From 7067898a560643d43bc413f051609c2beaed0436 Mon Sep 17 00:00:00 2001 From: Chris Wright Date: Tue, 8 Aug 2023 15:02:00 +0000 Subject: [PATCH] Bump tf version to 2.10 for aarch wheel compat --- .gitlab-ci.yml | 24 ++++++------------------ CHANGELOG.md | 8 ++++++++ README.md | 30 ++++++++++++++++-------------- build-wheels.sh | 8 +++++++- medaka/__init__.py | 2 +- requirements.txt | 2 +- 6 files changed, 39 insertions(+), 35 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1beab06..a8fe223 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -114,21 +114,11 @@ build:sdist: artifacts: paths: - wheelhouse-final/*.whl - only: - - tags - - -make-wheels-2010: - extends: .many-linux - image: "quay.io/pypa/manylinux2010_x86_64" - parallel: - matrix: - - PYWHEEL: [7, 8] - COMPUTE: ["gpu", "cpu"] - FLAVOUR: ["2010"] + #only: + #- tags -make-wheels-2014: +wheels-2014: extends: .many-linux image: "quay.io/pypa/manylinux2014_x86_64" parallel: @@ -138,7 +128,7 @@ make-wheels-2014: FLAVOUR: ["2014"] -make-wheels-2_28: +wheels-2_28: extends: .many-linux image: "quay.io/pypa/manylinux_2_28_x86_64" parallel: @@ -148,12 +138,10 @@ make-wheels-2_28: FLAVOUR: ["2_24"] -make-wheels-arm: +wheels-arm-2014: extends: .many-linux tags: - arm64 - variables: - DO_COUNT_TEST: 0 image: quay.io/pypa/manylinux2014_aarch64 before_script: # ARM CI image doesn't have git lfs, so need to jump some hoops @@ -166,7 +154,7 @@ make-wheels-arm: - GIT_SSL_NO_VERIFY=1 git lfs pull parallel: matrix: - - PYWHEEL: [7, 8, 9, 10] + - PYWHEEL: [8, 9, 10] COMPUTE: ["gpu"] FLAVOUR: ["2014"] diff --git a/CHANGELOG.md b/CHANGELOG.md index ed3a202..781e90b 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [v1.8.2] +### Added +* Updated features related to fetching of trimmed reads. +### Changed +* Refactored smolecule module. +* Faster inference and stitching of many short contigs. +* Tensorflow version 2.10 (allows for aarch64 wheels). + ## [v1.8.1] ### Added - Expose qualities parameter in medaka_consensus script with `-q` parameter. diff --git a/README.md b/README.md index d4ea975..a0f1dfd 100755 --- a/README.md +++ b/README.md @@ -37,21 +37,10 @@ Installation Medaka can be installed in one of several ways. -**Installation with conda** - -Perhaps the simplest way to start using medaka is -through conda; medaka is available via the -[bioconda](https://anaconda.org/bioconda/medaka) channel: - - conda create -n medaka -c conda-forge -c bioconda medaka - -Occasionally the conda releases lag behind the source code and -[PyPI](https://pypi.org/project/medaka/) releases. - **Installation with pip** -For those who prefer Python's native pacakage manager, medaka is also available -on pypi and can be installed using pip: +Official binary releases of medaka are available on +[PyPI](https://pypi.org/project/medaka/) and can be installed using pip: pip install medaka @@ -74,7 +63,20 @@ Using this method requires the user to provide several binaries: and place these within the `PATH`. `samtools/bgzip/tabix` version 1.14 and `minimap2` version 2.17 are recommended as these are those used in development -of medaka. +of medaka. (Newer versions are almost certainly fine). + +**Installation with conda** + +> The bioconda medaka packages are no longer supported by Oxford Nanopore Technologies. + +For those who prefer the conda package manager, medaka is available via the +[bioconda](https://anaconda.org/bioconda/medaka) channel: + + conda create -n medaka -c conda-forge -c bioconda medaka + +The bioconda releases lag behind the source code and [PyPI](https://pypi.org/project/medaka/) +releases. + **Installation from source** diff --git a/build-wheels.sh b/build-wheels.sh index d499d62..048db97 100755 --- a/build-wheels.sh +++ b/build-wheels.sh @@ -5,6 +5,8 @@ export MANYLINUX=1 export MEDAKA_DIST=1 export WITHDEFLATE=1 +arch=$(uname -m) + workdir=$1 shift @@ -65,7 +67,11 @@ if [[ "${DO_COUNT_TEST}" == "1" ]]; then else PYBIN="/opt/python/cp3${minor}-cp3${minor}m/bin" fi - "${PYBIN}"/pip install --prefer-binary -r requirements.txt + # don't look, these pyspoa builds were a manual affair + if [ "${arch}" = "arm64" ] || [ "${arch}" = "aarch64" ]; then + "${PYBIN}"/pip install https://github.com/nanoporetech/pyspoa/releases/download/v0.0.10/pyspoa-0.0.10-cp3${minor}-cp3${minor}-manylinux_2_17_aarch64.manylinux2014_aarch64.whl + fi + "${PYBIN}"/pip install --use-pep517 --prefer-binary -r requirements.txt "${PYBIN}"/pip install "${PACKAGE_NAME}" --no-index -f ./wheelhouse "${PYBIN}"/medaka_counts --print medaka/test/data/test_reads.bam utg000001l:10000-10010 done diff --git a/medaka/__init__.py b/medaka/__init__.py index 6afe8d0..884db4b 100755 --- a/medaka/__init__.py +++ b/medaka/__init__.py @@ -5,7 +5,7 @@ import subprocess import sys -__version__ = "1.8.1" +__version__ = "1.8.2" try: import parasail diff --git a/requirements.txt b/requirements.txt index 1c9daa8..befde08 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,7 @@ edlib grpcio h5py intervaltree -tensorflow~=2.8.0 +tensorflow~=2.10.0 numpy>=1.21.6 mappy ont_fast5_api