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mitsei/dlkit | dlkit/services/assessment.py | Bank.save_assessment_offered | def save_assessment_offered(self, assessment_offered_form, *args, **kwargs):
"""Pass through to provider AssessmentOfferedAdminSession.update_assessment_offered"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if assessment_offered_form.is... | python | def save_assessment_offered(self, assessment_offered_form, *args, **kwargs):
"""Pass through to provider AssessmentOfferedAdminSession.update_assessment_offered"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if assessment_offered_form.is... | [
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_assessment_taken_view | def use_comparative_assessment_taken_view(self):
"""Pass through to provider AssessmentTakenLookupSession.use_comparative_assessment_taken_view"""
self._object_views['assessment_taken'] = COMPARATIVE
# self._get_provider_session('assessment_taken_lookup_session') # To make sure the session is tr... | python | def use_comparative_assessment_taken_view(self):
"""Pass through to provider AssessmentTakenLookupSession.use_comparative_assessment_taken_view"""
self._object_views['assessment_taken'] = COMPARATIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_assessment_taken_view | def use_plenary_assessment_taken_view(self):
"""Pass through to provider AssessmentTakenLookupSession.use_plenary_assessment_taken_view"""
self._object_views['assessment_taken'] = PLENARY
# self._get_provider_session('assessment_taken_lookup_session') # To make sure the session is tracked
... | python | def use_plenary_assessment_taken_view(self):
"""Pass through to provider AssessmentTakenLookupSession.use_plenary_assessment_taken_view"""
self._object_views['assessment_taken'] = PLENARY
# self._get_provider_session('assessment_taken_lookup_session') # To make sure the session is tracked
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mitsei/dlkit | dlkit/services/assessment.py | Bank.get_assessment_taken_form | def get_assessment_taken_form(self, *args, **kwargs):
"""Pass through to provider AssessmentTakenAdminSession.get_assessment_taken_form_for_update"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.get_resource_form_for_update
# This method might be a bit s... | python | def get_assessment_taken_form(self, *args, **kwargs):
"""Pass through to provider AssessmentTakenAdminSession.get_assessment_taken_form_for_update"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.get_resource_form_for_update
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mitsei/dlkit | dlkit/services/assessment.py | Bank.save_assessment_taken | def save_assessment_taken(self, assessment_taken_form, *args, **kwargs):
"""Pass through to provider AssessmentTakenAdminSession.update_assessment_taken"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if assessment_taken_form.is_for_updat... | python | def save_assessment_taken(self, assessment_taken_form, *args, **kwargs):
"""Pass through to provider AssessmentTakenAdminSession.update_assessment_taken"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_assessment_part_view | def use_comparative_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_comparative_assessment_part_view"""
self._object_views['assessment_part'] = COMPARATIVE
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked... | python | def use_comparative_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_comparative_assessment_part_view"""
self._object_views['assessment_part'] = COMPARATIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_assessment_part_view | def use_plenary_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_plenary_assessment_part_view"""
self._object_views['assessment_part'] = PLENARY
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked
for... | python | def use_plenary_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_plenary_assessment_part_view"""
self._object_views['assessment_part'] = PLENARY
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_active_assessment_part_view | def use_active_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_active_assessment_part_view"""
self._operable_views['assessment_part'] = ACTIVE
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked
for... | python | def use_active_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_active_assessment_part_view"""
self._operable_views['assessment_part'] = ACTIVE
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_any_status_assessment_part_view | def use_any_status_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_any_status_assessment_part_view"""
self._operable_views['assessment_part'] = ANY_STATUS
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked... | python | def use_any_status_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_any_status_assessment_part_view"""
self._operable_views['assessment_part'] = ANY_STATUS
# self._get_provider_session('assessment_part_lookup_session') # To make sure the session is tracked... | [
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_sequestered_assessment_part_view | def use_sequestered_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_sequestered_assessment_part_view"""
