      0.0      if cbytes <= 0:
    200                                                   raise RuntimeError('error during blosc compression: %d' % cbytes)
-   201                                           
+   201
    202                                               # resize after compression
    203       200         1896      9.5      0.6      array.resize(dest, cbytes)
-   204                                           
+   204
    205       200          186      0.9      0.1      return dest
 
 *******************************************************************************
@@ -100,19 +100,19 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
 ==============================================================
     75                                           def decompress(source, dest):
     76                                               """Decompress data.
-    77                                           
+    77
     78                                               Parameters
     79                                               ----------
     80                                               source : bytes-like
     81                                                   Compressed data, including blosc header.
     82                                               dest : array-like
     83                                                   Object to decompress into.
-    84                                           
+    84
     85                                               Notes
     86                                               -----
     87                                               Assumes that the size of the destination buffer is correct for the size of
     88                                               the uncompressed data.
-    89                                           
+    89
     90                                               """
     91                                               cdef:
     92                                                   int ret
@@ -122,7 +122,7 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
     96                                                   array.array source_array
     97                                                   Py_buffer dest_buffer
     98                                                   size_t nbytes
-    99                                           
+    99
    100                                               # setup source buffer
    101       200          573      2.9      0.2      if PY2 and isinstance(source, array.array):
    102                                                   # workaround fact that array.array does not support new-style buffer
@@ -134,13 +134,13 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
    108       200          112      0.6      0.0          release_source_buffer = True
    109       200          144      0.7      0.1          PyObject_GetBuffer(source, &source_buffer, PyBUF_ANY_CONTIGUOUS)
    110       200           98      0.5      0.0          source_ptr = <char *> source_buffer.buf
-   111                                           
+   111
    112                                               # setup destination buffer
    113       200          552      2.8      0.2      PyObject_GetBuffer(dest, &dest_buffer,
    114                                                                  PyBUF_ANY_CONTIGUOUS | PyBUF_WRITEABLE)
    115       200          100      0.5      0.0      dest_ptr = <char *> dest_buffer.buf
    116       200           84      0.4      0.0      nbytes = dest_buffer.len
-   117                                           
+   117
    118                                               # perform decompression
    119       200         1856      9.3      0.8      if _get_use_threads():
    120                                                   # allow blosc to use threads internally
@@ -149,12 +149,12 @@ Line #      Hits         Time  Per Hit   % Time  Line Contents
    123                                               else:
    124                                                   with nogil:
    125                                                       ret = blosc_decompress_ctx(source_ptr, dest_ptr, nbytes, 1)
-   126                                           
+   126
    127                                               # release buffers
    128       200          754      3.8      0.3      if release_source_buffer:
    129       200          326      1.6      0.1          PyBuffer_Release(&source_buffer)
    130       200          165      0.8      0.1      PyBuffer_Release(&dest_buffer)
-   131                                           
+   131
    132                                               # handle errors
    133       200          128      0.6      0.1      if ret <= 0:
    134                                                   raise RuntimeError('error during blosc decompression: %d' % ret)

codecov.yml

@@ -0,0 +1,10 @@
+coverage:
+  status:
+    patch:
+      default:
+        target: auto
+    project:
+      default:
+        target: auto
+        threshold: 0.1
+comment: false

docs/Makefile

@@ -52,7 +52,7 @@ help:
 .PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
-	rm -rf $(BUILDDIR)/../_autoapi
+	rm -rf $(BUILDDIR)/../api
 
 .PHONY: html
 html: