minor tweaks to release notes for EasyBuild v4.8.0

easybuilders · Jul 7, 2023 · 93fb7a2 · 93fb7a2
1 parent 93efb2b
commit 93fb7a2
Showing 1 changed file with 35 additions and 24 deletions.
diff --git a/RELEASE_NOTES b/RELEASE_NOTES
@@ -22,30 +22,45 @@ feature release
     EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170),
     HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073),
     mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198),
-    NanoStat (#18201), oxDNA (#18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951),
-    plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180), pyMannKendall (#18044),
-    pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086), PyTorch-Image-Models (#18220), PyWBGT (#17980),
-    Safetensors (#18220), Sniffles (#18048), strace (#14381), Structure_threader (#18219), subset-bam (#18032), SVclone (#18084),
-    SVIM (#18071), Tapenade (#18109), TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894),
-    visdom (#18086), wrapt (#18125), xclip (#17055), xdotool (#17055)
+    NanoStat (#18201), oxDNA (#18175 + #18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951),
+    plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180),
+    pyMannKendall (#18044), pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086),
+    PyTorch-Image-Models (#18220), PyWBGT (#17980), Safetensors (#18220), Sniffles (#18048), strace (#14381),
+    Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), SVIM (#18071), Tapenade (#18109),
+    TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), visdom (#18086),
+    wrapt (#18125), xclip (#17055), xdotool (#17055)
 - added additional easyconfigs for various supported software packages, including:
-  - 3d dna, ABINIT 9.2.1, ABINIT 9.2.1, Abseil 20230125.2, affinity 20230524, affinity 20230524, AGAT 1.1.0, AIMAll 19.10.12, alleleCount 4.2.1, alleleIntegrator 0.8.8, AlphaPulldown 0.30.4, AlphaPulldown 0.30.4, AMS 2023.101, Anaconda3 2023.03, ANSYS 2023R1.eb, ASCAT 3.1.2, ASF SearchAPI, ATAT 3.36, attr 2.5.1, AUGUSTUS 3.5.0, Autoconf 2.71, Autoconf 2.71, AutoDock GPU, AutoDockSuite 4.2.6, Automake 1.16.5, Automake 1.16.5, Autotools 20220317, Autotools 20220317, axel 2.17.9, axel 2.17.9, Bandage 0.9.0, barrnap 0.9, BayesPrism 2.0, BayesTraits 3.0.2, BBMap 39.01, BGC Bayesian, binutils 2.40, BioPerl 1.7.8, Bismark 0.24.1, Bison 3.8.2, BLAST+ 2.14.0, BLAT 3.7, BLIS 0.9.0, boto3 1.26.163, Bowtie2 2.5.1, build 0.10.0, BUSCO 5.4.7, CalculiX CrunchiX, canu 2.2, CASA 6.5.5, ccache 4.6.3, cctbx base, cctbx base, CD HIT, Cellpose 2.2.2, Cellpose 2.2.2, CHERAB 1.4.0, CHERAB 1.4.0, Circuitscape 5.12.3, CLHEP 2.4.5.3, CLHEP 2.4.6.2, CmdStanR 0.5.2, CNVkit 0.9.10, corner 2.2.2, CppHeaderParser 2.7.4, CuCLARK 1.1, CUDA 12.1.1.eb, CUDA 12.2.0.eb, cuDNN 8.9.2.26, cutadapt 2.10, cutadapt 4.4, cuTENSOR 1.7.0.1, cuteSV 2.0.3, CVXOPT 1.3.1, DALI 2.1.2, DaliLite 4.1, Dalton 2020.1, datamash 1.8, deepTools 3.5.2, DEICODE 0.2.4, DendroPy 4.5.2, DIAMOND 2.1.8, dicom2nifti 2.3.0, DIRAC 23.0, DIRAC 23.0, dm haiku, DMTCP 3.0.0, dominate 2.8.0, dorado 0.3.0, dorado 0.3.1, dtcmp 1.1.4, duplex tools, dx toolkit, easel 0.48, EasyBuild 4.7.2.eb, ecFlow 5.7.0, EDirect 19.7.20230531, edlib 1.3.9, eggnog mapper, EIGENSOFT 7.2.1, elastix 5.0.0, ELPA 2021.11.001, Emacs 28.2, emcee 3.1.4, ETE 3.1.2, Exonerate 2.4.0, Extrae 4.0.4, FASTA 36.3.8i, fastp 0.20.1, fastp 0.23.4, FFTW 3.3.10, FFTW 3.3.10, FFTW.MPI 3.3.10, FLASH 2.2.00, flex 2.6.4, FlexiBLAS 3.3.1, FLUENT 2019R3.eb, fontconfig 2.14.2, foss 2023a.eb, FragPipe 20.