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ANDREA 0.1.0__tar.gz

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andrea-0.1.0/ANDREA.egg-info/PKG-INFO ADDED Viewed

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+Metadata-Version: 2.4
+Name: ANDREA
+Version: 0.1.0
+Summary: Platform for aggregated network discovery, simulation, inference, and benchmarking workflows.
+Author-email: Adrian Segura Ortiz <adrianseor.99@uma.es>, "George K. Georgakilas" <ggeorgakilas@athenarc.gr>, Theodore Dalamagas <dalamag@athenarc.gr>, "Jose F. Aldana-Montes" <jfaldana@uma.es>
+Maintainer-email: Adrian Segura Ortiz <adrianseor.99@uma.es>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/AdrianSeguraOrtiz/ANDREA
+Project-URL: Repository, https://github.com/AdrianSeguraOrtiz/ANDREA
+Project-URL: Issues, https://github.com/AdrianSeguraOrtiz/ANDREA/issues
+Project-URL: Documentation, https://github.com/AdrianSeguraOrtiz/ANDREA/tree/main/docs
+Keywords: gene regulatory networks,GRN inference,benchmarking,single-cell,systems biology,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Environment :: Web Environment
+Classifier: Framework :: FastAPI
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.5,>=2.0.2; python_version < "3.12"
+Requires-Dist: typer<0.24.0,>=0.23.1
+Requires-Dist: rich<16.0.0,>=15.0.0
+Requires-Dist: docker<8.0.0,>=7.1.0
+Requires-Dist: jsonschema<5.0.0,>=4.25.0
+Requires-Dist: pandas<3.0.0,>=2.3.0
+Requires-Dist: ortools<10.0,>=9.10
+Requires-Dist: fastapi<0.116.0,>=0.115.0
+Requires-Dist: uvicorn<0.35.0,>=0.34.0
+Requires-Dist: python-multipart<0.0.21,>=0.0.20
+Requires-Dist: aiofiles<25.0.0,>=24.1.0
+Provides-Extra: dev
+Requires-Dist: pytest<9.0.0,>=8.4.0; extra == "dev"
+Requires-Dist: httpx<0.29.0,>=0.28.0; extra == "dev"
+Requires-Dist: black<25.0.0,>=24.0.0; extra == "dev"
+Requires-Dist: isort<6.0.0,>=5.13.0; extra == "dev"
+Provides-Extra: release
+Requires-Dist: build<2.0.0,>=1.2.0; extra == "release"
+Requires-Dist: twine<7.0.0,>=6.0.0; extra == "release"
+Dynamic: license-file
+# ANDREA
+**Automated Network Discovery, Reproducible Evaluation and Analysis**
+ANDREA is a catalog-driven platform for generating benchmark expression
+datasets, running gene regulatory network (GRN) inference tools, evaluating
+inferred networks against reference truth and comparing networks across tools,
+contexts and runs. It exposes the same workflows through a command-line
+interface and local browser GUIs, while keeping public artifacts as plain JSON,
+CSV, SQLite and ZIP files.
+<p align="center">
+  <img src="docs/assets/andrea_overview.png" alt="ANDREA workflow overview" width="92%">
+</p>
+## What ANDREA Provides
+- A standardized catalog of simulator and inference-tool integrations, with
+  compatibility rules, parameter schemas, Docker wrappers and provenance
+  metadata.
