From e1d7147fa26b5cbb5ecfe26d024c76e933b057c8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 12:02:56 +0200
Subject: [PATCH 01/26] set new version number

---
 setup.py             | 2 +-
 src/isal/__init__.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 897db8b7..c9da227e 100644
--- a/setup.py
+++ b/setup.py
@@ -169,7 +169,7 @@ def build_isa_l(compiler_command: str, compiler_options: str):
 
 setup(
     name="isal",
-    version="0.8.1",
+    version="0.9.0-dev",
     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
index 9ebfc86f..c75bb223 100644
--- a/src/isal/__init__.py
+++ b/src/isal/__init__.py
@@ -39,4 +39,4 @@
     "__version__"
 ]
 
-__version__ = "0.8.1"
+__version__ = "0.9.0-dev"

From 9bfee4bdc6a0ef5766971a097bdad8ebcee5e7a1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:09:13 +0200
Subject: [PATCH 02/26] Add pypy as a possible version

---
 .github/workflows/ci.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6bff205d..09511f43 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -57,10 +57,12 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - 3.6
-          - 3.7
-          - 3.8
-          - 3.9
+          - "3.6"
+          - "3.7"
+          - "3.8"
+          - "3.9"
+          - "pypy-3.6"
+          - "pypy-3.7"
         os: ["ubuntu-latest"]
         include:
           - os: "macos-latest"

From 1d03c87d03a0a234d58f9d696c1535923426bec7 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:26:55 +0200
Subject: [PATCH 03/26] Fix tox

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 09511f43..c6a01eee 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -94,7 +94,7 @@ jobs:
         uses: ilammy/setup-nasm@v1.2.0
         if: runner.os == 'Windows'
       - name: Run tests
-        run: tox -e py3
+        run: tox
       - name: Upload coverage report
         uses: codecov/codecov-action@v1
 

From 4d0be0277c3cf50feb2ba0dd12a806e6a0cc5025 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:31:59 +0200
Subject: [PATCH 04/26] Fix default tox env

---
 tox.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index 702101e4..4c336802 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,7 +1,7 @@
 [tox]
 # Running plain tox will run the default environment (testenv) with the default
 # python3 interpreter of the user.
-envlist=py3
+envlist=testenv
 [testenv]
 deps=pytest
      coverage

From 3e41aa4b5d90a346ee5497086eba401a82b99444 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:40:21 +0200
Subject: [PATCH 05/26] Import non-default strategies conditionally

---
 src/isal/isal_zlib.pyx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/isal/isal_zlib.pyx b/src/isal/isal_zlib.pyx
index a880370a..d9ef6bf3 100644
--- a/src/isal/isal_zlib.pyx
+++ b/src/isal/isal_zlib.pyx
@@ -99,10 +99,13 @@ DEFLATED = zlib.DEFLATED
 
 # Strategies
 Z_DEFAULT_STRATEGY=zlib.Z_DEFAULT_STRATEGY
-Z_RLE=zlib.Z_RLE 
 Z_HUFFMAN_ONLY=zlib.Z_HUFFMAN_ONLY
 Z_FILTERED=zlib.Z_FILTERED
-Z_FIXED=zlib.Z_FIXED
+# Following strategies not supported on all versions of zlib.
+if hasattr(zlib, "Z_RLE"):
+    Z_RLE = zlib.Z_RLE
+if hasattr(zlib, "Z_FIXED"):
+   Z_FIXED=zlib.Z_FIXED
 
 # Flush methods
 Z_NO_FLUSH=zlib.Z_NO_FLUSH

From 47f7aee63ab096c0b228323227056a6b105564b2 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:48:37 +0200
Subject: [PATCH 06/26] test more during build

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c6a01eee..4fd41ab8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -162,7 +162,8 @@ jobs:
           # Fully test the build wheels again.
           CIBW_TEST_REQUIRES: "pytest"
           # Simple test that requires the project to be build correctly
-          CIBW_TEST_COMMAND: "pytest {project}/tests/test_igzip.py"
+          CIBW_TEST_COMMAND: >-
+            pytest {project}/tests/test_igzip.py {project}/tests/test_isal.py
       - name: Build sdist
         if: "runner.os == 'Linux'"
         run: python setup.py sdist

From cd98ba9a6fc30067e8449f6c0747731cb38e81b4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 14:52:45 +0200
Subject: [PATCH 07/26] Also build wheels for pypy and 32bit

