Merge branch 'blawrence/py39' into 'master'

Drop python 3.9 and macOS 10.15 support

See merge request minknow/pod5-file-format!449

Author: blawrence-ont

.gitlab-ci.yml

@@ -22,7 +22,7 @@ before_script:
 .parallel-py-versions:
   parallel:
     matrix:
-      - PYTHON_VERSION: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
+      - PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
 
 # ======================================
@@ -348,7 +348,9 @@ linux-aarch64-gcc9-release-build:
       - "lib_pod5*.whl"
 
 osx-arm64-clang15-release-build:
-  extends: [".build-osx-common"]
+  extends:
+    - .build-osx-common
+    - .parallel-py-versions
   tags:
     - osx_arm64
     - xcode-15.3
@@ -357,16 +359,9 @@ osx-arm64-clang15-release-build:
     CONAN_PROFILE: "macos-aarch64-appleclang-15.0.jinja"
     CONAN_PROFILE_CPPSTD: 20
     CMAKE_ARGS: "-DCMAKE_OSX_ARCHITECTURES=arm64"
-  parallel:
-    matrix:
-      - PYTHON_VERSION: ["3.9"]
-        MACOSX_DEPLOYMENT_TARGET: "10.15"
-        OUTPUT_SKU: "osx-10.15-arm64"
-        FORCE_PYTHON_PLATFORM: macosx_11_0_arm64
-      - PYTHON_VERSION: ["3.10", "3.11", "3.12", "3.13", "3.14"]
-        MACOSX_DEPLOYMENT_TARGET: "11.0"
-        OUTPUT_SKU: "osx-11.0-arm64"
-        FORCE_PYTHON_PLATFORM: macosx_11_0_arm64
+    MACOSX_DEPLOYMENT_TARGET: "14.0"
+    OUTPUT_SKU: "osx-14.0-arm64"
+    FORCE_PYTHON_PLATFORM: macosx_14_0_arm64
 
 
 # ======================================
@@ -626,35 +621,34 @@ conda_pytest:
     - python3 -m venv .venv/
     - source .venv/bin/activate
   script:
-    - pip install ./${LIB_WHEEL_GLOB} pod5-*.whl
+    - pip install ./${LIB_WHEEL_GLOB} pod5-*.whl setuptools
     - pip install -r ./benchmarks/image/requirements-benchmarks.txt
-    - export SLOW_5_VERSION=v1.0.0
     - ./benchmarks/image/install_slow5.sh
-    - export PATH="$(pwd)/slow5tools-${SLOW_5_VERSION}/:$PATH"
+    - export PATH="$(pwd)/slow5tools-v1.3.0/:$PATH"
     - ./benchmarks/run_benchmarks.py ./test_data/ ./benchmark-outputs
 
 benchmark-linux-x64:
   extends: [".benchmark"]
-  image: ${CI_REGISTRY}/traque/ont-docker-base/ont-base-python:3.9
+  image: ${CI_REGISTRY}/traque/ont-docker-base/ont-base-python:3.14
   tags:
     - linux
   needs:
     - linux-x64-gcc9-release-build
     - build-python-api
   variables:
-    LIB_WHEEL_GLOB: "lib_pod5*cp39*.whl"
+    LIB_WHEEL_GLOB: "lib_pod5*cp314*.whl"
 
 benchmark-linux-aarch64:
   extends: [".benchmark"]
-  image: ${CI_REGISTRY}/traque/ont-docker-base/ont-base-python:3.9
+  image: ${CI_REGISTRY}/traque/ont-docker-base/ont-base-python:3.14
   tags:
     - linux_aarch64
     - high-cpu
   needs:
     - linux-aarch64-gcc9-release-build
     - build-python-api
   variables:
-    LIB_WHEEL_GLOB: "lib_pod5*cp39*.whl"
+    LIB_WHEEL_GLOB: "lib_pod5*cp314*.whl"
 
 
 # ======================================
@@ -1277,8 +1271,5 @@ mlhub:
       }' \
       ${MLHUB_TRIGGER_URL}
   when: manual
-  parallel:
-    matrix:
-      - PYTHON_VERSION:
-        - "3.9"
-        - "3.12"
+  extends:
+    - .parallel-py-versions

CHANGELOG.md

@@ -13,6 +13,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Added missing licence files.
 
+### Removed
+
+- Removed Python 3.9 and macOS 10.15 support since they're EOL.
+
 
 ## [0.3.35]
 

benchmarks/image/install_slow5.sh

@@ -2,32 +2,34 @@
 
 set -e
 
-: "${SLOW_5_VERSION:=v1.0.0}"
+: "${SLOW_5_TOOLS_VERSION:=v1.3.0}"
+: "${SLOW_5_LIB_VERSION:=v1.3.1}"
 
 apt update
 apt install -y libzstd-dev libhdf5-dev
 
-wget "https://github.com/hasindu2008/slow5tools/releases/download/$SLOW_5_VERSION/slow5tools-$SLOW_5_VERSION-release.tar.gz"
-tar xvf "slow5tools-${SLOW_5_VERSION}-release.tar.gz"
+wget "https://github.com/hasindu2008/slow5tools/releases/download/${SLOW_5_TOOLS_VERSION}/slow5tools-${SLOW_5_TOOLS_VERSION}-release.tar.gz"
+tar xvf "slow5tools-${SLOW_5_TOOLS_VERSION}-release.tar.gz"
+rm "slow5tools-${SLOW_5_TOOLS_VERSION}-release.tar.gz"
 (
-    cd "slow5tools-${SLOW_5_VERSION}"
+    cd "slow5tools-${SLOW_5_TOOLS_VERSION}"
     ./configure
-    make zstd=1
+    make zstd=1 -j "$(nproc)"
 )
 
 # pyslow5 must be built with zstd support for fair comparison (otherwise default zlib is slower than zstd)
-git clone -b "${SLOW_5_VERSION}" https://github.com/hasindu2008/slow5lib
+git clone -b "${SLOW_5_LIB_VERSION}" https://github.com/hasindu2008/slow5lib
 
 (
     cd slow5lib/
 
     echo "Installing numpy"
     pip install numpy
 
-    make pyslow5
+    make pyslow5 -j "$(nproc)" 2> build_log.txt || (cat build_log.txt && exit)
     echo "Installing pyslow5"
     PYSLOW5_ZSTD=1 pip install dist/*.tar.gz
 
     # adding slow5 C API benchmarks
-    make zstd=1 && test/bench/build.sh
+    make zstd=1 -j "$(nproc)" && test/bench/build.sh
 )