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Gentoo's Bugzilla – Attachment 766881 Details for
Bug 835004
sci-chemistry/modeller-9.25 - except ImportError:
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sci-chemistry:modeller-9.25:20220312-180956.log
sci-chemistry:modeller-9.25:20220312-180956.log (text/plain), 46.05 KB, created by
Toralf Förster
on 2022-03-12 18:15:08 UTC
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hide
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Description:
sci-chemistry:modeller-9.25:20220312-180956.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2022-03-12 18:15:08 UTC
Size:
46.05 KB
patch
obsolete
> * Package: sci-chemistry/modeller-9.25 > * Repository: gentoo > * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_9 userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > >>>> Unpacking source... >>>> Unpacking modeller-9.25.tar.gz to /var/tmp/portage/sci-chemistry/modeller-9.25/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/modeller-9.25/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... >RefactoringTool: Skipping optional fixer: buffer >RefactoringTool: Skipping optional fixer: idioms >RefactoringTool: Skipping optional fixer: set_literal >RefactoringTool: Skipping optional fixer: ws_comma >RefactoringTool: Refactored modlib/modeller/__init__.py >--- modlib/modeller/__init__.py (original) >+++ modlib/modeller/__init__.py (refactored) >@@ -48,7 +48,7 @@ > return sys.maxsize > 2**32 > # This works on older Pythons, but not in Python 3 > else: >- return type(sys.dllhandle) == long >+ return type(sys.dllhandle) == int > > # Special processing on Windows to find _modeller.pyd and Modeller DLLs: > if hasattr(config, 'install_dir') and hasattr(sys, 'dllhandle'): >RefactoringTool: No changes to modlib/modeller/alignment.py >RefactoringTool: No changes to modlib/modeller/alnsequence.py >RefactoringTool: No changes to modlib/modeller/alnstructure.py >RefactoringTool: No changes to modlib/modeller/atom_type.py >RefactoringTool: Refactored modlib/modeller/coordinates.py >--- modlib/modeller/coordinates.py (original) >+++ modlib/modeller/coordinates.py (refactored) >@@ -147,7 +147,7 @@ > (startres, endres) = self._get_resind() > (startatm, endatm) = get_residue_atom_indices(self.seq, startres, > endres) >- return (range(startatm+1, endatm+1), self.seq) >+ return (list(range(startatm+1, endatm+1)), self.seq) > > atoms = property(__get_atoms, doc="List of all atoms in this chain") > >@@ -158,7 +158,7 @@ > def get_atom_indices(self): > (startind, endind) = get_residue_atom_indices(self.mdl, self._num, > self._num + 1) >- return range(startind + 1, endind + 1), self.mdl >+ return list(range(startind + 1, endind + 1)), self.mdl > > def __repr__(self): > # Get residue number before we do anything else. For alignment >@@ -252,7 +252,7 @@ > def get_atom_indices(self): > (startind, endind) = get_residue_atom_indices(self.mdl, self.offset, > self.offset + len(self)) >- return range(startind + 1, endind + 1), self.mdl >+ return list(range(startind + 1, endind + 1)), self.mdl > > def __getitem__(self, indx): > ret = modutil.handle_seq_indx(self, indx, self.mdl._indxres, >@@ -398,7 +398,7 @@ > return self.mdl.natm > > def get_atom_indices(self): >- return range(self.offset + 1, self.offset + len(self) + 1), self.mdl >+ return list(range(self.offset + 1, self.offset + len(self) + 1)), self.mdl > > def __getitem__(self, indx): > ret = modutil.handle_seq_indx(self, indx, self.mdl._indxatm, >RefactoringTool: No changes to modlib/modeller/density.py >RefactoringTool: No changes to modlib/modeller/energy_data.py >RefactoringTool: No changes to modlib/modeller/energy_profile.py >RefactoringTool: No changes to modlib/modeller/environ.py >RefactoringTool: No changes to modlib/modeller/excluded_pair.py >RefactoringTool: No changes to modlib/modeller/excluded_pair_list.py >RefactoringTool: No changes to modlib/modeller/features.py >RefactoringTool: No changes to modlib/modeller/forms.py >RefactoringTool: No changes to modlib/modeller/gbsa.py >RefactoringTool: No changes to modlib/modeller/group_restraints.py >RefactoringTool: Refactored modlib/modeller/id_table.py >--- modlib/modeller/id_table.py (original) >+++ modlib/modeller/id_table.py (refactored) >@@ -40,7 +40,7 @@ > def write_seqid_matrix(fh, coder, mat): > """Write a sequence identity matrix to a file""" > nseq = len(mat) >- print(" " * 9 + "".join([ s[:8] for s in coder ])) >+ print((" " * 9 + "".join([ s[:8] for s in coder ]))) > for n1 in range(nseq): > fh.write(coder[n1][:8] + " " + \ > "".join(["%8d" % (mat[n1][n2]+0.5) for n2 in range(nseq)])) >RefactoringTool: No changes to modlib/modeller/information.py >RefactoringTool: No changes to modlib/modeller/io_data.py >RefactoringTool: Refactored modlib/modeller/libraries.py >--- modlib/modeller/libraries.py (original) >+++ modlib/modeller/libraries.py (refactored) >@@ -32,7 +32,7 @@ > return BytesIO(*args) > else: > def _make_bytes_io(self, *args): >- from cStringIO import StringIO >+ from io import StringIO > return StringIO(*args) > > def __getstate__(self): >RefactoringTool: Refactored modlib/modeller/model.py >--- modlib/modeller/model.py (original) >+++ modlib/modeller/model.py (refactored) >@@ -121,7 +121,7 @@ > > def get_atom_indices(self): > """Get the indices of all atoms in this model""" >- return (range(1, self.natm+1), self) >+ return (list(range(1, self.natm+1)), self) > > def read(self, file, model_format='PDB', > model_segment=('FIRST:@', 'LAST:'), io=None, >@@ -340,7 +340,7 @@ > dope_score = sel.assess_dope() > scorer = normalized_dope.DOPEScorer(self) > z_score = scorer.get_z_score(dope_score) >- print(">> Normalized DOPE z score: %.3f" % z_score) >+ print((">> Normalized DOPE z score: %.3f" % z_score)) > return z_score > > def assess_normalized_dopehr(self): >@@ -351,7 +351,7 @@ > dope_score = sel.assess_dopehr() > scorer = normalized_dope.DOPEHRScorer(self) > z_score = scorer.get_z_score(dope_score) >- print(">> Normalized DOPE-HR z score: %.3f" % z_score) >+ print((">> Normalized DOPE-HR z score: %.3f" % z_score)) > return z_score > > def get_normalized_dope_profile(self): >RefactoringTool: Refactored modlib/modeller/model_topology.py >--- modlib/modeller/model_topology.py (original) >+++ modlib/modeller/model_topology.py (refactored) >@@ -50,7 +50,7 @@ > self.check_args = args > def __iter__(self): > return self >- def next(self): >+ def __next__(self): > while True: > atoms = self.__int_next() > if self.check_func is None \ >@@ -82,7 +82,7 @@ > self.check_args = args > def __iter__(self): > return self >- def next(self): >+ def __next__(self): > while True: > atoms = self.__int_next() > if self.check_func is None \ >RefactoringTool: No changes to modlib/modeller/modfile.py >RefactoringTool: No changes to modlib/modeller/normalized_dope.py >RefactoringTool: No changes to modlib/modeller/orient.py >RefactoringTool: No changes to modlib/modeller/parameters.py >RefactoringTool: Refactored modlib/modeller/physical.py >--- modlib/modeller/physical.py (original) >+++ modlib/modeller/physical.py (refactored) >@@ -31,7 +31,7 @@ > def __init__(self, default=1.0, **keys): > self._default = default > self._dict = {} >- for (term,val) in keys.items(): >+ for (term,val) in list(keys.items()): > term = eval("%s" % term) > self[term] = val > >RefactoringTool: No changes to modlib/modeller/profile.py >RefactoringTool: No changes to modlib/modeller/pseudo_atom.py >RefactoringTool: No changes to modlib/modeller/pseudo_atom_list.py >RefactoringTool: No changes to modlib/modeller/pssmdb.py >RefactoringTool: No changes to modlib/modeller/residue.py >RefactoringTool: No changes to modlib/modeller/restraints.py >RefactoringTool: No changes to modlib/modeller/rigid_body.py >RefactoringTool: No changes to modlib/modeller/rigid_body_list.py >RefactoringTool: Refactored modlib/modeller/salign.py >--- modlib/modeller/salign.py (original) >+++ modlib/modeller/salign.py (refactored) >@@ -38,8 +38,8 @@ > return aln.salign(auto_overhang=True, overhang_auto_limit=5, > overhang_factor=1, **keys) > except modeller.ModellerError: >- print("SALIGN with auto_overhang failed: %s" \ >- % str(sys.exc_info()[1])) >+ print(("SALIGN with auto_overhang failed: %s" \ >+ % str(sys.exc_info()[1]))) > print("Retrying without auto_overhang") > return aln.salign(**keys) > >@@ -118,13 +118,13 @@ > self.qscore = res.qscorepct > self.aln.write(file=output_aln_file, alignment_format='PIR') > better = True >- print("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty, >- res.qscorepct)) >+ print(("Qlty scrs %g\t%g\t%g" % (open_penalty, extend_penalty, >+ res.qscorepct))) > except modeller.ModellerError: >- print("Set of parameters %s %g %g resulted in the " >+ print(("Set of parameters %s %g %g resulted in the " > "following error\t%s" % (str(weights), open_penalty, > extend_penalty, >- str(sys.exc_info()[1]))) >+ str(sys.exc_info()[1])))) > return better > > >@@ -181,7 +181,7 @@ > best.try_struc_align(opfile, opfile2, fw2, ogp3d, egp3d, > align_block) > >- print("final max quality = %g" % best.qscore) >+ print(("final max quality = %g" % best.qscore)) > > if best.found_struc_align: > aln.clear() >RefactoringTool: Refactored modlib/modeller/saxsdata.py >--- modlib/modeller/saxsdata.py (original) >+++ modlib/modeller/saxsdata.py (refactored) >@@ -206,7 +206,7 @@ > try: > fh = open(saxsfilename,'r') > except: >- print("file "+saxsfilename+" not found :(") >+ print(("file "+saxsfilename+" not found :(")) > return > fh.close() > ns = 0 >@@ -225,8 +225,8 @@ > s_low = s_min - .001 > if (not s_hi): > s_hi = s_max + .001 >- print("s_min=%s, s_max=%s" % (str(s_min), str(s_max))) >- print("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi))) >+ print(("s_min=%s, s_max=%s" % (str(s_min), str(s_max)))) >+ print(("s_low=%s, s_hi=%s" % (str(s_low), str(s_hi)))) > self.ini_saxs(atmsel, > filename=formfacfilename, > s_min=s_min, s_max=s_max, maxs=ns, nmesh=ns, natomtyp=natomtyp, >RefactoringTool: No changes to modlib/modeller/schedule.py >RefactoringTool: No changes to modlib/modeller/secondary_structure.py >RefactoringTool: Refactored modlib/modeller/selection.py >--- modlib/modeller/selection.py (original) >+++ modlib/modeller/selection.py (refactored) >@@ -23,7 +23,7 @@ > return self.mdl.atoms[obj - 1] > else: > def next(self): >- obj = self.seliter.next() >+ obj = next(self.seliter) > return self.mdl.atoms[obj - 1] > > class selection(object): >@@ -52,7 +52,7 @@ > :rtype: list of ints > """ > if sys.version_info[:2] == (2,3): >- keys = self.__selection.keys() >+ keys = list(self.__selection.keys()) > keys.sort() > else: > keys = sorted(self.__selection.keys()) >@@ -722,9 +722,9 @@ > def assess(self, assessor, output='SHORT NO_REPORT', **vars): > """Assess with the given assessor object > (e.g. :class:`soap_loop.Scorer`).""" >- print(">> Model assessment by %s" % assessor.name) >+ print((">> Model assessment by %s" % assessor.name)) > molpdf, terms = assessor._assess(self, output=output, **vars) >- print("%s : %12.6f" % (assessor.name, molpdf)) >+ print(("%s : %12.6f" % (assessor.name, molpdf))) > return molpdf > > def _dope_energy(self, gprsr, name, output='SHORT NO_REPORT', >@@ -733,7 +733,7 @@ > nonbond_spline=1.), **vars): > """Internal function to do DOPE or DOPE-HR assessment""" > mdl = self.__mdl >- print(">> Model assessment by %s potential" % name) >+ print((">> Model assessment by %s potential" % name)) > edat = self.get_dope_energy_data() > old_gprsr = mdl.group_restraints > mdl.group_restraints = gprsr >@@ -744,7 +744,7 @@ > **vars) > finally: > mdl.group_restraints = old_gprsr >- print("%s score : %12.6f" % (name, molpdf)) >+ print(("%s score : %12.6f" % (name, molpdf))) > return molpdf > > def debug_function(self, residue_span_range=(0, 99999), >RefactoringTool: No changes to modlib/modeller/sequence.py >RefactoringTool: No changes to modlib/modeller/sequence_db.py >RefactoringTool: No changes to modlib/modeller/soap_loop.py >RefactoringTool: No changes to modlib/modeller/soap_peptide.py >RefactoringTool: No changes to modlib/modeller/soap_pp.py >RefactoringTool: No changes to modlib/modeller/soap_protein_od.py >RefactoringTool: No changes to modlib/modeller/superpose.py >RefactoringTool: No changes to modlib/modeller/symmetry.py >RefactoringTool: No changes to modlib/modeller/symmetry_list.py >RefactoringTool: No changes to modlib/modeller/terms.py >RefactoringTool: Refactored modlib/modeller/test.py >--- modlib/modeller/test.py (original) >+++ modlib/modeller/test.py (refactored) >@@ -2,7 +2,7 @@ > import modeller > import math > try: >- from cStringIO import StringIO >+ from io import StringIO > except ImportError: > from io import StringIO > import sys >@@ -150,7 +150,7 @@ > diff = abs(num1 - num2) > if msg is None: > msg = "%f != %f within %g" % (num1, num2, tolerance) >- self.assert_(diff < tolerance, msg) >+ self.assertTrue(diff < tolerance, msg) > > def run_capture_stdout(self, method, *args, **keys): > """Run a method and capture its standard output. Returns both the >RefactoringTool: No changes to modlib/modeller/topology.py >RefactoringTool: No changes to modlib/modeller/virtual_atom.py >RefactoringTool: No changes to modlib/modeller/automodel/__init__.py >RefactoringTool: No changes to modlib/modeller/automodel/allhmodel.py >RefactoringTool: No changes to modlib/modeller/automodel/assess.py >RefactoringTool: Refactored modlib/modeller/automodel/automodel.py >--- modlib/modeller/automodel/automodel.py (original) >+++ modlib/modeller/automodel/automodel.py (refactored) >@@ -203,13 +203,13 @@ > > def write_ok_summary(self, all, modeltyp): > """Print out a summary of all successfully generated models""" >- print("\n>> Summary of successfully produced %s:" % modeltyp) >- fields = [x for x in all[0].keys() if x.endswith(' score')] >+ print(("\n>> Summary of successfully produced %s:" % modeltyp)) >+ fields = [x for x in list(all[0].keys()) if x.endswith(' score')] > fields.sort() > fields = ['molpdf'] + fields > header = '%-25s ' % 'Filename' + " ".join(['%14s' % x for x in fields]) > print(header) >- print('-' * len(header)) >+ print(('-' * len(header))) > for mdl in all: > text = '%-25s' % mdl['name'] > for field in fields: >@@ -222,9 +222,9 @@ > > def write_failure_summary(self, all, modeltyp): > """Print out a summary of all failed models""" >- print("\n>> Summary of failed %s:" % modeltyp) >+ print(("\n>> Summary of failed %s:" % modeltyp)) > for mdl in all: >- print("%-25s %s" % (mdl['name'], mdl['failure'])) >+ print(("%-25s %s" % (mdl['name'], mdl['failure']))) > print('') > > def rd_restraints(self): >@@ -692,8 +692,8 @@ > elif atmsel.get_model() is not self: > raise ModellerError("selection is defined on the wrong model") > elif len(atmsel) < len(self.atoms): >- print("%d (of %d total) atoms selected for optimization" \ >- % (len(atmsel), len(self.atoms))) >+ print(("%d (of %d total) atoms selected for optimization" \ >+ % (len(atmsel), len(self.atoms)))) > return atmsel > > def mkhomcsr(self, atmsel, aln): >@@ -774,9 +774,9 @@ > selstd = selection(self).only_std_residues() > selca = selstd.only_atom_types('CA') > >- print("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \ >+ print(("%d atoms in HETATM/BLK residues constrained\n" % len(selhet) \ > + "to protein atoms within %.2f angstroms\n" % bond_distance \ >- + "and protein CA atoms within %.2f angstroms" % ca_distance) >+ + "and protein CA atoms within %.2f angstroms" % ca_distance)) > # Build the bonds first; this avoids duplicated CA-ligand bonds since > # make_distance() will not build restraints that are already on the > # nonbond exclusion list >@@ -823,8 +823,8 @@ > selhet = selhet.only_no_topology() > > # Intra-residue: >- print("%d atoms in residues without defined topology\n" % len(selhet) \ >- + "constrained to be rigid bodies") >+ print(("%d atoms in residues without defined topology\n" % len(selhet) \ >+ + "constrained to be rigid bodies")) > rsr = self.restraints > rsr.make_distance(selhet, selhet, aln=aln, > distance_rsr_model=7, maximal_distance=10.0, >@@ -898,8 +898,8 @@ > print("\nThe following CHARMM atom type assignments were made:") > print(" Atom Old type New type") > for atom, old_type, new_type in zip(sel, old_types, new_types): >- print(" %-20s %-15s %-15s" >- % (str(atom), fmt_typ(old_type), fmt_typ(new_type))) >+ print((" %-20s %-15s %-15s" >+ % (str(atom), fmt_typ(old_type), fmt_typ(new_type)))) > > def select_atoms(self): > """Select atoms to be optimized in the model building procedure. By >RefactoringTool: No changes to modlib/modeller/automodel/autosched.py >RefactoringTool: No changes to modlib/modeller/automodel/dope_loopmodel.py >RefactoringTool: No changes to modlib/modeller/automodel/dopehr_loopmodel.py >RefactoringTool: Refactored modlib/modeller/automodel/generate.py >--- modlib/modeller/automodel/generate.py (original) >+++ modlib/modeller/automodel/generate.py (refactored) >@@ -88,11 +88,11 @@ > to_rebuild.append(r) > _unbuild_ring(r, ring_atoms + extra_atoms) > if len(to_rebuild) > 0: >- print("The following %d residues contain 6-membered rings with " >+ print(("The following %d residues contain 6-membered rings with " > "poor geometries\nafter transfer from templates. Rebuilding " > "rings from internal coordinates:\n %s" \ > % (len(to_rebuild), >- "\n ".join([str(r) for r in to_rebuild]))) >+ "\n ".join([str(r) for r in to_rebuild])))) > mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') > > def read_xyz(mdl, aln): >RefactoringTool: Refactored modlib/modeller/automodel/loopmodel.py >--- modlib/modeller/automodel/loopmodel.py (original) >+++ modlib/modeller/automodel/loopmodel.py (refactored) >@@ -105,7 +105,7 @@ > lendef = len(self._defined_indices) > if lenall > lendef: > s = selection(self) - s >- print(""" >+ print((""" > The following %d atoms were not found in the input model's non-loop region, > and were added automatically by Modeller in order to determine correct > interactions between the loop and the rest of the protein: >@@ -115,7 +115,7 @@ > rest of the protein may exist (note, however, that the score of the loop does > not include protein-protein internal interactions, so will not be adversely > affected by any clashes).""" \ >-% (lenall - lendef, ", ".join([repr(a) for a in s]))) >+% (lenall - lendef, ", ".join([repr(a) for a in s])))) > > if self.loop.write_defined_only: > print(""" >@@ -406,7 +406,7 @@ > elif len(atmsel.only_no_topology()) > 0: > raise ModellerError("some selected residues have no topology") > else: >- print("%d atoms selected for loop refinement" % len(atmsel)) >+ print(("%d atoms selected for loop refinement" % len(atmsel))) > return atmsel > > def optimize_loop(self, atmsel, sched, actions): >RefactoringTool: No changes to modlib/modeller/automodel/parallel.py >RefactoringTool: No changes to modlib/modeller/automodel/randomize.py >RefactoringTool: No changes to modlib/modeller/automodel/refine.py >RefactoringTool: No changes to modlib/modeller/library_restraints/angles.py >RefactoringTool: No changes to modlib/modeller/library_restraints/bonds.py >RefactoringTool: No changes to modlib/modeller/library_restraints/chi1.py >RefactoringTool: No changes to modlib/modeller/library_restraints/chi2.py >RefactoringTool: No changes to modlib/modeller/library_restraints/chi3.py >RefactoringTool: No changes to modlib/modeller/library_restraints/chi4.py >RefactoringTool: No changes to modlib/modeller/library_restraints/impropers.py >RefactoringTool: No changes to modlib/modeller/library_restraints/omega_dihedrals.py >RefactoringTool: No changes to modlib/modeller/library_restraints/phi_psi.py >RefactoringTool: No changes to modlib/modeller/mmcif/data.py >RefactoringTool: Refactored modlib/modeller/mmcif/writer.py >--- modlib/modeller/mmcif/writer.py (original) >+++ modlib/modeller/mmcif/writer.py (refactored) >@@ -4,7 +4,7 @@ > # which works as far back as 2.3, so imports need to be protected by a > # version check > >-from __future__ import print_function >+ > import sys > import textwrap > >@@ -12,7 +12,7 @@ > if sys.version_info[0] >= 3: > _long_type = int > else: >- _long_type = long >+ _long_type = int > > class _LineWriter(object): > def __init__(self, writer, line_len=80): >RefactoringTool: No changes to modlib/modeller/optimizers/actions.py >RefactoringTool: Refactored modlib/modeller/optimizers/builtin_optimizer.py >--- modlib/modeller/optimizers/builtin_optimizer.py (original) >+++ modlib/modeller/optimizers/builtin_optimizer.py (refactored) >@@ -9,7 +9,7 @@ > # delete the key entirely, as __getstate__ must return a non-empty > # dict in order for our __setstate__ method to be called). > d = self.__dict__.copy() >- for key in self.__dict__.keys(): >+ for key in list(self.