PyPI project
abi-agent
24 indexed releases ยท newest sdist 1.5.7.1 with 421 indexed members
Files in 1.5.7.1 abi_agent-1.5.7.1.tar.gz
- docs/_base.py
- docs/diagrams/generate_abi_architecture_drawio.py
- docs/en/conf.py
- docs/zh/conf.py
- plugins/metagenomic_plasmid/scripts/dna_features_viz.py
- plugins/metagenomic_plasmid/scripts/plasmidfinder.py
- plugins/metagenomic_plasmid/scripts/pycirclize_viz.py
- plugins/metagenomic_plasmid/scripts/pyvis_viz.py
- plugins/rnaseq_expression/scripts/build_count_matrix.py
- scripts/amplicon_diversity.py
- scripts/analyze_scapp_plasmid_evidence.py
- scripts/audit_contract_coverage.py
- scripts/build_scapp_machine_evidence.py
- scripts/check_module_coverage.py
- scripts/check_release_identity.py
- scripts/create_real_data_case_study_figures.py
- scripts/create_scapp_paper_figure_specs.py
- scripts/emit_env_yamls.py
- scripts/generate_synthetic_taxonomy.py
- scripts/integrate_plasmid_supplement.py
- scripts/migration_gate.py
- scripts/reconstruct_scapp_truth.py
- scripts/repair_plasmid_standard_tables.py
- scripts/score_scapp_predictions.py
- scripts/setup_rnaseq_benchmark.py
- src/abi/__init__.py
- src/abi/_shared.py
- src/abi/agent/__init__.py
- src/abi/agent/context.py
- src/abi/agent/envelopes.py
- src/abi/agent/interface.py
- src/abi/agent_integrations.py
- src/abi/autoplasm/__init__.py
- src/abi/autoplasm/cli.py
- src/abi/autoplasm/config.py
- src/abi/autoplasm/dashboard.py
- src/abi/autoplasm/filesystem.py
- src/abi/autoplasm/json_utils.py
- src/abi/autoplasm/logger.py
- src/abi/autoplasm/normalize/__init__.py
- src/abi/autoplasm/normalize/abundance.py
- src/abi/autoplasm/normalize/annotation.py
- src/abi/autoplasm/normalize/plasmid_prediction.py
- src/abi/autoplasm/parsers.py
- src/abi/autoplasm/pipeline.py
- src/abi/autoplasm/planner.py
- src/abi/autoplasm/progress.py
- src/abi/autoplasm/report/__init__.py
- src/abi/autoplasm/report/html.py
- src/abi/autoplasm/report/markdown.py
- src/abi/autoplasm/resources.py
- src/abi/autoplasm/result_validation.py
- src/abi/autoplasm/sample_sheet.py
- src/abi/autoplasm/schemas.py
- src/abi/autoplasm/selectors.py
- src/abi/autoplasm/skills/__init__.py
- src/abi/autoplasm/skills/abundance.py
- src/abi/autoplasm/skills/annotation.py
- src/abi/autoplasm/skills/assembly.py
- src/abi/autoplasm/skills/base.py
- src/abi/autoplasm/skills/host_prediction.py
- src/abi/autoplasm/skills/plasmid_binning.py
- src/abi/autoplasm/skills/plasmid_detection.py
- src/abi/autoplasm/skills/qc.py
- src/abi/autoplasm/skills/registry.py
- src/abi/autoplasm/skills/statistics.py
- src/abi/autoplasm/skills/typing.py
- src/abi/autoplasm/skills/visualization.py
- src/abi/autoplasm/standard_tables.py
- src/abi/autoplasm/statistics.py
- src/abi/autoplasm/timeouts.py
- src/abi/cli.py
- src/abi/config.py
- src/abi/config_models.py
- src/abi/contracts/__init__.py
- src/abi/contracts/lint.py
- src/abi/contracts/lint_template.py
- src/abi/contracts/step_contract.py
- src/abi/dag.py
- src/abi/dag_planner.py
- src/abi/diagnostics.py
- src/abi/doctor.py
- src/abi/errors.py
- src/abi/execution_policy.py
- src/abi/executor.py
- src/abi/exporters/__init__.py
- src/abi/exporters/nextflow.py
- src/abi/exporters/snakemake.py
- src/abi/figures/__init__.py
- src/abi/figures/base.py
- src/abi/filesystem.py
- src/abi/interfaces.py
- src/abi/internal.py
- src/abi/jobs/__init__.py
- src/abi/jobs/client.py
