{bio}[foss/2023a] cryoCARE v0.3.1, CSBDeep v0.7.4 w/ CUDA 12.1.1 #20549

ThomasHoffmann77 · 2024-05-17T08:37:40Z

(created using eb --new-pr)

…RE031

github-actions · 2024-12-04T10:12:24Z

Updated software `CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb`

Diff against CSBDeep-0.7.4-foss-2023a.eb

easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb

diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
index 3b3b0f3765..1c31a6086b 100644
--- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a.eb
+++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
@@ -1,9 +1,10 @@
 # This easyconfig was created by the BEAR Software team at the University of Birmingham.
-# Update: Petr Král (INUITS)
+# update: foss/2023a thembl
 easyblock = 'PythonBundle'
 
 name = 'CSBDeep'
 version = '0.7.4'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = "https://csbdeep.bioimagecomputing.com/"
 description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE)."""
@@ -12,8 +13,9 @@ toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
     ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
     ('SciPy-bundle', '2023.07'),
-    ('TensorFlow', '2.13.0'),
+    ('TensorFlow', '2.15.1', versionsuffix),
     ('matplotlib', '3.7.2'),
     ('tqdm', '4.66.1'),
 ]
@@ -22,13 +24,13 @@ use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('tifffile', '2024.6.18', {
-        'source_tmpl': SOURCE_PY3_WHL,
-        'checksums': ['67299c0445fc47463bbc71f3cb4676da2ab0242b0c6c6542a0680801b4b97d8a'],
+    ('tifffile', '2023.9.26', {
+        'checksums': ['67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae'],
     }),
-    ('%(namelower)s', version, {
-        'source_tmpl': SOURCE_WHL,
-        'checksums': ['155d61827439373dc9c2a730a1ef621f7e373fea16599d583e0a70f1e48bd6db'],
+    (name, version, {
+        'modulename': '%(namelower)s',
+        'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
+        'checksums': ['85d6fc360bb33253ba6f543d75cf0cf123595f0ea4dd1fa76b1e5bc8fc55b901'],
     }),
 ]

Diff against CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
index fcd4c2441b..1c31a6086b 100644
--- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
@@ -1,4 +1,5 @@
 # This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# update: foss/2023a thembl
 easyblock = 'PythonBundle'
 
 name = 'CSBDeep'
@@ -8,15 +9,15 @@ versionsuffix = '-CUDA-%(cudaver)s'
 homepage = "https://csbdeep.bioimagecomputing.com/"
 description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE)."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('SciPy-bundle', '2022.05'),
-    ('TensorFlow', '2.11.0', versionsuffix),
-    ('matplotlib', '3.5.2'),
-    ('tqdm', '4.64.0'),
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.15.1', versionsuffix),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
@@ -27,9 +28,9 @@ exts_list = [
         'checksums': ['67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae'],
     }),
     (name, version, {
+        'modulename': '%(namelower)s',
         'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
         'checksums': ['85d6fc360bb33253ba6f543d75cf0cf123595f0ea4dd1fa76b1e5bc8fc55b901'],
-        'modulename': '%(namelower)s',
     }),
 ]

Diff against CSBDeep-0.7.4-foss-2022a.eb

easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb

diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
index e65992a566..1c31a6086b 100644
--- a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb
+++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb
@@ -1,20 +1,23 @@
 # This easyconfig was created by the BEAR Software team at the University of Birmingham.
+# update: foss/2023a thembl
 easyblock = 'PythonBundle'
 
 name = 'CSBDeep'
 version = '0.7.4'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = "https://csbdeep.bioimagecomputing.com/"
 description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE)."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('SciPy-bundle', '2022.05'),
-    ('TensorFlow', '2.11.0'),
-    ('matplotlib', '3.5.2'),
-    ('tqdm', '4.64.0'),
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.15.1', versionsuffix),
+    ('matplotlib', '3.7.2'),
+    ('tqdm', '4.66.1'),
 ]
 
 use_pip = True
@@ -25,9 +28,9 @@ exts_list = [
         'checksums': ['67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae'],
     }),
     (name, version, {
+        'modulename': '%(namelower)s',
         'source_tmpl': '%(namelower)s-%(version)s.tar.gz',
         'checksums': ['85d6fc360bb33253ba6f543d75cf0cf123595f0ea4dd1fa76b1e5bc8fc55b901'],
-        'modulename': '%(namelower)s',
     }),
 ]

Updated software `cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb`

Diff against cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb

easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb

diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb
index 9e6d24ecaf..4455451007 100644
--- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb
+++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,8 +1,8 @@
-# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2023/11
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/05
 easyblock = 'PythonBundle'
 
 name = 'cryoCARE'
-version = '0.3.0'
+version = '0.3.1'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/juglab/cryoCARE_pip'
@@ -21,18 +21,18 @@ identical, up to random noise, tomograms can be reconstructed.
 These two (even and odd) tomograms can be used as input to this cryoCARE        
 implementation."""
 
-toolchain = {'name': 'foss', 'version': '2022a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 
 dependencies = [
-    ('Python', '3.10.4'),
-    ('CUDA', '11.7.0', '', SYSTEM),
-    ('SciPy-bundle', '2022.05'),
-    ('TensorFlow', '2.11.0', versionsuffix),
-    ('mrcfile', '1.4.3'),
-    ('tqdm', '4.64.0'),
-    ('matplotlib', '3.5.2'),
-    ('CSBDeep', '0.7.4', versionsuffix),
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.15.1', versionsuffix),
+    ('mrcfile', '1.5.0'),
+    ('tqdm', '4.66.1'),
+    ('matplotlib', '3.7.2'),
+    ('CSBDeep', '0.7.4', versionsuffix),  # cryoCARE 0.3.1 requires < 0.8.0
 ]
 
 use_pip = True
@@ -40,11 +40,18 @@ sanity_pip_check = True
 
 exts_list = [
     (name, version, {
-        'patches': ['%(name)s-%(version)s_relax_requirements.patch'],
+        'patches': [
+            '%(name)s-0.3.0_relax_requirements.patch',
+            'cryoCARE-0.3.1_fix_np1.20.0deprecations.patch',
+        ],
+        'source_urls': ['https://github.com/juglab/cryoCARE_pip/archive/refs/tags/'],
+        'sources': ['v%(version)s.tar.gz'],
         'checksums': [
-            {'cryoCARE-0.3.0.tar.gz': '8885aeb03d1731de1958463bbf766fa9999f4480d71c3af09f711ee210ab9886'},
+            {'v0.3.1.tar.gz': 'faf1e06e4a893bf01a6a70b207b75c6ff190310d03fb9b9b56a4be7937935d54'},
             {'cryoCARE-0.3.0_relax_requirements.patch':
              'a44814f6e568f5fb618cf789d21a6b5714fbda78b4170ec8e868e50fb0f2a5c0'},
+            {'cryoCARE-0.3.1_fix_np1.20.0deprecations.patch':
+             'a25e3a540016db02d47b82e2104763e376340b80d0d1012ece7bb4a53f8bcdb9'}
         ],
     }),
 ]

Diff against cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb

easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb

diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb
index 81b96e34eb..4455451007 100644
--- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb
+++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,8 +1,8 @@
-# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2022/10
+# Thomas Hoffmann, EMBL Heidelberg, [email protected], 2024/05
 easyblock = 'PythonBundle'
 
 name = 'cryoCARE'
-version = '0.2.1'
+version = '0.3.1'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/juglab/cryoCARE_pip'
@@ -21,31 +21,38 @@ identical, up to random noise, tomograms can be reconstructed.
 These two (even and odd) tomograms can be used as input to this cryoCARE        
 implementation."""
 
