Merge branch 'gpimm/python_3.12_support' into 'master'

Add python 3.12 support

See merge request minknow/pod5-file-format!302

.gitlab-ci.yml

@@ -269,7 +269,7 @@ linux-x64-gcc9-release-build:
     PYTHON_ENABLED: "ON"
   parallel:
     matrix:
-      - PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+      - PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
 linux-aarch64-gcc9-release-build:
   image: quay.io/pypa/manylinux2014_aarch64
@@ -284,7 +284,7 @@ linux-aarch64-gcc9-release-build:
     PYTHON_ENABLED: "ON"
   parallel:
     matrix:
-      - PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+      - PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
 
 # ======================================
@@ -344,7 +344,7 @@ osx-x64-clang12-release-build:
       - PYTHON_VERSION: ["3.8.9", "3.9.13"]
         MACOSX_DEPLOYMENT_TARGET: "10.9"
         OUTPUT_SKU: "osx-10.9-x64"
-      - PYTHON_VERSION: ["3.10.10", "3.11.2"]
+      - PYTHON_VERSION: ["3.10.10", "3.11.2", "3.12.0"]
         MACOSX_DEPLOYMENT_TARGET: "10.9"
         OUTPUT_SKU: "osx-10.9-x64"
 
@@ -365,7 +365,7 @@ osx-arm64-clang13-release-build:
         MACOSX_DEPLOYMENT_TARGET: "10.9"
         OUTPUT_SKU: "osx-10.9-arm64"
         FORCE_PYTHON_PLATFORM: macosx_11_0_arm64
-      - PYTHON_VERSION: ["3.10.10", "3.11.2"]
+      - PYTHON_VERSION: ["3.10.10", "3.11.2", "3.12.0"]
         MACOSX_DEPLOYMENT_TARGET: "11.0"
         OUTPUT_SKU: "osx-11.0-arm64"
         FORCE_PYTHON_PLATFORM: macosx_11_0_arm64
@@ -385,14 +385,7 @@ osx-arm64-clang13-release-build:
   retry: 1
   before_script:
     - conan config install --verify-ssl=no "${CONAN_CONFIG_URL}"
-    - export PYENV="${HOME}/.pyenv/pyenv-win"
-    - export PYENV_ROOT="${PYENV}"
-    - export PYENV_HOME="${PYENV}"
-    - export PATH="${PYENV}/bin:${PYENV}/shims:${PATH}"
-    - if [[ -z $(pyenv install --list | grep "${PYTHON_VERSION}") ]]; then pyenv update; fi
-    - pyenv install ${PYTHON_VERSION} --skip-existing
-    - pyenv local ${PYTHON_VERSION}
-    - python -m venv .venv
+    - c:/Python${PYTHON_VERSION}/python -m venv .venv
     - source .venv/Scripts/activate
   script:
     - pod5_version="$(cmake -P ci/get_tag_version.cmake 2>&1)"
@@ -422,7 +415,7 @@ win-x64-msvc2017-release-build:
     OUTPUT_SKU: "win-x64"
   parallel:
     matrix:
-      - PYTHON_VERSION: ["3.8.0", "3.9.13", "3.10.10", "3.11.2"]
+      - PYTHON_VERSION: ["38", "39", "310", "311", "312"]
   artifacts:
     name: "${CI_JOB_NAME}-artifacts"
     paths:
@@ -480,7 +473,7 @@ build-python-api:
 .parallel-py-minor-ver: &parallel-py-minor-ver
   parallel:
     matrix:
-      - PY_MINOR_VER: ["8", "9", "10", "11"]
+      - PY_MINOR_VER: ["8", "9", "10", "11", "12"]
 
 tools-linux-x64:
   stage: test
@@ -544,7 +537,9 @@ pytest-linux-aarch64:
   needs:
     - linux-aarch64-gcc9-release-build
     - build-python-api
-  <<: *parallel-py-minor-ver
+  parallel:
+    matrix:
+      - PY_MINOR_VER: ["8", "9", "10", "11"] # TODO: Missing 12 as h5py doenst have binaries for 3.12 aarch64 yet
 
