Skip to content

Commit

Permalink
Merge pull request #203 from boegel/eb480_release_notes
Browse files Browse the repository at this point in the history
update release notes for EasyBuild v4.8.0
  • Loading branch information
boegel committed Jul 7, 2023
2 parents 94734f2 + 13bf206 commit 457ef5e
Show file tree
Hide file tree
Showing 5 changed files with 126 additions and 9 deletions.
3 changes: 3 additions & 0 deletions docs/changelog-docs.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,9 @@ search:

(for EasyBuild release notes, see [EasyBuild release notes][release_notes])

- **release 20230707.01** (*7 July 2023*): update
release notes for EasyBuild v4.8.0 (see
[EasyBuild v4.8.0 (7 July 2023)][release_notes_eb480])
- **release 20230527.01** (*27 May 2023*): update
release notes for EasyBuild v4.7.2 (see
[EasyBuild v4.7.2 (27 May 2023)][release_notes_eb472])
Expand Down
6 changes: 3 additions & 3 deletions docs/installation.md
Original file line number Diff line number Diff line change
Expand Up @@ -62,10 +62,10 @@ $ module load EasyBuild
$ module list

Currently Loaded Modules:
1) EasyBuild/4.7.2
1) EasyBuild/4.8.0

$ eb --version
This is EasyBuild 4.7.2 (framework: 4.7.2, easyblocks: 4.7.2) on host example.local
This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example.local
```

!!! tip
Expand Down Expand Up @@ -228,7 +228,7 @@ $ EB_VERBOSE=1 eb --version
>> 'python3' version: 3.6.8, which matches Python 3 version requirement (>= 3.5)
>> Selected Python command: python3 (/usr/bin/python3.6)
>> python3.6 -m easybuild.main --version
This is EasyBuild 4.7.2 (framework: 4.7.2, easyblocks: 4.7.2) on host example
This is EasyBuild 4.8.0 (framework: 4.8.0, easyblocks: 4.8.0) on host example
```


Expand Down
120 changes: 117 additions & 3 deletions docs/release-notes.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,124 @@ search:
# EasyBuild release notes {: #release_notes }

The latest version of EasyBuild provides support for building and
installing [**3,085** different software packages](../version-specific/supported-software),
installing [**3,161** different software packages](../version-specific/supported-software),
including 39 different (compiler) toolchains.
It contains 248 software-specific easyblocks and 41 generic easyblocks,
alongside 17,098 easyconfig files.
It contains 249 software-specific easyblocks and 42 generic easyblocks,
alongside 17,511 easyconfig files.


## EasyBuild v4.8.0 (7 July 2023) {: #release_notes_eb480 }

feature release

**framework**

- various enhancements, including:
- use version suffixes in PR title instead of Python versions when using `--new-pr` ([#4253](https://github.com/easybuilders/easybuild-framework/pull/4253) + [#4286](https://github.com/easybuilders/easybuild-framework/pull/4286))
- add script to find updated ECs for installed module ([#4271](https://github.com/easybuilders/easybuild-framework/pull/4271))
- various bug fixes, including:
- fix regex for extracting glibc version from output of '`ldd --version`' in Gentoo Linux ([#4290](https://github.com/easybuilders/easybuild-framework/pull/4290))
- allow versionsuffix to be set to None in `det_full_ec_version` ([#4292](https://github.com/easybuilders/easybuild-framework/pull/4292))
- other changes:
- stop running tests with Python 2.7 since it is no longer supported in GitHub Action ([#4267](https://github.com/easybuilders/easybuild-framework/pull/4267))
- replace `imp.load_source` by leveraging `importlib.util.module_from_spec` when using Python 3 ([#4280](https://github.com/easybuilders/easybuild-framework/pull/4280))