# Does this need to be re-implemented to match the other non-sub-package view setters?
self._containable_views['assessment_part'] = SEQUESTERED
... | python | def use_sequestered_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_sequestered_assessment_part_view"""
# Does this need to be re-implemented to match the other non-sub-package view setters?
self._containable_views['assessment_part'] = SEQUESTERED
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_unsequestered_assessment_part_view | def use_unsequestered_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_unsequestered_assessment_part_view"""
# Does this need to be re-implemented to match the other non-sub-package view setters?
self._containable_views['assessment_part'] = UNSEQUESTERED
... | python | def use_unsequestered_assessment_part_view(self):
"""Pass through to provider AssessmentPartLookupSession.use_unsequestered_assessment_part_view"""
# Does this need to be re-implemented to match the other non-sub-package view setters?
self._containable_views['assessment_part'] = UNSEQUESTERED
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mitsei/dlkit | dlkit/services/assessment.py | Bank.get_assessment_part_form | def get_assessment_part_form(self, *args, **kwargs):
"""Pass through to provider AssessmentPartAdminSession.get_assessment_part_form_for_update"""
# This method might be a bit sketchy. Time will tell.
if isinstance(args[-1], list) or 'assessment_part_record_types' in kwargs:
return s... | python | def get_assessment_part_form(self, *args, **kwargs):
"""Pass through to provider AssessmentPartAdminSession.get_assessment_part_form_for_update"""
# This method might be a bit sketchy. Time will tell.
if isinstance(args[-1], list) or 'assessment_part_record_types' in kwargs:
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mitsei/dlkit | dlkit/services/assessment.py | Bank.save_assessment_part | def save_assessment_part(self, assessment_part_form, *args, **kwargs):
"""Pass through to provider AssessmentPartAdminSession.update_assessment_part"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if assessment_part_form.is_for_update():
... | python | def save_assessment_part(self, assessment_part_form, *args, **kwargs):
"""Pass through to provider AssessmentPartAdminSession.update_assessment_part"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_asseessment_part_item_view | def use_comparative_asseessment_part_item_view(self):
"""Pass through to provider AssessmentPartItemSession.use_comparative_asseessment_part_item_view"""
self._object_views['asseessment_part_item'] = COMPARATIVE
# self._get_provider_session('assessment_part_item_session') # To make sure the sess... | python | def use_comparative_asseessment_part_item_view(self):
"""Pass through to provider AssessmentPartItemSession.use_comparative_asseessment_part_item_view"""
self._object_views['asseessment_part_item'] = COMPARATIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_assessment_part_item_view | def use_plenary_assessment_part_item_view(self):
"""Pass through to provider AssessmentPartItemSession.use_plenary_assessment_part_item_view"""
self._object_views['assessment_part_item'] = PLENARY
# self._get_provider_session('assessment_part_item_session') # To make sure the session is tracked
... | python | def use_plenary_assessment_part_item_view(self):
"""Pass through to provider AssessmentPartItemSession.use_plenary_assessment_part_item_view"""
self._object_views['assessment_part_item'] = PLENARY
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_sequence_rule_view | def use_comparative_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_comparative_sequence_rule_view"""
self._object_views['sequence_rule'] = COMPARATIVE
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
f... | python | def use_comparative_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_comparative_sequence_rule_view"""
self._object_views['sequence_rule'] = COMPARATIVE
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_sequence_rule_view | def use_plenary_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_plenary_sequence_rule_view"""
self._object_views['sequence_rule'] = PLENARY
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
for session i... | python | def use_plenary_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_plenary_sequence_rule_view"""
self._object_views['sequence_rule'] = PLENARY
