Created
June 19, 2024 12:16
-
-
Save natsukium/a1999c3c518e05ce4dfed42fad46fe1a to your computer and use it in GitHub Desktop.
system: x86_64-linux | build_time: 5 seconds | https://github.com/NixOS/nixpkgs/pull/320834
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Sourcing python-remove-tests-dir-hook | |
| Sourcing python-catch-conflicts-hook.sh | |
| Sourcing python-remove-bin-bytecode-hook.sh | |
| Sourcing pypa-build-hook | |
| Using pypaBuildPhase | |
| Sourcing python-runtime-deps-check-hook | |
| Using pythonRuntimeDepsCheckHook | |
| Sourcing pypa-install-hook | |
| Using pypaInstallPhase | |
| Sourcing python-imports-check-hook.sh | |
| Using pythonImportsCheckPhase | |
| Sourcing python-namespaces-hook | |
| Sourcing python-catch-conflicts-hook.sh | |
| Sourcing pytest-check-hook | |
| Using pytestCheckPhase | |
| @nix { "action": "setPhase", "phase": "unpackPhase" } | |
| Running phase: unpackPhase | |
| unpacking source archive /nix/store/pi5ym131bbsmbj8ic1ilynxf64l0z8p2-source | |
| source root is source | |
| setting SOURCE_DATE_EPOCH to timestamp 315619200 of file source/util/validate-outputs.py | |
| @nix { "action": "setPhase", "phase": "patchPhase" } | |
| Running phase: patchPhase | |
| @nix { "action": "setPhase", "phase": "updateAutotoolsGnuConfigScriptsPhase" } | |
| Running phase: updateAutotoolsGnuConfigScriptsPhase | |
| @nix { "action": "setPhase", "phase": "configurePhase" } | |
| Running phase: configurePhase | |
| no configure script, doing nothing | |
| @nix { "action": "setPhase", "phase": "buildPhase" } | |
| Running phase: buildPhase | |
| Executing pypaBuildPhase | |
| Creating a wheel... | |
| * Getting build dependencies for wheel... | |
| running egg_info | |
| creating modelcif.egg-info | |
| writing modelcif.egg-info/PKG-INFO | |
| writing dependency_links to modelcif.egg-info/dependency_links.txt | |
| writing requirements to modelcif.egg-info/requires.txt | |
| writing top-level names to modelcif.egg-info/top_level.txt | |
| writing manifest file 'modelcif.egg-info/SOURCES.txt' | |
| reading manifest file 'modelcif.egg-info/SOURCES.txt' | |
| reading manifest template 'MANIFEST.in' | |
| adding license file 'LICENSE' | |
| writing manifest file 'modelcif.egg-info/SOURCES.txt' | |
| * Building wheel... | |
| running bdist_wheel | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib | |
| creating build/lib/modelcif | |
| copying modelcif/__init__.py -> build/lib/modelcif | |
| copying modelcif/alignment.py -> build/lib/modelcif | |
| copying modelcif/associated.py -> build/lib/modelcif | |
| copying modelcif/data.py -> build/lib/modelcif | |
| copying modelcif/descriptor.py -> build/lib/modelcif | |
| copying modelcif/dumper.py -> build/lib/modelcif | |
| copying modelcif/model.py -> build/lib/modelcif | |
| copying modelcif/protocol.py -> build/lib/modelcif | |
| copying modelcif/qa_metric.py -> build/lib/modelcif | |
| copying modelcif/reader.py -> build/lib/modelcif | |
| copying modelcif/reference.py -> build/lib/modelcif | |
| copying modelcif/test.py -> build/lib/modelcif | |
| installing to build/bdist.linux-x86_64/wheel | |
| running install | |
| running install_lib | |
| creating build/bdist.linux-x86_64 | |
| creating build/bdist.linux-x86_64/wheel | |
| creating build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/__init__.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/alignment.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/associated.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/data.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/descriptor.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/dumper.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/model.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/protocol.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/qa_metric.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/reader.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/reference.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| copying build/lib/modelcif/test.py -> build/bdist.linux-x86_64/wheel/modelcif | |