-toolchain = {'name': 'foss', 'version': '2021a'}
+toolchain = {'name': 'foss', 'version': '2023a'}
 
 
 dependencies = [
-    ('Python', '3.9.5'),
-    ('CUDA', '11.3.1', '', SYSTEM),
-    ('SciPy-bundle', '2021.05'),
-    ('TensorFlow', '2.6.0', versionsuffix),
-    ('mrcfile', '1.3.0'),
-    ('tqdm', '4.61.2'),
-    ('matplotlib', '3.4.2'),
+    ('Python', '3.11.3'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('SciPy-bundle', '2023.07'),
+    ('TensorFlow', '2.15.1', versionsuffix),
+    ('mrcfile', '1.5.0'),
+    ('tqdm', '4.66.1'),
+    ('matplotlib', '3.7.2'),
+    ('CSBDeep', '0.7.4', versionsuffix),  # cryoCARE 0.3.1 requires < 0.8.0
 ]
 
 use_pip = True
 sanity_pip_check = True
 
 exts_list = [
-    ('tifffile', '2022.10.10', {
-        'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'],
-    }),
-    ('csbdeep', '0.7.2', {
-        'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'],
-    }),
     (name, version, {
-        'checksums': ['b66989acb6eadf771de08a46e4860d041113527205eebb2cf5d13ae3dc9cb43b'],
+        'patches': [
+            '%(name)s-0.3.0_relax_requirements.patch',
+            'cryoCARE-0.3.1_fix_np1.20.0deprecations.patch',
+        ],
+        'source_urls': ['https://github.com/juglab/cryoCARE_pip/archive/refs/tags/'],
+        'sources': ['v%(version)s.tar.gz'],
+        'checksums': [
+            {'v0.3.1.tar.gz': 'faf1e06e4a893bf01a6a70b207b75c6ff190310d03fb9b9b56a4be7937935d54'},
+            {'cryoCARE-0.3.0_relax_requirements.patch':
+             'a44814f6e568f5fb618cf789d21a6b5714fbda78b4170ec8e868e50fb0f2a5c0'},
+            {'cryoCARE-0.3.1_fix_np1.20.0deprecations.patch':
+             'a25e3a540016db02d47b82e2104763e376340b80d0d1012ece7bb4a53f8bcdb9'}
+        ],
     }),
 ]
 
@@ -55,4 +62,4 @@ sanity_check_commands = [
     'cryoCARE_predict.py --help',
 ]
 
-moduleclass = 'vis'
+moduleclass = 'bio'

{bio}[foss/2023a] cryoCARE v0.3.1, CSBDepp v0.7.4 w/ CUDA 12.1.1

4f6d8b3

ThomasHoffmann77 changed the title ~~{bio}[foss/2023a] cryoCARE v0.3.1, CSBDepp v0.7.4 w/ CUDA 12.1.1~~ {bio}[foss/2023a] cryoCARE v0.3.1, CSBDeep v0.7.4 w/ CUDA 12.1.1 May 17, 2024

ThomasHoffmann77 mentioned this pull request May 24, 2024

RELION5 draft for tomo support; 2nd try jfgrimm/easybuild-easyconfigs#6

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20 tasks

Merge branch 'easybuilders:develop' into 20240517103736_new_pr_cryoCA…

3365243

…RE031

github-actions bot added the update label Dec 4, 2024

ThomasHoffmann77 and others added 2 commits December 4, 2024 11:13

Update cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb

90ee19c

patch np1.20.0 deprecation

25dbff0

ThomasHoffmann77 mentioned this pull request Dec 5, 2024

{bio}[foss/2023a] RELION v5.0.0 w/ CUDA 12.1.1 #19678

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Thyre added the 2023a label Aug 18, 2025

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{bio}[foss/2023a] cryoCARE v0.3.1, CSBDeep v0.7.4 w/ CUDA 12.1.1 #20549

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Updated software CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb

Updated software cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb

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ThomasHoffmann77 commented May 17, 2024 •

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Updated software `CSBDeep-0.7.4-foss-2023a-CUDA-12.1.1.eb`

Updated software `cryoCARE-0.3.1-foss-2023a-CUDA-12.1.1.eb`