**easyblocks**

- add `PerlBundle` generic easyblock for installing a bundle of Perl modules ([#2945](https://github.com/easybuilders/easybuild-easyblocks/pull/2945))
- add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if `--rpath` is used ([#2952](https://github.com/easybuilders/easybuild-easyblocks/pull/2952))
- minor enhancements and updates, including:
- add support for NVIDIA Hopper CC 9.0 in LAMMPS ([#2941](https://github.com/easybuilders/easybuild-easyblocks/pull/2941))
- add support for `install_cmds` in `Binary` easyblock ([#2953](https://github.com/easybuilders/easybuild-easyblocks/pull/2953))
- various bug fixes, including:
- patch CMake's `UnixPaths.cmake` script if `--sysroot` is set ([#2248](https://github.com/easybuilders/easybuild-easyblocks/pull/2248))
- fix incorrect `sanity_check_step` for torchvision ([#2938](https://github.com/easybuilders/easybuild-easyblocks/pull/2938))
- update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes ([#2944](https://github.com/easybuilders/easybuild-easyblocks/pull/2944))
- improve handling of `optarch` in `Cargo` easyblock ([#2947](https://github.com/easybuilders/easybuild-easyblocks/pull/2947))
- reset modules loaded by `PythonPackage` to let `ExtensionEasyBlock` handle `multi_deps` correctly ([#2951](https://github.com/easybuilders/easybuild-easyblocks/pull/2951))
- other changes:
- stop running tests with Python 2.7 since it is no longer supported in GitHub Actions ([#2943](https://github.com/easybuilders/easybuild-easyblocks/pull/2943))