| running install_egg_info | |
| running egg_info | |
| writing modelcif.egg-info/PKG-INFO | |
| writing dependency_links to modelcif.egg-info/dependency_links.txt | |
| writing requirements to modelcif.egg-info/requires.txt | |
| writing top-level names to modelcif.egg-info/top_level.txt | |
| reading manifest file 'modelcif.egg-info/SOURCES.txt' | |
| reading manifest template 'MANIFEST.in' | |
| adding license file 'LICENSE' | |
| writing manifest file 'modelcif.egg-info/SOURCES.txt' | |
| Copying modelcif.egg-info to build/bdist.linux-x86_64/wheel/modelcif-0.9-py3.12.egg-info | |
| running install_scripts | |
| creating build/bdist.linux-x86_64/wheel/modelcif-0.9.dist-info/WHEEL | |
| creating '/build/source/dist/.tmp-aimcfqod/modelcif-0.9-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it | |
| adding 'modelcif/__init__.py' | |
| adding 'modelcif/alignment.py' | |
| adding 'modelcif/associated.py' | |
| adding 'modelcif/data.py' | |
| adding 'modelcif/descriptor.py' | |
| adding 'modelcif/dumper.py' | |
| adding 'modelcif/model.py' | |
| adding 'modelcif/protocol.py' | |
| adding 'modelcif/qa_metric.py' | |
| adding 'modelcif/reader.py' | |
| adding 'modelcif/reference.py' | |
| adding 'modelcif/test.py' | |
| adding 'modelcif-0.9.dist-info/LICENSE' | |
| adding 'modelcif-0.9.dist-info/METADATA' | |
| adding 'modelcif-0.9.dist-info/WHEEL' | |
| adding 'modelcif-0.9.dist-info/top_level.txt' | |
| adding 'modelcif-0.9.dist-info/RECORD' | |
| removing build/bdist.linux-x86_64/wheel | |
| Successfully built modelcif-0.9-py3-none-any.whl | |
| Finished creating a wheel... | |
| Finished executing pypaBuildPhase | |
| @nix { "action": "setPhase", "phase": "pythonRuntimeDepsCheckHook" } | |
| Running phase: pythonRuntimeDepsCheckHook | |
| Executing pythonRuntimeDepsCheck | |
| Checking runtime dependencies for modelcif-0.9-py3-none-any.whl | |
| Finished executing pythonRuntimeDepsCheck | |
| @nix { "action": "setPhase", "phase": "installPhase" } | |
| Running phase: installPhase | |
| Executing pypaInstallPhase | |
| Successfully installed modelcif-0.9-py3-none-any.whl | |
| Finished executing pypaInstallPhase | |
| @nix { "action": "setPhase", "phase": "pythonOutputDistPhase" } | |
| Running phase: pythonOutputDistPhase | |
| Executing pythonOutputDistPhase | |
| Finished executing pythonOutputDistPhase | |
| @nix { "action": "setPhase", "phase": "fixupPhase" } | |
| Running phase: fixupPhase | |
| shrinking RPATHs of ELF executables and libraries in /nix/store/04g4jl24c1bfrvgnac3s4j6zpxnaap7p-python3.12-modelcif-0.9 | |
| checking for references to /build/ in /nix/store/04g4jl24c1bfrvgnac3s4j6zpxnaap7p-python3.12-modelcif-0.9... | |
| patching script interpreter paths in /nix/store/04g4jl24c1bfrvgnac3s4j6zpxnaap7p-python3.12-modelcif-0.9 | |
| stripping (with command strip and flags -S -p) in /nix/store/04g4jl24c1bfrvgnac3s4j6zpxnaap7p-python3.12-modelcif-0.9/lib | |
| shrinking RPATHs of ELF executables and libraries in /nix/store/17vpzjaxv4rzq97z1rpvap6zyl8388l4-python3.12-modelcif-0.9-dist | |
| checking for references to /build/ in /nix/store/17vpzjaxv4rzq97z1rpvap6zyl8388l4-python3.12-modelcif-0.9-dist... | |
| patching script interpreter paths in /nix/store/17vpzjaxv4rzq97z1rpvap6zyl8388l4-python3.12-modelcif-0.9-dist | |
| Executing pythonRemoveTestsDir | |
| Finished executing pythonRemoveTestsDir | |
| @nix { "action": "setPhase", "phase": "installCheckPhase" } | |
| Running phase: installCheckPhase | |
| no Makefile or custom installCheckPhase, doing nothing | |
| @nix { "action": "setPhase", "phase": "pythonCatchConflictsPhase" } | |
| Running phase: pythonCatchConflictsPhase | |
| @nix { "action": "setPhase", "phase": "pythonRemoveBinBytecodePhase" } | |
| Running phase: pythonRemoveBinBytecodePhase | |