+- Four interoperable workflows:
+  `generate-data -> infer-network -> evaluate-inference -> compare-networks`.
+- Strict handoff bundles so outputs from one command can be consumed directly
+  by the next one.
+- Context-aware handling of global, group-level and column-level network
+  outputs, including emulated and aggregated execution strategies where
+  appropriate.
+- Cost-aware planning and execution orchestration for Dockerized simulator and
+  inference wrappers.
+- Evaluation reports and interactive comparison views for distance maps,
+  metric overlays and edge-level differences.
+- Support for temporary external Docker inference tools that follow ANDREA's
+  standard container contract.
+## Installation
+Install the release package:
+```sh
+pip install ANDREA
+```
+For a development checkout:
+```sh
+git clone https://github.com/AdrianSeguraOrtiz/ANDREA.git
+cd ANDREA
+python -m pip install -e ".[dev]"
+```
+Docker is required for workflows that execute simulator or inference wrappers.
+See [docs/installation.md](docs/installation.md) for the full setup notes.
+## Quick Start
+Inspect the CLI:
+```sh
+andrea --help
+andrea generate-data --help
+andrea infer-network --help
+andrea evaluate-inference --help
+andrea compare-networks --help
+```
+Open the local GUIs:
+```sh
+andrea gui generate-data
+andrea gui infer-network
+andrea gui evaluate-inference
+andrea gui compare-networks
+```
+The GUIs are local browser applications. ZIP bundles are mainly intended for
+GUI handoff; CLI and Python users can usually pass report JSON paths directly.
+## Workflows
+| Command | Purpose | Key outputs |
+|---|---|---|
+| `generate-data` | Build synthetic benchmark datasets from simulator catalogs. | `expression.tsv`, `truth/networks.csv`, manifests and analysis bundles. |
+| `infer-network` | Run catalog or external Docker inference tools against standardized datasets. | Per-run networks, merged normalized networks, graph exports and run reports. |
+| `evaluate-inference` | Score inferred networks against simulator or user-provided truth. | Metric tables, pairing tables, `evaluation_report.json` and visual summaries. |
+| `compare-networks` | Compare networks across tools, sources, parameters and contexts. | Distance tables, coordinates, `comparison.sqlite`, edge differences and reports. |
+See [docs/workflows.md](docs/workflows.md) for the workflow contracts and
+[docs/gui.md](docs/gui.md), [docs/cli.md](docs/cli.md) and
+[docs/core.md](docs/core.md) for GUI, command-line and Python usage.
+## Documentation
+- [Installation](docs/installation.md)
+- [Workflow contracts](docs/workflows.md)
+- [GUI guide](docs/gui.md)
+- [CLI guide](docs/cli.md)
+- [Core Python guide](docs/core.md)
+- [Catalogs and coverage](docs/catalogs.md)
+- [External Docker tools](docs/external-docker-tools.md)
+- [Full documentation index](docs/README.md)

