0.11.1
Site
Installation
Getting Started
Flowchart
Understanding the reports
Experimental Data
Custom Tests
Test Suite
Contributing
Credits
History
API Reference
Page
Index
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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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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
_
__author__ (in module memote)
__contains__() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
__email__ (in module memote)
__tablename__ (memote.suite.results.models.Result attribute)
__version__ (in module memote)
_init_worker() (in module memote.support.consistency)
_model_from_stream() (in module memote.suite.cli.runner)
_param (memote.suite.collect.ResultCollectionPlugin attribute)
_setup_gh_repo() (in module memote.suite.cli.runner)
_setup_travis_ci() (in module memote.suite.cli.runner)
_solve_metabolite_exchange() (in module memote.support.consistency)
_test_diff() (in module memote.suite.cli.reports)
_test_history() (in module memote.suite.cli.runner)
A
abort_if_false() (in module memote.suite.cli.callbacks)
absolute_extreme_coefficient_ratio() (in module memote.support.matrix)
add_environment_information() (memote.MemoteResult static method)
(memote.suite.results.MemoteResult static method)
(memote.suite.results.result.MemoteResult static method)
add_git() (memote.RepoResultManager static method)
(memote.suite.results.RepoResultManager static method)
(memote.suite.results.repo_result_manager.RepoResultManager static method)
addargs (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
annotate() (in module memote.utils)
apply() (memote.experimental.medium.Medium method)
author (memote.suite.results.models.Result attribute)
authored_on (memote.suite.results.models.Result attribute)
B
build_branch_structure() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
C
check_component_for_specific_sbo_term() (in module memote.support.sbo)
check_metabolites_formula_presence() (in module memote.support.basic)
check_row() (memote.experimental.checks.UnknownIdentifier method)
check_stoichiometric_consistency() (in module memote.support.consistency)
cli() (in module memote.suite.cli.runner)
close_boundaries_sensibly() (in module memote.support.helpers)
cobra_configuration (in module memote.support.consistency)
collect (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
collect_history() (memote.HistoryReport method)
(memote.suite.reporting.HistoryReport method)
(memote.suite.reporting.history.HistoryReport method)
COMPARTMENT_SHORTLIST (in module memote.support.helpers)
compound_matcher (in module memote.support.thermodynamics)
compute_score() (memote.Report method)
(memote.suite.reporting.Report method)
,
[1]
,
[2]
(memote.suite.reporting.report.Report method)
config_files (memote.suite.cli.config.ConfigFileProcessor attribute)
(memote.suite.cli.ConfigFileProcessor attribute)
config_section_schemas (memote.suite.cli.config.ConfigFileProcessor attribute)
(memote.suite.cli.ConfigFileProcessor attribute)
ConfigFileProcessor (class in memote.suite.cli)
(class in memote.suite.cli.config)
ConfigSectionSchema (class in memote.suite.cli.config)
ConfigSectionSchema.Memote (class in memote.suite.cli.config)
conftest (module)
confusion_matrix() (in module memote.support.essentiality)
CONTEXT_SETTINGS (in module memote.suite.cli)
D
degrees_of_freedom() (in module memote.support.matrix)
deployment (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
detect_energy_generating_cycles() (in module memote.support.consistency)
determine_miscellaneous_tests() (memote.Report method)
(memote.suite.reporting.Report method)
,
[1]
,
[2]
(memote.suite.reporting.report.Report method)
diff() (in module memote.suite.cli.reports)
diff_report() (in module memote)
(in module memote.suite.api)
DiffReport (class in memote)
(class in memote.suite.reporting)
(class in memote.suite.reporting.diff)
E
email (memote.suite.results.models.Result attribute)
ENERGY_COUPLES (in module memote.support.consistency)
EssentialityExperiment (class in memote.experimental.essentiality)
evaluate() (memote.experimental.essentiality.EssentialityExperiment method)
(memote.experimental.experiment.Experiment method)
(memote.experimental.growth.GrowthExperiment method)
evaluate_report() (memote.experimental.experimental_base.ExperimentalBase static method)
exclusive (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
Experiment (class in memote.experimental.experiment)