| @nix { "action": "setPhase", "phase": "pythonImportsCheckPhase" } | |
| Running phase: pythonImportsCheckPhase | |
| Executing pythonImportsCheckPhase | |
| Check whether the following modules can be imported: modelcif | |
| @nix { "action": "setPhase", "phase": "pytestCheckPhase" } | |
| Running phase: pytestCheckPhase | |
| Executing pytestCheckPhase | |
| ============================= test session starts ============================== | |
| platform linux -- Python 3.12.3, pytest-8.1.1, pluggy-1.4.0 | |
| rootdir: /build/source | |
| collecting ... | |
| collected 89 items / 2 deselected / 87 selected | |
| test/test_alignment.py . [ 1%] | |
| test/test_descriptor.py . [ 2%] | |
| test/test_dumper.py ............................ [ 34%] | |
| test/test_edit.py FF [ 36%] | |
| test/test_examples.py FFF [ 40%] | |
| test/test_main.py .............. [ 56%] | |
| test/test_make_mmcif.py .F [ 58%] | |
| test/test_model.py . [ 59%] | |
| test/test_qa_metric.py .... [ 64%] | |
| test/test_reader.py .F.F......................... [ 97%] | |
| test/test_reference.py .. [100%] | |
| =================================== FAILURES =================================== | |
| ________________________ Tests.test_model_with_assembly ________________________ | |
| self = <test_edit.Tests testMethod=test_model_with_assembly> | |
| def test_model_with_assembly(self): | |
| """Test read of Model with Assembly followed by write""" | |
| sin = StringIO(""" | |
| loop_ | |
| _entity.id | |
| _entity.type | |
| _entity.pdbx_description | |
| _entity.pdbx_number_of_molecules | |
| _entity.formula_weight | |
| _entity.details | |
| 1 polymer Nup84 2 100.0 . | |
| # | |
| loop_ | |
| _entity_poly_seq.entity_id | |
| _entity_poly_seq.num | |
| _entity_poly_seq.mon_id | |
| _entity_poly_seq.hetero | |
| 1 1 ALA . | |
| 1 2 CYS . | |
| # | |
| loop_ | |
| _struct_asym.id | |
| _struct_asym.entity_id | |
| _struct_asym.details | |
| A 1 'Model subunit A' | |
| # | |
| loop_ | |
| _ma_struct_assembly.ordinal_id | |
| _ma_struct_assembly.assembly_id | |
| _ma_struct_assembly.entity_id | |
| _ma_struct_assembly.asym_id | |
| _ma_struct_assembly.seq_id_begin | |
| _ma_struct_assembly.seq_id_end | |
| 1 1 1 A 1 2 | |
| # | |
| loop_ | |
| _ma_model_list.ordinal_id | |
| _ma_model_list.model_id | |
| _ma_model_list.model_group_id | |
| _ma_model_list.model_name | |
| _ma_model_list.model_group_name | |
| _ma_model_list.assembly_id | |
| _ma_model_list.data_id | |
| _ma_model_list.model_type | |
| _ma_model_list.model_type_other_details | |
| 1 1 1 'Best scoring model' 'All models' 1 4 'Homology model' . | |
| # | |
| loop_ | |
| _atom_site.group_PDB | |
| _atom_site.id | |
| _atom_site.type_symbol | |
| _atom_site.label_atom_id | |
| _atom_site.label_alt_id | |
| _atom_site.label_comp_id | |
| _atom_site.label_seq_id | |
| _atom_site.auth_seq_id | |
| _atom_site.pdbx_PDB_ins_code | |
| _atom_site.label_asym_id | |
| _atom_site.Cartn_x | |
| _atom_site.Cartn_y | |
| _atom_site.Cartn_z | |
| _atom_site.occupancy | |
| _atom_site.label_entity_id | |
| _atom_site.auth_asym_id | |
| _atom_site.B_iso_or_equiv | |
| _atom_site.pdbx_PDB_model_num | |
| ATOM 1 C CA . ALA 1 1 ? A 1.000 2.000 3.000 . 1 A . 1 | |
| """) | |
| > s, = modelcif.reader.read(sin) | |
| test/test_edit.py:85: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| modelcif/reader.py:929: in read | |
| return ihm.reader.read( | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:3918: in read | |
| more_data = r.read_file() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1131: in read_file | |
| return self._read_file_c() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1182: in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:1278: in __call__ | |
| s.sequence[seq_id - 1] = self.sysr.chem_comps.get_by_id(mon_id) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <ihm.reader._ChemCompIDMapper object at 0x7ffff5f321b0>, objid = 'ALA' | |
