{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.11 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0 by ThomasHoffmann77 · Pull Request #19157 · easybuilders/easybuild-easyconfigs

ThomasHoffmann77 · 2023-11-06T10:26:52Z

(created using eb --new-pr)
requires #19167

…MER 0.10.4 mrcfile/1.4.3 Cython/3.0.5 /w CUDA 12.0.0

verdurin · 2023-11-06T11:12:01Z

@ThomasHoffmann77 please let us know when you feel this is ready to review - we've received a request for Model-Angelo, so happy to take a look.

boegelbot · 2023-11-06T12:25:27Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6770202219
Last 100 lines of output from first failing test suite run:

    raise EasyBuildError(msg)
easybuild.tools.build_log.EasyBuildError: "Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 1160, in test_pr_sanity_check_paths
    for ec in self.changed_ecs:
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 301, in changed_ecs
    self._get_changed_easyconfigs()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 250, in _get_changed_easyconfigs
    ec = process_easyconfig(ec_file)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2087, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
easybuild.tools.build_log.EasyBuildError: "Failed to process easyconfig /home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb: Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

======================================================================
ERROR: test_pr_sha256_checksums (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure changed easyconfigs have SHA256 checksums in place.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2085, in process_easyconfig
    ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 518, in __init__
    self.local_var_naming(local_var_naming_check)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 823, in local_var_naming
    raise EasyBuildError(msg)
easybuild.tools.build_log.EasyBuildError: "Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 986, in test_pr_sha256_checksums
    for ec in self.changed_ecs:
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 301, in changed_ecs
    self._get_changed_easyconfigs()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 250, in _get_changed_easyconfigs
    ec = process_easyconfig(ec_file)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2087, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
easybuild.tools.build_log.EasyBuildError: "Failed to process easyconfig /home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb: Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

======================================================================
ERROR: test_r_libs_site_env_var (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2085, in process_easyconfig
    ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 518, in __init__
    self.local_var_naming(local_var_naming_check)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 823, in local_var_naming
    raise EasyBuildError(msg)
easybuild.tools.build_log.EasyBuildError: "Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 919, in test_r_libs_site_env_var
    for ec in self.parsed_easyconfigs:
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 276, in parsed_easyconfigs
    EasyConfigTest.parse_all_easyconfigs()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 201, in parse_all_easyconfigs
    cls._parsed_easyconfigs.extend(process_easyconfig(spec))
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2087, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
easybuild.tools.build_log.EasyBuildError: "Failed to process easyconfig /home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb: Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

======================================================================
ERROR: test_sanity_check_paths (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure specified sanity check paths adher to the requirements.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2085, in process_easyconfig
    ec = EasyConfig(spec, build_specs=build_specs, validate=validate, hidden=hidden)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 518, in __init__
    self.local_var_naming(local_var_naming_check)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 823, in local_var_naming
    raise EasyBuildError(msg)
easybuild.tools.build_log.EasyBuildError: "Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 903, in test_sanity_check_paths
    for ec in self.parsed_easyconfigs:
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 276, in parsed_easyconfigs
    EasyConfigTest.parse_all_easyconfigs()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 201, in parse_all_easyconfigs
    cls._parsed_easyconfigs.extend(process_easyconfig(spec))
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/framework/easyconfig/easyconfig.py", line 2087, in process_easyconfig
    raise EasyBuildError("Failed to process easyconfig %s: %s", spec, err.msg)
easybuild.tools.build_log.EasyBuildError: "Failed to process easyconfig /home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb: Use of 1 unknown easyconfig parameters detected in Model-Angelo_data-1.0.9.eb: install_type\nIf these are just local variables please rename them to start with 'local_', or try using --fix-deprecated-easyconfigs to do this automatically.\nFor more information, see https://easybuild.readthedocs.io/en/latest/Easyconfig-files-local-variables.html ."