- src/abi/jobs/service.py
- src/abi/json_utils.py
- src/abi/mcp/__init__.py
- src/abi/mcp/_tool_factory.py
- src/abi/mcp/server.py
- src/abi/openai_contracts.py
- src/abi/path_policy.py
- src/abi/permissions.py
- src/abi/plugin.py
- src/abi/plugins/__init__.py
- src/abi/plugins/amplicon_16s.py
- src/abi/plugins/easymetagenome/__init__.py
- src/abi/plugins/easymetagenome/adapters.py
- src/abi/plugins/easymetagenome/handlers.py
- src/abi/plugins/easymetagenome/report_manifest.py
- src/abi/plugins/easymetagenome/workflow.py
- src/abi/plugins/metagenomic_plasmid/__init__.py
- src/abi/plugins/metagenomic_plasmid/_engine/__init__.py
- src/abi/plugins/metagenomic_plasmid/_engine/cli.py
- src/abi/plugins/metagenomic_plasmid/_engine/config.py
- src/abi/plugins/metagenomic_plasmid/_engine/context_resolver.py
- src/abi/plugins/metagenomic_plasmid/_engine/dashboard.py
- src/abi/plugins/metagenomic_plasmid/_engine/filesystem.py
- src/abi/plugins/metagenomic_plasmid/_engine/json_utils.py
- src/abi/plugins/metagenomic_plasmid/_engine/logger.py
- src/abi/plugins/metagenomic_plasmid/_engine/normalize/__init__.py
- src/abi/plugins/metagenomic_plasmid/_engine/normalize/abundance.py
- src/abi/plugins/metagenomic_plasmid/_engine/normalize/annotation.py
- src/abi/plugins/metagenomic_plasmid/_engine/normalize/plasmid_prediction.py
- src/abi/plugins/metagenomic_plasmid/_engine/parsers.py
- src/abi/plugins/metagenomic_plasmid/_engine/pipeline.py
- src/abi/plugins/metagenomic_plasmid/_engine/pipeline_dag.py
- src/abi/plugins/metagenomic_plasmid/_engine/progress.py
- src/abi/plugins/metagenomic_plasmid/_engine/report/__init__.py
- src/abi/plugins/metagenomic_plasmid/_engine/report/html.py
- src/abi/plugins/metagenomic_plasmid/_engine/report/markdown.py
- src/abi/plugins/metagenomic_plasmid/_engine/resources.py
- src/abi/plugins/metagenomic_plasmid/_engine/result_validation.py
- src/abi/plugins/metagenomic_plasmid/_engine/sample_sheet.py
- src/abi/plugins/metagenomic_plasmid/_engine/schemas.py
- src/abi/plugins/metagenomic_plasmid/_engine/selectors.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/__init__.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/abundance.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/annotation.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/assembly.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/base.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/host_prediction.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/plasmid_binning.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/plasmid_detection.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/qc.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/registry.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/statistics.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/typing.py
- src/abi/plugins/metagenomic_plasmid/_engine/skills/visualization.py
- src/abi/plugins/metagenomic_plasmid/_engine/standard_tables.py
- src/abi/plugins/metagenomic_plasmid/_engine/statistics.py
- src/abi/plugins/metagenomic_plasmid/_engine/timeouts.py
- src/abi/plugins/metagenomic_plasmid/_engine/tool_defaults.py
- src/abi/plugins/metagenomic_plasmid/handlers.py
- src/abi/plugins/metatranscriptomics.py
- src/abi/plugins/rnaseq_expression.py
- src/abi/plugins/validator.py
- src/abi/plugins/viral_viwrap/__init__.py
- src/abi/plugins/viral_viwrap/artifact_mapper.py
