Merge pull request #209 from pycompression/release_1.7.0

rhpvorderman · web-flow · commit 58778eb5327c · 2024-08-09T14:19:53.000+02:00
Release 1.7.0
diff --git a/.github/release_checklist.md b/.github/release_checklist.md
@@ -2,9 +2,7 @@ Release checklist
 - [ ] Check outstanding issues on JIRA and Github.
 - [ ] Check [latest documentation](https://python-isal.readthedocs.io/en/latest/) looks fine.
 - [ ] Create a release branch.
-  - [ ] Set version to a stable number.
   - [ ] Change current development version in `CHANGELOG.rst` to stable version.
-  - [ ] Change the version in `__init__.py`
 - [ ] Check if the address sanitizer does not find any problems using `tox -e asan`
 - [ ] Merge the release branch into `main`.
 - [ ] Created an annotated tag with the stable version number. Include changes 
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -2,9 +2,6 @@ name: Continous integration
 
 on:
   pull_request:
-    paths-ignore:
-      - 'docs/**'
-      - '*.rst'
   push:
     branches:
       - develop
@@ -16,7 +13,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Set up Python 3.8
@@ -36,7 +33,7 @@ jobs:
           - twine_check
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Set up Python 3.8
@@ -67,12 +64,14 @@ jobs:
           - "pypy-3.10"
         os: ["ubuntu-latest"]
         include:
-          - os: "macos-latest"
-            python-version: 3.8
+          - os: "macos-13"
+            python-version: "3.8"
+          - os: "macos-14"
+            python-version: "3.10"
           - os: "windows-latest"
-            python-version: 3.8
+            python-version: "3.8"
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Set up Python ${{ matrix.python-version }}
@@ -108,7 +107,7 @@ jobs:
         python_version:
           - "3.8"
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - uses: uraimo/run-on-arch-action@v2.5.0
@@ -117,7 +116,11 @@ jobs:
           arch: none
           distro: none
           base_image: "--platform=linux/arm64 quay.io/pypa/manylinux2014_aarch64"
+          # versioningit needs an accessible git repository but the container
+          # is run as root, which is different from the repository user.
+          # use git config to override this.
           run: |-
+            git config --global --add safe.directory $PWD
             CFLAGS="-DNDEBUG -g0" python${{matrix.python_version}} -m pip install . pytest
             python${{matrix.python_version}} -m pytest tests
 
@@ -132,17 +135,17 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        os: ["ubuntu-latest", "macos-13", "windows-latest"]
         python_version: [ "python" ]
         include:
           - os: "ubuntu-latest"
             python_version: "pypy"
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Install miniconda.
-        uses: conda-incubator/setup-miniconda@v2.0.1 # https://github.com/conda-incubator/setup-miniconda.
+        uses: conda-incubator/setup-miniconda@v3 # https://github.com/conda-incubator/setup-miniconda.
         with:
           channels: conda-forge,defaults
       - name: Install requirements (universal)
@@ -168,7 +171,8 @@ jobs:
       matrix:
         os:
           - ubuntu-latest
-          - macos-latest
+          - macos-13
+          - macos-14
           - windows-latest
         cibw_archs_linux: ["x86_64"]
         cibw_before_all_linux:
@@ -186,9 +190,10 @@ jobs:
             cibw_archs_linux: "aarch64"
             cibw_before_all_linux: "true"  # The true command exits with 0
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
+          fetch-depth: 0  # Fetch everything to get accurately versioned tag.
       - uses: actions/setup-python@v2
         name: Install Python
       - name: Install cibuildwheel twine wheel
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
+src/isal/_version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "src/isal/isa-l"]
 	path = src/isal/isa-l
-	url = https://github.com/intel/isa-l.git
+	url = https://github.com/rhpvorderman/isa-l.git
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,6 +7,15 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 1.7.0
+-----------------
++ Include a patched ISA-L version 2.31. The applied patches make compilation
+  and wheelbuilding on MacOS ARM64 possible.
++ Fix a bug where READ and WRITE in isal.igzip were inconsistent with the
+  values in gzip on Python 3.13
++ Small simplifications to the ``igzip.compress`` function, which should lead
+  to less overhead.
+
 version 1.6.1
 -----------------
 + Fix a bug where streams that were passed to igzip_threaded.open where closed.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,2 +1,8 @@
 graft src/isal/isa-l
 include src/isal/*.h
+prune tests
+prune docs
+prune benchmark_scripts
+exclude requirements-docs.txt
+exclude codecov.yml
+exclude .readthedocs.yml
diff --git a/README.rst b/README.rst
@@ -101,8 +101,6 @@ Installation is supported on Linux, Windows and MacOS. For more advanced
 installation options check the `documentation
 <https://python-isal.readthedocs.io/en/stable/index.html#installation>`_.
 
-.. _differences-with-zlib-and-gzip-modules:
-
 python-isal as a dependency in your project
 -------------------------------------------
 
@@ -125,6 +123,8 @@ your project please list a python-isal dependency as follows.
 
