diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb
index 0ff99e5dcfa..1f2620e9f2c 100644
--- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb
@@ -23,10 +23,18 @@ toolchainopts = {'pic': True, 'cstd': 'c++98'}
 
 source_urls = [SOURCEFORGE_SOURCE]
 sources = [SOURCELOWER_TAR_GZ]
-patches = ['AMOS-%(version)s_GCC-4.7.patch']
+patches = [
+    'AMOS-%(version)s_GCC-4.7.patch',
+    'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch',
+    'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch',
+]
 checksums = [
-    '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b',  # amos-3.1.0.tar.gz
-    '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844',  # AMOS-3.1.0_GCC-4.7.patch
+    {'amos-3.1.0.tar.gz': '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b'},
+    {'AMOS-3.1.0_GCC-4.7.patch': '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844'},
+    {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch':
+     '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'},
+    {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch':
+     'e291d87b8cd27752474ee0e1f3acb44f9657cac50d5d6dcceca0efc6436f1fe1'},
 ]
 
 dependencies = [
diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch
new file mode 100644
index 00000000000..1c31a0a98a0
--- /dev/null
+++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch
@@ -0,0 +1,14 @@
+Replace deprecate NUCMER flag -maxmatch with --maxmatch (from MUMmer 4.0.0rc)
+see https://github.com/sanger-pathogens/circlator/issues/121 and https://github.com/mummer4/mummer/issues/49
+diff -ru amos-3.1.0.orig/src/Pipeline/minimus2.acf amos-3.1.0/src/Pipeline/minimus2.acf
+--- amos-3.1.0.orig/src/Pipeline/minimus2.acf	2011-07-25 01:27:26.000000000 +0200
++++ amos-3.1.0/src/Pipeline/minimus2.acf	2024-03-13 17:03:35.981707768 +0100
+@@ -54,7 +54,7 @@
+ 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ)
+ 
+ ## Getting overlaps 
+-20: $(NUCMER) -maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
++20: $(NUCMER) --maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX)
+ 21: $(SHOWCOORDS) -H -c -l -o -r -I $(MINID) $(ALIGN) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) 
+ 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB)
+ 
diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch
new file mode 100644
index 00000000000..82238b9a089
--- /dev/null
+++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch
@@ -0,0 +1,15 @@
+minimus2 needs delta-filter and show-coords but these were not set correctly like NUCMER
+author: Lara Peeters (HPC-UGent)
+diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefile.in
+--- amos-3.1.0.orig/src/Pipeline/Makefile.in	2011-08-05 05:08:07.000000000 +0200
++++ amos-3.1.0/src/Pipeline/Makefile.in	2024-03-14 12:31:16.218067000 +0100
+@@ -477,7 +477,8 @@
+                 echo '#!$(bindir)/runAmos -C' > "$(DESTDIR)$(bindir)/$$b"; \
+                 sed -e 's|^BINDIR[ 	]*=.*$$|BINDIR=$(bindir)|' \
+                     -e 's|^NUCMER[ 	]*=.*$$|NUCMER=$(NUCMER)|' \
+-                    -e 's|^DELTAFILTER[        ]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^DELTAFILTER[ 	]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \
++                    -e 's|^SHOWCOORDS[ 	]*=.*$$|SHOWCOORDS=$(SHOWCOORDS)|' \
+                     "$(DESTDIR)$(bindir)/$$f" >> "$(DESTDIR)$(bindir)/$$b" \
+                 || exit 1; \
+                 ;; \
diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..4dc70d8715f
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb
@@ -0,0 +1,28 @@
+easyblock = 'CMakeMake'
+
+name = 'Blosc'
+version = '1.21.5'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a',
+              'lib/libblosc.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..9e1b0949576
--- /dev/null
+++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb
@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Denis Kristak
+# Update: Thomas Hoffmann (EMBL)
+easyblock = 'CMakeMake'
+
+name = 'Blosc2'
+version = '2.13.2'
+
+homepage = 'https://www.blosc.org/'
+
+description = "Blosc, an extremely fast, multi-threaded, meta-compressor library"
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/Blosc/c-blosc2/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['f2adcd9615f138d1bb16dc27feadab1bb1eab01d77e5e2323d14ad4ca8c3ca21']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+sanity_check_paths = {
+    'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a',
+              'lib/libblosc2.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb
new file mode 100644
index 00000000000..754d1f6214b
--- /dev/null
+++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb
@@ -0,0 +1,30 @@
+easyblock = 'CMakeMake'
+
+name = 'DIAMOND'
+version = '2.1.9'
+
+homepage = 'https://github.com/bbuchfink/diamond'
+description = "Accelerated BLAST compatible local sequence aligner"
+
+toolchain = {'name': 'GCC', 'version': '13.2.0'}
+
+github_account = 'bbuchfink'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': [],
+}
+sanity_check_commands = ["%(namelower)s help"]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb
new file mode 100644
index 00000000000..3ad16c0cd87
--- /dev/null
+++ b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'denseweight'
+version = '0.1.2'
+
+homepage = 'https://github.com/steimi/denseweight'
+description = """
+This package implements the method for imbalanced regression DenseWeight. The corresponding
+paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow
+training machine learning models for regression tasks that emphasize performance for data
+points with rare target values in comparison to data points with more common target values.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('scikit-learn', '1.1.2'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('KDEpy', '1.1.9', {
+        'modulename': 'KDEpy',
+        'checksums': ['4bf0b2afd430ce5b40fafd98144de83d8b715d46fdf0f45fed2b5c2e9c40ce46'],
+    }),
+    (name, version, {
+        'checksums': ['281cf1fe4be364366363ee822b524620dcb629c5b9ff7852aa80f91a27c98b1e'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'ai'
diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb
new file mode 100644
index 00000000000..20a40cd3952
--- /dev/null
+++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb
@@ -0,0 +1,87 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC,
+#                                 Ghent University / The Francis Crick Institute
+# Authors::
+# * Wiktor Jurkowski <wiktor.jurkowski@gmail.com>
+# * Fotis Georgatos <fotis@cern.ch>
+# * George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# * Kenneth Hoste <kenneth.hoste@ugent.be>
+# * Adam Huffman <adam.huffman@crick.ac.uk>
+# * Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+# * J. Sassmannshausen <Crick HPC team>
+# * Dugan Witherick <dugan.witherick@warwick.ac.uk>
+# * Christoph Siegert <christoph.siegert@uni-leipzig.de>
+# License::   MIT/GPL
+
+name = 'GROMACS'
+version = '2024.1'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a CPU only build, containing both MPI and threadMPI binaries
+for both single and double precision.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+]
+checksums = [
+    {'gromacs-2024.1.tar.gz': '937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'},
+    {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
+     '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
+    {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
+     '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
+]
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('scikit-build', '0.17.6'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),
+    ('networkx', '3.2.1'),
+    ('mpi4py', '3.1.5'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.3.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb
new file mode 100644
index 00000000000..fbee4bfaee9
--- /dev/null
+++ b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb
@@ -0,0 +1,51 @@
+easyblock = 'Bundle'
+
+name = 'hdWGCNA'
+version = '0.3.00'
+versionsuffix = '-R-%(rver)s'
+local_biocver = '3.16'
+
+homepage = 'https://smorabit.github.io/hdWGCNA/'
+description = """hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high 
+ dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular 