----------------------------------------------------------------------
Ran 18487 tests in 901.828s

FAILED (errors=12)
ERROR: Not all tests were successful

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Please talk to my owner @boegel if you notice me acting stupid),
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ThomasHoffmann77 · 2023-11-06T12:41:31Z

@ThomasHoffmann77 please let us know when you feel this is ready to review - we've received a request for Model-Angelo, so happy to take a look.

@verdurin Tests still fail, but I remove 'draft'

easybuilders#19167

boegelbot · 2023-11-07T13:26:03Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6784676593
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 331, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 283, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
easybuild.tools.build_log.EasyBuildError: 'Missing dependencies: mrcfile/1.4.3-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 318, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 283, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
easybuild.tools.build_log.EasyBuildError: 'Missing dependencies: mrcfile/1.4.3-foss-2022a (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 868, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 283, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
easybuild.tools.build_log.EasyBuildError: 'Missing dependencies: mrcfile/1.4.3-foss-2022a (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 18492 tests in 864.552s

FAILED (errors=3)
ERROR: Not all tests were successful

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Please talk to my owner @boegel if you notice me acting stupid),
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…asyconfigs into 20231106112642_new_pr_Model-Angelo109

boegelbot · 2023-11-15T11:26:07Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6876442958
Output from first failing test suite run:

FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 97, in assertEqual
    super(TestCase, self).assertEqual(a, b)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/unittest/case.py", line 829, in assertEqual
    assertion_func(first, second, msg=msg)
AssertionError: 1 != 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/3.6.15/x64/lib/python3.6/site-packages/easybuild/base/testing.py", line 119, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 1:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/m/Model-Angelo_data/Model-Angelo_data-1.0.9.eb:98:14: E225 missing whitespace around operator

: 1 != 0:
DIFF:
- 1

----------------------------------------------------------------------
Ran 18532 tests in 716.581s

FAILED (failures=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

update to 1.0.10

….0.10-foss-2022a-CUDA-11.7.0.eb

…del-Angelo-1.0.11-foss-2022a-CUDA-11.7.0.eb update 1.0.10 -> 1.0.11

fix typo

sassy-crick · 2025-06-16T15:04:49Z

@ThomasHoffmann77 You might want to sync your PR with development, something like this:

eb --sync-pr-with-develop NUMBER_OF_PR

boegel · 2025-10-13T16:37:45Z

No longer relevant since 2022a toolchains are deprecated since foss/2025b was defined, see also https://docs.easybuild.io/policies/toolchains/, so closing...

github-actions · 2025-10-13T16:43:49Z

Updated software `Cython-3.0.5-GCCcore-11.3.0.eb`

Diff against Cython-0.29.37-GCCcore-13.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
index 8665d066e9..7e7fe1efff 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-0.29.37-GCCcore-13.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '0.29.37'
+version = '3.0.5'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,24 +13,26 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-sources = [SOURCE_TAR_GZ]
-checksums = ['f813d4a6dd94adee5d4ff266191d1d95bf6d4164a4facc535422c021b2504cfb']
+builddependencies = [('binutils', '2.38')]
 
-builddependencies = [
-    ('binutils', '2.42'),
-]
+dependencies = [('Python', '3.10.4')]
 
-dependencies = [
-    ('Python', '3.12.3'),
-]
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['39318348db488a2f24e7c84e08bdc82f2624853c0fea8b475ea0b70b27176492']
 
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
-sanity_check_commands = ["cython --version"]
+sanity_check_commands = [
+    'cython --version',
+]
 
 moduleclass = 'lang'

Diff against Cython-3.1.2-GCCcore-14.3.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
index 3b88ae00ab..7e7fe1efff 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.1.2-GCCcore-14.3.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.1.2'
+version = '3.0.5'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,24 +13,26 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '14.3.0'}
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['6bbf7a953fa6762dfecdec015e3b054ba51c0121a45ad851fa130f63f5331381']
+builddependencies = [('binutils', '2.38')]
 