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4fd41ab8..c61506cf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -156,9 +156,9 @@ jobs:
       - name: Build wheels
         run: cibuildwheel --output-dir dist
         env:
-          CIBW_BUILD: "cp3{6,7,8,9}-*"
-          CIBW_SKIP: "*-win32 *-manylinux_i686"  # Skip 32 bit.
+          CIBW_BUILD: "cp3{6,7,8,9}-*,pp3{6,7}-*"
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
+          CIBW_MANYLINUX_I686_IMAGE: "manylinux2014"
           # Fully test the build wheels again.
           CIBW_TEST_REQUIRES: "pytest"
           # Simple test that requires the project to be build correctly

From 83fdc8df6d4d8b5e0cbc09a56e3b16ce91cf1dc9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 15:53:01 +0200
Subject: [PATCH 08/26] Skip 32 bit

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c61506cf..ad3280d4 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -157,8 +157,8 @@ jobs:
         run: cibuildwheel --output-dir dist
         env:
           CIBW_BUILD: "cp3{6,7,8,9}-*,pp3{6,7}-*"
+          CIBW_SKIP: "*-win32 *-manylinux_i686"  # Skip 32 bit.
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
-          CIBW_MANYLINUX_I686_IMAGE: "manylinux2014"
           # Fully test the build wheels again.
           CIBW_TEST_REQUIRES: "pytest"
           # Simple test that requires the project to be build correctly

From 3808e309ef5bfd617fd6ae21c8798e7f04259df1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 15:53:21 +0200
Subject: [PATCH 09/26] testdeploy

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ad3280d4..413743d3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -130,7 +130,7 @@ jobs:
           PYTHON_ISAL_LINK_DYNAMIC: True
 
   deploy:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     needs: [lint, package-checks, test-static, test-dynamic]
     strategy:

From 8af02945f3fba7b7e53b1f13df9a0624e6ad3ef4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 16:04:07 +0200
Subject: [PATCH 10/26] Let cibuildwheel figure out supported pythons itself

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 413743d3..33766a46 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -156,7 +156,6 @@ jobs:
       - name: Build wheels
         run: cibuildwheel --output-dir dist
         env:
-          CIBW_BUILD: "cp3{6,7,8,9}-*,pp3{6,7}-*"
           CIBW_SKIP: "*-win32 *-manylinux_i686"  # Skip 32 bit.
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
           # Fully test the build wheels again.

From 43ec6ecd2ff0c0cac5dcfb81b05547e2b2b454b6 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 29 Mar 2021 16:46:47 +0200
Subject: [PATCH 11/26] Fix test for pypy

---
 tests/test_isal.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_isal.py b/tests/test_isal.py
index ba4eea8c..66104f9d 100644
--- a/tests/test_isal.py
+++ b/tests/test_isal.py
@@ -106,9 +106,9 @@ def test_compress_compressobj(data_size, level, wbits, memLevel):
                                         memLevel=memLevel)
     compressed = compressobj.compress(data) + compressobj.flush()
     if wbits in range(8, 16):
-        # In case a zlib header is used, determine the wbits automatically.
-        # For some reason it fails if wbits is set manually.
-        decompressed = zlib.decompress(compressed, wbits=0)
+        # TODO: Apparently the wbits level is not correctly implemented in
+        # ISA-L for the zlib stuff.
+        decompressed = zlib.decompress(compressed, wbits=15)
     else:
         decompressed = zlib.decompress(compressed, wbits=wbits)
     assert data == decompressed

From cdb99a0dd3becf1cd9b78b42d3ebb7eda2e2aef1 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 07:54:30 +0200
Subject: [PATCH 12/26] Add pypy support to the changelog

---
 CHANGELOG.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 24ed1995..a31a65b9 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,11 @@ 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 0.9.0-dev
+-----------------
++ Add support for pypy by adding pypy tests to the CI and setting up wheel
+  building support.
+
 version 0.8.1
 -----------------
 + Fix a bug where multi-member gzip files where read incorrectly due to an

From 035d09ec3e4a14cd87b6f12cd1a657c094d39abd Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 08:05:05 +0200
Subject: [PATCH 13/26] Only run wheel building when tag is pushed

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 33766a46..d5a8924f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -130,7 +130,7 @@ jobs:
           PYTHON_ISAL_LINK_DYNAMIC: True
 
   deploy:
-    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     needs: [lint, package-checks, test-static, test-dynamic]
     strategy:

From 062ac855661ac9f2941d340af80273d4afa49832 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 08:34:21 +0200
Subject: [PATCH 14/26] Add test for aarch64

---
 .github/workflows/ci.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d5a8924f..cf825fe0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -98,6 +98,30 @@ jobs:
       - name: Upload coverage report
         uses: codecov/codecov-action@v1
 
