Merge remote-tracking branch 'origin/develop' into fixints

Author: rhpvorderman

.github/workflows/ci.yml

@@ -44,6 +44,25 @@ jobs:
         run: tox -e docs
         env:
           PYTHON_ISAL_LINK_DYNAMIC: True
+  mypy:
+    needs: lint
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/[email protected]
+        with:
+          submodules: recursive
+      - name: Set up Python 3.6
+        uses: actions/[email protected]
+        with:
+          python-version: 3.6
+      - name: Install isal
+        run: sudo apt-get install libisal-dev
+      - name: Install tox and upgrade setuptools and pip
+        run: pip install --upgrade tox setuptools pip
+      - name: Mypy checks
+        run: tox -e mypy
+        env:
+          PYTHON_ISAL_LINK_DYNAMIC: True
   twine_check:
     needs: lint
     runs-on: ${{ matrix.os }}

CHANGELOG.rst

@@ -9,6 +9,8 @@ Changelog
 
 version 0.5.0-dev
 -----------------
++ Provided stubs (type-hint files) for ``isal_zlib`` and ``_isal`` modules.
+  Package is now tested with mypy to ensure correct type information.
 + The command-line interface now reads in blocks of 32K instead of 8K. This
   improves performance by about 6% when compressing and 11% when decompressing.
   A hidden ``-b`` flag was added to adjust the buffer size for benchmarks.

setup.py

@@ -128,7 +128,7 @@ def build_isa_l():
     zip_safe=False,
     packages=find_packages('src'),
     package_dir={'': 'src'},
-    package_data={'isal': ['*.pxd', '*.pyx',
+    package_data={'isal': ['*.pxd', '*.pyx', '*.pyi', 'py.typed',
                            # Include isa-l LICENSE and other relevant files
                            # with the binary distribution.
                            'isa-l/LICENSE', 'isa-l/README.md',

src/isal/_isal.pyi

@@ -0,0 +1,24 @@
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+ISAL_MAJOR_VERSION: int
+ISAL_MINOR_VERSION: int
+ISAL_PATCH_VERSION: int
+ISAL_VERSION: str

src/isal/igzip.py

@@ -36,7 +36,7 @@
 _COMPRESS_LEVEL_BEST = isal_zlib.ISAL_BEST_COMPRESSION
 
 try:
-    BadGzipFile = gzip.BadGzipFile
+    BadGzipFile = gzip.BadGzipFile  # type: ignore
 except AttributeError:  # Versions lower than 3.8 do not have BadGzipFile
     BadGzipFile = OSError
 
@@ -76,7 +76,8 @@ def open(filename, mode="rb", compresslevel=_COMPRESS_LEVEL_TRADEOFF,
             raise ValueError("Argument 'newline' not supported in binary mode")
 
     gz_mode = mode.replace("t", "")
-    if isinstance(filename, (str, bytes, os.PathLike)):
+    # __fspath__ method is os.PathLike
+    if isinstance(filename, (str, bytes)) or hasattr(filename, "__fspath__"):
         binary_file = IGzipFile(filename, gz_mode, compresslevel)
     elif hasattr(filename, "read") or hasattr(filename, "write"):
         binary_file = IGzipFile(None, gz_mode, compresslevel, filename)

src/isal/isal_zlib.pyi

@@ -0,0 +1,75 @@
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+ISAL_BEST_SPEED: int
+ISAL_BEST_COMPRESSION: int
+ISAL_DEFAULT_COMPRESSION: int
+Z_BEST_SPEED: int
+Z_BEST_COMPRESSION: int
+Z_DEFAULT_COMPRESSION: int
+
+DEF_BUF_SIZE: int
+DEF_MEM_LEVEL: int
+MAX_WBITS: int
+ISAL_DEFAULT_HIST_BITS: int
+
+DEFLATED: int
+
+Z_DEFAULT_STRATEGY: int
+Z_RLE: int
+Z_HUFFMAN_ONLY: int
+Z_FILTERED: int
+Z_FIXED: int
+
+ISAL_NO_FLUSH: int
+ISAL_SYNC_FLUSH: int
+ISAL_FULL_FLUSH: int
+
+Z_NO_FLUSH: int
+Z_SYNC_FLUSH: int
+Z_FINISH: int
+
+class IsalError(OSError): ...
+
+error: IsalError
+
+def adler32(data, value: int = ...) -> int: ...
+def crc32(data, value: int = ...) -> int: ...
+
+def compress(data, level: int = ..., wbits: int = ...) -> bytes: ...
+def decompress(data, wbits: int = ..., bufsize: int = ...) -> bytes: ...
+
+class Compress:
+    def compress(self, data) -> bytes: ...
+    def flush(self, mode: int = ...) -> bytes: ...
+
+class Decompress:
+    unused_data: bytes
+    unconsumed_tail: bytes
+    eof: bool
+    crc: int
+
+    def decompress(self, data, max_length: int = ...) -> bytes: ...
+    def flush(self, length: int = ...) -> bytes: ...
+
+def compressobj(level: int = ..., method: int = ..., wbits: int = ...,
+                memLevel: int = ..., strategy: int = ..., zdict = ...
+                ) -> Compress: ...
+def decompressobj(wbits: int = ..., zdict = ...) -> Decompress: ...

src/isal/py.typed

@@ -0,0 +1,21 @@
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+# Marker file for PEP 561.

tests/test_gzip_compliance.py

@@ -26,8 +26,8 @@
 import tempfile
 import unittest
 from subprocess import PIPE, Popen
-from test.support import _4G, bigmemtest
-from test.support.script_helper import assert_python_failure, assert_python_ok
+from test.support import _4G, bigmemtest  # type: ignore
+from test.support.script_helper import assert_python_failure, assert_python_ok  # type: ignore  # noqa: E501
 
 from isal import igzip
 

tests/test_zlib_compliance.py

@@ -19,8 +19,8 @@
 import random
 import sys
 import unittest
-from test import support
-from test.support import _1G, _4G, bigmemtest
+from test import support  # type: ignore
+from test.support import _1G, _4G, bigmemtest  # type: ignore
 
 import isal
 from isal import isal_zlib

tox.ini

@@ -41,12 +41,17 @@ commands=
 [testenv:lint]
 deps=flake8
      flake8-import-order
-     mypy
-# Linting does not need the installed package.
-skip_install=true
+skip_install=True
 commands =
     flake8 src tests setup.py benchmark.py
 
+[testenv:mypy]
+# pytest dep needed for mypy check
+deps=mypy
+     pytest
+commands =
+    mypy src/ tests/
+
 # Documentation should build on python version 3
 [testenv:docs]
 deps=-r requirements-docs.txt