-builddependencies = [
-    ('binutils', '2.44'),
-]
+dependencies = [('Python', '3.10.4')]
 
-dependencies = [
-    ('Python', '3.13.5'),
-]
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['39318348db488a2f24e7c84e08bdc82f2624853c0fea8b475ea0b70b27176492']
 
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
-sanity_check_commands = ["cython --version"]
+sanity_check_commands = [
+    'cython --version',
+]
 
 moduleclass = 'lang'

Diff against Cython-3.1.1-GCCcore-14.2.0.eb

easybuild/easyconfigs/c/Cython/Cython-3.1.1-GCCcore-14.2.0.eb

diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.1.1-GCCcore-14.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
index d14edc128a..7e7fe1efff 100644
--- a/easybuild/easyconfigs/c/Cython/Cython-3.1.1-GCCcore-14.2.0.eb
+++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.5-GCCcore-11.3.0.eb
@@ -1,7 +1,7 @@
 easyblock = 'PythonPackage'
 
 name = 'Cython'
-version = '3.1.1'
+version = '3.0.5'
 
 homepage = 'https://cython.org/'
 description = """
@@ -13,24 +13,26 @@ docurls = [
     'https://github.com/cython/cython',
 ]
 
-toolchain = {'name': 'GCCcore', 'version': '14.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-sources = [SOURCELOWER_TAR_GZ]
-checksums = ['505ccd413669d5132a53834d792c707974248088c4f60c497deb1b416e366397']
+builddependencies = [('binutils', '2.38')]
 
-builddependencies = [
-    ('binutils', '2.42'),
-]
+dependencies = [('Python', '3.10.4')]
 
-dependencies = [
-    ('Python', '3.13.1'),
-]
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['39318348db488a2f24e7c84e08bdc82f2624853c0fea8b475ea0b70b27176492']
 
 sanity_check_paths = {
     'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],
 }
 
-sanity_check_commands = ["cython --version"]
+sanity_check_commands = [
+    'cython --version',
+]
 
 moduleclass = 'lang'

Updated software `PyHMMER-0.10.4-gompi-2022a.eb`

Diff against PyHMMER-0.10.15-gompi-2023a.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
index 212f4e8f79..be6fcd40c6 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023a.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
@@ -1,40 +1,45 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02
-# Update: Petr Král (INUITS)
-
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.10.15'
+version = '0.10.4'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
-HMMER is a biological sequence analysis tool that uses profile hidden Markov
-models to search for sequence homologs. HMMER3 is developed and maintained by
+HMMER is a biological sequence analysis tool that uses profile hidden Markov    
+models to search for sequence homologs. HMMER3 is developed and maintained by   
 the Eddy/Rivas Laboratory at Harvard University.
 
-pyhmmer is a Python package, implemented using the Cython language, that
-provides bindings to HMMER3. It directly interacts with the HMMER internals,
+pyhmmer is a Python package, implemented using the Cython language, that        
+provides bindings to HMMER3. It directly interacts with the HMMER internals,    
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {}  # toolchain options, e.g. opt, pic, usempi, optarch, ...
+
 
 builddependencies = [
-    ('Cython', '3.0.8'),
+    # Cython 0.29.28 does not work
+    ('Cython', '3.0.5'),
 ]
-
 dependencies = [
-    ('Python', '3.11.3'),
-    ('HMMER', '3.4'),
-    ('psutil', '5.9.8')
+    ('Python', '3.10.4'),
+    ('HMMER', '3.3.2'),
 ]
 
+use_pip = True
+
 exts_list = [
-    ('%(namelower)s', version, {
-        # Requirement for `psutil` is too strict.
-        'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ",
-        'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'],
+    ('pyhmmer', version, {
+        'checksums': ['08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b'],
     }),
 ]
 
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+sanity_pip_check = True
 
 moduleclass = 'bio'

Diff against PyHMMER-0.10.15-gompi-2023b.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
index db7eeecc50..be6fcd40c6 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.15-gompi-2023b.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
@@ -1,38 +1,37 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02
-# Update: Petr Král (INUITS)
-
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.10.15'
+version = '0.10.4'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
-HMMER is a biological sequence analysis tool that uses profile hidden Markov
-models to search for sequence homologs. HMMER3 is developed and maintained by
+HMMER is a biological sequence analysis tool that uses profile hidden Markov    
+models to search for sequence homologs. HMMER3 is developed and maintained by   
 the Eddy/Rivas Laboratory at Harvard University.
 
