From 4689ab89e486d1569705fc167d6e1a178b247348 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 6 Mar 2025 11:29:53 +0100
Subject: [PATCH 1/4] adding easyconfigs: Boltz-1-0.4.1-foss-2023a.eb

---
 .../b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb     | 81 +++++++++++++++++++
 1 file changed, 81 insertions(+)
 create mode 100644 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.eb
new file mode 100644
index 000000000000..524a0b31a0ac
--- /dev/null
+++ b/easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb
@@ -0,0 +1,81 @@
+easyblock = 'PythonBundle'
+
+name = 'Boltz-1'
+version = '0.4.1'
+
+homepage = 'https://github.com/jwohlwend/boltz'
+description = """
+Boltz-1 is the state-of-the-art open-source model to predict biomolecular structures
+containing combinations of proteins, RNA, DNA, and other molecules.
+It also supports modified residues, covalent ligands and glycans, as well as
+conditioning the prediction on specified interaction pockets or contacts.
+"""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Python-bundle-PyPI', '2023.06'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('PyYAML', '6.0'),
+    ('PyTorch', '2.1.2'),
+    ('Hydra', '1.3.2'),
+    ('PyTorch-Lightning', '2.2.1'),
+    ('RDKit', '2024.03.3'),
+    ('dm-tree', '0.1.8'),
+    ('einops', '0.7.0'),
+    ('wandb', '0.16.1'),
+]
+
+use_pip = True
+
+# unpin strict dependencies versions
+local_preinstallopts = (
+    "sed -i -e "
+    r"'s/==.*/\",/g' -e "
+    "'s/torch>=2.2/torch/g' -e "
+    "'16d' -e "  # delete rdkit dep - pip check fail even RDKit is there
+    "'s/pandas>=2.2.2/pandas/g' "
+    "pyproject.toml && "
+)
+
+exts_list = [
+    ('urllib3', '2.0.7', {
+        'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'],
+    }),
+    ('ihm', '1.7', {
+        'checksums': ['f7d3b9a76d9652f7091bbd1c6bea044a1d40b35bcba9b64c8e51a061fc2463de'],
+    }),
+    ('frozendict', '2.4.5', {
+        'checksums': ['fd7add309789595c044c0155a0bddfa9d20c77f65de1e33a14aa3033b936ef63'],
+    }),
+    ('types-requests', '2.32.0.20240914', {
+        'modulename': False,
+        'checksums': ['2850e178db3919d9bf809e434eef65ba49d0e7e33ac92d588f4a5e295fffd405'],
+    }),
+    ('einx', '0.3.0', {
+        'checksums': ['17ff87c6a0f68ab358c1da489f00e95f1de106fd12ff17d0fb3e210aaa1e5f8c'],
+    }),
+    ('fairscale', '0.4.13', {
+        'checksums': ['1b797825c427f5dba92253fd0d8daa574e8bd651a2423497775fab1b30cfb768'],
+    }),
+    ('mashumaro', '3.14', {
+        'checksums': ['5ef6f2b963892cbe9a4ceb3441dfbea37f8c3412523f25d42e9b3a7186555f1d'],
+    }),
+    ('modelcif', '1.2', {
+        'checksums': ['517d2a7be67c96fd56dcc3b50cf7bb0b130958c325653d9925f9a5dbfe151d78'],
+    }),
+    ('boltz', version, {
+        'preinstallopts': local_preinstallopts,
+        'runtest': "cd %(start_dir)s && pytest -svv tests/",
+        'testinstall': True,
+        'checksums': ['7bc4081d578ac7be5972387546f9dd28723ce132264bc13f1d7471f2ce4aa56b'],
+    }),
+]
+
+sanity_pip_check = True
+
+sanity_check_commands = ["boltz 2>&1 | grep 'Usage: boltz'"]
+
+moduleclass = 'bio'

From 709c472d1c3dd1a9e8ff05155a3e6ddf20cf930c Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Thu, 6 Mar 2025 12:19:08 +0100
Subject: [PATCH 2/4] add hatchling as builddep

---
 easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb | 1 +
 1 file changed, 1 insertion(+)

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.eb
index 524a0b31a0ac..da532c9f1ab2 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.eb
@@ -13,6 +13,7 @@ conditioning the prediction on specified interaction pockets or contacts.
 
 toolchain = {'name': 'foss', 'version': '2023a'}
 
+builddependencies = [('hatchling', '1.18.0')]
 dependencies = [
     ('Python', '3.11.3'),
     ('Python-bundle-PyPI', '2023.06'),

From d9349e6feff79c187349b4208c90cfbcba574cd2 Mon Sep 17 00:00:00 2001
From: Pavel Tomanek <shavel.tom@gmail.com>
Date: Tue, 18 Mar 2025 15:23:46 +0100
Subject: [PATCH 3/4] update runtest to not store caches

---
 easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

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.eb
index da532c9f1ab2..9b3390477142 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.eb
@@ -69,7 +69,8 @@ exts_list = [
     }),
     ('boltz', version, {
         'preinstallopts': local_preinstallopts,
-        'runtest': "cd %(start_dir)s && pytest -svv tests/",
+        # export HOME to avoid saving large test caches to the user's /home/.boltz
+        'runtest': "export HOME=%(builddir)s && cd %(start_dir)s && pytest -svv tests/",
         'testinstall': True,
         'checksums': ['7bc4081d578ac7be5972387546f9dd28723ce132264bc13f1d7471f2ce4aa56b'],
     }),

From bba5e41fac434a6e3c1469834b9f79c622ac0e9d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 19 Mar 2025 15:44:56 +0100
Subject: [PATCH 4/4] don't explicitly set use_pip and sanity_pip_check in
 Boltz-1 easyconfig

---
 easybuild/easyconfigs/b/Boltz-1/Boltz-1-0.4.1-foss-2023a.eb | 4 ----
 1 file changed, 4 deletions(-)

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.eb
index 9b3390477142..3d6b0c2a2316 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.eb
@@ -29,8 +29,6 @@ dependencies = [
     ('wandb', '0.16.1'),
 ]
 
-use_pip = True
-
 # unpin strict dependencies versions
 local_preinstallopts = (
     "sed -i -e "
@@ -76,8 +74,6 @@ exts_list = [
     }),
 ]
 
-sanity_pip_check = True
-
 sanity_check_commands = ["boltz 2>&1 | grep 'Usage: boltz'"]
 
 moduleclass = 'bio'