andrea-0.1.0/ANDREA.egg-info/SOURCES.txt ADDED Viewed

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+LICENSE
+README.md
+pyproject.toml
+ANDREA.egg-info/PKG-INFO
+ANDREA.egg-info/SOURCES.txt
+ANDREA.egg-info/dependency_links.txt
+ANDREA.egg-info/entry_points.txt
+ANDREA.egg-info/requires.txt
+ANDREA.egg-info/top_level.txt
+andrea/__init__.py
+andrea/__main__.py
+andrea/config.py
+andrea/catalog_inference_tools/__init__.py
+andrea/catalog_inference_tools/input_specs/cell_cell_interactions.json
+andrea/catalog_inference_tools/input_specs/chromatin_accessibility.json
+andrea/catalog_inference_tools/input_specs/chromatin_regions.json
+andrea/catalog_inference_tools/input_specs/cluster_identities.json
+andrea/catalog_inference_tools/input_specs/cluster_markers.json
+andrea/catalog_inference_tools/input_specs/column_descriptors.json
+andrea/catalog_inference_tools/input_specs/column_phenotypes.json
+andrea/catalog_inference_tools/input_specs/enrichment_background.json
+andrea/catalog_inference_tools/input_specs/expression_matrix.json
+andrea/catalog_inference_tools/input_specs/grnboost_network.json
+andrea/catalog_inference_tools/input_specs/groups.json
+andrea/catalog_inference_tools/input_specs/interventions.json
+andrea/catalog_inference_tools/input_specs/lineage_tree.json
+andrea/catalog_inference_tools/input_specs/perturbation_design.json
+andrea/catalog_inference_tools/input_specs/prior_grn.json
+andrea/catalog_inference_tools/input_specs/prior_grn_by_group.json
+andrea/catalog_inference_tools/input_specs/pseudotime.json
+andrea/catalog_inference_tools/input_specs/replicates.json
+andrea/catalog_inference_tools/input_specs/spatial_coordinates.json
+andrea/catalog_inference_tools/input_specs/terms_of_interest.json
+andrea/catalog_inference_tools/input_specs/tf_list.json
+andrea/catalog_inference_tools/input_specs/timepoints.json
+andrea/catalog_inference_tools/schemas/dataset-manifest.schema.json
+andrea/catalog_inference_tools/schemas/input-spec.schema.json
+andrea/catalog_inference_tools/schemas/toolcost.schema.json
+andrea/catalog_inference_tools/schemas/toolspec.schema.json
+andrea/catalog_inference_tools/tools/aracne3/cost.json
+andrea/catalog_inference_tools/tools/aracne3/toolspec.json
+andrea/catalog_inference_tools/tools/cespgrn/cost.json
+andrea/catalog_inference_tools/tools/cespgrn/toolspec.json
+andrea/catalog_inference_tools/tools/clr/cost.json
+andrea/catalog_inference_tools/tools/clr/toolspec.json
+andrea/catalog_inference_tools/tools/dignet/cost.json
+andrea/catalog_inference_tools/tools/dignet/toolspec.json
+andrea/catalog_inference_tools/tools/genie3/cost.json
+andrea/catalog_inference_tools/tools/genie3/toolspec.json
+andrea/catalog_inference_tools/tools/grnboost2/cost.json
+andrea/catalog_inference_tools/tools/grnboost2/toolspec.json
+andrea/catalog_inference_tools/tools/infercsn/cost.json
+andrea/catalog_inference_tools/tools/infercsn/toolspec.json
+andrea/catalog_inference_tools/tools/inferelator3/cost.json
+andrea/catalog_inference_tools/tools/inferelator3/toolspec.json
+andrea/catalog_inference_tools/tools/kscreni/cost.json
+andrea/catalog_inference_tools/tools/kscreni/toolspec.json
+andrea/catalog_inference_tools/tools/lioness/cost.json
+andrea/catalog_inference_tools/tools/lioness/toolspec.json
+andrea/catalog_inference_tools/tools/metasem/cost.json
+andrea/catalog_inference_tools/tools/metasem/toolspec.json
+andrea/catalog_inference_tools/tools/miniex3/cost.json
+andrea/catalog_inference_tools/tools/miniex3/toolspec.json
+andrea/catalog_inference_tools/tools/pidc/cost.json
+andrea/catalog_inference_tools/tools/pidc/toolspec.json
+andrea/catalog_inference_tools/tools/planet/cost.json
+andrea/catalog_inference_tools/tools/planet/toolspec.json
+andrea/catalog_inference_tools/tools/ppcor/cost.json
+andrea/catalog_inference_tools/tools/ppcor/toolspec.json
+andrea/catalog_inference_tools/tools/pyscenic/cost.json
+andrea/catalog_inference_tools/tools/pyscenic/toolspec.json
+andrea/catalog_inference_tools/tools/scgenerai/cost.json
+andrea/catalog_inference_tools/tools/scgenerai/toolspec.json
+andrea/catalog_inference_tools/tools/scing/cost.json