 .. dependency end
 
+.. _differences-with-zlib-and-gzip-modules:
+
 Differences with zlib and gzip modules
 --------------------------------------
 
@@ -166,6 +166,28 @@ are also very welcome. Please report them on the `github issue tracker
 
 .. contributing end
 
+Development
+-----------
+.. development start
+
+The repository needs to be cloned recursively to make sure the
+`ISA-L <https://github.com/intel/isa-l>`_ repository is checked out:
+``git clone --recursive https://github.com/pycompression/python-isal.git``. If
+the repository is already checked out you can use ``git submodule update --init``.
+
+Patches should be made on a feature branch. To run the testing install ``tox``
+with ``pip install tox`` and run the commands ``tox -e lint`` and
+``tox``. That will run most of the testing that is also performed by the CI.
+For changes to the documentation run ``tox -e docs``. For changes to the C
+code please also run ``tox -e asan`` to check for memory leaks. This requires
+libasan to be installed.
+
+Building requires the 
+`ISA-L build requirements <https://github.com/intel/isa-l?tab=readme-ov-file#building-isa-l>`_ 
+as well.
+
+.. development end
+
 Acknowledgements
 ----------------
 
diff --git a/docs/conf.py b/docs/conf.py
@@ -4,27 +4,20 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-from distutils.dist import DistributionMetadata
-from pathlib import Path
-
-import pkg_resources
+from isal import __version__
 
 # -- Project information -----------------------------------------------------
 
 # Get package information from the installed package.
-package = pkg_resources.get_distribution("isal")
-metadata_file = Path(package.egg_info) / Path(package.PKG_INFO)
-metadata = DistributionMetadata(path=str(metadata_file))
 
 project = 'python-isal'
 copyright = '2020, Leiden University Medical Center'
 author = 'Leiden University Medical Center'
 
 # The short X.Y version
-version = package.parsed_version.base_version
+version = __version__
 # The full version, including alpha/beta/rc tags
-release = package.version
-
+release = __version__
 
 # -- General configuration ---------------------------------------------------
 
diff --git a/docs/index.rst b/docs/index.rst
@@ -158,6 +158,13 @@ Contributing
    :start-after: .. contributing start
    :end-before: .. contributing end
 
+===========
+Development
+===========
+.. include:: includes/README.rst
+   :start-after: .. development start
+   :end-before: .. development end
+
 ================
 Acknowledgements
 ================
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,10 @@
 [build-system]
-requires = ["setuptools>=51", "wheel"]
+requires = ["setuptools>=64", "versioningit>=1.1.0"]
 build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method="git"
+default-tag = "v0.0.0"
+
+[tool.versioningit.write]
+file = "src/isal/_version.py"
diff --git a/requirements-docs.txt b/requirements-docs.txt
@@ -1,4 +1,4 @@
 sphinx
-setuptools
 sphinx-rtd-theme
-sphinx-argparse
+# See https://github.com/sphinx-doc/sphinx-argparse/issues/56
+sphinx-argparse <0.5.0
diff --git a/setup.py b/setup.py
@@ -18,10 +18,15 @@
 from setuptools import Extension, find_packages, setup
 from setuptools.command.build_ext import build_ext
 
+import versioningit
+
 ISA_L_SOURCE = os.path.join("src", "isal", "isa-l")
 
+SYSTEM_IS_BSD = (sys.platform.startswith("freebsd") or
+                 sys.platform.startswith("netbsd"))
 SYSTEM_IS_UNIX = (sys.platform.startswith("linux") or
-                  sys.platform.startswith("darwin"))
+                  sys.platform.startswith("darwin") or
+                  SYSTEM_IS_BSD)
 SYSTEM_IS_WINDOWS = sys.platform.startswith("win")
 
 # Since pip builds in a temp directory by default, setting a fixed file in
@@ -113,7 +118,10 @@ def build_isa_l():
             cflags_param = "CFLAGS_aarch64"
         else:
             cflags_param = "CFLAGS_"
-        subprocess.run(["make", "-j", str(cpu_count), "-f", "Makefile.unx",
+        make_cmd = "make"
+        if SYSTEM_IS_BSD:
+            make_cmd = "gmake"
+        subprocess.run([make_cmd, "-j", str(cpu_count), "-f", "Makefile.unx",
                         "isa-l.h", "bin/isa-l.a",
                         f"{cflags_param}={build_env.get('CFLAGS', '')}"],
                        **run_args)
@@ -130,7 +138,7 @@ def build_isa_l():
 
 setup(
     name="isal",
-    version="1.6.1",
+    version=versioningit.get_version(),
     description="Faster zlib and gzip compatible compression and "
                 "decompression by providing python bindings for the ISA-L "
                 "library.",
diff --git a/src/isal/__init__.py b/src/isal/__init__.py
@@ -7,6 +7,7 @@
 
 from ._isal import (ISAL_MAJOR_VERSION, ISAL_MINOR_VERSION, ISAL_PATCH_VERSION,
                     ISAL_VERSION)
+from ._version import __version__
 
 __all__ = [
     "ISAL_MAJOR_VERSION",
@@ -15,5 +16,3 @@
     "ISAL_VERSION",
     "__version__"
 ]
-
-__version__ = "1.6.1"
diff --git a/src/isal/_version.pyi b/src/isal/_version.pyi
@@ -0,0 +1,8 @@
+# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010,
+# 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022
+# Python Software Foundation; All Rights Reserved
+
+# This file is part of python-isal which is distributed under the
+# PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2.
+
+__version__: int
diff --git a/src/isal/igzip.py b/src/isal/igzip.py
diff --git a/src/isal/isa-l b/src/isal/isa-l
diff --git a/src/isal/isal_zlibmodule.c b/src/isal/isal_zlibmodule.c

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+src/isal/_version.py`
	`2`	`+`
`1`	`3`	`# Byte-compiled / optimized / DLL files`
`2`	`4`	`__pycache__/`
`3`	`5`	`*.py[cod]`