+ and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies 
+ modules of highly co-expressed genes and provides context for these modules via statistical testing and biological 
+ knowledge sources. hdWGCNA uses datasets formatted as Seurat objects."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('R', '4.3.2'),
+    ('R-bundle-CRAN', '2023.12'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix),
+]
+
+exts_defaultclass = 'RPackage'
+exts_default_options = {
+    'sources': ['%(name)s_%(version)s.tar.gz'],
+    '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
+    ],
+}
+
+exts_list = [
+    ('tester', '0.1.7', {
+        'checksums': ['b9c645119c21c69450f3d366c911ed92ac7c14ef61652fd676a38fb9d420b5f4'],
+    }),
+    (name, version, {
+        'source_urls': ['https://github.com/smorabit/hdWGCNA/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['5ef9980f6d25b41af17ebad76722766db72fb8162d5ae7af4565893d26c9ed1f'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb
new file mode 100644
index 00000000000..486a2e560c3
--- /dev/null
+++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb
@@ -0,0 +1,41 @@
+easyblock = 'PythonBundle'
+
+name = 'loompy'
+version = '3.0.7'
+
+homepage = 'https://loompy.org/'
+description = "Python implementation of the Loom file format, an efficient file format for large omics datasets"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('poetry', '1.7.1'), ]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),  # for click
+    ('SciPy-bundle', '2023.07'),
+    ('h5py', '3.9.0'),
+    ('numba', '0.58.1'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('numpy-groupies', '0.10.2', {
+        'checksums': ['f920c4ded899f5975d94fc63d634e7c89622056bbab8cc98a44d4320a0ae8a12'],
+    }),
+    (name, version, {
+        'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/loompy'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["loompy --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb b/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb
new file mode 100644
index 00000000000..9ee68b714c8
--- /dev/null
+++ b/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb
@@ -0,0 +1,30 @@
+easyblock = 'PythonBundle'
+
+name = 'MetaDecoder'
+version = '1.0.19'
+
+homepage = 'https://github.com/liu-congcong/MetaDecoder'
+description = "An algorithm for clustering metagenomic sequences"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('Python-bundle-PyPI', '2023.10'),  # threadpoolctl
+    ('SciPy-bundle', '2023.11'),
+    ('scikit-learn', '1.4.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    (name, version, {
+        'source_urls': ['https://github.com/liu-congcong/MetaDecoder/archive/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': ['8b88813a97787bc56baa3100a576a9e56a0de02811c573573a2fffeb7e80623e'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb
new file mode 100644
index 00000000000..8b1d917815d
--- /dev/null
+++ b/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb
@@ -0,0 +1,24 @@
+easyblock = 'PythonPackage'
+
+name = 'networkx'
+version = '3.2.1'
+
+homepage = 'https://pypi.python.org/pypi/networkx'
+description = """NetworkX is a Python package for the creation, manipulation,
+and study of the structure, dynamics, and functions of complex networks."""
+
+toolchain = {'name': 'gfbf', 'version': '2023b'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['9f1bb5cf3409bf324e0a722c20bdb4c20ee39bf1c30ce8ae499c8502b0b5e0c6']
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # required for numpy, scipy, ...
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..9c1e920324e
--- /dev/null
+++ b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb
@@ -0,0 +1,34 @@
+easyblock = 'CMakeMake'
+
+name = 'Parallel-Hashmap'
+version = '1.3.12'
+
+homepage = 'https://github.com/greg7mdp/parallel-hashmap'
+description = """Parallel Hashmap is built on a modified version of
+Abseil's flat_hash_map. Parallel Hashmap has lower space requirements,
+is nearly as fast as the underlying flat_hash_map, and can be used from
+multiple threads with high levels of concurrency."""
+
+# There is no actual library built, so it can be at GCCcore level despite being a C++ "library"
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'greg7mdp'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['0cc203144321924cfbfcc401f42d8204c0dd24e2760c7a1c091baa16d9777c08']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+]
+
+configopts = '-DPHMAP_BUILD_TESTS=OFF -DPHMAP_BUILD_EXAMPLES=OFF'  # The test code doesn't build
+
+sanity_check_paths = {
+    'files': ['include/parallel_hashmap/phmap%s.h' % x for x in [
+        '', '_base', '_bits', '_config', '_dump', '_fwd_decl', '_utils'
+    ]],
+    'dirs': [],
+}
+
+moduleclass = 'lib'
diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
index ac77e85d5a0..2ee75d5ffc3 100644
--- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
+++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
@@ -674,10 +674,14 @@ exts_list = [
         'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'],
     }),
     ('Net::SSLeay', '1.92', {
+        'patches': ['Net-SSLeay-1.92_fix.patch'],
         'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ",
         'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz',
         'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'],
-        'checksums': ['47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'],
+        'checksums': [
+            {'Net-SSLeay-1.92.tar.gz': '47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'},
+            {'Net-SSLeay-1.92_fix.patch': '37790b10c5551bce92bc4bd7c98a92b0058fc16604272c7459a63096b52a8d1c'},
+        ],
     }),
     ('IO::Socket::SSL', '2.083', {
         'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz',
diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb
new file mode 100644
index 00000000000..51b07f31b27
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb
@@ -0,0 +1,76 @@
+# http://www.pytables.org/usersguide/installation.html
+# updated: Denis Kristak (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'PyTables'
+version = '3.9.2'
+
+homepage = 'https://www.pytables.org'
+description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope
+ with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the
+ NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical
+ parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing,
+ processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and 
+ disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions 
+ such as relational or object oriented databases."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'usempi': True}
+
+builddependencies = [
+    ('pkgconf', '2.0.3'),
+    ('CMake', '3.27.6'),
+    ('Ninja', '1.11.1'),
+    ('scikit-build', '0.17.6'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+    ('SciPy-bundle', '2023.11'),  # provides numexpr
+    ('HDF5', '1.14.3'),
+    ('LZO', '2.10'),
+    ('Blosc', '1.21.5'),
+    ('Blosc2', '2.13.2'),
+    ('py-cpuinfo', '9.0.0'),
+]
+
+use_pip = True
+
+exts_list = [
+    ('ndindex', '1.8', {
+        'checksums': ['5fc87ebc784605f01dd5367374cb40e8da8f2c30988968990066c5098a7eebe8'],
+    }),
+    # need to align version of blosc2 Python package with version of C Blosc2 used,
+    # see https://github.com/Blosc/python-blosc2/blob/main/RELEASE_NOTES.md
+    ('blosc2', '2.5.1', {
+        'checksums': ['47d5df50e7286edf81e629ece35f87f13f55c13c5e8545832188c420c75d1659'],
+        'preinstallopts': """sed -i 's/version=/cmake_args=["-DUSE_SYSTEM_BLOSC2=YES"], version=/g' setup.py && """,
+    }),
+    ('tables', version, {
+        'patches': [
+            'PyTables-3.8.0_fix-libs.patch',