+andrea/catalog_inference_tools/tools/scing/toolspec.json
+andrea/catalog_inference_tools/tools/scminer/cost.json
+andrea/catalog_inference_tools/tools/scminer/toolspec.json
+andrea/catalog_inference_tools/tools/scmtni/cost.json
+andrea/catalog_inference_tools/tools/scmtni/toolspec.json
+andrea/catalog_inference_tools/tools/scregulate/cost.json
+andrea/catalog_inference_tools/tools/scregulate/toolspec.json
+andrea/catalog_inference_tools/tools/scsgl/cost.json
+andrea/catalog_inference_tools/tools/scsgl/toolspec.json
+andrea/catalog_inference_tools/tools/simic/cost.json
+andrea/catalog_inference_tools/tools/simic/toolspec.json
+andrea/catalog_inference_tools/tools/tigress/cost.json
+andrea/catalog_inference_tools/tools/tigress/toolspec.json
+andrea/catalog_simulation_data_tools/__init__.py
+andrea/catalog_simulation_data_tools/input_specs/boolode_boolean_model.json
+andrea/catalog_simulation_data_tools/input_specs/boolode_initial_conditions.json
+andrea/catalog_simulation_data_tools/input_specs/boolode_interaction_strengths.json
+andrea/catalog_simulation_data_tools/input_specs/gnw_dynamical_network.json
+andrea/catalog_simulation_data_tools/input_specs/groundgan_causal_controller_checkpoint.json
+andrea/catalog_simulation_data_tools/input_specs/groundgan_causal_graph_pickle.json
+andrea/catalog_simulation_data_tools/input_specs/groundgan_model_checkpoint.json
+andrea/catalog_simulation_data_tools/input_specs/groundgan_reference_h5ad.json
+andrea/catalog_simulation_data_tools/input_specs/regulatory_network.json
+andrea/catalog_simulation_data_tools/input_specs/sergio_bifurcation_matrix.json
+andrea/catalog_simulation_data_tools/input_specs/sergio_master_regulators.json
+andrea/catalog_simulation_data_tools/input_specs/sergio_target_interactions.json
+andrea/catalog_simulation_data_tools/input_specs/syntren_externals_table.json
+andrea/catalog_simulation_data_tools/input_specs/syntren_source_network_sif.json
+andrea/catalog_simulation_data_tools/input_specs/tree_newick.json
+andrea/catalog_simulation_data_tools/schemas/benchmark-manifest.schema.json
+andrea/catalog_simulation_data_tools/schemas/ground-truth-manifest.schema.json
+andrea/catalog_simulation_data_tools/schemas/input-spec.schema.json
+andrea/catalog_simulation_data_tools/schemas/preflight-report.schema.json
+andrea/catalog_simulation_data_tools/schemas/scenario-request.schema.json
+andrea/catalog_simulation_data_tools/schemas/simulation-plan.schema.json
+andrea/catalog_simulation_data_tools/schemas/simulator-output-manifest.schema.json
+andrea/catalog_simulation_data_tools/schemas/simulator-runs.schema.json
+andrea/catalog_simulation_data_tools/schemas/simulatorcost.schema.json
+andrea/catalog_simulation_data_tools/schemas/simulatorspec.schema.json
+andrea/catalog_simulation_data_tools/simulators/boolode/cost.json
+andrea/catalog_simulation_data_tools/simulators/boolode/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/dyngen/cost.json
+andrea/catalog_simulation_data_tools/simulators/dyngen/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/genenetweaver/cost.json
+andrea/catalog_simulation_data_tools/simulators/genenetweaver/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/genespider2/cost.json
+andrea/catalog_simulation_data_tools/simulators/genespider2/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/groundgan/cost.json
+andrea/catalog_simulation_data_tools/simulators/groundgan/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/scmultisim/cost.json
+andrea/catalog_simulation_data_tools/simulators/scmultisim/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/sergio/cost.json
+andrea/catalog_simulation_data_tools/simulators/sergio/simulatorspec.json
+andrea/catalog_simulation_data_tools/simulators/syntren/cost.json
+andrea/catalog_simulation_data_tools/simulators/syntren/simulatorspec.json
+andrea/cli/__init__.py
+andrea/cli/app.py
+andrea/core/__init__.py
+andrea/core/commands/__init__.py
+andrea/core/commands/compare_networks/__init__.py
+andrea/core/commands/compare_networks/bundles.py
+andrea/core/commands/compare_networks/comparison.py