- src/abi/plugins/viral_viwrap/checker.py
- src/abi/plugins/viral_viwrap/command_builder.py
- src/abi/plugins/viral_viwrap/errors.py
- src/abi/plugins/viral_viwrap/handlers.py
- src/abi/plugins/viral_viwrap/parser.py
- src/abi/plugins/viral_viwrap/plan_outputs.py
- src/abi/plugins/viral_viwrap/runner.py
- src/abi/plugins/wgs_bacteria.py
- src/abi/provenance.py
- src/abi/report/__init__.py
- src/abi/report/citations.py
- src/abi/report/generic_report.py
- src/abi/report/html.py
- src/abi/report/limitations.py
- src/abi/report/methods.py
- src/abi/resource_downloader.py
- src/abi/resources.py
- src/abi/results.py
- src/abi/runtime_environment.py
- src/abi/runtime_lock.py
- src/abi/runtimes/__init__.py
- src/abi/runtimes/base.py
- src/abi/runtimes/hpc.py
- src/abi/runtimes/local.py
- src/abi/runtimes/nextflow.py
- src/abi/runtimes/snakemake.py
- src/abi/schemas.py
- src/abi/sciplot/__init__.py
- src/abi/sciplot/adapters.py
- src/abi/sciplot/api.py
- src/abi/sciplot/cli.py
- src/abi/sciplot/lint/__init__.py
- src/abi/sciplot/provenance/__init__.py
- src/abi/sciplot/renderers/__init__.py
- src/abi/sciplot/renderers/annotation_layout.py
- src/abi/sciplot/renderers/matplotlib_renderer.py
- src/abi/sciplot/renderers/plots/__init__.py
- src/abi/sciplot/renderers/plots/alpha_stats_boxplot.py
- src/abi/sciplot/renderers/plots/barplot.py
- src/abi/sciplot/renderers/plots/boxplot_with_points.py
- src/abi/sciplot/renderers/plots/differential_volcano.py
- src/abi/sciplot/renderers/plots/genus_heatmap.py
- src/abi/sciplot/renderers/plots/heatmap.py
- src/abi/sciplot/renderers/plots/lineplot.py
- src/abi/sciplot/renderers/plots/ordination_plot.py
- src/abi/sciplot/renderers/plots/pcoa_plot.py
- src/abi/sciplot/renderers/plots/phylogenetic_heatmap.py
- src/abi/sciplot/renderers/plots/phylum_stacked_bar.py
- src/abi/sciplot/renderers/plots/scatterplot.py
- src/abi/sciplot/renderers/plots/stacked_barplot.py
- src/abi/sciplot/renderers/plots/violin_with_box.py
- src/abi/sciplot/renderers/plots/volcano_plot.py
- src/abi/sciplot/schema/__init__.py
- src/abi/sciplot/schema/figure_spec.py
- src/abi/sciplot/schema/palette_spec.py
- src/abi/sciplot/schema/theme_spec.py
- src/abi/sciplot/tests/__init__.py
- src/abi/sciplot/tests/conftest.py
- src/abi/sciplot/tests/real_world_data.py
- src/abi/sciplot/tests/test_annotation_layout.py
- src/abi/sciplot/tests/test_barplot.py
- src/abi/sciplot/tests/test_biological_renderers.py
- src/abi/sciplot/tests/test_heatmap.py
- src/abi/sciplot/tests/test_lineplot.py
- src/abi/sciplot/tests/test_lint.py
- src/abi/sciplot/tests/test_matplotlib_renderer_unit.py
- src/abi/sciplot/tests/test_pcoa.py
- src/abi/sciplot/tests/test_render.py
- src/abi/sciplot/tests/test_renderer_contract.py
- src/abi/sciplot/tests/test_renderer_error_paths.py
- src/abi/sciplot/tests/test_schema.py
- src/abi/sciplot/tests/test_smoke_all_renderers.py
- src/abi/sciplot/tests/test_stacked_bar.py
- src/abi/sciplot/tests/test_unicode_rendering.py
- src/abi/sciplot/tests/test_volcano.py
- src/abi/sciplot/validators/__init__.py
- src/abi/skill_installer.py
- src/abi/step_runner.py
- src/abi/tables.py
- src/abi/testing.py
- src/abi/testing/__init__.py
- src/abi/testing/benchmark.py
- src/abi/timeouts.py
- src/abi/tool_catalog.py
- src/abi/tool_descriptors.py
- src/abi/tools.py
- src/abi/tsv_mapping.py
- src/abi/workflow/__init__.py
- src/abi/workflow/catalog.py