+            'PyTables-3.9.2_fix-find-blosc2-dep.patch',
+        ],
+        'checksums': [
+            {'tables-3.9.2.tar.gz': 'd470263c2e50c4b7c8635a0d99ac1ff2f9e704c24d71e5fa33c4529e7d0ad9c3'},
+            {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'},
+            {'PyTables-3.9.2_fix-find-blosc2-dep.patch':
+             'e2149f43da12d9ba26cca4c838f6e8a4694adab75c0f055b186674a017e41a55'},
+        ],
+    }),
+]
+
+local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree']
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+options = {'modulename': 'tables'}
+
+sanity_check_commands = ["%s --help" % x for x in local_bins]
+
+sanity_pip_check = True
+
+moduleclass = 'data'
diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch
new file mode 100644
index 00000000000..e832e65b278
--- /dev/null
+++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch
@@ -0,0 +1,20 @@
+determine installation prefix of Blosc2 dependency via $EBROOTBLOSC2, if defined,
+since mechanism to locate the library via blosc2-*.dist-info/RECORD doesn't work if blosc2 was not installed
+with vendored c-blosc2 library;
+author: Kenneth Hoste (HPC-UGent)
+--- tables-3.9.2/setup.py.orig	2024-03-14 19:17:54.100800849 +0100
++++ tables-3.9.2/setup.py	2024-03-14 19:22:04.099371064 +0100
+@@ -97,6 +97,13 @@
+ 
+ def get_blosc2_directories():
+     """Get Blosc2 directories for the C library"""
++    blosc2_root = os.getenv('EBROOTBLOSC2')
++    if blosc2_root:
++        library_path = Path(os.path.join(blosc2_root, 'lib'))
++        include_path = Path(os.path.join(blosc2_root, 'include'))
++        runtime_path = None
++        return include_path, library_path, runtime_path
++
+     try:
+         import blosc2
+     except ModuleNotFoundError:
diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb
new file mode 100644
index 00000000000..4ffea66d7cb
--- /dev/null
+++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb
@@ -0,0 +1,39 @@
+easyblock = 'PythonPackage'
+
+name = 'py-cpuinfo'
+version = '9.0.0'
+
+homepage = 'https://github.com/workhorsy/py-cpuinfo'
+description = "py-cpuinfo gets CPU info with pure Python."
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+
+dependencies = [
+    ('Python', '3.11.5'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+    'files': ['bin/cpuinfo'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = [
+    "cpuinfo",
+    "python -m cpuinfo",
+]
+
+options = {'modulename': 'cpuinfo'}
+
+sanity_pip_check = True
+
+moduleclass = 'tools'
diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
index 5c533ecb998..4e319447dd0 100644
--- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
+++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb
@@ -51,6 +51,8 @@ dependencies = [
     ('MPFR', '4.2.0'),  # for Rmpfr
     ('libgit2', '1.5.0'),
     ('OpenSSL', '1.1', '', SYSTEM),
+    ('protobuf', '23.0'),
+    ('jq', '1.6'),
 ]
 
 # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols.
@@ -3669,6 +3671,28 @@ exts_list = [
     ('ridge', '3.3', {
         'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'],
     }),
+    ('gdalUtilities', '1.2.5', {
+        'checksums': ['2a72e990080ad626205c78edc6614959b564413b7fc23132008b7259723571a7'],
+    }),
+    ('protolite', '2.3.0', {
+        'patches': ['protolite-2.3.0_use-c++17.patch'],
+        'checksums': [
+            {'protolite_2.3.0.tar.gz': '53ef24d51a8348f97bec39d254df3b97bd8b3d9bbffb81d6b06aad849cf78ce9'},
+            {'protolite-2.3.0_use-c++17.patch': 'fb5084c55dfbabc6f3e778accf4553f5c84f2bb0ab0ae84b3538c866a829afa4'},
+        ],