+andrea/core/commands/compare_networks/distances.py
+andrea/core/commands/compare_networks/loading.py
+andrea/core/commands/compare_networks/models.py
+andrea/core/commands/compare_networks/request.py
+andrea/core/commands/compare_networks/store.py
+andrea/core/commands/compare_networks/tables.py
+andrea/core/commands/compare_networks/utils.py
+andrea/core/commands/compare_networks/view.py
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+andrea/core/commands/compare_networks/view_assets/template.html
+andrea/core/commands/compare_networks/view_assets/view.css
+andrea/core/commands/compare_networks/view_assets/view.js
+andrea/core/commands/evaluate_inference/__init__.py
+andrea/core/commands/evaluate_inference/bundles.py
+andrea/core/commands/evaluate_inference/evaluation.py
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+andrea/core/commands/generate_data/bundles.py
+andrea/core/commands/generate_data/catalog.py
+andrea/core/commands/generate_data/cost_planner.py
+andrea/core/commands/generate_data/output_validation.py
+andrea/core/commands/generate_data/pipeline.py
+andrea/core/commands/generate_data/plan.py
+andrea/core/commands/generate_data/request.py
+andrea/core/commands/generate_data/scenario.py
+andrea/core/commands/generate_data/selection.py
+andrea/core/commands/generate_data/semantic.py
+andrea/core/commands/generate_data/shared.py
+andrea/core/commands/generate_data/backends/__init__.py
+andrea/core/commands/generate_data/backends/docker_runner.py
+andrea/core/commands/generate_data/backends/registry.py
+andrea/core/commands/infer_network/__init__.py
+andrea/core/commands/infer_network/bundles.py
+andrea/core/commands/infer_network/pipeline.py
+andrea/core/commands/infer_network/plan.py
+andrea/core/commands/infer_network/preflight.py
+andrea/core/commands/infer_network/run.py
+andrea/core/commands/infer_network/commons/__init__.py
+andrea/core/commands/infer_network/commons/artifacts.py
+andrea/core/commands/infer_network/commons/catalog.py
+andrea/core/commands/infer_network/commons/custom_tools.py
+andrea/core/commands/infer_network/commons/dataset.py
+andrea/core/commands/infer_network/commons/execution_state.py
+andrea/core/commands/infer_network/commons/merge.py
+andrea/core/commands/infer_network/commons/network_exports.py
+andrea/core/commands/infer_network/commons/planner.py
+andrea/core/commands/infer_network/commons/runtime_helpers.py
+andrea/core/commands/infer_network/commons/shared.py
+andrea/core/commands/infer_network/commons/threading.py
+andrea/core/commands/infer_network/commons/tool_rule_eval.py
+andrea/core/commands/infer_network/commons/tools.py
+andrea/core/shared/__init__.py
+andrea/core/shared/bundles.py
+andrea/core/shared/catalog_contracts.py
+andrea/core/shared/compatibility_rules.py
+andrea/core/shared/container_runtime.py
+andrea/core/shared/input_specs.py
+andrea/core/shared/input_validation.py
+andrea/core/shared/issues.py
+andrea/core/shared/json_io.py
+andrea/core/shared/network_context.py
+andrea/core/shared/param_validation.py
+andrea/core/shared/paths.py
+andrea/core/shared/progress.py
+andrea/core/shared/runtime_profile.py
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+andrea/gui/common/__init__.py
+andrea/gui/common/reproducibility.py
+andrea/gui/common/server_files.py
+andrea/gui/common/server_jobs.py
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+andrea/gui/compare_networks/static/index.html
+andrea/gui/compare_networks/static/styles.css
+andrea/gui/compare_networks/static/app/main.js
+andrea/gui/compare_networks/static/app/shared.js
+andrea/gui/evaluate_inference/__init__.py
+andrea/gui/evaluate_inference/server.py
+andrea/gui/evaluate_inference/static/index.html
+andrea/gui/evaluate_inference/static/styles.css
+andrea/gui/evaluate_inference/static/app/main.js
+andrea/gui/generate_data/__init__.py
+andrea/gui/generate_data/server.py
+andrea/gui/generate_data/static/index.html
+andrea/gui/generate_data/static/styles.css
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+andrea/gui/infer_network/static/app/ui/steps.js
+andrea/gui/infer_network/static/app/ui/toasts.js
+tests/test_cli_bootstrap.py

