Ticket #16848: npy201.txt

src\bundles\add_charge\src\process_lib.py:60:6: SyntaxError: Expected a module name
   |
58 |     return heavy_synonyms.get(heavy, [])
59 |
60 | from .5p_data import heavy_data, hyd_data
   |      ^
61 | for lib in sys.argv[1:]:
62 |     f = open(lib, "r")
   |

src\bundles\add_charge\src\process_lib.py:60:8: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
58 |     return heavy_synonyms.get(heavy, [])
59 |
60 | from .5p_data import heavy_data, hyd_data
   |        ^
61 | for lib in sys.argv[1:]:
62 |     f = open(lib, "r")
   |

src\bundles\add_charge\src\process_lib.py:60:15: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
58 |     return heavy_synonyms.get(heavy, [])
59 |
60 | from .5p_data import heavy_data, hyd_data
   |               ^
61 | for lib in sys.argv[1:]:
62 |     f = open(lib, "r")
   |

src\bundles\alphafold\src\alphafold21_predict_colab.py:78:5: SyntaxError: Expected a statement
   |
77 |     # The -x option logs each command with a prompt in front of it.
78 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |     ^
79 |     if _exit_code != 0:
80 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold21_predict_colab.py:78:14: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
77 |     # The -x option logs each command with a prompt in front of it.
78 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |              ^
79 |     if _exit_code != 0:
80 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold21_predict_colab.py:78:46: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
77 |     # The -x option logs each command with a prompt in front of it.
78 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                              ^
79 |     if _exit_code != 0:
80 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold21_predict_colab.py:78:48: SyntaxError: Expected an expression
   |
77 |     # The -x option logs each command with a prompt in front of it.
78 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                                ^
79 |     if _exit_code != 0:
80 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold21_predict_colab.py:634:5: SyntaxError: Expected a statement
    |
633 |     # Make a zip file of the predictions
634 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |     ^
635 |     
636 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold21_predict_colab.py:634:9: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
633 |     # Make a zip file of the predictions
634 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |         ^
635 |     
636 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold21_predict_colab.py:634:35: SyntaxError: Expected an identifier
    |
633 |     # Make a zip file of the predictions
634 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                   ^
635 |     
636 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold21_predict_colab.py:634:36: SyntaxError: Expected an identifier
    |
633 |     # Make a zip file of the predictions
634 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                    ^
635 |     
636 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold21_predict_colab.py:634:50: SyntaxError: Expected an expression
    |
633 |     # Make a zip file of the predictions
634 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                                  ^
635 |     
636 |     # Download predictions.
637 |     from google.colab import files
    |

src\bundles\alphafold\src\alphafold22_predict_colab.py:80:5: SyntaxError: Expected a statement
   |
79 |     # The -x option logs each command with a prompt in front of it.
80 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |     ^
81 |     if _exit_code != 0:
82 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold22_predict_colab.py:80:14: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
79 |     # The -x option logs each command with a prompt in front of it.
80 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |              ^
81 |     if _exit_code != 0:
82 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold22_predict_colab.py:80:46: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
79 |     # The -x option logs each command with a prompt in front of it.
80 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                              ^
81 |     if _exit_code != 0:
82 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold22_predict_colab.py:80:48: SyntaxError: Expected an expression
   |
79 |     # The -x option logs each command with a prompt in front of it.
80 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                                ^
81 |     if _exit_code != 0:
82 |         raise RuntimeError('Error running shell script %s, output in log file %s'
   |

src\bundles\alphafold\src\alphafold22_predict_colab.py:679:5: SyntaxError: Expected a statement
    |
678 |     # Make a zip file of the predictions
679 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |     ^
680 |     
681 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold22_predict_colab.py:679:9: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
678 |     # Make a zip file of the predictions
679 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |         ^
680 |     
681 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold22_predict_colab.py:679:35: SyntaxError: Expected an identifier
    |
678 |     # Make a zip file of the predictions
679 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                   ^
680 |     
681 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold22_predict_colab.py:679:36: SyntaxError: Expected an identifier
    |
678 |     # Make a zip file of the predictions
679 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                    ^
680 |     
681 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold22_predict_colab.py:679:50: SyntaxError: Expected an expression
    |
678 |     # Make a zip file of the predictions
679 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                                  ^
680 |     
681 |     # Download predictions.
682 |     from google.colab import files
    |

