unset `$CONDA_PREFIX` in configure step for Arrow by Flamefire · Pull Request #20414 · easybuilders/easybuild-easyconfigs

Flamefire · 2024-04-23T10:31:18Z

(created using eb --new-pr)

This fixes the configure process when a conda environment is active.

Relevant output from the configure step looks like:

-- Using CONDA approach to find dependencies
...
Using CONDA_PREFIX for ARROW_PACKAGE_PREFIX: /shared/earth/easybuild/rocky/8.4/x86_64/software/Mamba/23.1.0-4

jfgrimm · 2024-04-23T13:32:00Z

@Flamefire would you mind re-targetting this to the 5.0.x branch? this currently touches a lot of older easyconfigs, which have been archived in 5.0.x already

Flamefire · 2024-04-23T15:09:27Z

Test report by @Flamefire
FAILED
Build succeeded for 0 out of 14 (14 easyconfigs in total)
n1041 - Linux RHEL 8.7 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (icelake), Python 3.8.13
See https://gist.github.com/Flamefire/c5af556d8c3e1286986050ce5460acde for a full test report.

Flamefire · 2024-04-23T15:22:55Z

Turns out this option is too useful. If set it will not download/use any of the bundled software and hence will fail. If not set it might use conda if $CONDA_PREFIX is set in the environment.

So only thing we could do is preconfigopts = "unset CONDA_PREFIX; " which should fix the issue of Arrow not finding Snappy as it was trying to search the conda env.

Flamefire · 2024-04-23T16:33:15Z

Test report by @Flamefire
FAILED
Build succeeded for 13 out of 14 (14 easyconfigs in total)
n1539 - Linux RHEL 8.7 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (icelake), Python 3.8.13
See https://gist.github.com/Flamefire/45ddf4ed26ee1b8f2f00b2e89f9980b6 for a full test report.

Flamefire · 2024-04-24T07:49:03Z

Failure due to changed defaults in PythonPackage as I was installing in EB 4

jfgrimm · 2024-04-24T08:17:54Z

@boegelbot please test @ generoso
CORE_CNT=16

boegelbot · 2024-04-24T08:20:05Z

@jfgrimm: Request for testing this PR well received on login1

PR test command 'EB_PR=20414 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_20414 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 13354

Test results coming soon (I hope)...

Details

- notification for comment with ID 2074358097 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-04-24T10:16:22Z

Test report by @boegelbot
FAILED
Build succeeded for 11 out of 14 (14 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/b4b4056a14e15154be2e9abb1e13c9d6 for a full test report.

Flamefire · 2024-04-24T12:02:03Z

Test report by @boegelbot FAILED Build succeeded for 11 out of 14 (14 easyconfigs in total) cnx1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8 See https://gist.github.com/boegelbot/b4b4056a14e15154be2e9abb1e13c9d6 for a full test report.

Same issue here: 4.x -> 5.x changes

jfgrimm · 2024-04-24T12:09:15Z

hmm, I thought the bot used 5.0.x for PRs targetting that branch

branfosj · 2024-04-24T12:11:04Z

hmm, I thought the bot used 5.0.x for PRs targetting that branch

It is not automatatic and on jsc-zen3 only (I believe).

branfosj · 2024-04-24T12:11:28Z

@boegelbot please test @ jsc-zen3
CORE_CNT=16
EB_BRANCH=5.0.x

jfgrimm · 2024-04-24T12:13:31Z

hmm, I thought the bot used 5.0.x for PRs targetting that branch

It is not automatatic and on jsc-zen3 only (I believe).

thanks, haven't done anything on the 5.0.x easyconfigs branch for a while

boegelbot · 2024-04-24T12:20:14Z

@branfosj: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ "5.0.x" != 'develop' ]]; then EB_BRANCH="5.0.x" ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/"5.0.x" source init_env_easybuild_develop.sh; fi; EB_PR=20414 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH="5.0.x" /opt/software/slurm/bin/sbatch --job-name test_PR_20414 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 4029

Test results coming soon (I hope)...

Details

- notification for comment with ID 2074800172 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-04-24T15:56:00Z

Test report by @boegelbot
FAILED
Build succeeded for 26 out of 56 (14 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/8964ad34250089166ae00cf3026f3091 for a full test report.

Flamefire · 2024-04-25T07:26:26Z

Test report by @boegelbot FAILED Build succeeded for 26 out of 56 (14 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18 See https://gist.github.com/boegelbot/8964ad34250089166ae00cf3026f3091 for a full test report.

Unrelated issue when building CMake:

The C++ compiler does not support C++11 (e.g. std::unique_ptr).

github-actions · 2025-03-20T14:22:00Z

Updated software `Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb`

Diff against Boltz-1-0.4.1-foss-2023a.eb

easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb

diff --git a/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb b/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb
index 3d6b0c2a23..e0501d7ab9 100644
--- a/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb
+++ b/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb
@@ -2,6 +2,7 @@ easyblock = 'PythonBundle'
 
 name = 'Boltz-1'
 version = '0.4.1'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/jwohlwend/boltz'
 description = """
@@ -15,14 +16,15 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [('hatchling', '1.18.0')]
 dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
     ('SciPy-bundle', '2023.07'),
     ('Biopython', '1.83'),
     ('PyYAML', '6.0'),
-    ('PyTorch', '2.1.2'),
+    ('PyTorch', '2.1.2', versionsuffix),
     ('Hydra', '1.3.2'),
-    ('PyTorch-Lightning', '2.2.1'),
+    ('PyTorch-Lightning', '2.2.1', versionsuffix),
     ('RDKit', '2024.03.3'),
     ('dm-tree', '0.1.8'),
     ('einops', '0.7.0'),
@@ -38,7 +40,6 @@ local_preinstallopts = (
     "'s/pandas>=2.2.2/pandas/g' "
     "pyproject.toml && "
 )
-
 exts_list = [
     ('urllib3', '2.0.7', {
         'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'],

Updated software `Boltz-1-0.4.1-foss-2023a.eb`

Diff against Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb
index e0501d7ab9..3d6b0c2a23 100644
--- a/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb
@@ -2,7 +2,6 @@ easyblock = 'PythonBundle'
 
 name = 'Boltz-1'
 version = '0.4.1'
-versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/jwohlwend/boltz'
 description = """
@@ -16,15 +15,14 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 builddependencies = [('hatchling', '1.18.0')]
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),
     ('SciPy-bundle', '2023.07'),
     ('Biopython', '1.83'),
     ('PyYAML', '6.0'),
-    ('PyTorch', '2.1.2', versionsuffix),
+    ('PyTorch', '2.1.2'),
     ('Hydra', '1.3.2'),
-    ('PyTorch-Lightning', '2.2.1', versionsuffix),
+    ('PyTorch-Lightning', '2.2.1'),
     ('RDKit', '2024.03.3'),
     ('dm-tree', '0.1.8'),
     ('einops', '0.7.0'),
@@ -40,6 +38,7 @@ local_preinstallopts = (
     "'s/pandas>=2.2.2/pandas/g' "
     "pyproject.toml && "
 )
+
 exts_list = [
     ('urllib3', '2.0.7', {
         'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'],

