{vis}[foss/2020b] PyMol v2.4.0 w/ Python 3.8.6 #12582

ThomasHoffmann77 · 2021-04-13T12:40:02Z

(created using eb --new-pr)

…0_APBS_tools_plugin.patch, PyMol-2.4.0_openvr_header.patch

ThomasHoffmann77 · 2021-04-13T12:45:00Z

requires:

boegelbot · 2021-04-13T13:23:50Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/744743889
Output from first failing test suite run:

======================================================================
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
List of added easyconfig files in this PR:
Check whether any conflicts occur in software dependency graphs.
	PyMol-2.4.0-foss-2020b.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 155, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.1.0-foss-2020b, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (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 "test/easyconfigs/easyconfigs.py", line 139, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.1.0-foss-2020b, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 483, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.1.0-foss-2020b, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 930, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 745, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb
'use_pip' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb

----------------------------------------------------------------------
Ran 11811 tests in 495.636s

FAILED (failures=1, errors=3)
ERROR: Not all tests were successful.

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Please talk to my owner @boegel if you notice you me acting stupid),
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boegelbot · 2021-04-14T12:23:51Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/748075512
Output from first failing test suite run:

Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop

List of added easyconfig files in this PR:
	PyMol-2.4.0-foss-2020b.eb
======================================================================
ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 155, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.2.0-foss-2020b-egl, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (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 "test/easyconfigs/easyconfigs.py", line 139, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.2.0-foss-2020b-egl, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 483, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: glew/2.2.0-foss-2020b-egl, GLM/0.9.9.8, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 930, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 745, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb
'use_pip' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb

----------------------------------------------------------------------
Ran 11821 tests in 506.028s

FAILED (failures=1, errors=3)
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 you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

boegelbot · 2021-04-15T08:24:10Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/751151988
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 "test/easyconfigs/easyconfigs.py", line 155, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: GLM/0.9.9.8-foss-2020b, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (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 "test/easyconfigs/easyconfigs.py", line 139, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: GLM/0.9.9.8-foss-2020b, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 483, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 128, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: GLM/0.9.9.8-foss-2020b, msgpack-c/3.3.0-foss-2020b, mmtf-cpp/1.0.0-foss-2020b, OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0_Linux (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 930, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 745, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb
'use_pip' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb

----------------------------------------------------------------------
Ran 11838 tests in 507.385s

FAILED (failures=1, errors=3)
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 you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

Update APBS-3.0.0 dependency from binary to source

boegelbot · 2021-04-28T14:23:39Z

@ThomasHoffmann77: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/792744388
Output from first failing test suite run:

Found 12017 easyconfigs...
ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 156, in test_conflicts
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0-foss-2020b (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):
Failed to determine merge base (ec: 1, output: ''), falling back to specifying target branch develop

List of added easyconfig files in this PR:
  File "test/easyconfigs/easyconfigs.py", line 140, in test_dep_graph
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0-foss-2020b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 537, in test_dep_versions_per_toolchain_generation
    self.process_all_easyconfigs()
  File "test/easyconfigs/easyconfigs.py", line 129, in process_all_easyconfigs
    EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 460, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 323, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: OpenVR/1.0.17-foss-2020b, pdb2pqr/3.1.0-foss-2020b, APBS/3.0.0-foss-2020b (no easyconfig file or existing module found)'

======================================================================
FAIL: test_changed_files_pull_request (test.easyconfigs.easyconfigs.EasyConfigTest)
Specific checks only done for the (easyconfig) files that were changed in a pull request.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 985, in test_changed_files_pull_request
    self.check_python_packages(changed_ecs, added_ecs_filenames)
  File "test/easyconfigs/easyconfigs.py", line 799, in check_python_packages
    self.fail('\n'.join(failing_checks))
AssertionError: 'download_dep_fail' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb
'use_pip' should be set in exts_default_options in PyMol-2.4.0-foss-2020b.eb

----------------------------------------------------------------------
Ran 12027 tests in 576.027s

FAILED (failures=1, errors=3)
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 you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

boegel · 2024-01-13T18:43:55Z

closing this since foss/2020b is deprecated, see https://docs.easybuild.io/policies/toolchains

@ThomasHoffmann77 If PyMol is still relevant, please consider opening a new PR with a more recent toolchain

adding easyconfigs: PyMol-2.4.0-foss-2020b.eb and patches: PyMol-2.4.…

bb3d5d6

…0_APBS_tools_plugin.patch, PyMol-2.4.0_openvr_header.patch

update glew to 2.2.0

62d1ff1

adapt GLM toolchain

e6756dd

Update PyMol-2.4.0-foss-2020b.eb

fa37821

Update APBS-3.0.0 dependency from binary to source

guacke mentioned this pull request Oct 12, 2022

{vis}[foss/2020b] PyMOL v2.5.0 w/ Python 3.8.6 #16394

Merged

boegel added the new label Jan 13, 2024

boegel added this to the 4.x milestone Jan 13, 2024

boegel closed this Jan 13, 2024

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{vis}[foss/2020b] PyMol v2.4.0 w/ Python 3.8.6 #12582

{vis}[foss/2020b] PyMol v2.4.0 w/ Python 3.8.6 #12582

ThomasHoffmann77 commented Apr 13, 2021

ThomasHoffmann77 commented Apr 13, 2021 •

edited by boegel

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boegelbot commented Apr 28, 2021

boegel commented Jan 13, 2024

{vis}[foss/2020b] PyMol v2.4.0 w/ Python 3.8.6 #12582

{vis}[foss/2020b] PyMol v2.4.0 w/ Python 3.8.6 #12582

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ThomasHoffmann77 commented Apr 13, 2021

ThomasHoffmann77 commented Apr 13, 2021 • edited by boegel Loading

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boegelbot commented Apr 28, 2021

boegel commented Jan 13, 2024

ThomasHoffmann77 commented Apr 13, 2021 •

edited by boegel

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