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_active_sequence_rule_view | def use_active_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_active_sequence_rule_view"""
self._operable_views['sequence_rule'] = ACTIVE
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
for session i... | python | def use_active_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_active_sequence_rule_view"""
self._operable_views['sequence_rule'] = ACTIVE
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_any_status_sequence_rule_view | def use_any_status_sequence_rule_view(self):
"""Pass through to provider SequenceRuleLookupSession.use_any_status_sequence_rule_view"""
self._operable_views['sequence_rule'] = ANY_STATUS
# self._get_provider_session('sequence_rule_lookup_session') # To make sure the session is tracked
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"""Pass through to provider SequenceRuleLookupSession.use_any_status_sequence_rule_view"""
self._operable_views['sequence_rule'] = ANY_STATUS
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mitsei/dlkit | dlkit/services/assessment.py | Bank.save_sequence_rule | def save_sequence_rule(self, sequence_rule_form, *args, **kwargs):
"""Pass through to provider SequenceRuleAdminSession.update_sequence_rule"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if sequence_rule_form.is_for_update():
... | python | def save_sequence_rule(self, sequence_rule_form, *args, **kwargs):
"""Pass through to provider SequenceRuleAdminSession.update_sequence_rule"""
# Implemented from kitosid template for -
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_sequence_rule_enabler_view | def use_comparative_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_comparative_sequence_rule_enabler_view"""
self._object_views['sequence_rule_enabler'] = COMPARATIVE
# self._get_provider_session('sequence_rule_enabler_lookup_session') # To mak... | python | def use_comparative_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_comparative_sequence_rule_enabler_view"""
self._object_views['sequence_rule_enabler'] = COMPARATIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_sequence_rule_enabler_view | def use_plenary_sequence_rule_enabler_view(self):
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self._object_views['sequence_rule_enabler'] = PLENARY
# self._get_provider_session('sequence_rule_enabler_lookup_session') # To make sure the s... | python | def use_plenary_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_plenary_sequence_rule_enabler_view"""
self._object_views['sequence_rule_enabler'] = PLENARY
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_active_sequence_rule_enabler_view | def use_active_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_active_sequence_rule_enabler_view"""
self._operable_views['sequence_rule_enabler'] = ACTIVE
# self._get_provider_session('sequence_rule_enabler_lookup_session') # To make sure the s... | python | def use_active_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_active_sequence_rule_enabler_view"""
self._operable_views['sequence_rule_enabler'] = ACTIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_any_status_sequence_rule_enabler_view | def use_any_status_sequence_rule_enabler_view(self):
"""Pass through to provider SequenceRuleEnablerLookupSession.use_any_status_sequence_rule_enabler_view"""
self._operable_views['sequence_rule_enabler'] = ANY_STATUS
# self._get_provider_session('sequence_rule_enabler_lookup_session') # To mak... | python | def use_any_status_sequence_rule_enabler_view(self):
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self._operable_views['sequence_rule_enabler'] = ANY_STATUS
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mitsei/dlkit | dlkit/services/assessment.py | Bank.get_sequence_rule_enabler_form | def get_sequence_rule_enabler_form(self, *args, **kwargs):
"""Pass through to provider SequenceRuleEnablerAdminSession.get_sequence_rule_enabler_form_for_update"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.get_resource_form_for_update
# This method mi... | python | def get_sequence_rule_enabler_form(self, *args, **kwargs):
"""Pass through to provider SequenceRuleEnablerAdminSession.get_sequence_rule_enabler_form_for_update"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.get_resource_form_for_update
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mitsei/dlkit | dlkit/services/assessment.py | Bank.save_sequence_rule_enabler | def save_sequence_rule_enabler(self, sequence_rule_enabler_form, *args, **kwargs):