experimental (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
ExperimentalBase (class in memote.experimental.experimental_base)
ExperimentConfiguration (class in memote.experimental)
(class in memote.experimental.config)
F
filter_identifier() (in module memote.support.helpers)
filter_match_name() (in module memote.support.helpers)
filter_sbo_term() (in module memote.support.helpers)
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_blocked_metabolites() (in module memote.support.consistency)
find_bounds() (in module memote.support.helpers)
find_charge_unbalanced_reactions() (in module memote.support.consistency)
find_compartment_id_in_model() (in module memote.support.helpers)
find_components_without_annotation() (in module memote.support.annotation)
find_components_without_sbo_terms() (in module memote.support.sbo)
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_inconsistent_min_stoichiometry() (in module memote.support.consistency)
find_interchange_biomass_reactions() (in module memote.support.helpers)
find_mass_unbalanced_reactions() (in module memote.support.consistency)
find_met_in_model() (in module memote.support.helpers)
find_metabolites_not_consumed_with_open_bounds() (in module memote.support.consistency)
find_metabolites_not_produced_with_open_bounds() (in module memote.support.consistency)
find_objective_function() (in module memote.support.helpers)
find_orphans() (in module memote.support.consistency)
find_reactions_with_unbounded_flux_default_condition() (in module memote.support.consistency)
find_sink_reactions() (in module memote.support.helpers)
find_stoichiometrically_balanced_cycles() (in module memote.support.consistency)
find_thermodynamic_reversibility_index() (in module memote.support.thermodynamics)
find_top_level_complex() (in module memote.support.gpr_helpers)
find_transport_reactions() (in module memote.support.helpers)
find_transported_elements() (in module memote.support.helpers)
find_unconserved_metabolites() (in module memote.support.consistency)
format_and_score_diff_data() (memote.DiffReport method)
(memote.suite.reporting.DiffReport method)
(memote.suite.reporting.diff.DiffReport method)
format_failure() (in module memote.support.validation)
G
GENE_PRODUCT_ANNOTATIONS (in module memote.support.annotation)
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_biomass_flux() (in module memote.support.helpers)
get_config() (in module memote._version)
get_configured_tests() (memote.Report method)
(memote.suite.reporting.Report method)
,
[1]
,
[2]
(memote.suite.reporting.report.Report method)
get_filename() (memote.RepoResultManager method)
(memote.suite.results.RepoResultManager method)
(memote.suite.results.repo_result_manager.RepoResultManager method)
get_ids() (in module memote.utils)
get_ids_and_bounds() (in module memote.utils)
get_keywords() (in module memote._version)
get_minimal_growth_rate() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
get_path() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
get_result() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
get_smallest_compound_id() (in module memote.support.thermodynamics)
get_versions() (in module memote)
(in module memote._version)
git (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
git_get_keywords() (in module memote._version)
git_installed() (in module memote.suite.cli.callbacks)
git_pieces_from_vcs() (in module memote._version)
git_versions_from_keywords() (in module memote._version)
github_repository (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
github_username (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
GrowthExperiment (class in memote.experimental.growth)
H
HANDLERS (in module memote._version)
hexsha (memote.suite.results.models.Result attribute)
history() (in module memote.suite.cli.reports)
(in module memote.suite.cli.runner)
history_report() (in module memote)
(in module memote.suite.api)
HistoryManager (class in memote)
(class in memote.suite.results)
(class in memote.suite.results.history_manager)
HistoryReport (class in memote)
(class in memote.suite.reporting)
(class in memote.suite.reporting.history)
I
id (memote.suite.results.models.Result attribute)
is_modified() (in module memote.utils)
is_transport_reaction_annotations() (in module memote.support.helpers)
is_transport_reaction_formulae() (in module memote.support.helpers)
iter_branches() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
iter_commits() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