Updated software `CheckM-1.2.3-foss-2023b.eb`

Diff against CheckM-1.0.18-foss-2023a-Python-2.7.18.eb

easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.2.3-foss-2023b.eb
index c6ec903a1e..62c22732f0 100644
--- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2023a-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.2.3-foss-2023b.eb
@@ -1,52 +1,35 @@
 # Updated from previous config
 # Author: Pavel Grochal (INUITS)
+# Updated by: Filip Kružík (INUITS)
 # License: GPLv2
-# Update: Petr Král (INUITS)
 
 easyblock = 'PythonPackage'
 
 name = 'CheckM'
-version = '1.0.18'
-versionsuffix = '-Python-%(pyver)s'
+version = '1.2.3'
 
 homepage = 'https://github.com/Ecogenomics/CheckM'
-description = """CheckM provides a set of tools for assessing the quality of
-genomes recovered from isolates, single cells, or metagenomes."""
+description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates,
+ single cells, or metagenomes."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
-source_urls = [
-    'https://pypi.python.org/packages/source/c/checkm-genome',
-    'https://data.ace.uq.edu.au/public/CheckM_databases/',
-]
-sources = [
-    'checkm-genome-%(version)s.tar.gz',
-    {
-        'filename': 'checkm_data_2015_01_16.tar.gz',
-        'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s",
-    },
-]
-checksums = [
-    '0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7',  # checkm-genome-1.0.18.tar.gz
-    '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c',  # checkm_data_2015_01_16.tar.gz
-]
+source_urls = ['https://github.com/Ecogenomics/CheckM/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['5f8340e71d3256ba8cf407d27bdc7914d1aa86b14b2d63d1e32cceb325e5aa82']
 
+# Dependencies:
+# https://github.com/Ecogenomics/CheckM/blob/master/setup.py
 dependencies = [
-    ('Python', '2.7.18'),
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # numpy
     ('pplacer', '1.1.alpha19', '', SYSTEM),
     ('prodigal', '2.6.3'),
     ('HMMER', '3.4'),
-    ('SciPy-bundle', '2024.06', versionsuffix),
-    ('matplotlib', '2.2.5', versionsuffix),
-    ('Pysam', '0.20.0', versionsuffix),
-    ('DendroPy', '4.5.2', versionsuffix),
-]
-
-# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm
-postinstallcmds = [
-    "cp -a %(builddir)s/data %(installdir)s",
-    "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH "
-    "%(installdir)s/bin/checkm data setRoot %(installdir)s/data",
+    ('matplotlib', '3.8.2'),
+    ('Pysam', '0.22.0'),
+    ('DendroPy', '5.0.1'),
+    ('CheckM-Database', '2015_01_16', '', SYSTEM),
 ]
 
 sanity_check_paths = {

Updated software `CompareM-0.1.2-gfbf-2023b.eb`

Diff against CompareM-0.1.2-foss-2021b.eb

easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb

diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-gfbf-2023b.eb
index 9285994f57..ec81930b0c 100644
--- a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb
+++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-gfbf-2023b.eb
@@ -6,19 +6,17 @@ version = '0.1.2'
 homepage = 'https://github.com/dparks1134/CompareM'
 description = "A toolbox for comparative genomics."
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'gfbf', 'version': '2023b'}
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('matplotlib', '3.4.3'),
-    ('DIAMOND', '2.0.13'),
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),
+    ('matplotlib', '3.8.2'),
+    ('DIAMOND', '2.1.9'),
     ('prodigal', '2.6.3'),
 ]
 
 exts_list = [
-    ('future', '0.18.2', {
-        'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'],
-    }),
     ('biolib', '0.1.9', {
         'checksums': ['bc9ae68c6d76d46e4295fe0b1df5a48b575fe96374bd96d624c3330feb94856f'],
     }),

Updated software `DAS_Tool-1.1.7-foss-2023b-R-4.4.1.eb`

Diff against DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb

easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb

diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.7-foss-2023b-R-4.4.1.eb
index 4e5773b4b1..cafdb364b3 100644
--- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb
+++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.7-foss-2023b-R-4.4.1.eb
@@ -1,58 +1,66 @@
 easyblock = 'Tarball'
 
 name = 'DAS_Tool'
-version = '1.1.3'
+version = '1.1.7'
 versionsuffix = '-R-%(rver)s'
 
 homepage = 'https://github.com/cmks/DAS_Tool'
 description = """DAS Tool is an automated method that integrates the results of a flexible number of binning
  algorithms to calculate an optimized, non-redundant set of bins from a single assembly."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023b'}
 
 source_urls = ['https://github.com/cmks/DAS_Tool/archive/']
 sources = ['%(version)s.tar.gz']
-patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch']
+patches = ['DAS_Tool-1.1.7_defaultSearchEngBLAST+.patch']
 checksums = [
-    'c2d41a38a7a92d53d412ac3f2b8ab5b9fa64c56021aa5c4dd51fefd7c96b68f4',  # 1.1.3.tar.gz
-    'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a',  # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch
+    {'1.1.7.tar.gz': '3633b69242209ceee9cd523e3458adbe89da9c52ecd8724afef2e2099923c56c'},
+    {'DAS_Tool-1.1.7_defaultSearchEngBLAST+.patch': '5bee64984892910d0b68b73a517929f32abf0be7cb4786f1f7233ac56c70398b'},
 ]
 
 dependencies = [
-    ('R', '4.1.0'),
-    ('Python', '3.9.5'),
-    ('Ruby', '3.0.1'),
+    ('R', '4.4.1'),
+    ('Python', '3.11.5'),
+    ('R-bundle-CRAN', '2024.06'),
+    ('Ruby', '3.4.2'),
     ('pullseq', '1.0.2'),
     ('prodigal', '2.6.3'),
-    ('BLAST+', '2.11.0'),
+    ('BLAST+', '2.16.0'),
 ]
 
 exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'source_urls': [
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+}
 
 exts_list = [
-    (name, version, {
-        'modulename': 'DASTool',
-        'source_tmpl': 'DASTool_%(version)s.tar.gz',
-        'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'],
-        'checksums': ['050ba4fa061ceb398a6881652b4b5f14736581a35edd00ef9ae4cea986f38d18'],
+    ('docopt', '0.7.1', {
+        'checksums': ['9f473887e4607e9b21fd4ab02e802858d0ac2ca6dad9e357a9d884a47fe4b0ff'],
     }),
 ]
 
 postinstallcmds = [
     "cd %(installdir)s && unzip db.zip -d db",
     "chmod a+x %(installdir)s/DAS_Tool",
+    "chmod a+x %(installdir)s/src/*.sh",
+    "chmod a+x %(installdir)s/src/*.rb",
 ]
 
 sanity_check_paths = {
     'files': ['DAS_Tool', 'db/arc.all.faa', 'db/arc.scg.lookup'],
-    'dirs': ['DASTool/R'],
+    'dirs': ['src'],
 }
 