andrea-0.1.0/ANDREA.egg-info/dependency_links.txt ADDED Viewed

	@@ -0,0 +1 @@
1	+

andrea-0.1.0/ANDREA.egg-info/entry_points.txt ADDED Viewed

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1	+ [console_scripts]
2	+ andrea = andrea.__main__:main

andrea-0.1.0/ANDREA.egg-info/requires.txt ADDED Viewed

@@ -0,0 +1,23 @@
+typer<0.24.0,>=0.23.1
+rich<16.0.0,>=15.0.0
+docker<8.0.0,>=7.1.0
+jsonschema<5.0.0,>=4.25.0
+pandas<3.0.0,>=2.3.0
+ortools<10.0,>=9.10
+fastapi<0.116.0,>=0.115.0
+uvicorn<0.35.0,>=0.34.0
+python-multipart<0.0.21,>=0.0.20
+aiofiles<25.0.0,>=24.1.0
+[:python_version < "3.12"]
+numpy<2.5,>=2.0.2
+[dev]
+pytest<9.0.0,>=8.4.0
+httpx<0.29.0,>=0.28.0
+black<25.0.0,>=24.0.0
+isort<6.0.0,>=5.13.0
+[release]
+build<2.0.0,>=1.2.0
+twine<7.0.0,>=6.0.0

andrea-0.1.0/ANDREA.egg-info/top_level.txt ADDED Viewed

	@@ -0,0 +1 @@
1	+ andrea

andrea-0.1.0/LICENSE ADDED Viewed

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+MIT License
+Copyright (c) 2026 Adrián Segura
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