"""Pass through to provider SequenceRuleEnablerAdminSession.update_sequence_rule_enabler"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
if sequence_rule_e... | python | def save_sequence_rule_enabler(self, sequence_rule_enabler_form, *args, **kwargs):
"""Pass through to provider SequenceRuleEnablerAdminSession.update_sequence_rule_enabler"""
# Implemented from kitosid template for -
# osid.resource.ResourceAdminSession.update_resource
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_comparative_sequence_rule_enabler_rule_view | def use_comparative_sequence_rule_enabler_rule_view(self):
"""Pass through to provider SequenceRuleEnablerRuleLookupSession.use_comparative_sequence_rule_enabler_rule_view"""
self._object_views['sequence_rule_enabler_rule'] = COMPARATIVE
# self._get_provider_session('sequence_rule_enabler_rule_l... | python | def use_comparative_sequence_rule_enabler_rule_view(self):
"""Pass through to provider SequenceRuleEnablerRuleLookupSession.use_comparative_sequence_rule_enabler_rule_view"""
self._object_views['sequence_rule_enabler_rule'] = COMPARATIVE
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mitsei/dlkit | dlkit/services/assessment.py | Bank.use_plenary_sequence_rule_enabler_rule_view | def use_plenary_sequence_rule_enabler_rule_view(self):
"""Pass through to provider SequenceRuleEnablerRuleLookupSession.use_plenary_sequence_rule_enabler_rule_view"""
self._object_views['sequence_rule_enabler_rule'] = PLENARY
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self._object_views['sequence_rule_enabler_rule'] = PLENARY
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mitsei/dlkit | dlkit/records/assessment/basic/feedback_answer_records.py | FeedbackAnswerFormRecord._init_map | def _init_map(self):
"""stub"""
self.my_osid_object_form._my_map['confusedLearningObjectiveIds'] = \
self._confused_learning_objectives_metadata['default_list_values'][0]
self.my_osid_object_form._my_map['feedback'] = \
self._feedback_metadata['default_string_values'][0] | python | def _init_map(self):
"""stub"""
self.my_osid_object_form._my_map['confusedLearningObjectiveIds'] = \
self._confused_learning_objectives_metadata['default_list_values'][0]
self.my_osid_object_form._my_map['feedback'] = \
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mitsei/dlkit | dlkit/records/assessment/basic/feedback_answer_records.py | FeedbackAnswerFormRecord._init_metadata | def _init_metadata(self):
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mitsei/dlkit | dlkit/records/assessment/basic/feedback_answer_records.py | MultiLanguageFeedbacksAnswerFormRecord._init_metadata | def _init_metadata(self):
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mitsei/dlkit | dlkit/records/assessment/basic/feedback_answer_records.py | MultiLanguageFeedbacksAnswerFormRecord.clear_feedbacks | def clear_feedbacks(self):
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self._feedbacks_metadata['default_object_values'][0] | python | def clear_feedbacks(self):
"""stub"""
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raise NoAccess()
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theosysbio/means | src/means/inference/inference.py | _extract_params_from_i0 | def _extract_params_from_i0(only_variable_parameters, parameters_with_variability, initial_conditions_with_variability):
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theosysbio/means | src/means/inference/inference.py | InferenceWithRestarts.infer | def infer(self, number_of_processes=1, *args, **kwargs):
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nrcharles/caelum | caelum/tmy3.py | tmybasename | def tmybasename(usaf):
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nrcharles/caelum | caelum/tmy3.py | total | def total(usaf, field='GHI (W/m^2)'):
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mitsei/dlkit | dlkit/json_/proxy/managers.py | ProxyManager.get_proxy_session | def get_proxy_session(self):
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ND-CSE-30151/tock | tock/grammars.py | Grammar.is_contextfree | def is_contextfree(self):
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theosysbio/means | src/means/approximation/mea/moment_expansion_approximation.py | mea_approximation | def mea_approximation(model, max_order, closure='scalar', *closure_args, **closure_kwargs):
r"""
A wrapper around :class:`~means.approximation.mea.moment_expansion_approximation.MomentExpansionApproximation`.
