0.5.1
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Custom Tests
Test Suite
API Reference
Contributing
Credits
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Index
A
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B
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C
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D
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E
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F
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G
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H
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M
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N
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P
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R
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S
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T
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V
A
abort_if_false() (in module memote.suite.cli.callbacks)
addargs (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
annotate() (in module memote.utils)
B
boolean_chart() (in module memote.suite.reporting.plot)
build_index() (memote.suite.reporting.bag.ResultBagWrapper method)
C
check_metabolites_formula_presence() (in module memote.support.basic)
check_stoichiometric_consistency() (in module memote.support.consistency)
close_boundaries_sensibly() (in module memote.support.helpers)
collect (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
config_files (memote.suite.cli.config.ConfigFileProcessor attribute)
config_section_schemas (memote.suite.cli.config.ConfigFileProcessor attribute)
config_sections (memote.suite.cli.config.ConfigFileProcessor attribute)
ConfigFileProcessor (class in memote.suite.cli.config)
ConfigSectionSchema (class in memote.suite.cli.config)
ConfigSectionSchema.Memote (class in memote.suite.cli.config)
D
detect_energy_generating_cycles() (in module memote.support.consistency)
df2dict() (in module memote.support.helpers)
diff_report() (in module memote.suite.api)
DiffReport (class in memote.suite.reporting.reports.diff)
directory (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
E
exclusive (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
F
find_abc_tag_transporter() (in module memote.support.syntax)
find_biomass_precursors() (in module memote.support.biomass)
find_biomass_reaction() (in module memote.support.helpers)
find_blocked_biomass_precursors() (in module memote.support.biomass)
find_charge_imbalanced_reactions() (in module memote.support.consistency)
find_components_without_annotation() (in module memote.support.annotation)
find_converting_reactions() (in module memote.support.helpers)
find_deadends() (in module memote.support.consistency)
find_demand_reactions() (in module memote.support.helpers)
find_disconnected() (in module memote.support.consistency)
find_elementary_leakage_modes() (in module memote.support.consistency)
find_exchange_rxns() (in module memote.support.helpers)
find_false_demand_rxns() (in module memote.support.syntax)
find_false_exchange_rxns() (in module memote.support.syntax)
find_false_sink_rxns() (in module memote.support.syntax)
find_functional_units() (in module memote.support.helpers)
find_inconsistent_min_stoichiometry() (in module memote.support.consistency)
find_mass_imbalanced_reactions() (in module memote.support.consistency)
find_metabolites_consumed_with_closed_bounds() (in module memote.support.consistency)
find_metabolites_produced_with_closed_bounds() (in module memote.support.consistency)
find_orphans() (in module memote.support.consistency)
find_reaction_tag_transporter() (in module memote.support.syntax)
find_reactions_with_unbounded_flux_default_condition() (in module memote.support.consistency)
find_rxn_id_compartment_suffix() (in module memote.support.syntax)
find_rxn_id_suffix_compartment() (in module memote.support.syntax)
find_sink_reactions() (in module memote.support.helpers)
find_stoichiometrically_balanced_cycles() (in module memote.support.consistency)
find_transport_reactions() (in module memote.support.helpers)
find_transported_elements() (in module memote.support.helpers)
find_unconserved_metabolites() (in module memote.support.consistency)
find_universally_blocked_reactions() (in module memote.support.consistency)
find_untagged_demand_rxns() (in module memote.support.syntax)
find_untagged_exchange_rxns() (in module memote.support.syntax)
find_untagged_sink_rxns() (in module memote.support.syntax)
find_upper_case_mets() (in module memote.support.syntax)
G
generate_component_annotation_miriam_match() (in module memote.support.annotation)
generate_component_annotation_overview() (in module memote.support.annotation)
generate_component_id_namespace_overview() (in module memote.support.annotation)
get_basic_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_biomass_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_consistency_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_ids() (in module memote.utils)
get_model_ids() (memote.suite.reporting.bag.ResultBagWrapper method)
get_syntax_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
git (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
github_repository (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
github_username (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