**easyconfigs**

- added easyconfigs for `foss/2023a` ([#18264](https://github.com/easybuilders/easybuild-easyconfigs/pull/18264)) and `intel/2023a` ([#18275](https://github.com/easybuilders/easybuild-easyconfigs/pull/18275)) common toolchains
- added example easyconfig files for 76 new software packages:
- 3d-dna ([#9258](https://github.com/easybuilders/easybuild-easyconfigs/pull/9258)), affinity ([#18051](https://github.com/easybuilders/easybuild-easyconfigs/pull/18051)), AIMAll ([#13153](https://github.com/easybuilders/easybuild-easyconfigs/pull/13153)), alleleIntegrator ([#17923](https://github.com/easybuilders/easybuild-easyconfigs/pull/17923)), AlphaPulldown ([#17774](https://github.com/easybuilders/easybuild-easyconfigs/pull/17774)),
ASCAT ([#17923](https://github.com/easybuilders/easybuild-easyconfigs/pull/17923)), ASF-SearchAPI ([#18179](https://github.com/easybuilders/easybuild-easyconfigs/pull/18179)), ATAT ([#18213](https://github.com/easybuilders/easybuild-easyconfigs/pull/18213)), AutoDockSuite ([#9678](https://github.com/easybuilders/easybuild-easyconfigs/pull/9678)), axel ([#10961](https://github.com/easybuilders/easybuild-easyconfigs/pull/10961)), BayesPrism ([#17885](https://github.com/easybuilders/easybuild-easyconfigs/pull/17885)),
BGC-Bayesian-genomic-clines ([#18005](https://github.com/easybuilders/easybuild-easyconfigs/pull/18005)), CalculiX-CrunchiX ([#16805](https://github.com/easybuilders/easybuild-easyconfigs/pull/16805)), CASA ([#18055](https://github.com/easybuilders/easybuild-easyconfigs/pull/18055)), cctbx-base ([#17774](https://github.com/easybuilders/easybuild-easyconfigs/pull/17774)),
Circuitscape ([#16720](https://github.com/easybuilders/easybuild-easyconfigs/pull/16720)), CppHeaderParser ([#18272](https://github.com/easybuilders/easybuild-easyconfigs/pull/18272)), CuCLARK ([#9482](https://github.com/easybuilders/easybuild-easyconfigs/pull/9482)), cuteSV ([#18077](https://github.com/easybuilders/easybuild-easyconfigs/pull/18077)), DALI ([#18204](https://github.com/easybuilders/easybuild-easyconfigs/pull/18204)), DaliLite ([#17989](https://github.com/easybuilders/easybuild-easyconfigs/pull/17989)),
DEICODE ([#18181](https://github.com/easybuilders/easybuild-easyconfigs/pull/18181)), dm-haiku ([#18013](https://github.com/easybuilders/easybuild-easyconfigs/pull/18013)), dominate ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)), dx-toolkit ([#18232](https://github.com/easybuilders/easybuild-easyconfigs/pull/18232)), easel ([#18156](https://github.com/easybuilders/easybuild-easyconfigs/pull/18156)), ecFlow ([#15719](https://github.com/easybuilders/easybuild-easyconfigs/pull/15719)),
EDirect ([#17479](https://github.com/easybuilders/easybuild-easyconfigs/pull/17479)), FragPipe ([#18161](https://github.com/easybuilders/easybuild-easyconfigs/pull/18161)), GEM ([#18120](https://github.com/easybuilders/easybuild-easyconfigs/pull/18120)), gemelli ([#18120](https://github.com/easybuilders/easybuild-easyconfigs/pull/18120)), GLIMPSE ([#18163](https://github.com/easybuilders/easybuild-easyconfigs/pull/18163)), GRIDSS ([#18170](https://github.com/easybuilders/easybuild-easyconfigs/pull/18170)),
HOOMD-blue ([#18224](https://github.com/easybuilders/easybuild-easyconfigs/pull/18224)), KerasTuner ([#18197](https://github.com/easybuilders/easybuild-easyconfigs/pull/18197)), LayoutParser ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), LISFLOOD-FP ([#18194](https://github.com/easybuilders/easybuild-easyconfigs/pull/18194)), LuaRocks ([#18073](https://github.com/easybuilders/easybuild-easyconfigs/pull/18073)),
mannkendall ([#18043](https://github.com/easybuilders/easybuild-easyconfigs/pull/18043)), MOB-suite ([#16798](https://github.com/easybuilders/easybuild-easyconfigs/pull/16798)), molecularGSM ([#13150](https://github.com/easybuilders/easybuild-easyconfigs/pull/13150)), MONAI-Label ([#18180](https://github.com/easybuilders/easybuild-easyconfigs/pull/18180)), MView ([#18198](https://github.com/easybuilders/easybuild-easyconfigs/pull/18198)),
NanoStat ([#18201](https://github.com/easybuilders/easybuild-easyconfigs/pull/18201)), oxDNA ([#18175](https://github.com/easybuilders/easybuild-easyconfigs/pull/18175) + [#18214](https://github.com/easybuilders/easybuild-easyconfigs/pull/18214)), pastml ([#15336](https://github.com/easybuilders/easybuild-easyconfigs/pull/15336)), pbipa ([#18229](https://github.com/easybuilders/easybuild-easyconfigs/pull/18229)), Perl-bundle-CPAN ([#17970](https://github.com/easybuilders/easybuild-easyconfigs/pull/17970)), PheWeb ([#10951](https://github.com/easybuilders/easybuild-easyconfigs/pull/10951)),