__dict__.keys()): > if key.endswith("_modpt") or key.endswith("__optpt"): > d[key] = None > return d >@@ -21,7 +21,7 @@ > vars = params.copy() > self._update_params(vars, ok_keys, extravars) > for key in ok_keys: >- if key not in vars.keys() \ >+ if key not in list(vars.keys()) \ > and key not in ("edat", "libs", "actions", "schedule_scale"): > raise ValueError("a value must be given for %s" % key) > >RefactoringTool: No changes to modlib/modeller/optimizers/conjugate_gradients.py >RefactoringTool: No changes to modlib/modeller/optimizers/molecular_dynamics.py >RefactoringTool: Refactored modlib/modeller/optimizers/optimizer.py >--- modlib/modeller/optimizers/optimizer.py (original) >+++ modlib/modeller/optimizers/optimizer.py (refactored) >@@ -10,7 +10,7 @@ > return self.atmsel > > def _update_params(self, params, ok_keys, vars): >- for key in vars.keys(): >+ for key in list(vars.keys()): > if key in ok_keys: > params[key] = vars[key] > else: >RefactoringTool: No changes to modlib/modeller/optimizers/quasi_newton.py >RefactoringTool: No changes to modlib/modeller/optimizers/state_optimizer.py >RefactoringTool: No changes to modlib/modeller/parallel/communicator.py >RefactoringTool: Refactored modlib/modeller/parallel/data_types.py >--- modlib/modeller/parallel/data_types.py (original) >+++ modlib/modeller/parallel/data_types.py (refactored) >@@ -3,7 +3,7 @@ > import sys > > try: >- import cPickle as pickle >+ import pickle as pickle > except ImportError: > import pickle > >RefactoringTool: Refactored modlib/modeller/parallel/job.py >--- modlib/modeller/parallel/job.py (original) >+++ modlib/modeller/parallel/job.py (refactored) >@@ -106,7 +106,7 @@ > if id and id in pending_slaves: > slave = pending_slaves.pop(id) > connected_slaves[id] = slave >- print("Identified slave %s " % str(slave)) >+ print(("Identified slave %s " % str(slave))) > slave.accept_connection(sock) > slave.set_directory(self.cwd) > if sys.path[0] != '': >@@ -117,7 +117,7 @@ > return slave > elif id and id in connected_slaves: > slave = connected_slaves[id] >- print("Reconnect from slave %s " % str(slave)) >+ print(("Reconnect from slave %s " % str(slave))) > slave.accept_connection(sock) > else: > print("Ignoring request from unknown slave") >@@ -159,7 +159,7 @@ > """Run all tasks and return all the results, in the same order that they > were submitted, when all the jobs have completed.""" > tasks = self.tasks[:] >- print("Running %d tasks on %d slaves" % (len(tasks), len(self))) >+ print(("Running %d tasks on %d slaves" % (len(tasks), len(self)))) > self.push_tasks_to_slaves() > while True: > try: >@@ -174,7 +174,7 @@ > def yield_tasks_unordered(self): > """Run all tasks and return their results (as a generator), in > whatever order they complete.""" >- print("Running %d tasks on %d slaves" % (len(self.tasks), len(self))) >+ print(("Running %d tasks on %d slaves" % (len(self.tasks), len(self)))) > self.push_tasks_to_slaves() > while True: > try: >@@ -215,7 +215,7 @@ > task = obj.task_results() > if task: > # The slave completed its task >- print("%s on %s completed" % (str(task), str(obj))) >+ print(("%s on %s completed" % (str(task), str(obj)))) > if len(self.tasks) > 0: > obj.run_task(self.tasks.pop(0)) > return task >@@ -225,14 +225,14 @@ > except (NetworkError, TaskSetupError): > self.kill_slaves((obj,), sys.exc_info()[1]) > else: >- print("Warning: slave %s reports data, but is not running a task" \ >- % str(obj)) >+ print(("Warning: slave %s reports data, but is not running a task" \ >+ % str(obj))) > > def kill_slaves(self, slaves, err=""): > if err != "": > err = "(%s) " % err > for s in slaves: >- print("%s failed %s- removing from %s" % (s, err, self)) >+ print(("%s failed %s- removing from %s" % (s, err, self))) > task = s.kill() > if task: > self.tasks.append(task) >@@ -248,8 +248,8 @@ > timedout = [a for a in self if a.running_task() and \ > a.contact_timeout(self.heartbeat_timeout)] > if len(timedout) > 0: >- print("Did not hear from slaves %s in %d seconds" % \ >- (str(timedout), self.heartbeat_timeout)) >+ print(("Did not hear from slaves %s in %d seconds" % \ >+ (str(timedout), self.heartbeat_timeout))) > self.kill_slaves(timedout) > > def push_tasks_to_slaves(self): >@@ -264,8 +264,8 @@ > slave.run_task(t) > # If a network error occurred, kill the slave and requeue the task > except socket.error: >- print("slave %s failed on run task with %s; removing from job" \ >- % (slave, sys.exc_info()[1])) >+ print(("slave %s failed on run task with %s; removing from job" \ >+ % (slave, sys.exc_info()[1]))) > slave.kill() > self.tasks.insert(0, t) > self.expand_for_tasks() >RefactoringTool: No changes to modlib/modeller/parallel/local_slave.py >RefactoringTool: No changes to modlib/modeller/parallel/mypopen4.py >RefactoringTool: Refactored modlib/modeller/parallel/myspawn.py >--- modlib/modeller/parallel/myspawn.py (original) >+++ modlib/modeller/parallel/myspawn.py (refactored) >@@ -10,7 +10,7 @@ > ``output``.""" > > fp = open(output, "w") >- print("%s >& %s" % (cmd, output)) >+ print(("%s >& %s" % (cmd, output))) > if sys.platform == 'win32': > _myspawn_win32(cmd, fp) > else: >@@ -27,4 +27,4 @@ > # Ignore Windows "file not found" errors, so that behavior is consistent > # between Unix and Windows > except WindowsError: >- print("WindowsError: %s (ignored)" % sys.exc_info()[1]) >+ print(("WindowsError: %s (ignored)" % sys.exc_info()[1])) >RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_job.py >RefactoringTool: No changes to modlib/modeller/parallel/sge_pe_slave.py >RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_array.py >--- modlib/modeller/parallel/sge_qsub_array.py (original) >+++ modlib/modeller/parallel/sge_qsub_array.py (refactored) >@@ -36,7 +36,7 @@ > outlines = output.readlines() > output.close() > for