| newcls = None | |
| def get_by_id(self, objid, newcls=None): | |
| # Don't modify class of standard residue types | |
| if objid in self._standard_by_id: | |
| obj = self._standard_by_id[objid] | |
| if objid not in self._obj_by_id: | |
| self._obj_by_id[objid] = obj | |
| > self.system_list.append(obj) | |
| E AttributeError: 'NoneType' object has no attribute 'append' | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:148: AttributeError | |
| ______________________ Tests.test_model_without_assembly _______________________ | |
| self = <test_edit.Tests testMethod=test_model_without_assembly> | |
| def test_model_without_assembly(self): | |
| """Test read of Model without Assembly followed by write""" | |
| sin = StringIO(""" | |
| loop_ | |
| _entity.id | |
| _entity.type | |
| _entity.pdbx_description | |
| _entity.pdbx_number_of_molecules | |
| _entity.formula_weight | |
| _entity.details | |
| 1 polymer Nup84 2 100.0 . | |
| # | |
| loop_ | |
| _entity_poly_seq.entity_id | |
| _entity_poly_seq.num | |
| _entity_poly_seq.mon_id | |
| _entity_poly_seq.hetero | |
| 1 1 ALA . | |
| 1 2 CYS . | |
| # | |
| loop_ | |
| _struct_asym.id | |
| _struct_asym.entity_id | |
| _struct_asym.details | |
| A 1 'Model subunit A' | |
| # | |
| loop_ | |
| _ma_model_list.ordinal_id | |
| _ma_model_list.model_id | |
| _ma_model_list.model_group_id | |
| _ma_model_list.model_name | |
| _ma_model_list.model_group_name | |
| _ma_model_list.assembly_id | |
| _ma_model_list.data_id | |
| _ma_model_list.model_type | |
| _ma_model_list.model_type_other_details | |
| 1 1 1 'Best scoring model' 'All models' . 4 'Homology model' . | |
| # | |
| loop_ | |
| _atom_site.group_PDB | |
| _atom_site.id | |
| _atom_site.type_symbol | |
| _atom_site.label_atom_id | |
| _atom_site.label_alt_id | |
| _atom_site.label_comp_id | |
| _atom_site.label_seq_id | |
| _atom_site.auth_seq_id | |
| _atom_site.pdbx_PDB_ins_code | |
| _atom_site.label_asym_id | |
| _atom_site.Cartn_x | |
| _atom_site.Cartn_y | |
| _atom_site.Cartn_z | |
| _atom_site.occupancy | |
| _atom_site.label_entity_id | |
| _atom_site.auth_asym_id | |
| _atom_site.B_iso_or_equiv | |
| _atom_site.pdbx_PDB_model_num | |
| ATOM 1 C CA . ALA 1 1 ? A 1.000 2.000 3.000 . 1 A . 1 | |
| """) | |
| > s, = modelcif.reader.read(sin) | |
| test/test_edit.py:148: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| modelcif/reader.py:929: in read | |
| return ihm.reader.read( | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:3918: in read | |
| more_data = r.read_file() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1131: in read_file | |
| return self._read_file_c() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1182: in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:1278: in __call__ | |
| s.sequence[seq_id - 1] = self.sysr.chem_comps.get_by_id(mon_id) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <ihm.reader._ChemCompIDMapper object at 0x7ffff5e39160>, objid = 'ALA' | |
| newcls = None | |
| def get_by_id(self, objid, newcls=None): | |
| # Don't modify class of standard residue types | |
| if objid in self._standard_by_id: | |
| obj = self._standard_by_id[objid] | |
| if objid not in self._obj_by_id: | |
| self._obj_by_id[objid] = obj | |
| > self.system_list.append(obj) | |
| E AttributeError: 'NoneType' object has no attribute 'append' | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:148: AttributeError | |
| _______________________ Tests.test_convert_bcif_example ________________________ | |
| self = <test_examples.Tests testMethod=test_convert_bcif_example> | |
| @unittest.skipIf(msgpack is None, "BinaryCIF needs msgpack") | |
| def test_convert_bcif_example(self): | |
| """Test convert_bcif example""" | |
| with utils.temporary_directory() as tmpdir: | |
| from_input = get_example_path("input") | |
| to_input = os.path.join(tmpdir, 'input') | |
| os.mkdir(to_input) | |