-pyhmmer is a Python package, implemented using the Cython language, that
-provides bindings to HMMER3. It directly interacts with the HMMER internals,
+pyhmmer is a Python package, implemented using the Cython language, that        
+provides bindings to HMMER3. It directly interacts with the HMMER internals,    
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2023b'}
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {}  # toolchain options, e.g. opt, pic, usempi, optarch, ...
+
 
 builddependencies = [
-    ('Cython', '3.0.10'),
+    # Cython 0.29.28 does not work
+    ('Cython', '3.0.5'),
 ]
-
 dependencies = [
-    ('Python', '3.11.5'),
-    ('HMMER', '3.4'),
-    ('psutil', '6.1.0')
+    ('Python', '3.10.4'),
+    ('HMMER', '3.3.2'),
 ]
 
+use_pip = True
+
 exts_list = [
-    ('%(namelower)s', version, {
-        # Requirement for `psutil` is too strict.
-        'preinstallopts': "sed -i 's/psutil ~=5.8/psutil >=5.8/g' setup.cfg && ",
-        'checksums': ['bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921'],
+    ('pyhmmer', version, {
+        'checksums': ['08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b'],
     }),
 ]
 
@@ -41,4 +40,6 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
 }
 
+sanity_pip_check = True
+
 moduleclass = 'bio'

Diff against PyHMMER-0.10.6-gompi-2023a.eb

easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb

diff --git a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
index 387076e15d..be6fcd40c6 100644
--- a/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.6-gompi-2023a.eb
+++ b/easybuild/easyconfigs/p/PyHMMER/PyHMMER-0.10.4-gompi-2022a.eb
@@ -1,33 +1,37 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
 easyblock = 'PythonBundle'
 
 name = 'PyHMMER'
-version = '0.10.6'
+version = '0.10.4'
 
 homepage = 'https://github.com/althonos/pyhmmer'
 description = """
-HMMER is a biological sequence analysis tool that uses profile hidden Markov
-models to search for sequence homologs. HMMER3 is developed and maintained by
+HMMER is a biological sequence analysis tool that uses profile hidden Markov    
+models to search for sequence homologs. HMMER3 is developed and maintained by   
 the Eddy/Rivas Laboratory at Harvard University.
 
-pyhmmer is a Python package, implemented using the Cython language, that
-provides bindings to HMMER3. It directly interacts with the HMMER internals,
+pyhmmer is a Python package, implemented using the Cython language, that        
+provides bindings to HMMER3. It directly interacts with the HMMER internals,    
 which has the following advantages over CLI wrappers (like hmmer-py)"""
 
-toolchain = {'name': 'gompi', 'version': '2023a'}
+toolchain = {'name': 'gompi', 'version': '2022a'}
+toolchainopts = {}  # toolchain options, e.g. opt, pic, usempi, optarch, ...
+
 
 builddependencies = [
-    ('Cython', '3.0.7'),
+    # Cython 0.29.28 does not work
+    ('Cython', '3.0.5'),
 ]
 dependencies = [
-    ('Python', '3.11.3'),
-    ('HMMER', '3.4'),
-    ('psutil', '5.9.8')
+    ('Python', '3.10.4'),
+    ('HMMER', '3.3.2'),
 ]
 