andrea-0.1.0/PKG-INFO ADDED Viewed

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+Metadata-Version: 2.4
+Name: ANDREA
+Version: 0.1.0
+Summary: Platform for aggregated network discovery, simulation, inference, and benchmarking workflows.
+Author-email: Adrian Segura Ortiz <adrianseor.99@uma.es>, "George K. Georgakilas" <ggeorgakilas@athenarc.gr>, Theodore Dalamagas <dalamag@athenarc.gr>, "Jose F. Aldana-Montes" <jfaldana@uma.es>
+Maintainer-email: Adrian Segura Ortiz <adrianseor.99@uma.es>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/AdrianSeguraOrtiz/ANDREA
+Project-URL: Repository, https://github.com/AdrianSeguraOrtiz/ANDREA
+Project-URL: Issues, https://github.com/AdrianSeguraOrtiz/ANDREA/issues
+Project-URL: Documentation, https://github.com/AdrianSeguraOrtiz/ANDREA/tree/main/docs
+Keywords: gene regulatory networks,GRN inference,benchmarking,single-cell,systems biology,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Environment :: Web Environment
+Classifier: Framework :: FastAPI
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <3.14,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.5,>=2.0.2; python_version < "3.12"
+Requires-Dist: typer<0.24.0,>=0.23.1
+Requires-Dist: rich<16.0.0,>=15.0.0
+Requires-Dist: docker<8.0.0,>=7.1.0
+Requires-Dist: jsonschema<5.0.0,>=4.25.0
+Requires-Dist: pandas<3.0.0,>=2.3.0
+Requires-Dist: ortools<10.0,>=9.10
+Requires-Dist: fastapi<0.116.0,>=0.115.0
+Requires-Dist: uvicorn<0.35.0,>=0.34.0
+Requires-Dist: python-multipart<0.0.21,>=0.0.20
+Requires-Dist: aiofiles<25.0.0,>=24.1.0
+Provides-Extra: dev
+Requires-Dist: pytest<9.0.0,>=8.4.0; extra == "dev"
+Requires-Dist: httpx<0.29.0,>=0.28.0; extra == "dev"
+Requires-Dist: black<25.0.0,>=24.0.0; extra == "dev"
+Requires-Dist: isort<6.0.0,>=5.13.0; extra == "dev"
+Provides-Extra: release
+Requires-Dist: build<2.0.0,>=1.2.0; extra == "release"
+Requires-Dist: twine<7.0.0,>=6.0.0; extra == "release"
+Dynamic: license-file
+# ANDREA
+**Automated Network Discovery, Reproducible Evaluation and Analysis**
+ANDREA is a catalog-driven platform for generating benchmark expression
+datasets, running gene regulatory network (GRN) inference tools, evaluating
+inferred networks against reference truth and comparing networks across tools,
+contexts and runs. It exposes the same workflows through a command-line
+interface and local browser GUIs, while keeping public artifacts as plain JSON,
+CSV, SQLite and ZIP files.
+<p align="center">
+  <img src="docs/assets/andrea_overview.png" alt="ANDREA workflow overview" width="92%">
+</p>
+## What ANDREA Provides
+- A standardized catalog of simulator and inference-tool integrations, with
+  compatibility rules, parameter schemas, Docker wrappers and provenance
+  metadata.
+- Four interoperable workflows:
+  `generate-data -> infer-network -> evaluate-inference -> compare-networks`.
+- Strict handoff bundles so outputs from one command can be consumed directly
+  by the next one.
+- Context-aware handling of global, group-level and column-level network
+  outputs, including emulated and aggregated execution strategies where
+  appropriate.
+- Cost-aware planning and execution orchestration for Dockerized simulator and
+  inference wrappers.
+- Evaluation reports and interactive comparison views for distance maps,
+  metric overlays and edge-level differences.
+- Support for temporary external Docker inference tools that follow ANDREA's
+  standard container contract.
+## Installation
+Install the release package:
+```sh
+pip install ANDREA
+```
+For a development checkout:
+```sh
+git clone https://github.com/AdrianSeguraOrtiz/ANDREA.git
+cd ANDREA
+python -m pip install -e ".[dev]"
+```
+Docker is required for workflows that execute simulator or inference wrappers.
+See [docs/installation.md](docs/installation.md) for the full setup notes.
+## Quick Start
+Inspect the CLI:
+```sh
+andrea --help
+andrea generate-data --help
+andrea infer-network --help
+andrea evaluate-inference --help
+andrea compare-networks --help
+```
+Open the local GUIs:
+```sh
+andrea gui generate-data
+andrea gui infer-network
+andrea gui evaluate-inference
+andrea gui compare-networks
+```
+The GUIs are local browser applications. ZIP bundles are mainly intended for
+GUI handoff; CLI and Python users can usually pass report JSON paths directly.
+## Workflows
+| Command | Purpose | Key outputs |
+|---|---|---|
+| `generate-data` | Build synthetic benchmark datasets from simulator catalogs. | `expression.tsv`, `truth/networks.csv`, manifests and analysis bundles. |
+| `infer-network` | Run catalog or external Docker inference tools against standardized datasets. | Per-run networks, merged normalized networks, graph exports and run reports. |
+| `evaluate-inference` | Score inferred networks against simulator or user-provided truth. | Metric tables, pairing tables, `evaluation_report.json` and visual summaries. |
+| `compare-networks` | Compare networks across tools, sources, parameters and contexts. | Distance tables, coordinates, `comparison.sqlite`, edge differences and reports. |
+See [docs/workflows.md](docs/workflows.md) for the workflow contracts and
+[docs/gui.md](docs/gui.md), [docs/cli.md](docs/cli.md) and
+[docs/core.md](docs/core.md) for GUI, command-line and Python usage.
+## Documentation
+- [Installation](docs/installation.md)
+- [Workflow contracts](docs/workflows.md)
+- [GUI guide](docs/gui.md)
+- [CLI guide](docs/cli.md)
+- [Core Python guide](docs/core.md)
+- [Catalogs and coverage](docs/catalogs.md)
+- [External Docker tools](docs/external-docker-tools.md)
+- [Full documentation index](docs/README.md)