Ci fixes by akutuva21 · Pull Request #112 · RuleWorld/PyBioNetGen

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.

akutuva21 · 2026-07-20T18:06:38Z

You merged the last PR too early before CI completed, so here's some small updates to ensure it passes

…test mocks - bngfile.py: replaced conf.get('stdout') with self.suppress (conf was removed in the upstream deferred-app-setup refactor) - test_csimulator.py: patch get_conf() instead of the removed module-level conf attribute, matching the upstream csimulator architecture

…s_to_bngparser add_empty_block creates empty block attributes but does not populate active_blocks (only the real parser does that via add_block with an argument). The test needs active_blocks populated so bngmodel.__init__ does not raise BNGModelError before reaching the assertion.

…asses_path_options_to_bngparser The merged code now passes verbose=self.verbose to BNGParser, so the expected call must include verbose=False for the default case.