+use_pip = True
+
 exts_list = [
     ('pyhmmer', version, {
-        'checksums': ['47e017ccc523046400312afc937d4d68306f6ca0ed82e313deb3697d4fd8ccff'],
+        'checksums': ['08bc02aadf0f113df2b2912478bb02be9daf5d322df9c72bcd07fa01fe53a87b'],
     }),
 ]
 
@@ -36,4 +40,6 @@ sanity_check_paths = {
     'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
 }
 
+sanity_pip_check = True
+
 moduleclass = 'bio'

{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHM…

cf238ea

…MER 0.10.4 mrcfile/1.4.3 Cython/3.0.5 /w CUDA 12.0.0

ThomasHoffmann77 marked this pull request as draft November 6, 2023 10:27

fix style. fix model path

0e11586

ThomasHoffmann77 changed the title ~~{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHMMER 0.10.4 mrcfile/1.4.3 Cython/3.0.5 /w CUDA 12.0.0~~ {bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHMMER 0.10.4 mrcfile/1.4.3 Cython/3.0.5 /w CUDA 11.7.0 Nov 6, 2023

ThomasHoffmann77 added 2 commits November 6, 2023 11:55

fix model path

bc5f17e

fix sanity check path

03fa0b3

ThomasHoffmann77 added 2 commits November 6, 2023 12:16

styles

8307f9a

mrcfile sanity check paths

fbb117c

ThomasHoffmann77 marked this pull request as ready for review November 6, 2023 12:42

ThomasHoffmann77 and others added 3 commits November 6, 2023 13:50

Update Model-Angelo_data-1.0.9.eb

5253a2a

ModelAngelo_data: remove install_type

e7c3066

Delete easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb

ba89d28

easybuilders#19167

ThomasHoffmann77 changed the title ~~{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHMMER 0.10.4 mrcfile/1.4.3 Cython/3.0.5 /w CUDA 11.7.0~~ {bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0 Nov 7, 2023

verdurin and others added 2 commits November 7, 2023 17:13

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

a0a7e40

…asyconfigs into 20231106112642_new_pr_Model-Angelo109

modextravars->modextrapaths for TORCH_HOME

88708c7

modextravars->modextrapaths for TORCH_HOME; fix style

71c73bb

fix patch of get_esm_models for handling multiple paths in

f41fd6b

ThomasHoffmann77 marked this pull request as draft November 17, 2023 19:44

ThomasHoffmann77 mentioned this pull request Nov 21, 2023

RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb with models and missing dependencies #18359

Closed

1 task

ThomasHoffmann77 marked this pull request as ready for review November 23, 2023 13:38

ThomasHoffmann77 added 2 commits November 27, 2023 11:34

Update Model-Angelo-1.0.9-foss-2022a-CUDA-11.7.0.eb

d881b0f

update to 1.0.10

Rename Model-Angelo-1.0.9-foss-2022a-CUDA-11.7.0.eb to Model-Angelo-1…

f49a62d

….0.10-foss-2022a-CUDA-11.7.0.eb

ThomasHoffmann77 changed the title ~~{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.9 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0~~ {bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.10 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0 Nov 27, 2023

Update and rename Model-Angelo-1.0.10-foss-2022a-CUDA-11.7.0.eb to Mo…

b6e0464

…del-Angelo-1.0.11-foss-2022a-CUDA-11.7.0.eb update 1.0.10 -> 1.0.11

ThomasHoffmann77 changed the title ~~{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.10 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0~~ {bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.11 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0 Nov 28, 2023

Update Model-Angelo-1.0.11-foss-2022a-CUDA-11.7.0.eb

3900822

fix typo

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{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.11 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0#19157

{bio}[foss/2022a,gompi/2022a,GCCcore/11.3.0] Model-Angelo v1.0.11 PyHMMER 0.10.4 Cython/3.0.5 /w CUDA 11.7.0#19157
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ThomasHoffmann77 commented Nov 6, 2023 •

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Updated software `Cython-3.0.5-GCCcore-11.3.0.eb`

Updated software `PyHMMER-0.10.4-gompi-2022a.eb`