src\bundles\alphafold\src\alphafold_predict_colab.py:76:5: SyntaxError: Expected a statement
   |
75 |     # The -x option logs each command with a prompt in front of it.
76 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |     ^
77 |     
78 | def install_hmmer(install_log = 'install_log.txt'):
   |

src\bundles\alphafold\src\alphafold_predict_colab.py:76:14: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
75 |     # The -x option logs each command with a prompt in front of it.
76 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |              ^
77 |     
78 | def install_hmmer(install_log = 'install_log.txt'):
   |

src\bundles\alphafold\src\alphafold_predict_colab.py:76:46: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
75 |     # The -x option logs each command with a prompt in front of it.
76 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                              ^
77 |     
78 | def install_hmmer(install_log = 'install_log.txt'):
   |

src\bundles\alphafold\src\alphafold_predict_colab.py:76:48: SyntaxError: Expected an expression
   |
75 |     # The -x option logs each command with a prompt in front of it.
76 |     !bash -x "{filename}" >> "{install_log}" 2>&1
   |                                                ^
77 |     
78 | def install_hmmer(install_log = 'install_log.txt'):
   |

src\bundles\alphafold\src\alphafold_predict_colab.py:567:5: SyntaxError: Expected a statement
    |
566 |     # Make a zip file of the predictions
567 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |     ^
568 |     
569 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold_predict_colab.py:567:9: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
566 |     # Make a zip file of the predictions
567 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |         ^
568 |     
569 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold_predict_colab.py:567:35: SyntaxError: Expected an identifier
    |
566 |     # Make a zip file of the predictions
567 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                   ^
568 |     
569 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold_predict_colab.py:567:36: SyntaxError: Expected an identifier
    |
566 |     # Make a zip file of the predictions
567 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                    ^
568 |     
569 |     # Download predictions.
    |

src\bundles\alphafold\src\alphafold_predict_colab.py:567:50: SyntaxError: Expected an expression
    |
566 |     # Make a zip file of the predictions
567 |     !cd {output_dir} ; zip -q -r ../results.zip *
    |                                                  ^
568 |     
569 |     # Download predictions.
570 |     from google.colab import files
    |

src\bundles\alphafold\src\colabfold_predict.py:168:3: SyntaxError: Expected a statement
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict.py:168:12: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |            ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict.py:168:19: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict.py:168:30: SyntaxError: Expected an expression
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                              ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict.py:168:35: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                                   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict.py:169:3: SyntaxError: Expected a statement
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |   ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict.py:169:29: SyntaxError: Expected an expression
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |                             ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict.py:169:35: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |                                   ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict.py:172:3: SyntaxError: Expected a statement
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |   ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:14: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |              ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:26: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                          ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:39: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                       ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:45: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                             ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:52: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                    ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:58: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                          ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:63: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                               ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:172:76: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                                            ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict.py:195:20: SyntaxError: Expected an expression
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                    ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict.py:195:21: SyntaxError: Invalid assignment target
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                     ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict.py:195:45: SyntaxError: Invalid assignment target
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                                             ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict.py:222:3: SyntaxError: Expected a statement
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |   ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:12: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |            ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:18: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                  ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:34: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                  ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:40: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                        ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:46: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                              ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:52: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                                    ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:222:58: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                                          ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict.py:305:3: SyntaxError: Expected a statement
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |   ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict.py:305:12: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |            ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict.py:305:44: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |                                            ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict.py:305:46: SyntaxError: Expected an expression
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |                                              ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict_test.py:168:3: SyntaxError: Expected a statement
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict_test.py:168:12: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |            ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict_test.py:168:19: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict_test.py:168:30: SyntaxError: Expected an expression
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                              ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict_test.py:168:35: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
    |                                   ^
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |

src\bundles\alphafold\src\colabfold_predict_test.py:169:3: SyntaxError: Expected a statement
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |   ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict_test.py:169:29: SyntaxError: Expected an expression
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |                             ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict_test.py:169:35: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
167 |   relax = 'relaxed' if energy_minimize else 'unrelaxed'
168 |   !cp -p *_{relax}_rank_001_*.pdb best_model.pdb
169 |   !cp -p *_scores_rank_001_*.json best_model_pae.json
    |                                   ^
170 |
171 |   # Make a zip file of the predictions
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:3: SyntaxError: Expected a statement
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |   ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:14: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |              ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:26: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                          ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:39: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                       ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:45: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                             ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:52: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                    ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:58: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                          ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:63: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                               ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:172:76: SyntaxError: Expected an expression
    |
171 |   # Make a zip file of the predictions
172 |   !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt
    |                                                                            ^
173 |
174 |   # Download predictions.
    |

src\bundles\alphafold\src\colabfold_predict_test.py:195:20: SyntaxError: Expected an expression
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                    ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict_test.py:195:21: SyntaxError: Invalid assignment target
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                     ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict_test.py:195:45: SyntaxError: Invalid assignment target
    |
193 | #
194 | def report_gpu_type():
195 |   gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name
    |                                             ^
196 |   gpu_name = gpu_name_lines[0]
197 |   print(f'Using {gpu_name} graphics processor')
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:3: SyntaxError: Expected a statement
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |   ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:12: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |            ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:18: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                  ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:34: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                  ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:40: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                        ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:46: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                              ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:52: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                                    ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:222:58: SyntaxError: Expected an expression
    |
220 |   occur if different sequences are run when computing MSA.
221 |   '''
222 |   !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta
    |                                                          ^
223 |
224 | # ================================================================================================
    |

src\bundles\alphafold\src\colabfold_predict_test.py:305:3: SyntaxError: Expected a statement
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |   ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict_test.py:305:12: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |            ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict_test.py:305:44: SyntaxError: Simple statements must be separated by newlines or semicolons
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |                                            ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\alphafold\src\colabfold_predict_test.py:305:46: SyntaxError: Expected an expression
    |
304 |   # The -x option logs each command with a prompt in front of it.
305 |   !bash -x "{filename}" >> "{install_log}" 2>&1
    |                                              ^
306 |   if _exit_code != 0:
307 |     raise RuntimeError('Error running shell script %s, output in log file %s'
    |

src\bundles\atomic\src\structure.py:865:20: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
    |
863 |             from numpy import unique, in1d
864 |             sel_rids = unique(rids[asel])
865 |             ares = in1d(rids, sel_rids)
    |                    ^^^^ NPY201
866 |             if ares.sum() > na:
867 |                 # Promote to entire residues
    |
    = help: Replace with `numpy.isin`

src\bundles\atomic\src\structure.py:873:23: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
    |
871 |                 ssids = r.secondary_structure_ids
872 |                 sel_ssids = unique(ssids[asel])
873 |                 ass = in1d(ssids, sel_ssids)
    |                       ^^^^ NPY201
874 |                 if ass.sum() > na:
875 |                     # Promote to secondary structure
    |
    = help: Replace with `numpy.isin`

src\bundles\atomic\src\structure.py:887:30: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
    |
885 |                         cids = array(r.chain_ids)
886 |                         sel_cids = unique(cids[asel])
887 |                         ac = in1d(cids, sel_cids)
    |                              ^^^^ NPY201
888 |                         if ac.sum() > na:
889 |                             # Promote to entire chains
    |
    = help: Replace with `numpy.isin`

src\bundles\atomic\src\structure.py:1038:20: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
     |
1036 |             from numpy import in1d, invert
1037 |             matched_chain_ids = atoms.filter(a).unique_chain_ids
1038 |             mask = in1d(atoms.chain_ids, matched_chain_ids)
     |                    ^^^^ NPY201
1039 |             if '<' in operator:
1040 |                 expand_by = atoms.filter(mask)
     |
     = help: Replace with `numpy.isin`

src\bundles\map_data\src\arrays.py:256:12: NPY201 [*] `np.product` will be removed in NumPy 2.0. Use `numpy.prod` instead.
    |
254 |   for k in range(size[2]):
255 |     indices[k,:,:,2] = k
256 |   volume = product(size)
    |            ^^^^^^^ NPY201
257 |   indices = reshape(indices, (volume, 3))
258 |   return indices
    |
    = help: Replace with `numpy.prod`

src\bundles\map_data\src\readarray.py:233:13: NPY201 [*] `np.product` will be removed in NumPy 2.0. Use `numpy.prod` instead.
    |
231 |     vtype = dtype(value_type)
232 |     tsize = vtype.itemsize
233 |     bytes = product(size, dtype=float64)*float(tsize)
    |             ^^^^^^^ NPY201
234 |     mbytes = bytes / 2**20
235 |     sz = ','.join(['%d' % s for s in size])
    |
    = help: Replace with `numpy.prod`