- src/abi/workflow/compiled_plan.py
- src/abi/workflow/execution.py
- src/abi/workflow/figure_specs.py
- src/abi/workflow/manifest.py
- src/abi/workflow/validation.py
- tests/__init__.py
- tests/conftest.py
- tests/integration/test_abi_cli.py
- tests/integration/test_cli_gaps.py
- tests/integration/test_compiled_plan_plugins.py
- tests/integration/test_docker_execution.py
- tests/integration/test_dry_run.py
- tests/integration/test_easymetagenome_handlers.py
- tests/integration/test_golden_traces.py
- tests/integration/test_tool_catalog_integration.py
- tests/integration/test_viwrap_compatibility_runner.py
- tests/integration/test_workflow_coordinator.py
- tests/performance/test_core_performance.py
- tests/smoke/__init__.py
- tests/smoke/test_amplicon_benchmark.py
- tests/smoke/test_amplicon_smoke.py
- tests/smoke/test_dry_run_smoke.py
- tests/smoke/test_metatranscriptomics_benchmark.py
- tests/smoke/test_plasmid_benchmark.py
- tests/smoke/test_real_plugin_runs.py
- tests/smoke/test_rnaseq_benchmark.py
- tests/smoke/test_tool_smoke.py
- tests/smoke/test_wgs_benchmark.py
- tests/test_amplicon_16s_plugin.py
- tests/test_cli.py
- tests/test_config.py
- tests/test_dag.py
- tests/test_dag_planner.py
- tests/test_documentation_artifacts.py
- tests/test_metatranscriptomics_plugin.py
- tests/test_report.py
- tests/test_rnaseq_expression_plugin.py
- tests/test_schemas.py
- tests/test_sdk_boundaries.py
- tests/test_tables.py
- tests/test_tsv_mapping.py
- tests/test_wgs_bacteria_plugin.py
- tests/unit/test_abi_dag.py
- tests/unit/test_abi_plugins.py
- tests/unit/test_agent_integration_assets.py
- tests/unit/test_agent_integrations.py
- tests/unit/test_agent_interface.py
- tests/unit/test_agent_query_helpers.py
- tests/unit/test_amplicon_diversity.py
- tests/unit/test_analyze_scapp_plasmid_evidence.py
- tests/unit/test_architecture_diagram.py
- tests/unit/test_autoplasm_shims.py
- tests/unit/test_benchmark.py
- tests/unit/test_build_scapp_machine_evidence.py
- tests/unit/test_cli_helpers.py
- tests/unit/test_cloud_release_lock.py
- tests/unit/test_compiled_plan.py
- tests/unit/test_compiled_plan_runtime.py
- tests/unit/test_config.py
- tests/unit/test_config_models.py
- tests/unit/test_container_runtime.py
- tests/unit/test_context_resolver.py
- tests/unit/test_contract_exempt.py
- tests/unit/test_contract_lint.py
- tests/unit/test_contracts.py
- tests/unit/test_contracts_validators.py
- tests/unit/test_create_real_data_case_study_figures.py
- tests/unit/test_create_scapp_paper_figure_specs.py
- tests/unit/test_dag_planner_helpers.py
- tests/unit/test_dag_planner_paths.py
- tests/unit/test_declarative_plugin.py
- tests/unit/test_diagnostics.py
- tests/unit/test_docker_configuration.py
- tests/unit/test_doctor.py
- tests/unit/test_documentation_artifacts.py
- tests/unit/test_download_scripts.py
- tests/unit/test_easymetagenome_plugin.py
- tests/unit/test_engine_json_utils.py
- tests/unit/test_engine_logger.py
- tests/unit/test_engine_selectors.py
- tests/unit/test_errors.py
- tests/unit/test_execution_policy.py
- tests/unit/test_executor.py
- tests/unit/test_executor_boundaries.py
- tests/unit/test_figures.py
- tests/unit/test_figures_engine.py
- tests/unit/test_figures_helpers.py
- tests/unit/test_filesystem.py
- tests/unit/test_hpc_boundaries.py
- tests/unit/test_hpc_runtime.py
- tests/unit/test_integrate_plasmid_supplement.py
- tests/unit/test_interfaces.py