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See :class:... | python | def mea_approximation(model, max_order, closure='scalar', *closure_args, **closure_kwargs):
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theosysbio/means | src/means/approximation/mea/moment_expansion_approximation.py | MomentExpansionApproximation._generate_problem_left_hand_side | def _generate_problem_left_hand_side(self, n_counter, k_counter):
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theosysbio/means | src/means/approximation/mea/moment_expansion_approximation.py | MomentExpansionApproximation._generate_mass_fluctuation_kinetics | def _generate_mass_fluctuation_kinetics(self, central_moments, dmu_over_dt, n_counter):
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theosysbio/means | src/means/approximation/mea/moment_expansion_approximation.py | MomentExpansionApproximation._substitute_raw_with_central | def _substitute_raw_with_central(self, central_moments_exprs, central_from_raw_exprs, n_counter, k_counter):
r"""
Takes the expressions for central moments, and substitute the symbols representing raw moments,
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theosysbio/means | src/means/approximation/mea/raw_to_central.py | raw_to_central | def raw_to_central(n_counter, species, k_counter):
"""
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.. math::
\mathbf{M_{x^n}} = \sum_{k_1=0}^{n_1} ... \sum_{k_d=0}^{n_d} \mathbf{{n \choose k}} (-1)^{\mathbf{n-k}} \mu^{\mathbf... | python | def raw_to_central(n_counter, species, k_counter):
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delfick/harpoon | harpoon/formatter.py | MergedOptionStringFormatter.get_string | def get_string(self, key):
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Vagrants/blackbird | blackbird/sr71.py | main | def main():
"""
main
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"""
main
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Add command line arguments to each section in config.
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Vagrants/blackbird | blackbird/sr71.py | BlackBird._create_threads | def _create_threads(self):
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:rtype: ``osid.proxy.ProxySession``
:raise: ``OperationFailed`` -- unable to complete request
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mitsei/dlkit | dlkit/authz_adapter/grading/sessions.py | GradeSystemSearchSession.get_grade_systems_by_search | def get_grade_systems_by_search(self, grade_system_query, grade_system_search):
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# Implemented from azosid template for -
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.set_query_sequence | def set_query_sequence(self,seq):
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:type seq: string
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.target_range | def target_range(self):
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a = self.alignment_ranges
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.actual_query_range | def actual_query_range(self):
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.set_reference | def set_reference(self,ref):
"""Set the reference sequence
:param ref: reference sequence
:type ref: string
"""
self._options = self._options._replace(reference = ref) | python | def set_reference(self,ref):
"""Set the reference sequence
:param ref: reference sequence
:type ref: string
"""
self._options = self._options._replace(reference = ref) | [
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.get_alignment_strings | def get_alignment_strings(self,min_intron_size=68):
"""Process the alignment to get information like
the alignment strings for each exon. These strings are used by the pretty print.
:returns: String representation of the alignment in an easy to read format
:rtype: string
"""
qseq = self.quer... | python | def get_alignment_strings(self,min_intron_size=68):
"""Process the alignment to get information like
the alignment strings for each exon. These strings are used by the pretty print.
:returns: String representation of the alignment in an easy to read format
:rtype: string
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.print_alignment | def print_alignment(self,chunk_size=40,min_intron_size=68):
"""print the nice looking alignment. Must have data accessable from get_query_sequence() and get_refernece_sequencec()
:returns: Pretty print string.
:rtype: string
"""
has_qual = True
if not self.query_quality: has_qual = False
... | python | def print_alignment(self,chunk_size=40,min_intron_size=68):
"""print the nice looking alignment. Must have data accessable from get_query_sequence() and get_refernece_sequencec()
:returns: Pretty print string.
:rtype: string
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has_qual = True
if not self.query_quality: has_qual = False
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.get_PSL | def get_PSL(self,min_intron_size=68):
"""Get a PSL object representation of the alignment.
:returns: PSL representation
:rtype: PSL
"""
from seqtools.format.psl import PSL
matches = sum([x[0].length for x in self.alignment_ranges]) # 1. Matches - Number of matching bases that aren't repeats
... | python | def get_PSL(self,min_intron_size=68):
"""Get a PSL object representation of the alignment.