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:38:9: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
37 | if len(sys.argv)!=2:
38 |   print "Missing file argument\nUsage: sample.py FILE"
   |         ^
39 |   sys.exit()
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:44:11: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
42 | x=xdrfile(sys.argv[1]) 
43 | for f in x:   #iterates frames
44 |     print "%8s %8s %8s %8s   Step: %8d "%("Atom","X","Y","Z",f.step) #print header
   |           ^
45 |     for i,a in enumerate(f.x):  #iterate atoms
46 |       print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:46:13: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
44 |     print "%8s %8s %8s %8s   Step: %8d "%("Atom","X","Y","Z",f.step) #print header
45 |     for i,a in enumerate(f.x):  #iterate atoms
46 |       print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z
   |             ^
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:49:35: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
47 | def test(fn):
48 |     x=xdrfile(fn)
49 |     if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1
   |                                   ^
50 |     for k,f in enumerate(x):
51 |         if f.step != step1+k: print "incorrect step",f.step,step1+k,k
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:51:37: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
49 |     if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1
50 |     for k,f in enumerate(x):
51 |         if f.step != step1+k: print "incorrect step",f.step,step1+k,k
   |                                     ^
52 |         if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
53 |         if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:52:48: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
50 |     for k,f in enumerate(x):
51 |         if f.step != step1+k: print "incorrect step",f.step,step1+k,k
52 |         if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
   |                                                ^
53 |         if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
54 |         if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:53:66: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
51 |         if f.step != step1+k: print "incorrect step",f.step,step1+k,k
52 |         if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
53 |         if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
   |                                                                  ^
54 |         if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
55 |         for i in range(DIM):
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:54:60: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
52 |         if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
53 |         if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
54 |         if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
   |                                                            ^
55 |         for i in range(DIM):
56 |             for j in range(DIM):
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:57:66: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
55 |         for i in range(DIM):
56 |             for j in range(DIM):
57 |                 if fabs(f.box[i][j] - box1[i][j]) > toler: print "box incorrect",f.box[i][j],box1[i][j]
   |                                                                  ^
58 |         for i in range(x.natoms):
59 |             for j in range(DIM):
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:61:56: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
59 |             for j in range(DIM):
60 |                 target = (i+1)*3.7 + (j+1)
61 |                 if  f.x[i][j] - target > toler : print "x incorrect"
   |                                                        ^
62 |     print fn,"OK"
   |

src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:62:11: SyntaxError: Simple statements must be separated by newlines or semicolons
   |
60 |                 target = (i+1)*3.7 + (j+1)
61 |                 if  f.x[i][j] - target > toler : print "x incorrect"
62 |     print fn,"OK"
   |           ^
63 |
64 | test("../test.trr")
   |

src\bundles\std_commands\src\align.py:312:37: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
    |
310 |     for s, a in atoms.by_structure:
311 |         satoms = s.atoms
312 |         catoms.append(satoms.filter(in1d(satoms.chain_ids, a.unique_chain_ids)))
    |                                     ^^^^ NPY201
313 |     from chimerax.atomic import concatenate, Atoms
314 |     return concatenate(catoms, Atoms)
    |
    = help: Replace with `numpy.isin`

src\bundles\std_commands\src\sym.py:447:16: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead.
    |
445 |         mmcif_cids = mmcif_chain_ids(atoms, self.from_mmcif)
446 |         from numpy import in1d, logical_not
447 |         mask = in1d(mmcif_cids, chain_ids)
    |                ^^^^ NPY201
448 |         included_atoms = atoms.filter(mask)
449 |         logical_not(mask,mask)
    |
    = help: Replace with `numpy.isin`

Found 113 errors.
[*] 8 fixable with the `--fix` option.