+    }),
+    ('jqr', '1.3.1', {
+        'checksums': ['e22461e75ff7e57fe502dc7d16c5e5fe9f8e4cbe042b5eadad06fc37394f9f36'],
+    }),
+    ('geojson', '0.3.5', {
+        'checksums': ['e425c8579dc9cf5e3c1f71db3b0eed8225e5ed7ea88b6c861f800f60fc07402a'],
+    }),
+    ('geojsonio', '0.11.3', {
+        'checksums': ['7168eb3571440479f0cbdd005ff9db3233d3c91fc10d37fb0eb200793da3402b'],
+    }),
+    ('MODIStsp', '2.1.0', {
+        'checksums': ['9416bf2a32faf4ae7159f50ba56ac7924852af59f932223b2268aedfa1769fda'],
+    }),
 ]
 
 moduleclass = 'lang'
diff --git a/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch b/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch
new file mode 100644
index 00000000000..a73741e3a1e
--- /dev/null
+++ b/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch
@@ -0,0 +1,14 @@
+make sure that protolite using -std=gnu++17 instead of -std=gnu++14 (default in R 4.2.2)
+required to fix compilation problems like:
+error: string_view in namespace std does not name a type
+author: Kenneth Hoste (HPC-UGent)
+--- protolite/configure.orig	2024-01-10 10:50:16.030350785 +0100
++++ protolite/configure	2024-01-10 10:50:52.847841896 +0100
+@@ -87,6 +87,7 @@
+ 
+ # Write to Makevars
+ sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars
++echo 'CXX_STD = CXX17' >> src/Makevars
+ 
+ # Look for 'protoc' compiler
+ if [ `command -v protoc` ]; then
diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb
new file mode 100644
index 00000000000..59c1fa24feb
--- /dev/null
+++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb
@@ -0,0 +1,21 @@
+name = 'SLEPc'
+version = '3.20.1'
+
+homepage = 'https://slepc.upv.es'
+description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
+ of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
+ either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
+ partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': True}
+
+source_urls = ['https://slepc.upv.es/download/distrib']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5a36b664895881d3858d0644f56bf7bb922bdab70d732fa11cbf6442fec11806']
+
+dependencies = [('PETSc', '3.20.3')]
+
+petsc_arch = 'installed-arch-linux2-c-opt'
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb
new file mode 100644
index 00000000000..b799671e0f0
--- /dev/null
+++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb
@@ -0,0 +1,40 @@
+easyblock = 'PythonBundle'
+
+name = 'scVelo'
+version = '0.3.1'
+
+homepage = "https://scvelo.org"
+description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using
+ dynamical modeling."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+builddependencies = [('hatchling', '1.18.0')]
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('numba', '0.58.1'),
+    ('anndata', '0.10.5.post1'),
+    ('scanpy', '1.9.8'),
+    ('loompy', '3.0.7'),
+    ('umap-learn', '0.5.5'),
+    ('scikit-learn', '1.3.1'),
+    ('matplotlib', '3.7.2'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('scvelo', version, {
+        'patches': ['scVelo-0.3.1_dep-fix.patch'],
+        'preinstallopts': "sed -i 's/scikit-learn>=0.21.2, <1.2.0/scikit-learn>=0.21.2/' pyproject.toml && ",
+        'checksums': [
+            {'scvelo-0.3.1.tar.gz': '3a41a73b29e091268c40f08dc57a63eab5dfc2bd8a57e564cf1a6aca5e4d5d22'},
+            {'scVelo-0.3.1_dep-fix.patch': 'c8d1b41518f4b7b6528bcb00861287d9f1d96d419a4b3ce98599ea1d8cb59503'},
+        ],
+    }),
+]
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch
new file mode 100644
index 00000000000..10c26136ce7
--- /dev/null
+++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch
@@ -0,0 +1,216 @@