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, freetype 2.13.0, GATE 9.2, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0.eb, GCCcore 11.4.0.eb, GCTA 1.94.1, GDRCopy 2.3.1, Geant4 11.0.2, Geant4 11.1.2, Geant4 data, GEM 1.5.1, GEM 1.5.1, gemelli 0.0.9, GEMMA 0.98.5, gengetopt 2.23, GenomeTools 1.6.2, GetOrganelle 1.7.7.0, gfbf 2023a.eb, gffread 0.12.7, git 2.41.0, glew 2.2.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GMAP GSNAP, GMAP GSNAP, GMP 6.2.1, gompi 2023a.eb, gperf 3.1, graphite2 1.3.14, GRIDSS 2.13.2, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2023.1, GROMACS 2023.1, GSL 2.7, Gurobi 10.0.1, HDF5 1.12.2, HDF5 1.12.2, help2man 1.49.3, hifiasm 0.19.5, Highway 1.0.4, HMMER 3.3.2, HOOMD blue, Horovod 0.25.0, HPL 2.3, HPL 2.3, hwloc 2.9.1, iimpi 2023a.eb, imagecodecs 2022.9.26, imkl FFTW, Infernal 1.1.4, intel 2023a.eb, InterProScan 5.62, intltool 0.51.0, IQ TREE, IQ TREE, ISA L, ITK 5.2.1, ITSTool 2.0.7, JAGS 4.3.2, jq 1.5, Julia 1.9.0, jxrlib 1.1, KerasTuner 1.3.5, kim api, LAMMPS 23Jun2022, LASTZ 1.02.00, LayoutParser 0.3.4, LayoutParser 0.3.4, LERC 4.0.0, libavif 0.11.1, libcircle 0.3, libde265 1.0.11, libevent 2.1.8, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, libpciaccess 0.17, libpspio 0.2.4, libpspio 0.2.4, libpspio 0.2.4, libSBML 5.19.0, libsodium 1.0.18, libtool 2.4.7, LISFLOOD FP, LISFLOOD FP, LMDB 0.9.29, LMfit 1.2.1, lpsolve 5.5.2.11, LSD2 2.4.1, LuaJIT 2.1.0, LuaRocks 3.9.2, lwgrp 1.0.5, lxml 4.9.2, M4 1.4.19, MAFFT 7.505, MAGeCK 0.5.9.5, mannkendall 1.1.1, MATLAB 2023a.eb, MaxQuant 2.4.2.0.eb, MCR R2022a.5.eb, MedPy 0.4.0, meshio 5.3.4, Meson 1.1.1, Mesquite 2.3.0, MetaEuk 6, minimap2 2.26, MITObim 1.9.1, MMseqs2 14, MOB suite, molecularGSM 20190826, MONAI Label, MONAI Label, MPFR 4.2.0, mpifileutils 0.11.1, MuJoCo 2.2.2, MultiQC 1.14, MUMmer 4.0.0rc1, MUSCLE 5.1.0, MUST 1.7.1, MView 1.67, NAMD 2.14, nanoget 1.18.1, nanomath 1.3.0, NanoStat 1.6.0, NanoStat 1.6.0, ncbi vdb, ncbi vdb, NCCL 2.18.3, NCO 5.0.6, ncurses 6.4.eb, netCDF 4.7.4, networkx 3.0, Nextflow 23.04.2.eb, ngspice 39, Ninja 1.11.1, nnU Net, ont fast5, OpenBLAS 0.3.23, OpenFOAM v2112, OpenMM 7.4.1, OpenMPI 4.1.5, OpenPGM 5.2.122, openpyxl 3.1.2, OSU Micro, oxDNA 3.5.2, pagmo 2.18.0, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, pastml 1.9.34, patchelf 0.18.0, pbipa 1.8.0, PEAR 0.9.11, Perl 5.36.1, Perl 5.36.1, Perl bundle, PheWeb 1.1.20, pigz 2.7, pkg config, plinkliftover 0.3.0, PLUMED 2.5.4, PLUMED 2.5.4, PMIx 4.2.4, pmt 1.1.0, popscle 0.1, popt 1.16, POT 0.9.0, prodigal 2.6.3, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyBioLib 1.1.988, PyCalib 20230531, Pychopper 2.3.1, pycocotools 2.0.6, pydicom seg, pyfaidx 0.7.2.1, pygmo 2.18.0, pyiron 0.3.0, pyMannKendall 1.4.3, PyOpenCL 2021.2.13, pypmt 1.1.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, pyspoa 0.0.9, Python 3.11.3, python isal, python mujoco, python parasail, PyTorch 1.13.1, pytorch CycleGAN, PyTorch Image, PyTorch Image, PyWBGT 1.0.0, PyWBGT 1.0.0, PyYAML 6.0, qcat 1.1.0, QuantumESPRESSO 6.6, rasterio 1.3.8, regionmask 0.10.0, RNA SeQC, ROOT 6.26.06, RSEM 1.3.3, Ruby 3.2.2, Rust 1.70.0, Safetensors 0.3.1, Safetensors 0.3.1, samblaster 0.1.26, ScaFaCoS 1.0.4, ScaLAPACK 2.2.0, scArches 0.5.6, segemehl 0.3.4, SEPP 4.5.1, seqtk 1.4, SimpleITK 2.1.0, Sniffles 2.0.7, SortMeRNA 2.1, SPAdes 3.15.4, spoa 4.0.7, spoa 4.0.7, SRA Toolkit, STAR 2.7.10b, stardist 0.8.3, statsmodels 0.14.0, strace 5.14, Structure_threader 1.3.10, subset bam, Subversion 1.14.2, SuiteSparse 5.13.0, SUNDIALS 6.2.0, SUNDIALS 6.2.0, SUNDIALS 6.5.1, SVclone 1.1.2, SVIM 2.0.0, Tapenade 3.16, TensorFlow 2.8.4, TensorFlow 2.9.1, TensorFlow 2.9.1, TensorFlow Graphics, tidymodels 1.1.0, timm 0.6.13, tmux 3.3a, tmux 3.3a, tmux 3.3a.eb, tokenizers 0.13.3, TopHat 2.1.2, TopHat 2.1.2, torchaudio 0.12.0, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2, Transformers 4.30.2, Triangle 1.6, Trinity 2.15.1, Trinotate 4.0.1, UCC 1.2.0, UCC CUDA, UCX 1.14.1, UCX CUDA, Ultralytics 8.0.92, util linux, VASP 6.3.2, visdom 0.2.4, Voro++ 0.4.6, VTK 9.0.1, VTK 9.2.6, WhatsHap 1.7, wrapt 1.15.0, wrapt 1.15.0, X11 20230603, xarray 2023.4.2, xclip 0.13, xdotool 3.20211022.1, Xerces C++, Xerces C++, XlsxWriter 3.1.2, XML LibXML, xorg macros, yaml cpp, Yasm 1.3.0, ZeroMQ 4.3.4, zfp 1.0.0, zlib 1.2.13, zlib ng, Zopfli 1.0.3