J
jsonify() (in module memote.utils)
L
largest_compartment_id_met() (in module memote.support.helpers)
load() (memote.experimental.config.ExperimentConfiguration method)
(memote.RepoResultManager method)
(memote.ReportConfiguration class method)
(memote.ResultManager method)
(memote.SQLResultManager method)
(memote.experimental.ExperimentConfiguration method)
(memote.experimental.essentiality.EssentialityExperiment method)
(memote.experimental.experimental_base.ExperimentalBase method)
(memote.experimental.growth.GrowthExperiment method)
(memote.suite.reporting.ReportConfiguration class method)
(memote.suite.reporting.config.ReportConfiguration class method)
(memote.suite.results.RepoResultManager method)
(memote.suite.results.ResultManager method)
(memote.suite.results.SQLResultManager method)
(memote.suite.results.repo_result_manager.RepoResultManager method)
(memote.suite.results.result_manager.ResultManager method)
(memote.suite.results.sql_result_manager.SQLResultManager method)
load_cobra_model() (in module memote.support.validation)
load_essentiality() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
load_growth() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
load_history() (memote.HistoryManager method)
(memote.suite.results.HistoryManager method)
(memote.suite.results.history_manager.HistoryManager method)
load_medium() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
location (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
log_json_incompatible_types() (in module memote.utils)
LOGGER (in module memote)
(in module memote.suite.cli)
(in module memote.suite.cli.callbacks)
(in module memote.suite.cli.reports)
(in module memote.suite.cli.runner)
(in module memote.suite.collect)
(in module memote.suite.reporting)
,
[1]
(in module memote.suite.reporting.history)
(in module memote.suite.reporting.report)
(in module memote.suite.reporting.snapshot)
(in module memote.support.annotation)
(in module memote.support.consistency)
(in module memote.support.essentiality)
(in module memote.support.helpers)
(in module memote.support.matrix)
(in module memote.support.sbo)
logger (in module memote.support.thermodynamics)
LOGGER (in module test_biomass)
LONG_VERSION_PY (in module memote._version)
M
map_metabolite2kegg() (in module memote.support.thermodynamics)
matrix_rank() (in module memote.support.matrix)
Medium (class in memote.experimental.medium)
memote (module)
memote._version (module)
memote.experimental (module)
memote.experimental.checks (module)
memote.experimental.config (module)
memote.experimental.essentiality (module)
memote.experimental.experiment (module)
memote.experimental.experimental_base (module)
memote.experimental.growth (module)
memote.experimental.medium (module)
memote.experimental.schemata (module)
memote.experimental.tabular (module)
memote.jinja2_extension (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.config (module)
memote.suite.reporting.diff (module)
memote.suite.reporting.history (module)
memote.suite.reporting.report (module)
memote.suite.reporting.snapshot (module)
memote.suite.results (module)
memote.suite.results.history_manager (module)
memote.suite.results.models (module)
memote.suite.results.repo_result_manager (module)
memote.suite.results.result (module)
memote.suite.results.result_manager (module)
memote.suite.results.sql_result_manager (module)
memote.suite.templates (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.data (module)
memote.support.essentiality (module)
memote.support.gpr_helpers (module)
memote.support.helpers (module)
memote.support.matrix (module)
memote.support.sbo (module)
memote.support.thermodynamics (module)
memote.support.validation (module)
memote.utils (module)
memote_result (memote.suite.results.models.Result attribute)
MemoteExtension (class in memote)
(class in memote.jinja2_extension)
MemoteResult (class in memote)
(class in memote.suite.results)
(class in memote.suite.results.result)
merge() (memote.ReportConfiguration method)
(memote.suite.reporting.ReportConfiguration method)
(memote.suite.reporting.config.ReportConfiguration method)
METABOLITE_ANNOTATIONS (in module memote.support.annotation)
metabolites_per_compartment() (in module memote.support.helpers)
METANETX_SHORTLIST (in module memote.support.helpers)
model (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
model() (memote.suite.collect.ResultCollectionPlugin method)
N
new() (in module memote.suite.cli.runner)
normalize() (memote.jinja2_extension.MemoteExtension static method)