:returns: PSL representation
:rtype: PSL
"""
from seqtools.format.psl import PSL
matches = sum([x[0].length for x in self.alignment_ranges]) # 1. Matches - Number of matching bases that aren't repeats
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.get_SAM | def get_SAM(self,min_intron_size=68):
"""Get a SAM object representation of the alignment.
:returns: SAM representation
:rtype: SAM
"""
from seqtools.format.sam import SAM
#ar is target then query
qname = self.alignment_ranges[0][1].chr
flag = 0
if self.strand == '-': flag = 16
... | python | def get_SAM(self,min_intron_size=68):
"""Get a SAM object representation of the alignment.
:returns: SAM representation
:rtype: SAM
"""
from seqtools.format.sam import SAM
#ar is target then query
qname = self.alignment_ranges[0][1].chr
flag = 0
if self.strand == '-': flag = 16
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.construct_cigar | def construct_cigar(self,min_intron_size=68):
"""Create a CIGAR string from the alignment
:returns: CIGAR string
:rtype: string
"""
# goes target query
ar = self.alignment_ranges
cig = ''
if ar[0][1].start > 1: # soft clipped
cig += str(ar[0][1].start-1)+'S'
for i in range(l... | python | def construct_cigar(self,min_intron_size=68):
"""Create a CIGAR string from the alignment
:returns: CIGAR string
:rtype: string
"""
# goes target query
ar = self.alignment_ranges
cig = ''
if ar[0][1].start > 1: # soft clipped
cig += str(ar[0][1].start-1)+'S'
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jason-weirather/py-seq-tools | seqtools/align.py | Alignment.get_target_transcript | def get_target_transcript(self,min_intron=1):
"""Get the mapping of to the target strand
:returns: Transcript mapped to target
:rtype: Transcript
"""
if min_intron < 1:
sys.stderr.write("ERROR minimum intron should be 1 base or longer\n")
sys.exit()
#tx = Transcript()
rngs = [... | python | def get_target_transcript(self,min_intron=1):
"""Get the mapping of to the target strand
:returns: Transcript mapped to target
:rtype: Transcript
"""
if min_intron < 1:
sys.stderr.write("ERROR minimum intron should be 1 base or longer\n")
sys.exit()
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rngs = [... | [
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mitsei/dlkit | dlkit/json_/learning/queries.py | ProficiencyQuery.match_resource_id | def match_resource_id(self, resource_id, match):
"""Sets the resource ``Id`` for this query.
arg: resource_id (osid.id.Id): a resource ``Id``
arg: match (boolean): ``true`` if a positive match, ``false``
for a negative match
raise: NullArgument - ``resource_id`` i... | python | def match_resource_id(self, resource_id, match):
"""Sets the resource ``Id`` for this query.
arg: resource_id (osid.id.Id): a resource ``Id``
arg: match (boolean): ``true`` if a positive match, ``false``
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mitsei/dlkit | dlkit/json_/learning/queries.py | ProficiencyQuery.match_objective_id | def match_objective_id(self, objective_id, match):
"""Sets the objective ``Id`` for this query.
arg: objective_id (osid.id.Id): an objective ``Id``
arg: match (boolean): ``true`` for a positive match,
``false`` for a negative match
raise: NullArgument - ``objectiv... | python | def match_objective_id(self, objective_id, match):
"""Sets the objective ``Id`` for this query.
arg: objective_id (osid.id.Id): an objective ``Id``
arg: match (boolean): ``true`` for a positive match,
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mitsei/dlkit | dlkit/json_/learning/queries.py | ProficiencyQuery.match_completion | def match_completion(self, start, end, match):
"""Sets the completion for this query to match completion percentages between the given range inclusive.
arg: start (decimal): start of range
arg: end (decimal): end of range
arg: match (boolean): ``true`` for a positive match,
... | python | def match_completion(self, start, end, match):
"""Sets the completion for this query to match completion percentages between the given range inclusive.
arg: start (decimal): start of range
arg: end (decimal): end of range
arg: match (boolean): ``true`` for a positive match,
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mitsei/dlkit | dlkit/json_/learning/queries.py | ProficiencyQuery.match_level_id | def match_level_id(self, grade_id, match):
"""Sets the level grade ``Id`` for this query.
arg: grade_id (osid.id.Id): a grade ``Id``
arg: match (boolean): ``true`` for a positive match,
``false`` for a negative match
raise: NullArgument - ``grade_id`` is ``null``
... | python | def match_level_id(self, grade_id, match):
"""Sets the level grade ``Id`` for this query.
arg: grade_id (osid.id.Id): a grade ``Id``
arg: match (boolean): ``true`` for a positive match,
``false`` for a negative match
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRangeFromString | def GenomicRangeFromString(range_string,payload=None,dir=None):
"""Constructor for a GenomicRange object that takes a string"""
m = re.match('^(.+):(\d+)-(\d+)$',range_string)
if not m:
sys.stderr.write("ERROR bad genomic range string\n"+range_string+"\n")
sys.exit()
chr = m.group(1)
start = int(m.g... | python | def GenomicRangeFromString(range_string,payload=None,dir=None):
"""Constructor for a GenomicRange object that takes a string"""
m = re.match('^(.+):(\d+)-(\d+)$',range_string)
if not m:
sys.stderr.write("ERROR bad genomic range string\n"+range_string+"\n")
sys.exit()
chr = m.group(1)
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.copy | def copy(self):
"""Create a new copy of selfe. does not do a deep copy for payload
:return: copied range
:rtype: GenomicRange
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return type(self)(self.chr,
self.start+self._start_offset,
self.end,
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return type(self)(self.chr,
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.get_bed_array | def get_bed_array(self):
"""Return a basic three meber bed array representation of this range
:return: list of [chr,start (0-indexed), end (1-indexed]
:rtype: list
"""
arr = [self.chr,self.start-1,self.end]
if self.dir:
arr.append(self.dir)
return arr | python | def get_bed_array(self):
"""Return a basic three meber bed array representation of this range
:return: list of [chr,start (0-indexed), end (1-indexed]
:rtype: list
"""
arr = [self.chr,self.start-1,self.end]
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.equals | def equals(self,gr):
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:rtype: bool
"""
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""" check for equality. does not consider direction
:param gr: another genomic range
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.get_range_string | def get_range_string(self):
""" get the range string represetation. similar to the default input for UCSC genome browser
:return: representation by string like chr2:801-900
:rtype: string
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:param type: use_direction
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:param use_direction: false by default
:param type: GenomicRange
:param type: use_direction
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.overlaps | def overlaps(self,in_genomic_range,padding=0):
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""" The size of the overlap
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.merge | def merge(self,range2):
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jason-weirather/py-seq-tools | seqtools/range/__init__.py | GenomicRange.subtract | def subtract(self,range2):
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mitsei/dlkit | dlkit/json_/relationship/searches.py | RelationshipSearchResults.get_relationships | def get_relationships(self):
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svetlyak40wt/python-cl-conditions | example/example.py | parse_log_entry | def parse_log_entry(text):
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svetlyak40wt/python-cl-conditions | example/example.py | log_analyzer | def log_analyzer(path):
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svetlyak40wt/python-cl-conditions | example/example.py | log_analyzer2 | def log_analyzer2(path):
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OpenAgInitiative/openag_python | openag/cli/db/__init__.py | init | def init(db_url, api_url):
"""
Initialize the database server. Sets some configuration parameters on the
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documents into those databases, and sets up replication with the cloud
server if one has already been selected.
"""
... | python | def init(db_url, api_url):
"""
Initialize the database server. Sets some configuration parameters on the
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OpenAgInitiative/openag_python | openag/cli/db/__init__.py | clear | def clear():
"""
Clear all data on the local server. Useful for debugging purposed.
"""
utils.check_for_local_server()
click.confirm(
"Are you sure you want to do this? It will delete all of your data",
abort=True
)
server = Server(config["local_server"]["url"])
for db_na... | python | def clear():
"""
Clear all data on the local server. Useful for debugging purposed.
"""
utils.check_for_local_server()
click.confirm(
"Are you sure you want to do this? It will delete all of your data",
abort=True
)
server = Server(config["local_server"]["url"])
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OpenAgInitiative/openag_python | openag/cli/db/__init__.py | load_fixture | def load_fixture(fixture_file):
"""
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and uses it to populate the database. Fuxture files should consist of a
dictionary mapping database names to arrays of objects to store in those
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"""
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"""
Populate the database from a JSON file. Reads the JSON file FIXTURE_FILE
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OpenAgInitiative/openag_python | openag/cli/db/__init__.py | update_module_types | def update_module_types():
"""
Download the repositories for all of the firmware_module_type records and
update them using the `module.json` files from the repositories themselves.
Currently only works for git repositories.
"""
local_url = config["local_server"]["url"]
server = Server(local_... | python | def update_module_types():
"""
Download the repositories for all of the firmware_module_type records and
update them using the `module.json` files from the repositories themselves.
Currently only works for git repositories.
"""
local_url = config["local_server"]["url"]
server = Server(local_... | [
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matham/pyflycap2 | pyflycap2/utils.py | strip_comments | def strip_comments(code):
'''Returns the headers with comments removed.
'''
single_comment = compile('//.*') # single line comment
multi_comment = compile('/\\*\\*.*?\\*/', re.DOTALL) # multiline comment
code = sub(single_comment, '', code)
code = sub(multi_comment, '', code)
return... | python | def strip_comments(code):
'''Returns the headers with comments removed.
'''
single_comment = compile('//.*') # single line comment
multi_comment = compile('/\\*\\*.*?\\*/', re.DOTALL) # multiline comment
code = sub(single_comment, '', code)
code = sub(multi_comment, '', code)
return... | [
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matham/pyflycap2 | pyflycap2/utils.py | parse_prototype | def parse_prototype(prototype):
'''Returns a :attr:`FunctionSpec` instance from the input.
'''
val = ' '.join(prototype.splitlines())
f = match(func_pat, val) # match the whole function
if f is None:
raise Exception('Cannot parse function prototype "{}"'.format(val))
ftp, pointer... | python | def parse_prototype(prototype):
'''Returns a :attr:`FunctionSpec` instance from the input.
'''
val = ' '.join(prototype.splitlines())
f = match(func_pat, val) # match the whole function
if f is None:
raise Exception('Cannot parse function prototype "{}"'.format(val))
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matham/pyflycap2 | pyflycap2/utils.py | parse_struct | def parse_struct(type_name, body, name):
'''Returns a :attr:`StructSpec` instance from the input.
'''
type_name, name = type_name.strip(), name.strip()
lines = [l.strip() for l in body.splitlines() if l.strip()]
members = []
for line in lines:
m = match(variable_pat, line)
... | python | def parse_struct(type_name, body, name):
'''Returns a :attr:`StructSpec` instance from the input.
'''
type_name, name = type_name.strip(), name.strip()
lines = [l.strip() for l in body.splitlines() if l.strip()]
members = []
for line in lines:
m = match(variable_pat, line)
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matham/pyflycap2 | pyflycap2/utils.py | parse_enum | def parse_enum(type_name, body, name):
'''Returns a :attr:`EnumSpec` instance from the input.
'''
type_name, name = type_name.strip(), name.strip()
lines = [l.strip(' ,') for l in body.splitlines() if l.strip(', ')]
members = []
for line in lines:
vals = [v.strip() for v in line... | python | def parse_enum(type_name, body, name):
'''Returns a :attr:`EnumSpec` instance from the input.
'''
type_name, name = type_name.strip(), name.strip()
lines = [l.strip(' ,') for l in body.splitlines() if l.strip(', ')]
members = []
for line in lines:
vals = [v.strip() for v in line... | [
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