H
history_report() (in module memote.suite.api)
HistoryReport (class in memote.suite.reporting.reports.history)
M
memote (module)
memote.suite (module)
memote.suite.api (module)
memote.suite.cli (module)
memote.suite.cli.callbacks (module)
memote.suite.cli.config (module)
memote.suite.cli.reports (module)
memote.suite.cli.runner (module)
memote.suite.collect (module)
memote.suite.reporting (module)
memote.suite.reporting.bag (module)
memote.suite.reporting.plot (module)
memote.suite.reporting.reports (module)
memote.suite.reporting.reports.diff (module)
memote.suite.reporting.reports.history (module)
memote.suite.reporting.reports.report (module)
memote.suite.reporting.reports.snapshot (module)
memote.support (module)
memote.support.annotation (module)
memote.support.basic (module)
memote.support.biomass (module)
memote.support.consistency (module)
memote.support.consistency_helpers (module)
memote.support.helpers (module)
memote.support.syntax (module)
memote.utils (module)
memote.version_info (module)
model (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
model() (memote.suite.collect.ResultCollectionPlugin method)
N
nullspace() (in module memote.support.consistency_helpers)
P
probe_git() (in module memote.suite.cli.callbacks)
pytest_namespace() (memote.suite.collect.ResultCollectionPlugin method)
pytest_report_teststatus() (memote.suite.collect.ResultCollectionPlugin method)
pytest_runtest_call() (memote.suite.collect.ResultCollectionPlugin method)
pytest_runtest_teardown() (memote.suite.collect.ResultCollectionPlugin method)
R
read_only_model() (memote.suite.collect.ResultCollectionPlugin method)
register_with() (in module memote.utils)
render_html() (memote.suite.reporting.reports.diff.DiffReport method)
(memote.suite.reporting.reports.history.HistoryReport method)
(memote.suite.reporting.reports.report.Report method)
(memote.suite.reporting.reports.snapshot.SnapshotReport method)
Report (class in memote.suite.reporting.reports.report)
ResultBagWrapper (class in memote.suite.reporting.bag)
ResultCollectionPlugin (class in memote.suite.collect)
results (memote.suite.collect.ResultCollectionPlugin attribute)
run_fba() (in module memote.support.helpers)
S
scatter_line_chart() (in module memote.suite.reporting.plot)
section_names (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
show_versions() (in module memote.version_info)
skip (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
snapshot_report() (in module memote.suite.api)
SnapshotReport (class in memote.suite.reporting.reports.snapshot)
solver (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
stoichiometry_matrix() (in module memote.support.consistency_helpers)
sum_biomass_weight() (in module memote.support.biomass)
T
test_annotation (module)
test_basic (module)
test_blocked_reactions() (in module test_consistency)
test_compartments_presence() (in module test_basic)
test_consistency (module)
test_detect_energy_generating_cycles() (in module test_consistency)
test_find_deadends() (in module test_consistency)
test_find_disconnected() (in module test_consistency)
test_find_metabolites_consumed_with_closed_bounds() (in module test_consistency)
test_find_metabolites_produced_with_closed_bounds() (in module test_consistency)
test_find_orphans() (in module test_consistency)
test_find_pure_metabolic_reactions() (in module test_basic)
test_find_reactions_unbounded_flux_default_condition() (in module test_consistency)
test_find_stoichiometrically_balanced_cycles() (in module test_consistency)
test_find_transport_reactions() (in module test_basic)
test_find_unique_metabolites() (in module test_basic)
test_gene_protein_reaction_rule_presence() (in module test_basic)
test_genes_presence() (in module test_basic)
test_metabolic_coverage() (in module test_basic)
test_metabolite_annotation_overview() (in module test_annotation)
test_metabolite_annotation_presence() (in module test_annotation)
test_metabolite_annotation_wrong_ids() (in module test_annotation)
test_metabolite_id_namespace_consistency() (in module test_annotation)
test_metabolites_charge_presence() (in module test_basic)
test_metabolites_formula_presence() (in module test_basic)
test_metabolites_presence() (in module test_basic)
test_model() (in module memote.suite.api)
test_model_id_presence() (in module test_basic)
test_ngam_presence() (in module test_basic)
test_protein_complex_presence() (in module test_basic)
test_reaction_annotation_overview() (in module test_annotation)
test_reaction_annotation_presence() (in module test_annotation)
test_reaction_annotation_wrong_ids() (in module test_annotation)
test_reaction_charge_balance() (in module test_consistency)
test_reaction_id_namespace_consistency() (in module test_annotation)
test_reaction_mass_balance() (in module test_consistency)
test_reactions_presence() (in module test_basic)
test_stoichiometric_consistency() (in module test_consistency)
test_transport_reaction_gpr_presence() (in module test_basic)
test_transport_reaction_presence() (in module test_basic)
truncate() (in module memote.utils)
V
validate_collect() (in module memote.suite.cli.callbacks)
validate_model() (in module memote.suite.cli.callbacks)
validate_pytest_args() (in module memote.suite.cli.callbacks)
validate_repository() (in module memote.suite.cli.callbacks)
validate_username() (in module memote.suite.cli.callbacks)