{ai,bio}[foss/2024a] AlphaFold3 v3.0.0, jax-triton v0.2.0, jaxtyping v0.2.36, dm-tree v0.1.8 w/ CUDA 12.6.0 DRAFT!

[ThomasHoffmann77]

(created using eb --new-pr)

• {compiler,devel}[GCCcore/13.3.0,foss/2024a] Triton v3.1.0, Clang v19.0.0_10dc3a8 w/ CUDA 12.6.0 #22064
• {lib}[foss/2024a] dm-haiku v0.0.13, tensorstore v0.1.69 w/ CUDA 12.6.0 #22028
• {ai}[gfbf/2024a] jax v0.4.34, ml_dtypes v0.5.0 w/ CUDA 12.6.0 WIP #21924
• {bio}[foss/2024a] AlphaFold3 WIP #21864 (pybind11, RDkit)

TODO: "alphafold3 3.0.0 requires rdkit, which is not installed." although RDKit is dependency

[github-actions]

Updated software dm-tree-0.1.8-GCC-13.3.0.eb

Diff against dm-tree-0.1.8-GCCcore-12.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
index bf55444d00..7d7f0a7982 100644
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
@@ -8,16 +8,22 @@ description = """dm-tree provides tree, a library for working with nested data s
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430']
+patches = ['dm-tree-0.1.8_pybind11.patch']
+checksums = [
+    {'dm-tree-0.1.8.tar.gz': '0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'},
+    {'dm-tree-0.1.8_pybind11.patch': '1ed433eda86d46333d735dfea9eecf9d007ba0ca8b1bc610c6f02cd478b8d131'},
+]
 
 builddependencies = [
-    ('binutils', '2.40'),
-    ('CMake', '3.26.3'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Abseil', '20240722.0'),
 ]
-dependencies = [('Python', '3.11.3')]
 
 download_dep_fail = True
 

Diff against dm-tree-0.1.8-GCCcore-11.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
old mode 100755
new mode 100644
index 94b5023db0..7d7f0a7982
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
@@ -8,16 +8,22 @@ description = """dm-tree provides tree, a library for working with nested data s
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430']
+patches = ['dm-tree-0.1.8_pybind11.patch']
+checksums = [
+    {'dm-tree-0.1.8.tar.gz': '0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'},
+    {'dm-tree-0.1.8_pybind11.patch': '1ed433eda86d46333d735dfea9eecf9d007ba0ca8b1bc610c6f02cd478b8d131'},
+]
 
 builddependencies = [
-    ('binutils', '2.38'),
-    ('CMake', '3.23.1'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Abseil', '20240722.0'),
 ]
-dependencies = [('Python', '3.10.4')]
 
 download_dep_fail = True
 

Diff against dm-tree-0.1.6-GCCcore-10.3.0.eb

easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb

diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
index de8beea149..7d7f0a7982 100644
--- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb
+++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCC-13.3.0.eb
@@ -1,23 +1,29 @@
 easyblock = 'PythonPackage'
 
 name = 'dm-tree'
-version = '0.1.6'
+version = '0.1.8'
 
 homepage = 'https://github.com/deepmind/tree'
 description = """dm-tree provides tree, a library for working with nested data structures. In a way,
 tree generalizes the builtin map function which only supports flat sequences, and
 allows to apply a function to each "leaf" preserving the overall structure."""
 
-toolchain = {'name': 'GCCcore', 'version': '10.3.0'}
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
 
 sources = [SOURCELOWER_TAR_GZ]
-checksums = ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a']
+patches = ['dm-tree-0.1.8_pybind11.patch']
+checksums = [
+    {'dm-tree-0.1.8.tar.gz': '0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'},
+    {'dm-tree-0.1.8_pybind11.patch': '1ed433eda86d46333d735dfea9eecf9d007ba0ca8b1bc610c6f02cd478b8d131'},
+]
 
 builddependencies = [
-    ('binutils', '2.36.1'),
-    ('Bazel', '3.7.2'),
+    ('pybind11', '2.12.0'),
+]
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Abseil', '20240722.0'),
 ]
-dependencies = [('Python', '3.9.5')]
 
 download_dep_fail = True
 

[ThomasHoffmann77]

dm-tree pybind11 patch taken from debian: https://udd.debian.org/patches.cgi?src=dm-tree&version=0.1.8-3