+  test-arch:
+    name: Test on ${{ matrix.distro }} ${{ matrix.arch }}
+    runs-on: "ubuntu-latest"
+    needs: lint
+    strategy:
+      matrix:
+        distro: [ "ubuntu20.04" ]
+        arch: ["aarch64"]
+    steps:
+      - uses: actions/checkout@v2.3.4
+        with:
+          submodules: recursive
+      - uses: uraimo/run-on-arch-action@v2.0.9
+        name: Build & run test
+        with:
+          arch: ${{ matrix.arch }}
+          distro: ${{ matrix.distro }}
+          install: |
+            apt-get update -q -y
+            apt-get install -q -y python3 python3-pip build-essential gcc binutils automake autoconf
+          run: |
+            python3 -m pip install -U setuptools pip wheel tox
+            tox -e py3
+
   # Test if the python-isal conda package can be build. Which is linked
   # dynamically to the conda isa-l package.
   test-dynamic:

From 2bb9453048aef3569ce82d88bc2f885a098cb0a8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 08:50:57 +0200
Subject: [PATCH 15/26] Install libtool

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index cf825fe0..4f41d10c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -117,10 +117,10 @@ jobs:
           distro: ${{ matrix.distro }}
           install: |
             apt-get update -q -y
-            apt-get install -q -y python3 python3-pip build-essential gcc binutils automake autoconf
+            apt-get install -q -y python3 python3-pip gcc binutils automake autoconf libtool
           run: |
             python3 -m pip install -U setuptools pip wheel tox
-            tox -e py3
+            tox
 
   # Test if the python-isal conda package can be build. Which is linked
   # dynamically to the conda isa-l package.

From 3b315a5a2c22fed84d9fe48beadc6bb2f98ff939 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 09:58:59 +0200
Subject: [PATCH 16/26] Enable aarch64 wheel building

---
 .github/workflows/ci.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4f41d10c..5011d2c9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -177,11 +177,18 @@ jobs:
       - name: Install nasm (Windows)
         uses: ilammy/setup-nasm@v1.2.0
         if: runner.os == 'Windows'
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v1.0.1
+        with:
+          platforms: arm64
       - name: Build wheels
         run: cibuildwheel --output-dir dist
         env:
           CIBW_SKIP: "*-win32 *-manylinux_i686"  # Skip 32 bit.
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014"
+          CIBW_MANYLINUX_AARCH64_IMAGE: "manylinux2014"
+          CIBW_ARCHS_LINUX: "x86_64 aarch64"
           # Fully test the build wheels again.
           CIBW_TEST_REQUIRES: "pytest"
           # Simple test that requires the project to be build correctly

From c82f542d5771dc2318152c044d4abb20985ff607 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 09:59:41 +0200
Subject: [PATCH 17/26] Test deploy

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5011d2c9..8265a445 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -154,7 +154,7 @@ jobs:
           PYTHON_ISAL_LINK_DYNAMIC: True
 
   deploy:
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
     needs: [lint, package-checks, test-static, test-dynamic]
     strategy:

From 4d1b38b6a687850b2cba8231f3c5dfcd40942232 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 10:33:37 +0200
Subject: [PATCH 18/26] Only run arch check on main/develop

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8265a445..2b6f3eea 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -99,6 +99,7 @@ jobs:
         uses: codecov/codecov-action@v1
 
   test-arch:
+    if: startsWith(github.ref, 'refs/tags') || github.ref == refs/heads/develop || github.ref == refs/heads/main
     name: Test on ${{ matrix.distro }} ${{ matrix.arch }}
     runs-on: "ubuntu-latest"
     needs: lint
@@ -154,9 +155,9 @@ jobs:
           PYTHON_ISAL_LINK_DYNAMIC: True
 
   deploy:
-    #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
-    needs: [lint, package-checks, test-static, test-dynamic]
+    needs: [lint, package-checks, test-static, test-dynamic, test-arch]
     strategy:
       matrix:
         os: ["macos-latest", "ubuntu-latest", "windows-latest"]

From d65ccd12941327d6d9073aabe9758b552525cf68 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:04:04 +0200
Subject: [PATCH 19/26] Add missing quotes

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2b6f3eea..41ae68c0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -99,7 +99,7 @@ jobs:
         uses: codecov/codecov-action@v1
 
   test-arch:
-    if: startsWith(github.ref, 'refs/tags') || github.ref == refs/heads/develop || github.ref == refs/heads/main
+    if: startsWith(github.ref, 'refs/tags') || github.ref == 'refs/heads/develop' || github.ref == 'refs/heads/main'
     name: Test on ${{ matrix.distro }} ${{ matrix.arch }}
     runs-on: "ubuntu-latest"
     needs: lint

From 2545acfaa14f725ed5bf2544d9fb9ff17c9e8153 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:17:09 +0200
Subject: [PATCH 20/26] Update changelog

---
 CHANGELOG.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a31a65b9..c1d689ad 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -9,6 +9,9 @@ Changelog
 
 version 0.9.0-dev
 -----------------
++ Fix a bug where a AttributeError was triggered when zlib.Z_RLE or
+  zlib.Z_FIXED were not present.
++ Add support for Linux aarch64 builds.
 + Add support for pypy by adding pypy tests to the CI and setting up wheel
   building support.
 

From 99d79b859a572dfa7b8cafbf605b34b7be6d571a Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:24:29 +0200
Subject: [PATCH 21/26] Also install dynamic linking on PyPy

---
 .github/workflows/ci.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 41ae68c0..05c81de2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -136,6 +136,10 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python_version: ["python"]
+        include:
+          - os: "ubuntu-latest"
+            python_version: "pypy"
     steps:
       - uses: actions/checkout@v2.3.4
         with:
@@ -145,7 +149,7 @@ jobs:
         with:
           channels: conda-forge,defaults
       - name: Install requirements (universal)
-        run: conda install isa-l python tox
+        run: conda install isa-l ${{ matrix.python_version}} tox
       - name: Set MSVC developer prompt
         uses: ilammy/msvc-dev-cmd@v1.6.0
         if: runner.os == 'Windows'

From ab84108bb9288d02fca039e19e6144d58b1e97c7 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:28:57 +0200
Subject: [PATCH 22/26] Add extra library include dir

---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index c9da227e..2e19f1a9 100644
--- a/setup.py
+++ b/setup.py
@@ -62,6 +62,7 @@ def build_extension(self, ext):
             for prefix in possible_prefixes:
                 if Path(prefix, "include", "isa-l").exists():
                     ext.include_dirs = [os.path.join(prefix, "include")]
+                    ext.library_dirs = [os.path.join(prefix, "lib")]
                     break   # Only one include directory is needed.
                 # On windows include is in Library apparently
                 elif Path(prefix, "Library", "include", "isa-l").exists():

From a7b9d6541a53859b3acc71a4ecbaf9045590814b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:32:57 +0200
Subject: [PATCH 23/26] Make sure coverage errors with PyPy are ignored

---
 tox.ini | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index 4c336802..aca29b9e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,8 +10,9 @@ passenv=
 commands =
     # Create HTML coverage report for humans and xml coverage report for external services.
     coverage run --source=isal -m py.test tests
-    coverage html
-    coverage xml
+    # Ignore errors during report generation. Pypy does not generate proper coverage reports.
+    coverage html -i
+    coverage xml -i
 
 [testenv:coverage]
 # Separate test environment for cython coverage.

From 203ad209f2c141df7a58e656957f0fd98117a589 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:36:47 +0200
Subject: [PATCH 24/26] Fix tox command

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 05c81de2..a9e56d94 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -154,7 +154,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1.6.0
         if: runner.os == 'Windows'
       - name: Run tests (dynamic link)
-        run: tox -e py3
+        run: tox
         env:
           PYTHON_ISAL_LINK_DYNAMIC: True
 

From 8c0bd03ce10210506f4794c0551a3c517333563d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 12:37:24 +0200
Subject: [PATCH 25/26] Remove custom name

---
 .github/workflows/ci.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a9e56d94..17bf2c4e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -100,7 +100,6 @@ jobs:
 
   test-arch:
     if: startsWith(github.ref, 'refs/tags') || github.ref == 'refs/heads/develop' || github.ref == 'refs/heads/main'
-    name: Test on ${{ matrix.distro }} ${{ matrix.arch }}
     runs-on: "ubuntu-latest"
     needs: lint
     strategy:

From c8e73a5220ecf590e574527e83dd1e5dfc0574bc Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Mar 2021 14:35:55 +0200
Subject: [PATCH 26/26] Stable version number

---
 CHANGELOG.rst        | 2 +-
 setup.py             | 2 +-
 src/isal/__init__.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index c1d689ad..f6554898 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,7 +7,7 @@ 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 0.9.0-dev
+version 0.9.0
 -----------------
 + Fix a bug where a AttributeError was triggered when zlib.Z_RLE or
   zlib.Z_FIXED were not present.
diff --git a/setup.py b/setup.py
index 2e19f1a9..170385ff 100644
--- a/setup.py
+++ b/setup.py
@@ -170,7 +170,7 @@ def build_isa_l(compiler_command: str, compiler_options: str):
 
 setup(
     name="isal",
-    version="0.9.0-dev",
+    version="0.9.0",
     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
index c75bb223..c03589f7 100644
--- a/src/isal/__init__.py
+++ b/src/isal/__init__.py
@@ -39,4 +39,4 @@
     "__version__"
 ]
 
-__version__ = "0.9.0-dev"
+__version__ = "0.9.0"