| shutil.copy(os.path.join(from_input, "ligands.cif"), to_input) | |
| > subprocess.check_call([sys.executable, | |
| get_example_path("convert_bcif.py")], | |
| cwd=tmpdir) | |
| test/test_examples.py:89: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| popenargs = (['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/convert_bcif.py'],) | |
| kwargs = {'cwd': '/build/tmpxv4uhpf2'}, retcode = 1 | |
| cmd = ['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/convert_bcif.py'] | |
| def check_call(*popenargs, **kwargs): | |
| """Run command with arguments. Wait for command to complete. If | |
| the exit code was zero then return, otherwise raise | |
| CalledProcessError. The CalledProcessError object will have the | |
| return code in the returncode attribute. | |
| The arguments are the same as for the call function. Example: | |
| check_call(["ls", "-l"]) | |
| """ | |
| retcode = call(*popenargs, **kwargs) | |
| if retcode: | |
| cmd = kwargs.get("args") | |
| if cmd is None: | |
| cmd = popenargs[0] | |
| > raise CalledProcessError(retcode, cmd) | |
| E subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/convert_bcif.py']' returned non-zero exit status 1. | |
| /nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/lib/python3.12/subprocess.py:413: CalledProcessError | |
| ----------------------------- Captured stderr call ----------------------------- | |
| Traceback (most recent call last): | |
| File "/build/source/examples/convert_bcif.py", line 11, in <module> | |
| systems = modelcif.reader.read(fh, format='mmCIF') | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/build/source/modelcif/reader.py", line 929, in read | |
| return ihm.reader.read( | |
| ^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 3918, in read | |
| more_data = r.read_file() | |
| ^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1131, in read_file | |
| return self._read_file_c() | |
| ^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1182, in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/build/source/modelcif/reader.py", line 170, in __call__ | |
| s = self.sysr.chem_comps.get_by_id( | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 148, in get_by_id | |
| self.system_list.append(obj) | |
| ^^^^^^^^^^^^^^^^^^^^^^^ | |
| AttributeError: 'NoneType' object has no attribute 'append' | |
| __________________________ Tests.test_ligands_example __________________________ | |
| self = <test_examples.Tests testMethod=test_ligands_example> | |
| def test_ligands_example(self): | |
| """Test ligands example""" | |
| with utils.temporary_directory() as tmpdir: | |
| subprocess.check_call([sys.executable, | |
| get_example_path("ligands.py")], | |
| cwd=tmpdir) | |
| # Make sure that a complete output file was produced and that we | |
| # can read it | |
| with open(os.path.join(tmpdir, 'output.cif')) as fh: | |
| contents = fh.readlines() | |
| self.assertEqual(len(contents), 324) | |
| with open(os.path.join(tmpdir, 'output.cif')) as fh: | |
| > s, = modelcif.reader.read(fh) | |
| test/test_examples.py:79: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| modelcif/reader.py:929: in read | |
| return ihm.reader.read( | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:3918: in read | |
| more_data = r.read_file() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1131: in read_file | |
| return self._read_file_c() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1182: in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| modelcif/reader.py:170: in __call__ | |
| s = self.sysr.chem_comps.get_by_id( | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <ihm.reader._ChemCompIDMapper object at 0x7ffff5e42a80>, objid = 'ALA' | |
| newcls = <class 'ihm.LPeptideChemComp'> | |
| def get_by_id(self, objid, newcls=None): | |
| # Don't modify class of standard residue types | |
| if objid in self._standard_by_id: | |
| obj = self._standard_by_id[objid] | |
| if objid not in self._obj_by_id: | |