line in outlines: >- print(line.rstrip('\r\n')) >+ print((line.rstrip('\r\n'))) > a.require_clean_exit() > self._set_jobid(outlines) > >RefactoringTool: No changes to modlib/modeller/parallel/sge_qsub_job.py >RefactoringTool: Refactored modlib/modeller/parallel/sge_qsub_slave.py >--- modlib/modeller/parallel/sge_qsub_slave.py (original) >+++ modlib/modeller/parallel/sge_qsub_slave.py (refactored) >@@ -38,7 +38,7 @@ > qsub = "qsub -S /bin/sh -o '%s' -N '%s' %s %s" % \ > (output, name, self.standard_options, self._options) > cmd = "%s -slave %s" % (path, id) >- print("%s | %s" % (cmd, qsub)) >+ print(("%s | %s" % (cmd, qsub))) > a = MyPopen4(qsub) > (input, output) = (a.stdin, a.stdout) > input.write(cmd + '\n') >@@ -46,7 +46,7 @@ > outlines = output.readlines() > output.close() > for line in outlines: >- print(line.rstrip('\r\n')) >+ print((line.rstrip('\r\n'))) > a.require_clean_exit() > self._set_jobid(outlines) > >RefactoringTool: No changes to modlib/modeller/parallel/slave.py >RefactoringTool: No changes to modlib/modeller/parallel/slave_communicator.py >RefactoringTool: Refactored modlib/modeller/parallel/slaveloop.py >--- modlib/modeller/parallel/slaveloop.py (original) >+++ modlib/modeller/parallel/slaveloop.py (refactored) >@@ -51,14 +51,14 @@ > master.send_data(communicator.ErrorWrapper(detail)) > except socket.error: > detail2 = sys.exc_info()[1] >- print("Warning: ignored exception " + str(detail2) \ >+ print(("Warning: ignored exception " + str(detail2) \ > + " when trying to send error state " \ >- + str(detail) + " back to master") >+ + str(detail) + " back to master")) > raise detail > raise > > def run(self): >- print("Slave startup: connect to master at %s" % self.addr) >+ print(("Slave startup: connect to master at %s" % self.addr)) > (host, port, identifier) = self.addr.split(":", 2) > port = int(port) > lock = threading.Lock() >RefactoringTool: No changes to modlib/modeller/parallel/slavestate.py >RefactoringTool: No changes to modlib/modeller/parallel/ssh_slave.py >RefactoringTool: No changes to modlib/modeller/parallel/task.py >RefactoringTool: No changes to modlib/modeller/scripts/align_strs_seq.py >RefactoringTool: No changes to modlib/modeller/scripts/asgl_principal_components.py >RefactoringTool: No changes to modlib/modeller/scripts/cispeptide.py >RefactoringTool: No changes to modlib/modeller/scripts/complete_pdb.py >RefactoringTool: No changes to modlib/modeller/scripts/fit.py >RefactoringTool: No changes to modlib/modeller/scripts/principal_components.py >RefactoringTool: No changes to modlib/modeller/scripts/sequence_srch.py >RefactoringTool: Refactored modlib/modeller/top_interpreter/__init__.py >--- modlib/modeller/top_interpreter/__init__.py (original) >+++ modlib/modeller/top_interpreter/__init__.py (refactored) >@@ -65,7 +65,7 @@ > if len(line) > 0: > try: > self._parse_top_ini_line(line.split(None, 4), vars) >- except TypeError, detail: >+ except TypeError as detail: > mod_log_write("read_top__E> " + str(detail)) > mod_log_write(" top.ini line: " + line) > raise >@@ -113,7 +113,7 @@ > self._set_top_vars(vars) > try: > fh = self._open_include_file(self.variables['include_file']) >- except IOError, detail: >+ except IOError as detail: > mod_log_write("runlines__E> " + str(detail)) > mod_log_write(" TOP Command line: " + line) > raise >@@ -160,7 +160,7 @@ > indxca = self._run_top_cmd(cmd, indxca, lines, callstack, > subrout) > _modeller.mod_top_post() >- except (IndexError, SyntaxError, TypeError), detail: >+ except (IndexError, SyntaxError, TypeError) as detail: > mod_log_write("runlines__E> " + str(detail)) > mod_log_write(" TOP Command line: " + line) > raise >RefactoringTool: No changes to modlib/modeller/top_interpreter/commands.py >RefactoringTool: Refactored modlib/modeller/top_interpreter/topcmds.py >--- modlib/modeller/top_interpreter/topcmds.py (original) >+++ modlib/modeller/top_interpreter/topcmds.py (refactored) >@@ -19,7 +19,7 @@ > if not isinstance(vars, (list, tuple)): > vars = (vars,) > for var in vars: >- if keys.has_key(var): >+ if var in keys: > args.append(keys[var]) > else: > args.append(self.vars[var]) >RefactoringTool: Refactored modlib/modeller/top_interpreter/util.py >--- modlib/modeller/top_interpreter/util.py (original) >+++ modlib/modeller/top_interpreter/util.py (refactored) >@@ -1,7 +1,7 @@ > import _modeller > > def set_topvars(topvardict, vars, topini): >- for name in topvardict.keys(): >+ for name in list(topvardict.keys()): > value = topvardict[name] > if value is None: > continue >RefactoringTool: Refactored modlib/modeller/top_interpreter/variables.py >--- modlib/modeller/top_interpreter/variables.py (original) >+++ modlib/modeller/top_interpreter/variables.py (refactored) >@@ -32,11 +32,11 @@ > def __init__(self, topcmds): > self._topcmds = topcmds > self._topvars = {} >- for var in self._deftops.keys(): >+ for var in list(self._deftops.keys()): > self._ourvars[var] = self._deftops[var] >- for var in self._edat_members.keys(): >+ for var in list(self._edat_members.keys()): > self._ourvars[var] = self._edat_members[var] >- for var in self._io_members.keys(): >+ for var in list(self._io_members.keys()): > self._ourvars[var] = self._io_members[var] > > def __setitem__(self, key, value): >RefactoringTool: No changes to modlib/modeller/util/array.py >RefactoringTool: No changes to modlib/modeller/util/logger.py >RefactoringTool: No changes to modlib/modeller/util/matrix.py >RefactoringTool: No changes to modlib/modeller/util/modlist.py >RefactoringTool: Refactored modlib/modeller/util/modobject.py >--- modlib/modeller/util/modobject.py (original) >+++ modlib/modeller/util/modobject.py (refactored) >@@ -1,8 +1,8 @@ > class modobject(object): > def __setattr__(self, name, val): > if name not in dir(self): >- print("runcmd_____W>: creation of new member '%s' in %s: " >- "possible typo!" % (name, str(self))) >+ print(("runcmd_____W>: creation of new member '%s' in %s: " >+ "possible typo!" % (name, str(self)))) > object.