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{chem}[gfbf/2023a] MDTraj v1.10.0 w/ Python 3.11.3 #22129

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{chem}[gfbf/2023a] MDTraj v1.10.0 w/ Python 3.11.3 #22129

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@hvelab hvelab commented Jan 7, 2025

(created using eb --new-pr)

@github-actions github-actions bot added the update label Jan 7, 2025
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github-actions bot commented Jan 7, 2025 •
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Updated software MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb

Diff against MDTraj-1.10.0-gfbf-2023a.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
index 77acffa94a..4b87ad2420 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
@@ -5,6 +5,8 @@ easyblock = 'PythonBundle'
 name = 'MDTraj'
 version = '1.10.0'
 
+versionsuffix = "-Python-3.11.3"
+
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
 
@@ -14,7 +16,7 @@ toolchainopts = {'openmp': True}
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('zlib', '1.2.13'),
+    ('zlib', '1.2.11'),
 ]
 
 use_pip = True
Diff against MDTraj-1.9.9-gfbf-2023a.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
index 8f17291298..4b87ad2420 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
@@ -1,9 +1,11 @@
-# Updated: Pavel Grochal (INUITS)
+# Updated: Helena Vela (HPCNow!)
 
 easyblock = 'PythonBundle'
 
 name = 'MDTraj'
-version = '1.9.9'
+version = '1.10.0'
+
+versionsuffix = "-Python-3.11.3"
 
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
@@ -14,19 +16,25 @@ toolchainopts = {'openmp': True}
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('zlib', '1.2.13'),
+    ('zlib', '1.2.11'),
 ]
 
 use_pip = True
 exts_list = [
-    ('pyparsing', '3.1.0', {
-        'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'],
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    ('pymbar', '3.1', {
+        # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475
+        'source_urls': ['https://github.com/choderalab/pymbar/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'],
     }),
     ('astunparse', '1.6.3', {
         'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
     }),
     ('mdtraj', version, {
-        'checksums': ['1b03f7ac753af5ca07cf874842689c8d49e791ee1242510875581df6100ca15e'],
+        'checksums': ['7d518b5a53b498f52686567e0191e9ee41a725b3296a8dbcac24fe824ed4af8f'],
     }),
 ]
Diff against MDTraj-1.9.7-foss-2021b.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
index 9bf0a45a67..4b87ad2420 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
@@ -1,19 +1,21 @@
-# Updated: Pavel Grochal (INUITS)
+# Updated: Helena Vela (HPCNow!)
 
 easyblock = 'PythonBundle'
 
 name = 'MDTraj'
-version = '1.9.7'
+version = '1.10.0'
+
+versionsuffix = "-Python-3.11.3"
 
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 toolchainopts = {'openmp': True}
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
     ('zlib', '1.2.11'),
 ]
 
@@ -32,7 +34,7 @@ exts_list = [
         'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
     }),
     ('mdtraj', version, {
-        'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'],
+        'checksums': ['7d518b5a53b498f52686567e0191e9ee41a725b3296a8dbcac24fe824ed4af8f'],
     }),
 ]

Updated software MDTraj-1.10.0-gfbf-2023a.eb

Diff against MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
index 4b87ad2420..77acffa94a 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a-Python-3.11.3.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
@@ -5,8 +5,6 @@ easyblock = 'PythonBundle'
 name = 'MDTraj'
 version = '1.10.0'
 
-versionsuffix = "-Python-3.11.3"
-
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
 
@@ -16,7 +14,7 @@ toolchainopts = {'openmp': True}
 dependencies = [
     ('Python', '3.11.3'),
     ('SciPy-bundle', '2023.07'),
-    ('zlib', '1.2.11'),
+    ('zlib', '1.2.13'),
 ]
 
 use_pip = True
Diff against MDTraj-1.9.9-gfbf-2023a.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
index 8f17291298..77acffa94a 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.9-gfbf-2023a.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
@@ -1,9 +1,9 @@
-# Updated: Pavel Grochal (INUITS)
+# Updated: Helena Vela (HPCNow!)
 
 easyblock = 'PythonBundle'
 
 name = 'MDTraj'
-version = '1.9.9'
+version = '1.10.0'
 
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
@@ -19,14 +19,20 @@ dependencies = [
 
 use_pip = True
 exts_list = [
-    ('pyparsing', '3.1.0', {
-        'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'],
+    ('astor', '0.8.1', {
+        'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'],
+    }),
+    ('pymbar', '3.1', {
+        # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475
+        'source_urls': ['https://github.com/choderalab/pymbar/archive/'],
+        'sources': ['%(version)s.tar.gz'],
+        'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'],
     }),
     ('astunparse', '1.6.3', {
         'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
     }),
     ('mdtraj', version, {
-        'checksums': ['1b03f7ac753af5ca07cf874842689c8d49e791ee1242510875581df6100ca15e'],
+        'checksums': ['7d518b5a53b498f52686567e0191e9ee41a725b3296a8dbcac24fe824ed4af8f'],
     }),
 ]
Diff against MDTraj-1.9.7-foss-2021b.eb

easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb

diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
index 9bf0a45a67..77acffa94a 100644
--- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021b.eb
+++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.10.0-gfbf-2023a.eb
@@ -1,20 +1,20 @@
-# Updated: Pavel Grochal (INUITS)
+# Updated: Helena Vela (HPCNow!)
 
 easyblock = 'PythonBundle'
 
 name = 'MDTraj'
-version = '1.9.7'
+version = '1.10.0'
 
 homepage = 'https://mdtraj.org'
 description = "Read, write and analyze MD trajectories with only a few lines of Python code."
 
-toolchain = {'name': 'foss', 'version': '2021b'}
+toolchain = {'name': 'gfbf', 'version': '2023a'}
 toolchainopts = {'openmp': True}
 
 dependencies = [
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('zlib', '1.2.11'),
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('zlib', '1.2.13'),
 ]
 
 use_pip = True
@@ -32,7 +32,7 @@ exts_list = [
         'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'],
     }),
     ('mdtraj', version, {
-        'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'],
+        'checksums': ['7d518b5a53b498f52686567e0191e9ee41a725b3296a8dbcac24fe824ed4af8f'],
     }),
 ]

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@hvelab