 # Help gets printed correctly, but the error code is 1
-sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version]
+sanity_check_commands = ['DAS_Tool -v | grep "DAS Tool %s"' % version]
 
 modextrapaths = {
-    'PATH': '',
+    'PATH': ['src', ''],
     'R_LIBS_SITE': '',
 }

Updated software `DendroPy-5.0.1-GCCcore-13.2.0.eb`

Diff against DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-5.0.1-GCCcore-13.2.0.eb
index 9d1f416412..373072cd66 100644
--- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.3.0-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-5.0.1-GCCcore-13.2.0.eb
@@ -7,26 +7,24 @@
 # $Id$
 #
 ##
-# Update: Petr Král (INUITS)
 easyblock = 'PythonPackage'
 
 name = 'DendroPy'
-version = '4.5.2'
-versionsuffix = '-Python-%(pyver)s'
+version = '5.0.1'
 
 homepage = 'https://dendropy.org/'
 description = """A Python library for phylogenetics and phylogenetic computing:
 reading, writing, simulation, processing and manipulation of phylogenetic trees
 (phylogenies) and characters."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 sources = [SOURCE_TAR_GZ]
-checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101']
+checksums = ['f2815e7649a6fe2924ff3fdf00a660c948dc6f3316e303b8b022f74cc75ca42e']
 
 builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Python', '2.7.18')]
+dependencies = [('Python', '3.11.5')]
 
 fix_python_shebang_for = ['bin/*.py']

Updated software `EasyBuild-5.0.0.eb`

Diff against EasyBuild-0.5.0.0beta2.eb

easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta2.eb

diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0.eb
index 20b240d70a..18d894aa77 100644
--- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-0.5.0.0beta2.eb
+++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.0.0.eb
@@ -1,50 +1,47 @@
 easyblock = 'EB_EasyBuildMeta'
 
 name = 'EasyBuild'
-version = '0.5.0.0beta2'
+version = '5.0.0'
 
-homepage = 'https://easybuild.io'
+homepage = 'https://easybuilders.github.io/easybuild'
 description = """EasyBuild is a software build and installation framework
  written in Python that allows you to install software in a structured,
  repeatable and robust way."""
 
 toolchain = SYSTEM
 
+source_urls = [
+    # easybuild-framework
+    'https://files.pythonhosted.org/packages/6b/1d/4b81b9f5f64fa9ba364f3a328410c8fa3657c7d2f49ac542e5eb12d8ae31/',
+    # easybuild-easyblocks
+    'https://files.pythonhosted.org/packages/38/dd/403149f8543f80399e2ab021465b1e3a500616bcc74ceba26ddbdc8ea757/',
+    # easybuild-easyconfigs
+    'https://files.pythonhosted.org/packages/5b/e4/db43afd003d83eb20de8c1f7745eaeddc6a559d95d066ad3bef69c751862/',
+]
+# note: subdirectory for each unpacked source tarball is renamed because custom easyblock in older EasyBuild version
+# that is used for installing EasyBuild with EasyBuild expects subdirectories with '-' rather than '_';
+# see also https://github.com/easybuilders/easybuild-easyblocks/pull/3358
 sources = [
     {
-        'filename': 'easybuild-framework-v%s.tar.gz' % version[2:],
-        'git_config': {
-            'url': 'https://github.com/easybuilders',
-            'repo_name': 'easybuild-framework',
-            'tag': 'easybuild-framework-v%s' % version[2:],
-            'keep_git_dir': True,
-        },
+        'filename': 'easybuild_framework-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_framework-%(version)s easybuild-framework-%(version)s",
     },
     {
-        'filename': 'easybuild-easyblocks-v%s.tar.gz' % version[2:],
-        'git_config': {
-            'url': 'https://github.com/easybuilders',
-            'repo_name': 'easybuild-easyblocks',
-            'tag': 'easybuild-easyblocks-v%s' % version[2:],
-            'keep_git_dir': True,
-        },
+        'filename': 'easybuild_easyblocks-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_easyblocks-%(version)s easybuild-easyblocks-%(version)s",
     },
     {
-        'filename': 'easybuild-easyconfigs-v%s.tar.gz' % version[2:],
-        'git_config': {
-            'url': 'https://github.com/easybuilders',
-            'repo_name': 'easybuild-easyconfigs',
-            'tag': 'easybuild-easyconfigs-v%s' % version[2:],
-            'keep_git_dir': True,
-        },
+        'filename': 'easybuild_easyconfigs-%(version)s.tar.gz',
+        'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s",
     },
 ]
 checksums = [
-    None,
-    None,
-    None,
+    {'easybuild_framework-5.0.0.tar.gz': '7c1a40ad7aab135aeb316f78d5b16232604cd455e0bdf44f0a4d2b3552a41484'},
+    {'easybuild_easyblocks-5.0.0.tar.gz': '691facfa259172eea40dbcffde9f253927b95f71507e28c7d8fb4cf023a5c091'},
+    {'easybuild_easyconfigs-5.0.0.tar.gz': '3a15933e42a01badbf3d5aed3596a8f76f96fac1d5b56149e5be12bf4d7bef7c'},
 ]
 
+# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?)
 # EasyBuild is a (set of) Python packages, so it depends on Python
 # usually, we want to use the system Python, so no actual Python dependency is listed
 allow_system_deps = [('Python', SYS_PYTHON_VERSION)]

Updated software `FragGeneScan-1.32-GCCcore-13.2.0.eb`

Diff against FragGeneScan-1.31-GCCcore-12.3.0.eb

easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.32-GCCcore-13.2.0.eb
index 8466e596a3..01aadb816e 100644
--- a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.32-GCCcore-13.2.0.eb
@@ -1,20 +1,20 @@
 easyblock = 'MakeCp'
 
 name = 'FragGeneScan'
-version = '1.31'
+version = '1.32'
 
 homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/'
 description = "FragGeneScan is an application for finding (fragmented) genes in short reads."
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = ['%(name)s%(version)s.tar.gz']
-checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c']
+checksums = ['54db8dab643f791aae7b05c310fe0d88ecb07db306211185c4c8524734f334c4']
 
 builddependencies = [('binutils', '2.40')]
 
-dependencies = [('Perl', '5.36.1')]
+dependencies = [('Perl', '5.38.0')]
 
 fix_perl_shebang_for = ['*.pl']

Updated software `IDBA-UD-1.1.3-GCCcore-13.2.0.eb`

Diff against IDBA-UD-1.1.3-GCCcore-12.3.0.eb

easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-13.2.0.eb
index 83d24a82ee..64328da2a8 100644
--- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-13.2.0.eb
@@ -24,7 +24,7 @@ locally to generate some missing k-mers in low-depth regions. With these technol
 can iterate k value of de Bruijn graph to a very large value with less gaps and less branches
 to form long contigs in both low-depth and high-depth regions."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s']
 sources = ['idba-%(version)s.tar.gz']

Updated software `idemux-0.1.6-GCCcore-12.3.0.eb`

Diff against idemux-0.1.6-GCCcore-10.2.0.eb

easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb

diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-12.3.0.eb
index c801e2d60d..287a89f83e 100644
--- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb
+++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-12.3.0.eb
@@ -1,5 +1,6 @@
 # Author: Pavel Grochal (INUITS)
 # License: GPLv2
+# Update: Petr Král (INUITS)
 
 easyblock = 'PythonBundle'
 
@@ -10,24 +11,22 @@ homepage = 'https://github.com/Lexogen-Tools/idemux'
 description = """idemux - inline barcode demultiplexing
 Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool."""
 
-toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 builddependencies = [
-    ('binutils', '2.35'),
+    ('binutils', '2.40'),
 ]
 
 dependencies = [
-    ('Python', '3.8.6'),
-    ('coverage', '5.5'),
+    ('Python', '3.11.3'),
+    ('coverage', '7.2.3'),
+    ('tqdm', '4.66.1'),
 ]
 
 exts_list = [
-    ('pytest-runner', '5.3.0', {
+    ('pytest-runner', '6.0.1', {
         'modulename': 'ptr',
-        'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'],
-    }),
-    ('tqdm', '4.60.0', {
-        'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'],
+        'checksums': ['70d4739585a7008f37bf4933c013fdb327b8878a5a69fcbb3316c88882f0f49b'],
     }),
     (name, version, {
         'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'],

Updated software `MaxBin-2.2.7-gompi-2023b.eb`

Diff against MaxBin-2.2.7-gompi-2023a-Python-2.7.18.eb

easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2023a-Python-2.7.18.eb

diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2023b.eb
index afcf7432a6..cdf029c7db 100644
--- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2023a-Python-2.7.18.eb
+++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2023b.eb
@@ -2,26 +2,22 @@ easyblock = 'MakeCp'
 
 name = 'MaxBin'
 version = '2.2.7'
-versionsuffix = '-Python-%(pyver)s'
 
 # https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work
 homepage = 'https://sourceforge.net/projects/maxbin/'
 description = """MaxBin is software for binning assembled metagenomic sequences
 based on an Expectation-Maximization algorithm."""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2023b'}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = [SOURCE_TAR_GZ]
 checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e']
 
-builddependencies = [('binutils', '2.40')]
-
 dependencies = [
-    ('Python', '2.7.18'),
-    ('Perl', '5.36.1'),
-    ('Bowtie2', '2.5.4', versionsuffix),
-    ('FragGeneScan', '1.31'),
+    ('Perl', '5.38.0'),
+    ('Bowtie2', '2.5.4'),
+    ('FragGeneScan', '1.32'),
     ('HMMER', '3.4'),
     ('IDBA-UD', '1.1.3'),
 ]

Updated software `PyTorch-2.3.0-foss-2023b.eb`

Diff against PyTorch-2.1.2-foss-2023b.eb

easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.3.0-foss-2023b.eb
index b4b25bd33e..308397336a 100644
--- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.3.0-foss-2023b.eb
@@ -1,5 +1,5 @@
 name = 'PyTorch'
-version = '2.1.2'
+version = '2.3.0'
 
 homepage = 'https://pytorch.org/'
 description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration.
@@ -11,7 +11,6 @@ source_urls = [GITHUB_RELEASE]
 sources = ['%(namelower)s-v%(version)s.tar.gz']
 patches = [
     'PyTorch-1.7.0_disable-dev-shm-test.patch',
-    'PyTorch-1.11.1_skip-test_init_from_local_shards.patch',
     'PyTorch-1.12.1_add-hypothesis-suppression.patch',
     'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch',
     'PyTorch-1.12.1_fix-TestTorch.test_to.patch',
@@ -23,39 +22,34 @@ patches = [
     'PyTorch-1.13.1_skip-tests-without-fbgemm.patch',
     'PyTorch-2.0.1_avoid-test_quantization-failures.patch',
     'PyTorch-2.0.1_fix-skip-decorators.patch',
-    'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch',
     'PyTorch-2.0.1_fix-vsx-loadu.patch',
-    'PyTorch-2.0.1_no-cuda-stubs-rpath.patch',
     'PyTorch-2.0.1_skip-failing-gradtest.patch',
     'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch',
     'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch',
-    'PyTorch-2.1.0_disable-gcc12-warning.patch',
-    'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch',
-    'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch',
-    'PyTorch-2.1.0_fix-validationError-output-test.patch',
     'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch',
     'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch',
-    'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch',
     'PyTorch-2.1.0_remove-test-requiring-online-access.patch',
     'PyTorch-2.1.0_skip-diff-test-on-ppc.patch',
     'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch',
     'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch',
-    'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch',
-    'PyTorch-2.1.0_skip-test_wrap_bad.patch',
-    'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch',
-    'PyTorch-2.1.2_fix-test_memory_profiler.patch',
-    'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch',
-    'PyTorch-2.1.2_fix-vsx-vector-abs.patch',
-    'PyTorch-2.1.2_fix-vsx-vector-div.patch',
     'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch',
-    'PyTorch-2.1.2_skip-memory-leak-test.patch',
     'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch',
+    'PyTorch-2.3.0_disable_test_linear_package_if_no_half_types_are_available.patch',
+    'PyTorch-2.3.0_disable_DataType_dependent_test_if_tensorboard_is_not_available.patch',
+    'PyTorch-2.3.0_skip-test_init_from_local_shards.patch',
+    'PyTorch-2.3.0_no-cuda-stubs-rpath.patch',
+    'PyTorch-2.3.0_disable-gcc12-warning.patch',
+    'PyTorch-2.3.0_fix-test_extension_backend-without-vectorization.patch',
+    'PyTorch-2.3.0_disable_tests_which_need_network_download.patch',
+    'PyTorch-2.3.0_avoid_caffe2_test_cpp_jit.patch',
+    'PyTorch-2.3.0_fix_missing_masked_load_for_int_type.patch',
+    'PyTorch-2.3.0_skip_test_var_mean_differentiable.patch',
+    'PyTorch-2.3.0_skip_test_sdpa_nn_functional_scaled_dot_product_attention_cpu.patch',
+    'PyTorch-2.3.0_fix-mkldnn-avx512-f32-bias.patch',
 ]
 checksums = [
-    {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'},
+    {'pytorch-v2.3.0.tar.gz': '69579513b26261bbab32e13b7efc99ad287fcf3103087f2d4fdf1adacd25316f'},
     {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'},
-    {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch':
-     '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'},
     {'PyTorch-1.12.1_add-hypothesis-suppression.patch':
      'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'},
     {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch':
@@ -75,28 +69,16 @@ checksums = [
     {'PyTorch-2.0.1_avoid-test_quantization-failures.patch':
      '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'},
     {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'},
-    {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch':
-     '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'},
     {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'},
-    {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'},
     {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'},
     {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch':
      '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'},
     {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch':
      '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'},
-    {'PyTorch-2.1.0_disable-gcc12-warning.patch': 'c858b8db0010f41005dc06f9a50768d0d3dc2d2d499ccbdd5faf8a518869a421'},
-    {'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch':
-     'b15b1291a3c37bf6a4982cfbb3483f693acb46a67bc0912b383fd98baf540ccf'},
-    {'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch':
-     '84bb51a719abc677031a7a3dfe4382ff098b0cbd8b39b8bed2a7fa03f80ac1e9'},
-    {'PyTorch-2.1.0_fix-validationError-output-test.patch':
-     '7eba0942afb121ed92fac30d1529447d892a89eb3d53c565f8e9d480e95f692b'},
     {'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch':
      '3793b4b878be1abe7791efcbd534774b87862cfe7dc4774ca8729b6cabb39e7e'},
     {'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch':
      'aef38adf1210d0c5455e91d7c7a9d9e5caad3ae568301e0ba9fc204309438e7b'},
-    {'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch':
-     '0ac36411e76506b3354c85a8a1260987f66af947ee52ffc64230aee1fa02ea8b'},
     {'PyTorch-2.1.0_remove-test-requiring-online-access.patch':
      '35184b8c5a1b10f79e511cc25db3b8a5585a5d58b5d1aa25dd3d250200b14fd7'},
     {'PyTorch-2.1.0_skip-diff-test-on-ppc.patch': '394157dbe565ffcbc1821cd63d05930957412156cc01e949ef3d3524176a1dda'},
@@ -104,22 +86,34 @@ checksums = [
      '6298daf9ddaa8542850eee9ea005f28594ab65b1f87af43d8aeca1579a8c4354'},
     {'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch':
      '5229ca88a71db7667a90ddc0b809b2c817698bd6e9c5aaabd73d3173cf9b99fe'},
-    {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch':
-     '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'},
-    {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'},
-    {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch':
-     'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'},
-    {'PyTorch-2.1.2_fix-test_memory_profiler.patch':
-     '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'},
-    {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch':
-     'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'},
-    {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'},
-    {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'},
     {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch':
      '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'},
-    {'PyTorch-2.1.2_skip-memory-leak-test.patch': '8d9841208e8a00a498295018aead380c360cf56e500ef23ca740adb5b36de142'},
     {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch':
      'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'},
+    {'PyTorch-2.3.0_disable_test_linear_package_if_no_half_types_are_available.patch':
+     '23416f2d9d5226695ec3fbea0671e3650c655c19deefd3f0f8ddab5afa50f485'},
+    {'PyTorch-2.3.0_disable_DataType_dependent_test_if_tensorboard_is_not_available.patch':
+     '0dcbdfde6752c3ff54c5376f521b4a742167669feb7f0f1d4e1d4d55f72b664f'},
+    {'PyTorch-2.3.0_skip-test_init_from_local_shards.patch':
+     '90ed9c2870f57ee6dc032d00873a37e2217a2b92a13035ded1c25ad5306455f2'},
+    {'PyTorch-2.3.0_no-cuda-stubs-rpath.patch':
+     '7ba26824b5def7379cff02ae821a080698e6affea0da45bc846e9ecb89939cb1'},
+    {'PyTorch-2.3.0_disable-gcc12-warning.patch':
+     'a8a624e1a2a5f4c82610173e50bd0f853e49bd5621b432f5aac689f9f6eb1514'},
+    {'PyTorch-2.3.0_fix-test_extension_backend-without-vectorization.patch':
+     '36aa2d5ba175be17f4e996f4fb2d544fe477d4a0bd0644cd59a85063779afc8e'},
+    {'PyTorch-2.3.0_disable_tests_which_need_network_download.patch':
+     'b7fd1a5135dfd4098cdc054182f7bf84a23ac98462a00477712182b5442da855'},
+    {'PyTorch-2.3.0_avoid_caffe2_test_cpp_jit.patch':
+     '041adcd91d994b8c2ab57d227f081cd57e572c157117b37171e1eb8eb576f8fc'},
+    {'PyTorch-2.3.0_fix_missing_masked_load_for_int_type.patch':
+     'aa6ff764f3f7bf84372a8a257fe1b4ae6dc4b9744ad35f0f9015f2696c62a41e'},
+    {'PyTorch-2.3.0_skip_test_var_mean_differentiable.patch':
+     '9703fd0f1fca8916f6d79d83e9a7efe8e3f717362a5fdaa8f5d9da90d0c75018'},
+    {'PyTorch-2.3.0_skip_test_sdpa_nn_functional_scaled_dot_product_attention_cpu.patch':
+     '7955f2655db3da18606574fdcbc5990be24098f49ad1db5e86ea756ea1cc506f'},
+    {'PyTorch-2.3.0_fix-mkldnn-avx512-f32-bias.patch':
+     'ee07d21c3ac7aeb0bd0e39507b18a417b9125284a529102929c4b5c6727c2976'},
 ]
 
 osdependencies = [OS_PKG_IBVERBS_DEV]
@@ -131,6 +125,9 @@ builddependencies = [
     ('pytest-flakefinder', '1.1.0'),
     ('pytest-rerunfailures', '14.0'),
     ('pytest-shard', '0.1.2'),
+    ('tlparse', '0.3.5'),
+    ('optree', '0.13.0'),
+    ('unittest-xml-reporting', '3.1.0'),
 ]
 
 dependencies = [
@@ -169,15 +166,24 @@ excluded_tests = {
         # intermittent failures on various systems
         # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712
         'distributed/rpc/test_tensorpipe_agent',
+        # This test is expected to fail when run in their CI, but won't in our case.
+        # It just checks for a "CI" env variable
+        'test_ci_sanity_check_fail',
+        # This fails consistently and is disabled upstream
+        # See https://github.com/pytorch/pytorch/issues/100152 and
+        # https://github.com/pytorch/pytorch/pull/124712
+        'test_cpp_extensions_open_device_registration',
+
     ]
 }
 
-runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error  --verbose %(excluded_tests)s'
+local_test_opts = '--continue-through-error --pipe-logs --verbose %(excluded_tests)s'
+runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py ' + local_test_opts
 
 # Especially test_quantization has a few corner cases that are triggered by the random input values,
 # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030
 # So allow a low number of tests to fail as the tests "usually" succeed
-max_failed_tests = 2
+max_failed_tests = 6
 
 tests = ['PyTorch-check-cpp-extension.py']

Updated software `PyVista-0.44.2-foss-2024a.eb`

Diff against PyVista-0.43.8-foss-2022a.eb

easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb

diff --git a/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb b/easybuild/easyconfigs/p/PyVista/PyVista-0.44.2-foss-2024a.eb
index 7dcea9255c..558796e254 100644
--- a/easybuild/easyconfigs/p/PyVista/PyVista-0.43.8-foss-2022a.eb
+++ b/easybuild/easyconfigs/p/PyVista/PyVista-0.44.2-foss-2024a.eb
@@ -1,21 +1,22 @@
 easyblock = 'PythonBundle'
 
 name = 'PyVista'
-version = '0.43.8'
+version = '0.44.2'
 
 homepage = 'https://docs.pyvista.org/'
 description = """
 3D plotting and mesh analysis through a streamlined interface for the
 Visualization Toolkit (VTK)"""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('VTK', '9.2.2'),
-    ('imageio', '2.22.2'),
-    ('matplotlib', '3.5.2'),
-    ('Pillow', '9.1.1'),
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+    ('VTK', '9.3.1'),  # require vtk<9.4.0
+    ('imageio', '2.36.1'),
+    ('matplotlib', '3.9.2'),
+    ('Pillow', '10.4.0'),
 ]
 
 exts_list = [
@@ -28,21 +29,12 @@ exts_list = [
     ('colorcet', '3.1.0', {
         'checksums': ['2921b3cd81a2288aaf2d63dbc0ce3c26dcd882e8c389cc505d6886bf7aa9a4eb'],
     }),
-    ('commonmark', '0.9.1', {
-        'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'],
-    }),
-    ('rich', '12.6.0', {
-        'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'],
-    }),
     ('meshio', '5.3.5', {
         'checksums': ['f21f01abd9f29ba06ea119304b3d39e610421cfe93b9dd23362834919f87586d'],
     }),
-    ('pooch', '1.6.0', {
-        'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'],
-    }),
     ('pyvista', version, {
         'use_pip_extras': 'colormaps,io',
-        'checksums': ['b9220753ae94fb8ca3047d291a706a4046b06659016c0000c184b5f24504f8d0'],
+        'checksums': ['db65943c3c1c9ba49fe16f5a25a5bc23b74bf1ea7a38aae4ef9c4dc5838ccf5e'],
     }),
 ]

Updated software `pairtools-1.1.2-gfbf-2023a.eb`

Diff against pairtools-1.1.2-gfbf-2024a.eb

easybuild/easyconfigs/p/pairtools/pairtools-1.1.2-gfbf-2024a.eb

diff --git a/easybuild/easyconfigs/p/pairtools/pairtools-1.1.2-gfbf-2024a.eb b/easybuild/easyconfigs/p/pairtools/pairtools-1.1.2-gfbf-2023a.eb
index 55a37d3cad..c1580fc017 100644
--- a/easybuild/easyconfigs/p/pairtools/pairtools-1.1.2-gfbf-2024a.eb
+++ b/easybuild/easyconfigs/p/pairtools/pairtools-1.1.2-gfbf-2023a.eb
@@ -8,20 +8,20 @@ description = """pairtools is a simple and fast command-line framework to proces
  from a Hi-C experiment. pairtools perform various operations on Hi-C pairs and
  occupy the middle position in a typical Hi-C data processing pipeline."""
 
-toolchain = {'name': 'gfbf', 'version': '2024a'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 
 builddependencies = [
-    ('Cython', '3.0.10'),
+    ('Cython', '3.0.7'),
 ]
 
 dependencies = [
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('matplotlib', '3.9.2'),
-    ('Pysam', '0.22.1'),
-    ('PyYAML', '6.0.2'),
-    ('hatchling', '1.24.2'),
-    ('Python-bundle-PyPI', '2024.06'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('matplotlib', '3.7.2'),
+    ('Pysam', '0.22.0'),
+    ('PyYAML', '6.0'),
+    ('hatchling', '1.18.0'),
 ]
 
 exts_list = [

Updated software `prodigal-2.6.3-GCCcore-13.2.0.eb`

Diff against prodigal-2.6.3-GCCcore-12.3.0.eb

easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb
index 09e71ae376..22a2163f6d 100644
--- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-13.2.0.eb
@@ -22,7 +22,7 @@ description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm
    is a microbial (bacterial and archaeal) gene finding program developed
    at Oak Ridge National Laboratory and the University of Tennessee."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/hyattpd/Prodigal/archive/']
 sources = ['v%(version)s.tar.gz']

Updated software `pullseq-1.0.2-GCCcore-13.2.0.eb`

Diff against pullseq-1.0.2-GCCcore-10.3.0.eb

easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-13.2.0.eb
index bd94483da5..31c5331e3a 100644
--- a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-13.2.0.eb
@@ -6,18 +6,18 @@ version = '1.0.2'
 homepage = 'https://github.com/bcthomas/pullseq'
 description = "Utility program for extracting sequences from a fasta/fastq file"
 
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://github.com/bcthomas/pullseq/archive/']
 sources = ['%(version)s.tar.gz']
 checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f']
 
 builddependencies = [
-    ('binutils', '2.36.1'),
-    ('Autotools', '20210128'),
+    ('binutils', '2.40'),
+    ('Autotools', '20220317'),
 ]
 dependencies = [
-    ('PCRE', '8.44'),
+    ('PCRE', '8.45'),
 ]
 
 preconfigopts = "./bootstrap && "

Updated software `RSeQC-5.0.1-foss-2023a.eb`

Diff against RSeQC-4.0.0-foss-2021b.eb

easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb

diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-5.0.1-foss-2023a.eb
index 4d9921d2ad..9230167fb1 100644
--- a/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb
+++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-5.0.1-foss-2023a.eb
@@ -1,11 +1,12 @@
 # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
 # Author: Adam Huffman
 # The Francis Crick Institute
+# Update: Petr Král (INUITS)
 
 easyblock = 'PythonPackage'
 
 name = 'RSeQC'
-version = '4.0.0'
+version = '5.0.1'
 
 homepage = 'http://rseqc.sourceforge.net/'
 description = """RSeQC provides a number of useful modules that can
@@ -15,17 +16,17 @@ description = """RSeQC provides a number of useful modules that can
  evaluate sequencing saturation, mapped reads distribution, coverage
  uniformity, strand specificity, transcript level RNA integrity etc."""
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = [SOURCE_TAR_GZ]
-checksums = ['5b44932bad669c6d9190c5c111d181e868fb40077ed20c16c0881f67fbcc669b']
+checksums = ['3c7d458784861af352d8da3f4f1cc8941934b37643164e9b74f929a32bd9ca80']
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('Pysam', '0.17.0'),
-    ('bx-python', '0.8.13'),
-    ('pyBigWig', '0.3.18'),
+    ('Python', '3.11.3'),
+    ('Pysam', '0.22.0'),
+    ('bx-python', '0.10.0'),
+    ('pyBigWig', '0.3.22'),
 ]
 
 fix_python_shebang_for = ['bin/*.py']

Updated software `Ruby-3.4.2-GCCcore-13.2.0.eb`

Diff against Ruby-3.0.3-GCCcore-12.3.0.eb

easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.4.2-GCCcore-13.2.0.eb
index 6ece8c58eb..fbf5b305f0 100644
--- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.4.2-GCCcore-13.2.0.eb
@@ -1,21 +1,22 @@
 name = 'Ruby'
-version = '3.0.3'
+version = '3.4.2'
 
 homepage = 'https://www.ruby-lang.org'
 description = """Ruby is a dynamic, open source programming language with
  a focus on simplicity and productivity. It has an elegant syntax that is
  natural to read and easy to write."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
 
 source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s']
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac']
+checksums = ['41328ac21f2bfdd7de6b3565ef4f0dd7543354d37e96f157a1552a6bd0eb364b']
 
 dependencies = [
     ('binutils', '2.40'),  # needed for gem
     ('zlib', '1.2.13'),
     ('OpenSSL', '1.1', '', SYSTEM),
+    ('libyaml', '0.2.5'),
 ]
 
 moduleclass = 'lang'

Updated software `VTK-9.3.1-foss-2024a.eb`

Diff against VTK-9.2.6-foss-2023a.eb

easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb

diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.3.1-foss-2024a.eb
index b01bd65e22..5866f71672 100644
--- a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/v/VTK/VTK-9.3.1-foss-2024a.eb
@@ -2,13 +2,12 @@
 # Authors::
 # * Fotis Georgatos <[email protected]>
 # * Robert Mijakovic <[email protected]>
-# Update: Pavel Tománek (Inuits)
 ##
 
 easyblock = 'CMakeNinja'
 
 name = 'VTK'
-version = '9.2.6'
+version = '9.3.1'
 
 homepage = 'https://www.vtk.org'
 description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for
@@ -17,7 +16,7 @@ description = """The Visualization Toolkit (VTK) is an open-source, freely avail
  algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques
  such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s']
@@ -27,23 +26,23 @@ sources = [
 ]
 patches = [('vtk-version.egg-info', '.')]
 checksums = [
-    {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'},
-    {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'},
+    {'VTK-9.3.1.tar.gz': '8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8'},
+    {'VTKData-9.3.1.tar.gz': '299569eba74413ee90cc5073511e82a957d7d685deb0a9f16362e2714e4e7f6f'},
     {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'},
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('Ninja', '1.11.1'),
+    ('CMake', '3.29.3'),
+    ('Ninja', '1.12.1'),
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('XZ', '5.4.2'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('XZ', '5.4.5'),
     ('libGLU', '9.0.3'),
-    ('X11', '20230603'),
-    ('Qt5', '5.15.10'),
+    ('X11', '20240607'),
+    ('Qt6', '6.7.2'),
 ]
 
 separate_build_dir = True
@@ -59,8 +58,8 @@ configopts += "-DPython3_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s
 configopts += "-DPython3_LIBRARY=$EBROOTPYTHON/lib/libpython%(pyshortver)s.so "
 # Other
 configopts += "-DVTK_USE_MPI=ON "
-configopts += "-DVTK_QT_VERSION=5 "
-configopts += "-DQt5_DIR=$EBROOTQT5 "
+configopts += "-DVTK_QT_VERSION=6 "
+configopts += "-DQt6_DIR=$EBROOTQT6 "
 configopts += "-DVTK_MODULE_ENABLE_VTK_GuiSupportQt=YES "
 configopts += "-DVTK_MODULE_ENABLE_VTK_ViewsQt=YES"

Flamefire · 2025-03-26T14:25:12Z

Test report by @Flamefire
FAILED
Build succeeded for 28 out of 30 (12 easyconfigs in total)
i7009 - Linux Rocky Linux 8.9 (Green Obsidian), x86_64, AMD EPYC 7702 64-Core Processor (zen2), Python 3.8.17
See https://gist.github.com/Flamefire/9a0ca870182757bb7674d0febbde65c2 for a full test report.

Flamefire · 2025-03-26T14:57:12Z

Test report by @Flamefire
SUCCESS
Build succeeded for 12 out of 12 (12 easyconfigs in total)
n1263 - Linux RHEL 8.9 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (icelake), Python 3.8.17
See https://gist.github.com/Flamefire/caceee42e4ef8130fda6b7c003717a37 for a full test report.

Flamefire · 2025-03-27T02:13:23Z

Test report by @Flamefire
FAILED
Build succeeded for 11 out of 13 (12 easyconfigs in total)
i8027 - Linux Rocky Linux 8.9 (Green Obsidian), x86_64, AMD EPYC 7352 24-Core Processor (zen2), 8 x NVIDIA NVIDIA A100-SXM4-40GB, 555.42.06, Python 3.8.17
See https://gist.github.com/Flamefire/b1e3dd9bedc8e2d61205cae6f3798c46 for a full test report.

Flamefire · 2025-03-28T02:47:51Z

Test report by @Flamefire
FAILED
Build succeeded for 172 out of 247 (12 easyconfigs in total)
c111 - Linux AlmaLinux 9.4, x86_64, AMD EPYC 9334 32-Core Processor (zen4), 4 x NVIDIA NVIDIA H100, 560.35.03, Python 3.9.18
See https://gist.github.com/Flamefire/8149bb355eafdaf23c1743bfe9edc94c for a full test report.

Thyre · 2025-08-18T12:35:25Z

This PR contains a few deprecated (and / or ) archived EasyConfigs by now. We should probably just remove them, and focus on the supported ones.

Flamefire · 2025-08-26T12:59:41Z

Rebased to remove old ECs

boegel · 2025-10-13T16:52:00Z

@Flamefire Anything using a toolchain older than 2022b is deprecated or no longer supported, so if this is still relevant it needs another cleanup round...

Flamefire · 2025-10-14T07:33:15Z

This just adds a simple line with a trivial env variable unset. I think it is much easier to just merge it even it does a simple change to ECs of deprecated toolchains.

akesandgren

LGTM

akesandgren · 2025-10-15T13:36:49Z

@boegelbot Please test @ jsc-zen3

boegelbot · 2025-10-15T13:40:11Z

@akesandgren: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=20414 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_20414 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 8406

Test results coming soon (I hope)...

Details

- notification for comment with ID 3406491707 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-10-15T15:29:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 9 out of 9 (9 easyconfigs in total)
jsczen3c2.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/afa2103a11abc7d157e71f3181fbf742 for a full test report.

akesandgren · 2025-10-15T15:59:06Z

Going in, thanks @Flamefire!

Flamefire marked this pull request as ready for review April 23, 2024 10:35

Flamefire force-pushed the 20240423122900_new_pr_Arrow0120 branch 2 times, most recently from 7768c94 to 103b2a4 Compare April 23, 2024 12:08

Flamefire marked this pull request as draft April 23, 2024 13:05

Flamefire force-pushed the 20240423122900_new_pr_Arrow0120 branch from 103b2a4 to a9b0c55 Compare April 23, 2024 14:07

Flamefire changed the base branch from develop to 5.0.x April 23, 2024 14:08

Flamefire marked this pull request as ready for review April 24, 2024 12:00

boegel mentioned this pull request May 2, 2024

{bio}[foss/2023a] Single-cell-python-bundle v2024.02 #20116

Merged

38 tasks

github-actions Bot added change new update workflow labels Mar 20, 2025

Flamefire changed the base branch from 5.0.x to develop March 26, 2025 09:36

Thyre added bug fix 2020b issues & PRs related to 2020b 2021a 2021b issues & PRs related to 2021b 2023a 2022a 2022b and removed change labels Aug 18, 2025

Fix Arrow configure in Conda envs

b20701e

Flamefire force-pushed the 20240423122900_new_pr_Arrow0120 branch from 7b87ea2 to b20701e Compare August 26, 2025 12:59

github-actions Bot added the change label Aug 26, 2025

Thyre removed the 2020b issues & PRs related to 2020b label Aug 26, 2025

akesandgren approved these changes Oct 15, 2025

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akesandgren added this to the next release (5.2.0?) milestone Oct 15, 2025

akesandgren merged commit 7548456 into easybuilders:develop Oct 15, 2025
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Flamefire deleted the 20240423122900_new_pr_Arrow0120 branch October 16, 2025 07:54

boegel changed the title ~~Fix Arrow configure in Conda envs~~ unset $CONDA_PREFIX in configure step for Arrow Dec 19, 2025

boegel removed the change label Dec 19, 2025

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Updated software Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb

Updated software Boltz-1-0.4.1-foss-2023a.eb

Updated software CheckM-1.2.3-foss-2023b.eb

Updated software CompareM-0.1.2-gfbf-2023b.eb

Updated software DAS_Tool-1.1.7-foss-2023b-R-4.4.1.eb

Updated software DendroPy-5.0.1-GCCcore-13.2.0.eb

Updated software EasyBuild-5.0.0.eb

Updated software FragGeneScan-1.32-GCCcore-13.2.0.eb

Updated software IDBA-UD-1.1.3-GCCcore-13.2.0.eb

Updated software idemux-0.1.6-GCCcore-12.3.0.eb

Updated software MaxBin-2.2.7-gompi-2023b.eb

Updated software PyTorch-2.3.0-foss-2023b.eb

Updated software PyVista-0.44.2-foss-2024a.eb

Updated software pairtools-1.1.2-gfbf-2023a.eb

Updated software prodigal-2.6.3-GCCcore-13.2.0.eb

Updated software pullseq-1.0.2-GCCcore-13.2.0.eb

Updated software RSeQC-5.0.1-foss-2023a.eb

Updated software Ruby-3.4.2-GCCcore-13.2.0.eb

Updated software VTK-9.3.1-foss-2024a.eb

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branfosj commented Apr 24, 2024 •

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Updated software `Boltz-1-0.4.1-foss-2023a-CUDA-12.1.1.eb`

Updated software `Boltz-1-0.4.1-foss-2023a.eb`

Updated software `CheckM-1.2.3-foss-2023b.eb`

Updated software `CompareM-0.1.2-gfbf-2023b.eb`

Updated software `DAS_Tool-1.1.7-foss-2023b-R-4.4.1.eb`

Updated software `DendroPy-5.0.1-GCCcore-13.2.0.eb`

Updated software `EasyBuild-5.0.0.eb`

Updated software `FragGeneScan-1.32-GCCcore-13.2.0.eb`

Updated software `IDBA-UD-1.1.3-GCCcore-13.2.0.eb`

Updated software `idemux-0.1.6-GCCcore-12.3.0.eb`

Updated software `MaxBin-2.2.7-gompi-2023b.eb`

Updated software `PyTorch-2.3.0-foss-2023b.eb`

Updated software `PyVista-0.44.2-foss-2024a.eb`

Updated software `pairtools-1.1.2-gfbf-2023a.eb`

Updated software `prodigal-2.6.3-GCCcore-13.2.0.eb`

Updated software `pullseq-1.0.2-GCCcore-13.2.0.eb`

Updated software `RSeQC-5.0.1-foss-2023a.eb`

Updated software `Ruby-3.4.2-GCCcore-13.2.0.eb`

Updated software `VTK-9.3.1-foss-2024a.eb`