| self._obj_by_id[objid] = obj | |
| > self.system_list.append(obj) | |
| E AttributeError: 'NoneType' object has no attribute 'append' | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:148: AttributeError | |
| _________________________ Tests.test_mkmodbase_example _________________________ | |
| self = <test_examples.Tests testMethod=test_mkmodbase_example> | |
| def test_mkmodbase_example(self): | |
| """Test mkmodbase example""" | |
| with utils.temporary_directory() as tmpdir: | |
| > subprocess.check_call([sys.executable, | |
| get_example_path("mkmodbase.py")], | |
| cwd=tmpdir) | |
| test/test_examples.py:54: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| popenargs = (['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/mkmodbase.py'],) | |
| kwargs = {'cwd': '/build/tmpizrp91fj'}, retcode = 1 | |
| cmd = ['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/mkmodbase.py'] | |
| def check_call(*popenargs, **kwargs): | |
| """Run command with arguments. Wait for command to complete. If | |
| the exit code was zero then return, otherwise raise | |
| CalledProcessError. The CalledProcessError object will have the | |
| return code in the returncode attribute. | |
| The arguments are the same as for the call function. Example: | |
| check_call(["ls", "-l"]) | |
| """ | |
| retcode = call(*popenargs, **kwargs) | |
| if retcode: | |
| cmd = kwargs.get("args") | |
| if cmd is None: | |
| cmd = popenargs[0] | |
| > raise CalledProcessError(retcode, cmd) | |
| E subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/examples/mkmodbase.py']' returned non-zero exit status 1. | |
| /nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/lib/python3.12/subprocess.py:413: CalledProcessError | |
| ----------------------------- Captured stderr call ----------------------------- | |
| Traceback (most recent call last): | |
| File "/build/source/examples/mkmodbase.py", line 211, in <module> | |
| s, = modelcif.reader.read(fh) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/build/source/modelcif/reader.py", line 929, in read | |
| return ihm.reader.read( | |
| ^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 3918, in read | |
| more_data = r.read_file() | |
| ^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1131, in read_file | |
| return self._read_file_c() | |
| ^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1182, in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/build/source/modelcif/reader.py", line 170, in __call__ | |
| s = self.sysr.chem_comps.get_by_id( | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 148, in get_by_id | |
| self.system_list.append(obj) | |
| ^^^^^^^^^^^^^^^^^^^^^^^ | |
| AttributeError: 'NoneType' object has no attribute 'append' | |
| _______________________________ Tests.test_mini ________________________________ | |
| self = <test_make_mmcif.Tests testMethod=test_mini> | |
| @unittest.skipIf(sys.version_info[0] < 3, "make-mmcif.py needs Python 3") | |
| def test_mini(self): | |
| """Check that make-mmcif works given only basic atom info""" | |
| incif = utils.get_input_file_name(TOPDIR, 'mini.cif') | |
| > subprocess.check_call([sys.executable, MAKE_MMCIF, incif]) | |
| test/test_make_mmcif.py:26: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| popenargs = (['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/util/make-mmcif.py', '/build/source/test/input/mini.cif'],) | |
| kwargs = {}, retcode = 1 | |
| cmd = ['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/util/make-mmcif.py', '/build/source/test/input/mini.cif'] | |
| def check_call(*popenargs, **kwargs): | |
| """Run command with arguments. Wait for command to complete. If | |
| the exit code was zero then return, otherwise raise | |
| CalledProcessError. The CalledProcessError object will have the | |
| return code in the returncode attribute. | |
| The arguments are the same as for the call function. Example: | |