- tests/unit/test_internal_helpers.py
- tests/unit/test_internal_runtime.py
- tests/unit/test_job_service.py
- tests/unit/test_json_utils.py
- tests/unit/test_limitations_enforcement.py
- tests/unit/test_lint_template.py
- tests/unit/test_local_runtime.py
- tests/unit/test_logger.py
- tests/unit/test_mcp_ext.py
- tests/unit/test_mcp_server.py
- tests/unit/test_mcp_tool_factory.py
- tests/unit/test_metagenomic_plasmid_policy.py
- tests/unit/test_module_coverage_gate.py
- tests/unit/test_nextflow_exporter.py
- tests/unit/test_nextflow_ext.py
- tests/unit/test_nextflow_runtime.py
- tests/unit/test_normalize.py
- tests/unit/test_parsers.py
- tests/unit/test_path_policy.py
- tests/unit/test_permissions.py
- tests/unit/test_pipeline_dag.py
- tests/unit/test_planner.py
- tests/unit/test_plugin_artifact_alignment.py
- tests/unit/test_progress_dashboard.py
- tests/unit/test_provenance.py
- tests/unit/test_provenance_ext.py
- tests/unit/test_public_errors.py
- tests/unit/test_public_exports.py
- tests/unit/test_reconstruct_scapp_truth.py
- tests/unit/test_recovery_actions.py
- tests/unit/test_registry.py
- tests/unit/test_repair_plasmid_standard_tables.py
- tests/unit/test_report_citations.py
- tests/unit/test_report_generic.py
- tests/unit/test_report_html.py
- tests/unit/test_report_limitations.py
- tests/unit/test_report_methods.py
- tests/unit/test_resource_boundaries.py
- tests/unit/test_resource_downloader.py
- tests/unit/test_resource_helpers.py
- tests/unit/test_resource_paths.py
- tests/unit/test_resources.py
- tests/unit/test_result_validation.py
- tests/unit/test_results.py
- tests/unit/test_results_ext.py
- tests/unit/test_rnaseq_deseq2_command.py
- tests/unit/test_rnaseq_featurecounts.py
- tests/unit/test_rnaseq_parsers.py
- tests/unit/test_runtime_lock.py
- tests/unit/test_sample_sheet.py
- tests/unit/test_sciplot_adapters.py
- tests/unit/test_sciplot_adapters_more.py
- tests/unit/test_sciplot_api.py
- tests/unit/test_sciplot_cli_ext.py
- tests/unit/test_sciplot_lineplot.py
- tests/unit/test_sciplot_lint.py
- tests/unit/test_sciplot_palette.py
- tests/unit/test_sciplot_theme.py
- tests/unit/test_sciplot_validators.py
- tests/unit/test_score_scapp_predictions.py
and 21 more members in this release
Indexed releases
- 1.5.7.1
abi_agent-1.5.7.1.tar.gz421 members - 1.5.7.1
abi_agent-1.5.7.1-py3-none-any.whl214 members - 1.5.6
abi_agent-1.5.6.tar.gz390 members - 1.5.6
abi_agent-1.5.6-py3-none-any.whl211 members - 1.5.5
abi_agent-1.5.5.tar.gz371 members - 1.5.5
abi_agent-1.5.5-py3-none-any.whl219 members - 1.5.3
abi_agent-1.5.3.tar.gz353 members - 1.5.3
abi_agent-1.5.3-py3-none-any.whl209 members - 1.5.1
abi_agent-1.5.1.tar.gz286 members - 1.5.1
abi_agent-1.5.1-py3-none-any.whl192 members - 1.5.0
abi_agent-1.5.0.tar.gz277 members - 1.5.0
abi_agent-1.5.0-py3-none-any.whl192 members - 1.3.3
abi_agent-1.3.3.tar.gz237 members - 1.3.3
abi_agent-1.3.3-py3-none-any.whl169 members - 1.3.2
abi_agent-1.3.2.tar.gz207 members - 1.3.2
abi_agent-1.3.2-py3-none-any.whl141 members - 1.2.0
abi_agent-1.2.0.tar.gz197 members - 1.2.0
abi_agent-1.2.0-py3-none-any.whl139 members - 1.1.0
abi_agent-1.1.0.tar.gz161 members - 1.1.0
abi_agent-1.1.0-py3-none-any.whl123 members - 1.0.0
abi_agent-1.0.0.tar.gz150 members - 1.0.0
abi_agent-1.0.0-py3-none-any.whl118 members - 0.2.0
abi_agent-0.2.0.tar.gz119 members - 0.2.0
abi_agent-0.2.0-py3-none-any.whl87 members