+  - 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)
   - enhance sanity check for recent LibTIFF easyconfigs (#17975)
-  - update JupyterLab v3.5.0 to set JUPYTERLAB_SETTINGS_DIR and JUPYTERLAB_WORKSPACES_DIR on module load (#17982)
-  - add RBesT extension to R 4.2.1 + 4.2.2 (+ missing epitools extension for R 4.2.2) (#18029)
-  - add svglite extension to R 4.2.1 + 4.2.2 (#18063)
-  - add FKSUM + haldensify extensions to R 4.2.2 (#18122)
+  - update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module (#17982)
   - use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167)
   - update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173)
-  - add Polychrome, shinycssloaders, princurve extensions to R 4.2.2 (#18195)
-  - add TrajectoryUtils + slingshot extensions to R-bundle-Bioconductor 3.16 (#18196)
-  - add extra packages to recent R easyconfigs (#18245)
-  - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18246)
+  - add extra packages to recent R easyconfigs (#18029, #18063, #18122, #18195, #18245)
+  - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18196, #18246)
 - various bug fixes, including:
   - add patches to fix TensorFlow 2.7.1 on POWER (#16795)
-  - fix TensorFlow-2.8.4-foss-2021b.eb (#17058)
+  - fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ foss/2021b (#17058)
   - stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998)
   - add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007)
   - fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030)
@@ -58,8 +73,7 @@ feature release
   - update homepage for NWChem 7.x (#18184)
   - update homepage for SUNDIALS 5.x and 6.x (#18186)
   - add missing source_urls for SimpleITK (#18212)
-  - patch oxDNA/oxpy to use correct pip install prefix (#18214)
-  - patch files for QT5-5.17.7-GCCcore-12.20.0.eb for SIGSTKSZ in glibc 2.34 (#18230)
+  - use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (#18230)
   - fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231)
   - fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235)
   - use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236)
@@ -68,17 +82,14 @@ feature release
   - update source url for pkgconf (#18271)
 - other changes:
   - stop running easyconfig unit tests with Python 2.7 (#18006)
-  - fix toolchain for networkx-3.0 foss-2022b -> gfbf-2022b (#18061)
+  - fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b) (#18061)
   - remove unused PyTorch patch (#18062)
-  - allow multiply dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098)
-  - use UCC 1.2.0 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18127)
-  - use PMIx 4.2.4 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18144)
-  - remove old UCC (1.1.0) from GCCcore 12.3.0 (#18145)
+  - allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098)
   - bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188)
   - remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222)
   - remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223)
   - remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260)
-  - change base for intel/2023.03 to GCCcore/12.3.0 (#18263)
+  - change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a) (#18263)
 
 
 v4.7.2 (27 May 2023)