| check_call(["ls", "-l"]) | |
| """ | |
| retcode = call(*popenargs, **kwargs) | |
| if retcode: | |
| cmd = kwargs.get("args") | |
| if cmd is None: | |
| cmd = popenargs[0] | |
| > raise CalledProcessError(retcode, cmd) | |
| E subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/bin/python3.12', '/build/source/util/make-mmcif.py', '/build/source/test/input/mini.cif']' returned non-zero exit status 1. | |
| /nix/store/zwvdwiw0zg5liz6lkkkqyab035parhld-python3-3.12.3/lib/python3.12/subprocess.py:413: CalledProcessError | |
| ----------------------------- Captured stderr call ----------------------------- | |
| Traceback (most recent call last): | |
| File "/build/source/util/make-mmcif.py", line 58, in <module> | |
| fhout, [add_modelcif_info(s) for s in modelcif.reader.read(fh)]) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/build/source/modelcif/reader.py", line 929, in read | |
| return ihm.reader.read( | |
| ^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 3918, in read | |
| more_data = r.read_file() | |
| ^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1131, in read_file | |
| return self._read_file_c() | |
| ^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py", line 1182, in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 1278, in __call__ | |
| s.sequence[seq_id - 1] = self.sysr.chem_comps.get_by_id(mon_id) | |
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| File "/nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py", line 148, in get_by_id | |
| self.system_list.append(obj) | |
| ^^^^^^^^^^^^^^^^^^^^^^^ | |
| AttributeError: 'NoneType' object has no attribute 'append' | |
| _________________________ Tests.test_assembly_handler __________________________ | |
| self = <test_reader.Tests testMethod=test_assembly_handler> | |
| def test_assembly_handler(self): | |
| """Test _AssemblyHandler and _AssemblyDetailsHandler""" | |
| cif = """ | |
| loop_ | |
| _entity_poly_seq.entity_id | |
| _entity_poly_seq.num | |
| _entity_poly_seq.mon_id | |
| 1 1 ALA | |
| 1 2 ALA | |
| # | |
| loop_ | |
| _struct_asym.id | |
| _struct_asym.entity_id | |
| _struct_asym.details | |
| A 1 Nup84 | |
| # | |
| loop_ | |
| _ma_struct_assembly.ordinal_id | |
| _ma_struct_assembly.assembly_id | |
| _ma_struct_assembly.entity_id | |
| _ma_struct_assembly.asym_id | |
| _ma_struct_assembly.seq_id_begin | |
| _ma_struct_assembly.seq_id_end | |
| 1 1 1 A 1 2 | |
| 2 1 1 A 1 1 | |
| 3 1 1 A . . | |
| # | |
| loop_ | |
| _ma_struct_assembly_details.assembly_id | |
| _ma_struct_assembly_details.assembly_name | |
| _ma_struct_assembly_details.assembly_description | |
| 1 foo bar | |
| """ | |
| > s, = modelcif.reader.read(StringIO(cif)) | |
| test/test_reader.py:496: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| modelcif/reader.py:929: in read | |
| return ihm.reader.read( | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:3918: in read | |
| more_data = r.read_file() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1131: in read_file | |
| return self._read_file_c() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1182: in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:1278: in __call__ | |
| s.sequence[seq_id - 1] = self.sysr.chem_comps.get_by_id(mon_id) | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <ihm.reader._ChemCompIDMapper object at 0x7ffff5e41d00>, objid = 'ALA' | |
| newcls = None | |
| def get_by_id(self, objid, newcls=None): | |
| # Don't modify class of standard residue types | |
| if objid in self._standard_by_id: | |
| obj = self._standard_by_id[objid] | |
| if objid not in self._obj_by_id: | |
| self._obj_by_id[objid] = obj | |
| > self.system_list.append(obj) | |
| E AttributeError: 'NoneType' object has no attribute 'append' | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:148: AttributeError | |
| _________________________ Tests.test_chem_comp_handler _________________________ | |