plinkliftover ([#18136](https://github.com/easybuilders/easybuild-easyconfigs/pull/18136)), pmt ([#18052](https://github.com/easybuilders/easybuild-easyconfigs/pull/18052)), PyBioLib ([#18124](https://github.com/easybuilders/easybuild-easyconfigs/pull/18124)), Pychopper ([#10344](https://github.com/easybuilders/easybuild-easyconfigs/pull/10344)), pydicom-seg ([#18180](https://github.com/easybuilders/easybuild-easyconfigs/pull/18180)),
pyMannKendall ([#18044](https://github.com/easybuilders/easybuild-easyconfigs/pull/18044)), pypmt ([#18045](https://github.com/easybuilders/easybuild-easyconfigs/pull/18045)), python-mujoco ([#18253](https://github.com/easybuilders/easybuild-easyconfigs/pull/18253)), pytorch-CycleGAN-pix2pix ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)),
PyTorch-Image-Models ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), PyWBGT ([#17980](https://github.com/easybuilders/easybuild-easyconfigs/pull/17980)), Safetensors ([#18220](https://github.com/easybuilders/easybuild-easyconfigs/pull/18220)), Sniffles ([#18048](https://github.com/easybuilders/easybuild-easyconfigs/pull/18048)), strace ([#14381](https://github.com/easybuilders/easybuild-easyconfigs/pull/14381)),
Structure_threader ([#18219](https://github.com/easybuilders/easybuild-easyconfigs/pull/18219)), subset-bam ([#18032](https://github.com/easybuilders/easybuild-easyconfigs/pull/18032)), SVclone ([#18084](https://github.com/easybuilders/easybuild-easyconfigs/pull/18084)), SVIM ([#18071](https://github.com/easybuilders/easybuild-easyconfigs/pull/18071)), Tapenade ([#18109](https://github.com/easybuilders/easybuild-easyconfigs/pull/18109)),
TensorFlow-Graphics ([#17465](https://github.com/easybuilders/easybuild-easyconfigs/pull/17465)), timm ([#17787](https://github.com/easybuilders/easybuild-easyconfigs/pull/17787)), Trinotate ([#18124](https://github.com/easybuilders/easybuild-easyconfigs/pull/18124)), Ultralytics ([#17894](https://github.com/easybuilders/easybuild-easyconfigs/pull/17894)), visdom ([#18086](https://github.com/easybuilders/easybuild-easyconfigs/pull/18086)),
wrapt ([#18125](https://github.com/easybuilders/easybuild-easyconfigs/pull/18125)), xclip ([#17055](https://github.com/easybuilders/easybuild-easyconfigs/pull/17055)), xdotool ([#17055](https://github.com/easybuilders/easybuild-easyconfigs/pull/17055))
- added additional easyconfigs for various supported software packages, including:
- AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0,
boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10,
corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1,
datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3,
elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2,
FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1,
Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1,
hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2,
Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0,
lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1,
minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3,
Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2,
OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1,
PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6,
pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3,
python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4,
seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0,
tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0,
UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2,
XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7
- minor enhancements, including:
- add CI check for `-DCMAKE_BUILD_TYPE`, should use `build_type` instead ([#14008](https://github.com/easybuilders/easybuild-easyconfigs/pull/14008))
- enhance sanity check for recent LibTIFF easyconfigs ([#17975](https://github.com/easybuilders/easybuild-easyconfigs/pull/17975))
- update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module ([#17982](https://github.com/easybuilders/easybuild-easyconfigs/pull/17982))
- use custom easyblock for Rust 1.65.0 ([#18174](https://github.com/easybuilders/easybuild-easyconfigs/pull/18174)) and Rust 1.70.0 ([#18167](https://github.com/easybuilders/easybuild-easyconfigs/pull/18167))
- update easyconfig for Nextflow 23.04.2 to use `install_cmds` ([#18173](https://github.com/easybuilders/easybuild-easyconfigs/pull/18173))
- add extra packages to recent R easyconfigs ([#18029](https://github.com/easybuilders/easybuild-easyconfigs/pull/18029), [#18063](https://github.com/easybuilders/easybuild-easyconfigs/pull/18063), [#18122](https://github.com/easybuilders/easybuild-easyconfigs/pull/18122), [#18195](https://github.com/easybuilders/easybuild-easyconfigs/pull/18195), [#18245](https://github.com/easybuilders/easybuild-easyconfigs/pull/18245))
- add extra packages to recent R-bundle-Bioconductor easyconfigs ([#18196](https://github.com/easybuilders/easybuild-easyconfigs/pull/18196), [#18246](https://github.com/easybuilders/easybuild-easyconfigs/pull/18246))
- various bug fixes, including:
- add patches to fix TensorFlow 2.7.1 on POWER ([#16795](https://github.com/easybuilders/easybuild-easyconfigs/pull/16795))
- fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ `foss/2021b` ([#17058](https://github.com/easybuilders/easybuild-easyconfigs/pull/17058))
- stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 ([#17998](https://github.com/easybuilders/easybuild-easyconfigs/pull/17998))
- add pkgconfig as build dependency for nodejs , required for finding ICU dependency ([#18007](https://github.com/easybuilders/easybuild-easyconfigs/pull/18007))
- fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 ([#18030](https://github.com/easybuilders/easybuild-easyconfigs/pull/18030))
- update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies ([#18041](https://github.com/easybuilders/easybuild-easyconfigs/pull/18041))
- fix `--sanity-check-only` for MAGeCK v0.5.9.4 ([#18047](https://github.com/easybuilders/easybuild-easyconfigs/pull/18047))
- enable building static libs and check for `libexslt.*` in libxslt ([#18064](https://github.com/easybuilders/easybuild-easyconfigs/pull/18064))
- add `-pthread` flag for dorado ([#18072](https://github.com/easybuilders/easybuild-easyconfigs/pull/18072))
- add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 ([#18087](https://github.com/easybuilders/easybuild-easyconfigs/pull/18087))
- add missing pkgconf build dependency for XML-LibXML v2.0208 ([#18159](https://github.com/easybuilders/easybuild-easyconfigs/pull/18159))
- update homepage for NWChem 7.x ([#18184](https://github.com/easybuilders/easybuild-easyconfigs/pull/18184))
- update homepage for SUNDIALS 5.x and 6.x ([#18186](https://github.com/easybuilders/easybuild-easyconfigs/pull/18186))
- add missing `source_urls` for SimpleITK ([#18212](https://github.com/easybuilders/easybuild-easyconfigs/pull/18212))
- use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 ([#18230](https://github.com/easybuilders/easybuild-easyconfigs/pull/18230))
- fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) ([#18231](https://github.com/easybuilders/easybuild-easyconfigs/pull/18231))
- fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks ([#18235](https://github.com/easybuilders/easybuild-easyconfigs/pull/18235))
- use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 ([#18236](https://github.com/easybuilders/easybuild-easyconfigs/pull/18236))
- update `source_urls` for Velvet 1.2.10 ([#18237](https://github.com/easybuilders/easybuild-easyconfigs/pull/18237))
- use upstream patch for symbol compatibility in XZ 5.2.5 ([#18250](https://github.com/easybuilders/easybuild-easyconfigs/pull/18250))
- update source url for pkgconf ([#18271](https://github.com/easybuilders/easybuild-easyconfigs/pull/18271))
- other changes:
- stop running easyconfig unit tests with Python 2.7 ([#18006](https://github.com/easybuilders/easybuild-easyconfigs/pull/18006))
- fix toolchain for networkx-3.0 (`foss/2022b` -> `gfbf/2022b`) ([#18061](https://github.com/easybuilders/easybuild-easyconfigs/pull/18061))
- remove unused PyTorch patch ([#18062](https://github.com/easybuilders/easybuild-easyconfigs/pull/18062))
- allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match ([#18098](https://github.com/easybuilders/easybuild-easyconfigs/pull/18098))
- bump OpenSSL 1.1 wrapper fallback to 1.1.1u ([#18188](https://github.com/easybuilders/easybuild-easyconfigs/pull/18188))
- remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion ([#18222](https://github.com/easybuilders/easybuild-easyconfigs/pull/18222))
- remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB ([#18223](https://github.com/easybuilders/easybuild-easyconfigs/pull/18223))
- remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs ([#18260](https://github.com/easybuilders/easybuild-easyconfigs/pull/18260))
- change base compiler for `intel/2023.03` to `GCCcore/12.3.0` (required to use it as intel/2023a) ([#18263](https://github.com/easybuilders/easybuild-easyconfigs/pull/18263))


## EasyBuild v4.7.2 (27 May 2023) {: #release_notes_eb472 }
Expand Down
Loading

0 comments on commit 457ef5e

Please sign in to comment.