Merge branch 'tf-bump' into 'dev'

Bump tf version to 2.10 for aarch wheel compat

See merge request research/medaka!551

.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"]
 

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.

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**
 

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

medaka/__init__.py

@@ -5,7 +5,7 @@
 import subprocess
 import sys
 
-__version__ = "1.8.1"
+__version__ = "1.8.2"
 
 try:
     import parasail

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