| self = <test_reader.Tests testMethod=test_chem_comp_handler> | |
| def test_chem_comp_handler(self): | |
| """Test ChemCompHandler and ChemCompDescriptorHandler""" | |
| cif = """ | |
| loop_ | |
| _chem_comp.id | |
| _chem_comp.type | |
| _chem_comp.name | |
| _chem_comp.formula | |
| _chem_comp.ma_provenance | |
| MET 'L-peptide linking' . . . | |
| CYS 'D-peptide linking' CYSTEINE . ? | |
| ALA 'L-peptide linking' ALANINE . 'CCD Core' | |
| MATYPE 'L-PEPTIDE LINKING' 'MODELARCHIVE COMPONENT' . 'CCD MA' | |
| MYTYPE 'L-PEPTIDE LINKING' 'MY CUSTOM COMPONENT' . 'CCD local' | |
| # | |
| loop_ | |
| _ma_chem_comp_descriptor.ordinal_id | |
| _ma_chem_comp_descriptor.chem_comp_id | |
| _ma_chem_comp_descriptor.chem_comp_name | |
| _ma_chem_comp_descriptor.type | |
| _ma_chem_comp_descriptor.value | |
| _ma_chem_comp_descriptor.details | |
| _ma_chem_comp_descriptor.software_id | |
| 1 MYTYPE 'ignored' 'InChI Key' XDAOLTSRNUSPPH-XMMPIXPASA-N foo 1 | |
| 2 MYTYPE ? 'IUPAC Name' foobar . . | |
| # | |
| loop_ | |
| _entity_poly_seq.entity_id | |
| _entity_poly_seq.num | |
| _entity_poly_seq.mon_id | |
| _entity_poly_seq.hetero | |
| 1 1 MET . | |
| 1 2 CYS . | |
| 1 3 ALA . | |
| 1 4 MATYPE . | |
| 1 5 MYTYPE . | |
| """ | |
| > s, = modelcif.reader.read(StringIO(cif)) | |
| test/test_reader.py:1141: | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| modelcif/reader.py:929: in read | |
| return ihm.reader.read( | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:3918: in read | |
| more_data = r.read_file() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1131: in read_file | |
| return self._read_file_c() | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/format.py:1182: in _read_file_c | |
| eof, more_data = _format.ihm_read_file(self._c_format) | |
| modelcif/reader.py:170: in __call__ | |
| s = self.sysr.chem_comps.get_by_id( | |
| _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ | |
| self = <ihm.reader._ChemCompIDMapper object at 0x7ffff59366c0>, objid = 'MET' | |
| newcls = <class 'ihm.LPeptideChemComp'> | |
| def get_by_id(self, objid, newcls=None): | |
| # Don't modify class of standard residue types | |
| if objid in self._standard_by_id: | |
| obj = self._standard_by_id[objid] | |
| if objid not in self._obj_by_id: | |
| self._obj_by_id[objid] = obj | |
| > self.system_list.append(obj) | |
| E AttributeError: 'NoneType' object has no attribute 'append' | |
| /nix/store/102i0r7340abrqdzxhw7blnld6x4zscd-python3.12-ihm-1.2/lib/python3.12/site-packages/ihm/reader.py:148: AttributeError | |
| =========================== short test summary info ============================ | |
| FAILED test/test_edit.py::Tests::test_model_with_assembly - AttributeError: 'NoneType' object has no attribute 'append' | |
| FAILED test/test_edit.py::Tests::test_model_without_assembly - AttributeError: 'NoneType' object has no attribute 'append' | |
| FAILED test/test_examples.py::Tests::test_convert_bcif_example - subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqya... | |
| FAILED test/test_examples.py::Tests::test_ligands_example - AttributeError: 'NoneType' object has no attribute 'append' | |
| FAILED test/test_examples.py::Tests::test_mkmodbase_example - subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqya... | |
| FAILED test/test_make_mmcif.py::Tests::test_mini - subprocess.CalledProcessError: Command '['/nix/store/zwvdwiw0zg5liz6lkkkqya... | |
| FAILED test/test_reader.py::Tests::test_assembly_handler - AttributeError: 'NoneType' object has no attribute 'append' | |
| FAILED test/test_reader.py::Tests::test_chem_comp_handler - AttributeError: 'NoneType' object has no attribute 'append' | |
| ================== 8 failed, 79 passed, 2 deselected in 1.07s ================== | |
| /nix/store/d3dzfy4amjl826fb8j00qp1d9887h7hm-stdenv-linux/setup: line 1579: pop_var_context: head of shell_variables not a function context |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment