{bio}[foss/2025a] ESM-2 v2.0.0

[WilleBell]

(created using eb --new-pr)

Depends on:

• {ai}[foss/2025a] PyTorch v2.9.1, Triton v3.5.1 w/ CUDA 12.8.0 from wheels #25267

[github-actions]

Updated software ESM-2-2.0.0-foss-2025a.eb

Diff against ESM-2-2.0.0-foss-2023a.eb

easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
index 232a7493b4..5ca8f5e968 100644
--- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
@@ -8,15 +8,16 @@ description = """ESM-2 outperforms all tested single-sequence protein language m
  across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate
  accurate structure predictions end to end directly from the sequence of a protein."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('Java', '11', '', SYSTEM),  # needed by ANTLR4 runtime
+    ('Java', '21', '', SYSTEM),  # needed by ANTLR4 runtime
 ]
 
 dependencies = [
-    ('Python', '3.11.3'),
-    ('PyTorch', '2.1.2'),
+    ('Python', '3.13.1'),
+    ('PyTorch', '2.9.1', '-whl'),
+    ('PyYAML', '6.0.2'),
 ]
 
 # omegaconf is required for esmfold (in addition to OpenFold-1.0.1)

Diff against ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
index a16798bd82..5ca8f5e968 100644
--- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
@@ -2,23 +2,22 @@ easyblock = 'PythonBundle'
 
 name = 'ESM-2'
 version = '2.0.0'
-versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/facebookresearch/esm'
 description = """ESM-2 outperforms all tested single-sequence protein language models
  across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate
  accurate structure predictions end to end directly from the sequence of a protein."""
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('Java', '11', '', SYSTEM),  # needed by ANTLR4 runtime
+    ('Java', '21', '', SYSTEM),  # needed by ANTLR4 runtime
 ]
 
 dependencies = [
-    ('CUDA', '12.1.1', '', SYSTEM),
-    ('Python', '3.11.3'),
-    ('PyTorch', '2.1.2', versionsuffix),
+    ('Python', '3.13.1'),
+    ('PyTorch', '2.9.1', '-whl'),
+    ('PyYAML', '6.0.2'),
 ]
 
 # omegaconf is required for esmfold (in addition to OpenFold-1.0.1)

Diff against ESM-2-2.0.0-foss-2022b.eb

easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb

diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
index f459d4d28a..5ca8f5e968 100644
--- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb
+++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2025a.eb
@@ -8,15 +8,16 @@ description = """ESM-2 outperforms all tested single-sequence protein language m
  across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate
  accurate structure predictions end to end directly from the sequence of a protein."""
 
-toolchain = {'name': 'foss', 'version': '2022b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 
 builddependencies = [
-    ('Java', '11', '', SYSTEM),  # needed by ANTLR4 runtime
+    ('Java', '21', '', SYSTEM),  # needed by ANTLR4 runtime
 ]
 
 dependencies = [
-    ('Python', '3.10.8'),
-    ('PyTorch', '1.13.1'),
+    ('Python', '3.13.1'),
+    ('PyTorch', '2.9.1', '-whl'),
+    ('PyYAML', '6.0.2'),
 ]
 
 # omegaconf is required for esmfold (in addition to OpenFold-1.0.1)
@@ -30,7 +31,11 @@ exts_list = [
     }),
     ('fair-esm', version, {
         'modulename': "esm, esm.pretrained",
-        'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'],
+        'patches': ['%(name)s-%(version)s_fix_dataclass.patch'],
+        'checksums': [
+            {'fair-esm-2.0.0.tar.gz': '4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'},
+            {'fair-esm-2.0.0_fix_dataclass.patch': 'f3ce414d5ccad5980200ccd86b16740edb4b4e14075208991d867faa00fd0d8a'},
+        ],
     }),
 ]