 .versions-matrix-pyenv-and-venv: &versions-matrix-pyenv-and-venv
   parallel:
@@ -557,6 +552,8 @@ pytest-linux-aarch64:
         PYTHON_VERSION: "3.10.10"
       - PY_MINOR_VER: "11"
         PYTHON_VERSION: "3.11.2"
+      - PY_MINOR_VER: "12"
+        PYTHON_VERSION: "3.12.0"
 
 pytest-osx-x64:
   extends: [".pytest"]
@@ -590,19 +587,10 @@ pytest-win-x64:
     - win-x64-msvc2017-release-build
     - build-python-api
   before_script:
-      # pyenv doesn't live on the PATH by default (and pyenv-win doesn't have `pyenv init`)
-    - export PYENV=~/.pyenv/pyenv-win
-    - export PATH=${PYENV}/bin:${PYENV}/shims:${PATH}
-    # needs PYTHON_VERSION set, and optionally VENV_BIN_DIR
-    - if [[ -z $( pyenv install --list | grep "${PYTHON_VERSION}" ) ]]; then pyenv update; fi
-    - pyenv install --skip-existing ${PYTHON_VERSION}
-    - pyenv global ${PYTHON_VERSION}
-    - python --version
-      # with pyenv, we don't have to use `python3` (and `python` also works on Windows)
-    - python -m venv .venv/
+    - c:/Python3${PY_MINOR_VER}/python -m venv .venv
     - source .venv/Scripts/activate
-    - python -m pip install --upgrade pip
     - python --version
+    - python -m pip install --upgrade pip
   <<: *versions-matrix-pyenv-and-venv
 
 
@@ -978,6 +966,7 @@ mlhub:
       - PYTHON_VERSION:
         - "3.8"
         - "3.11"
+        - "3.12"
 
 
 # ======================================

CHANGELOG.md

@@ -7,6 +7,11 @@ All notable changes, updates, and fixes to pod5 will be documented here
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.2]
+
+## Added
+
+- Support for Python 3.12
 
 ## [0.3.1] 2023-11-10
 
@@ -33,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Removed python3.7 support
 
+
 ## [0.2.9] 2023-11-02
 
 ### Fixed
@@ -51,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove exposed artifactory URL env var from gitlab ci config.
 - `convert to_fast5` writes byte encoded read_ids to match Minkow (was `str`)
 
+
 ## [0.2.7] 2023-09-11
 
 ### Added

ci/setup_python_osx.sh

@@ -15,7 +15,7 @@ git clone https://github.com/gregneagle/relocatable-python.git
 echo "Generating python ${version} into ${destination}"
 
 os_version="10.9"
-if [[ "${version}" == "3.10.10" || "${version}" == "3.11.2" ]]; then
+if [[ "${version}" == "3.10.10" || "${version}" == "3.11.2" || "${version}" == "3.12.0" ]]; then
     os_version="11"
 fi
 

docs/requirements.txt

@@ -2,4 +2,4 @@ sphinx-rtd-theme
 sphinx==v5.3.0
 myst-parser
 # Paths are relative to project root for ReadTheDocs and docs/Makefile
-pod5==0.3.1
+pod5==0.3.2

python/pod5/pyproject.toml

@@ -22,17 +22,17 @@ classifiers=[
 ]
 
 dependencies = [
-    "lib_pod5 == 0.3.1",
+    "lib_pod5 == 0.3.2",
     "iso8601",
     'importlib-metadata; python_version<"3.8"',
     "more_itertools",
     "numpy >= 1.21.0",
     'typing-extensions; python_version<"3.8"',
-    "pyarrow ~= 11.0.0",
+    "pyarrow ~= 14.0.0",
     "pytz",
     "packaging",
     "polars~=0.19",
-    "h5py~=3.8.0",
+    "h5py~=3.10.0",
     "vbz_h5py_plugin",
     "tqdm"
 ]