(memote.MemoteExtension static method)
NotThisMethod
nullspace() (in module memote.support.consistency_helpers)
number_independent_conservation_relations() (in module memote.support.matrix)
O
online() (in module memote.suite.cli.runner)
open_boundaries() (in module memote.support.helpers)
open_exchanges() (in module memote.support.helpers)
P
plus_or_dot() (in module memote._version)
probe_git() (in module memote.suite.cli.callbacks)
pytest_configure() (memote.suite.collect.ResultCollectionPlugin method)
pytest_generate_tests() (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
REACTION_ANNOTATIONS (in module memote.support.annotation)
read_tabular() (in module memote.experimental.tabular)
record_git_info() (memote.RepoResultManager method)
(memote.suite.results.RepoResultManager method)
(memote.suite.results.repo_result_manager.RepoResultManager method)
register_vcs_handler() (in module memote._version)
register_with() (in module memote.utils)
render() (in module memote._version)
render_git_describe() (in module memote._version)
render_git_describe_long() (in module memote._version)
render_html() (memote.Report method)
(memote.suite.reporting.Report method)
,
[1]
,
[2]
(memote.suite.reporting.report.Report method)
render_json() (memote.Report method)
(memote.suite.reporting.Report method)
,
[1]
,
[2]
(memote.suite.reporting.report.Report method)
render_pep440() (in module memote._version)
render_pep440_old() (in module memote._version)
render_pep440_post() (in module memote._version)
render_pep440_pre() (in module memote._version)
RepoResultManager (class in memote)
(class in memote.suite.results)
(class in memote.suite.results.repo_result_manager)
Report (class in memote)
(class in memote.suite.reporting)
,
[1]
,
[2]
(class in memote.suite.reporting.report)
report() (in module memote.suite.cli.reports)
ReportConfiguration (class in memote)
(class in memote.suite.reporting)
(class in memote.suite.reporting.config)
Result (class in memote.suite.results.models)
ResultCollectionPlugin (class in memote.suite.collect)
ResultManager (class in memote)
(class in memote.suite.results)
(class in memote.suite.results.result_manager)
run() (in module memote.suite.cli.runner)
run_command() (in module memote._version)
run_fba() (in module memote.support.helpers)
run_sbml_validation() (in module memote.support.validation)
S
sbml_version() (memote.suite.collect.ResultCollectionPlugin method)
SCHEMA (memote.experimental.essentiality.EssentialityExperiment attribute)
(memote.experimental.experimental_base.ExperimentalBase attribute)
(memote.experimental.growth.GrowthExperiment attribute)
(memote.experimental.medium.Medium attribute)
show_versions() (in module memote)
(in module memote.utils)
skip (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
snapshot() (in module memote.suite.cli.reports)
snapshot_report() (in module memote)
(in module memote.suite.api)
SnapshotReport (class in memote)
(class in memote.suite.reporting)
(class in memote.suite.reporting.snapshot)
solver (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
solver_timeout (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
SQLResultManager (class in memote)
(class in memote.suite.results)
(class in memote.suite.results.sql_result_manager)
stdout_notifications() (in module memote.utils)
stoichiometry_matrix() (in module memote.support.consistency_helpers)
store() (memote.RepoResultManager method)
(memote.ResultManager method)
(memote.SQLResultManager method)
(memote.suite.results.RepoResultManager method)
(memote.suite.results.ResultManager method)
(memote.suite.results.SQLResultManager method)
(memote.suite.results.repo_result_manager.RepoResultManager method)
(memote.suite.results.result_manager.ResultManager method)
(memote.suite.results.sql_result_manager.SQLResultManager method)
sum_biomass_weight() (in module memote.support.biomass)
T
tags (memote.jinja2_extension.MemoteExtension attribute)
(memote.MemoteExtension attribute)
test_absolute_extreme_coefficient_ratio() (in module test_matrix)
test_annotation (module)
test_basic (module)
test_biomass (module)
test_biomass_consistency() (in module test_biomass)
test_biomass_default_production() (in module test_biomass)
test_biomass_open_production() (in module test_biomass)
test_biomass_precursors_default_production() (in module test_biomass)
test_biomass_precursors_open_production() (in module test_biomass)
test_biomass_presence() (in module test_biomass)