__setattr__(self, name, val) > > def __getstate__(self): >@@ -11,7 +11,7 @@ > # delete the key entirely, as __getstate__ must return a non-empty > # dict in order for our __setstate__ method to be called). > d = self.__dict__.copy() >- for key in self.__dict__.keys(): >+ for key in list(self.__dict__.keys()): > if key.endswith("_modpt"): > d[key] = None > return d >RefactoringTool: Refactored modlib/modeller/util/modutil.py >--- modlib/modeller/util/modutil.py (original) >+++ modlib/modeller/util/modutil.py (refactored) >@@ -17,7 +17,7 @@ > else: > return indx > elif isinstance(indx, slice): >- return range(*indx.indices(len(seqtype))) >+ return list(range(*indx.indices(len(seqtype)))) > elif lookup_func is not None: > args = lookup_args + (indx,) > int_indx = lookup_func(*args) >RefactoringTool: Files that were modified: >RefactoringTool: modlib/modeller/__init__.py >RefactoringTool: modlib/modeller/alignment.py >RefactoringTool: modlib/modeller/alnsequence.py >RefactoringTool: modlib/modeller/alnstructure.py >RefactoringTool: modlib/modeller/atom_type.py >RefactoringTool: modlib/modeller/coordinates.py >RefactoringTool: modlib/modeller/density.py >RefactoringTool: modlib/modeller/energy_data.py >RefactoringTool: modlib/modeller/energy_profile.py >RefactoringTool: modlib/modeller/environ.py >RefactoringTool: modlib/modeller/excluded_pair.py >RefactoringTool: modlib/modeller/excluded_pair_list.py >RefactoringTool: modlib/modeller/features.py >RefactoringTool: modlib/modeller/forms.py >RefactoringTool: modlib/modeller/gbsa.py >RefactoringTool: modlib/modeller/group_restraints.py >RefactoringTool: modlib/modeller/id_table.py >RefactoringTool: modlib/modeller/information.py >RefactoringTool: modlib/modeller/io_data.py >RefactoringTool: modlib/modeller/libraries.py >RefactoringTool: modlib/modeller/model.py >RefactoringTool: modlib/modeller/model_topology.py >RefactoringTool: modlib/modeller/modfile.py >RefactoringTool: modlib/modeller/normalized_dope.py >RefactoringTool: modlib/modeller/orient.py >RefactoringTool: modlib/modeller/parameters.py >RefactoringTool: modlib/modeller/physical.py >RefactoringTool: modlib/modeller/profile.py >RefactoringTool: modlib/modeller/pseudo_atom.py >RefactoringTool: modlib/modeller/pseudo_atom_list.py >RefactoringTool: modlib/modeller/pssmdb.py >RefactoringTool: modlib/modeller/residue.py >RefactoringTool: modlib/modeller/restraints.py >RefactoringTool: modlib/modeller/rigid_body.py >RefactoringTool: modlib/modeller/rigid_body_list.py >RefactoringTool: modlib/modeller/salign.py >RefactoringTool: modlib/modeller/saxsdata.py >RefactoringTool: modlib/modeller/schedule.py >RefactoringTool: modlib/modeller/secondary_structure.py >RefactoringTool: modlib/modeller/selection.py >RefactoringTool: modlib/modeller/sequence.py >RefactoringTool: modlib/modeller/sequence_db.py >RefactoringTool: modlib/modeller/soap_loop.py >RefactoringTool: modlib/modeller/soap_peptide.py >RefactoringTool: modlib/modeller/soap_pp.py >RefactoringTool: modlib/modeller/soap_protein_od.py >RefactoringTool: modlib/modeller/superpose.py >RefactoringTool: modlib/modeller/symmetry.py >RefactoringTool: modlib/modeller/symmetry_list.py >RefactoringTool: modlib/modeller/terms.py >RefactoringTool: modlib/modeller/test.py >RefactoringTool: modlib/modeller/topology.py >RefactoringTool: modlib/modeller/virtual_atom.py >RefactoringTool: modlib/modeller/automodel/__init__.py >RefactoringTool: modlib/modeller/automodel/allhmodel.py >RefactoringTool: modlib/modeller/automodel/assess.py >RefactoringTool: modlib/modeller/automodel/automodel.py >RefactoringTool: modlib/modeller/automodel/autosched.py >RefactoringTool: modlib/modeller/automodel/dope_loopmodel.py >RefactoringTool: modlib/modeller/automodel/dopehr_loopmodel.py >RefactoringTool: modlib/modeller/automodel/generate.py >RefactoringTool: modlib/modeller/automodel/loopmodel.py >RefactoringTool: modlib/modeller/automodel/parallel.py >RefactoringTool: modlib/modeller/automodel/randomize.py >RefactoringTool: modlib/modeller/automodel/refine.py >RefactoringTool: modlib/modeller/library_restraints/angles.py >RefactoringTool: modlib/modeller/library_restraints/bonds.py >RefactoringTool: modlib/modeller/library_restraints/chi1.py >RefactoringTool: modlib/modeller/library_restraints/chi2.py >RefactoringTool: modlib/modeller/library_restraints/chi3.py >RefactoringTool: modlib/modeller/library_restraints/chi4.py >RefactoringTool: modlib/modeller/library_restraints/impropers.py >RefactoringTool: modlib/modeller/library_restraints/omega_dihedrals.py >RefactoringTool: modlib/modeller/library_restraints/phi_psi.py >RefactoringTool: modlib/modeller/mmcif/data.py >RefactoringTool: modlib/modeller/mmcif/writer.py >RefactoringTool: modlib/modeller/optimizers/actions.py >RefactoringTool: modlib/modeller/optimizers/builtin_optimizer.py >RefactoringTool: modlib/modeller/optimizers/conjugate_gradients.py >RefactoringTool: modlib/modeller/optimizers/molecular_dynamics.py >RefactoringTool: modlib/modeller/optimizers/optimizer.py >RefactoringTool: modlib/modeller/optimizers/quasi_newton.py >RefactoringTool: modlib/modeller/optimizers/state_optimizer.py >RefactoringTool: modlib/modeller/parallel/communicator.py >RefactoringTool: modlib/modeller/parallel/data_types.py >RefactoringTool: modlib/modeller/parallel/job.py >RefactoringTool: modlib/modeller/parallel/local_slave.py >RefactoringTool: modlib/modeller/parallel/mypopen4.py >RefactoringTool: modlib/modeller/parallel/myspawn.py >RefactoringTool: modlib/modeller/parallel/sge_pe_job.py >RefactoringTool: modlib/modeller/parallel/sge_pe_slave.py >RefactoringTool: modlib/modeller/parallel/sge_qsub_array.py >RefactoringTool: modlib/modeller/parallel/sge_qsub_job.py >RefactoringTool: modlib/modeller/parallel/sge_qsub_slave.py >RefactoringTool: modlib/modeller/parallel/slave.py >RefactoringTool: modlib/modeller/parallel/slave_communicator.py >RefactoringTool: modlib/modeller/parallel/slaveloop.py >RefactoringTool: modlib/modeller/parallel/slavestate.py >RefactoringTool: modlib/modeller/parallel/ssh_slave.py >RefactoringTool: modlib/modeller/parallel/task.py >RefactoringTool: modlib/modeller/scripts/align_strs_seq.py >RefactoringTool: modlib/modeller/scripts/asgl_principal_components.py >RefactoringTool: modlib/modeller/scripts/cispeptide.py >RefactoringTool: modlib/modeller/scripts/complete_pdb.py >RefactoringTool: modlib/modeller/scripts/fit.py >RefactoringTool: modlib/modeller/scripts/principal_components.py >RefactoringTool: modlib/modeller/scripts/sequence_srch.py >RefactoringTool: modlib/modeller/top_interpreter/__init__.py >RefactoringTool: modlib/modeller/top_interpreter/commands.py >RefactoringTool: modlib/modeller/top_interpreter/topcmds.py >RefactoringTool: modlib/modeller/top_interpreter/util.py >RefactoringTool: modlib/modeller/top_interpreter/variables.py >RefactoringTool: modlib/modeller/util/array.py >RefactoringTool: modlib/modeller/util/logger.py >RefactoringTool: modlib/modeller/util/matrix.py >RefactoringTool: modlib/modeller/util/modlist.py >RefactoringTool: modlib/modeller/util/modobject.py >RefactoringTool: modlib/modeller/util/modutil.py >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25 ... > * python3_9: running distutils-r1_run_phase python_compile >python3.9 setup.py build -j 4 >Package glib-2.0 was not found in the pkg-config search path. >Perhaps you should add the directory containing `glib-2.0.pc' >to the PKG_CONFIG_PATH environment variable >Package 'glib-2.0', required by 'virtual:world', not found >Traceback (most recent call last): > File "/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig/setup.py", line 25, in <module> > glib = pkgconfig("glib-2.0") > File "/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig/setup.py", line 19, in pkgconfig > for token in getoutput(["pkg-config", "--libs", > File "/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig/setup.py", line 11, in getoutput > return subprocess.check_output(args, universal_newlines=True) > File "/usr/lib/python3.9/subprocess.py", line 424, in check_output > return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, > File "/usr/lib/python3.9/subprocess.py", line 528, in run > raise CalledProcessError(retcode, process.args, >subprocess.CalledProcessError: Command '['pkg-config', '--libs', '--cflags', 'glib-2.0']' returned non-zero exit status 1. > * ERROR: sci-chemistry/modeller-9.25::gentoo failed (compile phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 127: Called src_compile > * environment, line 3251: Called distutils-r1_src_compile > * environment, line 1402: Called _distutils-r1_run_foreach_impl 'python_compile' > * environment, line 565: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' > * environment, line 2903: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' > * environment, line 2389: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' > * environment, line 2387: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' > * environment, line 917: Called distutils-r1_run_phase 'python_compile' > * environment, line 1392: Called python_compile > * environment, line 2685: Called distutils-r1_python_compile > * environment, line 1203: Called esetup.py 'build' '-j' '4' > * environment, line 1928: Called die > * The specific snippet of code: > * "${@}" || die -n; > * > * If you need support, post the output of `emerge --info '=sci-chemistry/modeller-9.25::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/modeller-9.25::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-chemistry:modeller-9.25:20220312-180956.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/modeller-9.25/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/modeller-9.25/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25/src/swig' > * S: '/var/tmp/portage/sci-chemistry/modeller-9.25/work/modeller-9.25' >
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