+Move scvi-tools to optional-dependencies and remove `torch` dependency
+
+From b8d80f7934a305888a61417f7aa22de2e426b81a Mon Sep 17 00:00:00 2001
+From: Michal Klein <46717574+michalk8@users.noreply.github.com>
+Date: Wed, 7 Feb 2024 22:15:53 +0100
+Subject: [PATCH 1/4] Remove hard `scvi-tools` dependency
+
+---
+ .github/workflows/ci.yml |  2 +-
+ pyproject.toml           |  7 +++++--
+ scvelo/tools/__init__.py | 12 ++++++++++--
+ 3 files changed, 16 insertions(+), 5 deletions(-)
+
+diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
+index fd341688..f8058c62 100644
+--- a/.github/workflows/ci.yml
++++ b/.github/workflows/ci.yml
+@@ -45,7 +45,7 @@ jobs:
+             fail-fast: false
+             matrix:
+                 os: [ubuntu-latest]
+-                python-version: [3.9, "3.10"]
++                python-version: ["3.9", "3.10"]
+         steps:
+             - uses: actions/checkout@v2
+             - name: Set up Python ${{ matrix.python-version }}
+diff --git a/pyproject.toml b/pyproject.toml
+index a0184458..5f747c2c 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -50,11 +50,13 @@ dependencies = [
+     "pandas>=1.1.1, !=1.4.0",
+     "scipy>=1.4.1",
+     "scikit-learn>=0.21.2, <1.2.0",
+-    "scvi-tools>=0.20.1",
+     "matplotlib>=3.3.0"
+ ]
+ 
+ [project.optional-dependencies]
++vi = [
++    "scvi-tools>=0.20.1",
++]
+ louvain = [
+     "igraph",
+     "louvain"
+@@ -78,7 +80,8 @@ dev = [
+     "pybind11",
+     "pytest-cov",
+     "igraph",
+-    "setuptools_scm"
++    "scvi-tools>=0.20.1",
++    "setuptools_scm",
+ ]
+ docs = [
+     # Just until rtd.org understands pyproject.toml
+diff --git a/scvelo/tools/__init__.py b/scvelo/tools/__init__.py
+index b2e3e126..3a40aff1 100644
+--- a/scvelo/tools/__init__.py
++++ b/scvelo/tools/__init__.py
+@@ -1,3 +1,5 @@
++import contextlib
++
+ from scanpy.tools import diffmap, dpt, louvain, tsne, umap
+ 
+ from ._em_model import ExpectationMaximizationModel
+@@ -11,7 +13,6 @@
+     recover_latent_time,
+ )
+ from ._steady_state_model import SecondOrderSteadyStateModel, SteadyStateModel
+-from ._vi_model import VELOVI
+ from .paga import paga
+ from .rank_velocity_genes import rank_velocity_genes, velocity_clusters
+ from .score_genes_cell_cycle import score_genes_cell_cycle
+@@ -23,6 +24,10 @@
+ from .velocity_graph import velocity_graph
+ from .velocity_pseudotime import velocity_map, velocity_pseudotime
+ 
++with contextlib.suppress(ImportError):
++    from ._vi_model import VELOVI
++
++
+ __all__ = [
+     "align_dynamics",
+     "differential_kinetic_test",
+@@ -54,5 +59,8 @@
+     "SteadyStateModel",
+     "SecondOrderSteadyStateModel",
+     "ExpectationMaximizationModel",
+-    "VELOVI",
+ ]
++if "VELOVI" in locals():
++    __all__ += ["VELOVI"]
++
++del contextlib
+
+From 12e91cf0015df8917669e8242afd38c9b7291f82 Mon Sep 17 00:00:00 2001
+From: Michal Klein <46717574+michalk8@users.noreply.github.com>
+Date: Wed, 7 Feb 2024 22:37:00 +0100
+Subject: [PATCH 2/4] Skip VELOVI tests if `scvi-tools` not installed
+
+---
+ pyproject.toml               |  1 -
+ tests/tools/test_vi_model.py | 12 ++++++++++--
+ 2 files changed, 10 insertions(+), 3 deletions(-)
+
+diff --git a/pyproject.toml b/pyproject.toml
+index 5f747c2c..71cd881b 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -80,7 +80,6 @@ dev = [
+     "pybind11",
+     "pytest-cov",
+     "igraph",
+-    "scvi-tools>=0.20.1",
+     "setuptools_scm",
+ ]
+ docs = [
+diff --git a/tests/tools/test_vi_model.py b/tests/tools/test_vi_model.py
+index 15592072..241896d8 100644
+--- a/tests/tools/test_vi_model.py
++++ b/tests/tools/test_vi_model.py
+@@ -1,7 +1,15 @@
+-from scvi.data import synthetic_iid
++# isort: skip_file
++import pytest
++import contextlib
+ 
+ import scvelo as scv
+-from scvelo.tools import VELOVI
++
++with contextlib.suppress(ImportError):
++    from scvi.data import synthetic_iid
++    from scvelo.tools import VELOVI
++
++
++_ = pytest.importorskip("scvi")
+ 
+ 
+ def test_preprocess_data():
+
+From cfd4fa096e8b25161fc71467d02bf4036b0f5e75 Mon Sep 17 00:00:00 2001
+From: Michal Klein <46717574+michalk8@users.noreply.github.com>
+Date: Wed, 7 Feb 2024 22:43:16 +0100
+Subject: [PATCH 3/4] Remove `torch` dependency
+
+---
+ scvelo/tools/_core.py      | 4 ----
+ scvelo/tools/_vi_module.py | 4 +++-
+ 2 files changed, 3 insertions(+), 5 deletions(-)
+
+diff --git a/scvelo/tools/_core.py b/scvelo/tools/_core.py
+index df352bc0..92b18212 100644
+--- a/scvelo/tools/_core.py
++++ b/scvelo/tools/_core.py
+@@ -1,8 +1,6 @@
+ from abc import abstractmethod
+ from typing import NamedTuple
+ 
+-import torch
+-
+ from anndata import AnnData
+ 
+ 
+@@ -13,8 +11,6 @@ class _REGISTRY_KEYS_NT(NamedTuple):
+ 
+ REGISTRY_KEYS = _REGISTRY_KEYS_NT()
+ 
+-DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus()
+-
+ 
+ class BaseInference:
+     """Base Inference class for all velocity methods."""
+diff --git a/scvelo/tools/_vi_module.py b/scvelo/tools/_vi_module.py
+index 4c5ecc81..c211da75 100644
+--- a/scvelo/tools/_vi_module.py
++++ b/scvelo/tools/_vi_module.py
+@@ -11,7 +11,9 @@
+ from scvi.module.base import auto_move_data, BaseModuleClass, LossOutput
+ from scvi.nn import Encoder, FCLayers
+ 
+-from ._core import DEFAULT_ACTIVATION_FUNCTION, REGISTRY_KEYS
++from ._core import REGISTRY_KEYS
++
++DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus()
+ 
+ torch.backends.cudnn.benchmark = True
+ 
+
+From e03ed96918361f3d124ee178c4bda1cfee0e83cb Mon Sep 17 00:00:00 2001
+From: Michal Klein <46717574+michalk8@users.noreply.github.com>
+Date: Wed, 7 Feb 2024 22:51:35 +0100
+Subject: [PATCH 4/4] Remove unused `skip_file`
+
+---
+ tests/tools/test_vi_model.py | 5 +++--
+ 1 file changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/tests/tools/test_vi_model.py b/tests/tools/test_vi_model.py
+index 241896d8..d8ecc0c8 100644
+--- a/tests/tools/test_vi_model.py
++++ b/tests/tools/test_vi_model.py
+@@ -1,11 +1,12 @@
+-# isort: skip_file
+-import pytest
+ import contextlib
+ 
++import pytest
++
+ import scvelo as scv
+ 
+ with contextlib.suppress(ImportError):
+     from scvi.data import synthetic_iid
++
+     from scvelo.tools import VELOVI
+ 
+ 
\ No newline at end of file
diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..d0ee82a07da
--- /dev/null
+++ b/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb
@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'Vim'
+version = "9.1.0004"
+
+homepage = 'http://www.vim.org'
+description = """ Vim is an advanced text editor that seeks to provide the power 
+ of the de-facto Unix editor 'Vi', with a more complete feature set. """
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/refs/tags/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['b930d02549e246a220d6ee95a4ef4938e56881e33b82e992e9439ac0f9fc7c13']
+
+builddependencies = [
+    ('binutils', '2.40'),
+]
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Perl', '5.36.1'),
+    ('PCRE', '8.45'),
+]
+
+configopts = "--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes"
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'bin/vimtutor', 'bin/xxd'],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = ['%(namelower)s --version']
+
+moduleclass = 'tools'