test_biomass_specific_sbo_presence() (in module test_sbo)
test_blocked_reactions() (in module test_consistency)
test_compartments_presence() (in module test_basic)
test_consistency (module)
test_degrees_of_freedom() (in module test_matrix)
test_demand_specific_sbo_presence() (in module test_sbo)
test_detect_energy_generating_cycles() (in module test_consistency)
test_direct_metabolites_in_biomass() (in module test_biomass)
TEST_DIRECTORY (in module memote.suite)
test_essential_precursors_not_in_biomass() (in module test_biomass)
test_essentiality (module)
test_exchange_specific_sbo_presence() (in module test_sbo)
test_fast_growth_default() (in module test_biomass)
test_fbc_presence() (in module test_sbml)
test_find_candidate_irreversible_reactions() (in module test_thermodynamics)
test_find_constrained_pure_metabolic_reactions() (in module test_basic)
test_find_constrained_transport_reactions() (in module test_basic)
test_find_deadends() (in module test_consistency)
test_find_disconnected() (in module test_consistency)
test_find_duplicate_metabolites_in_compartments() (in module test_basic)
test_find_duplicate_reactions() (in module test_basic)
test_find_medium_metabolites() (in module test_basic)
test_find_metabolites_not_consumed_with_open_bounds() (in module test_consistency)
test_find_metabolites_not_produced_with_open_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_reactions_with_identical_genes() (in module test_basic)
test_find_reactions_with_partially_identical_annotations() (in module test_basic)
test_find_reversible_oxygen_reactions() (in module test_basic)
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_gam_in_biomass() (in module test_biomass)
test_gene_essentiality_from_data_qualitative() (in module test_essentiality)
test_gene_product_annotation_overview() (in module test_annotation)
test_gene_product_annotation_presence() (in module test_annotation)
test_gene_product_annotation_wrong_ids() (in module test_annotation)
test_gene_protein_reaction_rule_presence() (in module test_basic)
test_gene_sbo_presence() (in module test_sbo)
test_gene_specific_sbo_presence() (in module test_sbo)
test_genes_presence() (in module test_basic)
test_growth (module)
test_growth_from_data_qualitative() (in module test_growth)
test_inconsistent_min_stoichiometry() (in module test_consistency)
test_matrix (module)
test_matrix_rank() (in module test_matrix)
test_metabolic_coverage() (in module test_basic)
test_metabolic_reaction_specific_sbo_presence() (in module test_sbo)
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_metabolite_sbo_presence() (in module test_sbo)
test_metabolite_specific_sbo_presence() (in module test_sbo)
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)
(in module memote.suite.api)
test_model_id_presence() (in module test_basic)
test_ngam_presence() (in module test_basic)
test_number_independent_conservation_relations() (in module test_matrix)
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_reaction_sbo_presence() (in module test_sbo)
test_reactions_presence() (in module test_basic)
test_sbml (module)
test_sbml_level() (in module test_sbml)
test_sbo (module)
test_sink_specific_sbo_presence() (in module test_sbo)
test_stoichiometric_consistency() (in module test_consistency)
test_thermodynamics (module)
test_transport_reaction_gpr_presence() (in module test_basic)
test_transport_reaction_specific_sbo_presence() (in module test_sbo)
test_unconserved_metabolites() (in module test_consistency)
TOLERANCE_THRESHOLD (in module memote.support.consistency)
translate_reaction() (in module memote.support.thermodynamics)
TRANSPORT_RXN_SBO_TERMS (in module memote.support.helpers)
truncate() (in module memote.utils)
TRUTHY (memote.experimental.experimental_base.ExperimentalBase attribute)
U
UnknownIdentifier (class in memote.experimental.checks)
V
validate() (memote.experimental.config.ExperimentConfiguration method)
(memote.experimental.ExperimentConfiguration method)
(memote.experimental.essentiality.EssentialityExperiment method)
(memote.experimental.experimental_base.ExperimentalBase method)
(memote.experimental.medium.Medium method)
validate_collect() (in module memote.suite.cli.callbacks)
validate_experimental() (in module memote.suite.cli.callbacks)
validate_model() (in module memote)
(in module memote.suite.api)
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)
VersioneerConfig (class in memote._version)
versions_from_parentdir() (in module memote._version)
W
wrapper (in module memote.utils)