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CHANGELOG.md
CONTRIBUTING.md
LICENSE
Makefile
POLICY.md
README.md
VERSIONING.md
conftest.py
mkdocs.yml
pyproject.toml
ruff.toml
uv.lock
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atlas/bibliography/refs.yaml
atlas/cases/01_physics/overdamped-langevin-st/case-overdamped-fokker-planck-baseline.yaml
atlas/claims/README.md
atlas/claims/01_physics/ctmc-schnakenberg/claim-schnakenberg-ep-rate-definition.yaml
atlas/claims/01_physics/ctmc-seifert/claim-seifert-ep.yaml
atlas/claims/01_physics/overdamped-langevin-st/claim-ep-nonnegative-isothermal.yaml
atlas/claims/01_physics/overdamped-langevin-st/claim-overdamped-anomalous-ep-limitation.yaml
atlas/domains/00_golden/proxy-other.yaml
atlas/domains/00_golden/subsystem-langevin.yaml
atlas/domains/00_golden/supersystem-network.yaml
atlas/domains/01_physics/biochemical-cme.yaml
atlas/domains/01_physics/ctmc-schnakenberg.yaml
atlas/domains/01_physics/domain_ctmc_seifert.yaml
atlas/domains/01_physics/overdamped-langevin-st.yaml
atlas/domains/01_physics/overdamped-nonisothermal-langevin.yaml
atlas/domains/01_physics/quantum-lindblad.yaml
atlas/domains/01_physics/underdamped-langevin-st.yaml
atlas/relations/00_golden/coarsegrain-super-to-proxy.yaml
atlas/relations/00_golden/composition-sub-to-super.yaml
atlas/relations/00_golden/coupling-proxy-to-sub.yaml
atlas/relations/01_physics/biochemical-cme-to-ctmc.yaml
atlas/relations/01_physics/ctmc-coarsegraining-hidden-variables.yaml
atlas/relations/01_physics/ctmc-to-diffusion-limit.yaml
atlas/relations/01_physics/overdamped-nonisothermal-anomalous-ep.yaml
atlas/relations/01_physics/quantum-lindblad-to-ctmc-classical-limit.yaml
atlas/relations/01_physics/underdamped-to-overdamped-limit.yaml
atlas/schema/domain.schema.json
atlas/schema/relation.schema.json
dist/packs/.gitkeep
docs/atlas_graph.mmd
docs/cases_conventions.md
docs/claims.md
docs/composition_integrity.md
docs/compute.md
docs/compute_cases.md
docs/contract.md
docs/contribution.md
docs/developer-guide.md
docs/effective-closure.md
docs/gen_pages.py
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docs/metrics.md
docs/releases.md
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src/entropy_table/__init__.py
src/entropy_table/_version.py
src/entropy_table/cli.py
src/entropy_table.egg-info/PKG-INFO
src/entropy_table.egg-info/SOURCES.txt
src/entropy_table.egg-info/dependency_links.txt
src/entropy_table.egg-info/entry_points.txt
src/entropy_table.egg-info/requires.txt
src/entropy_table.egg-info/top_level.txt
src/entropy_table/commands/__init__.py
src/entropy_table/commands/analyze_health.py
src/entropy_table/commands/build_index.py
src/entropy_table/commands/extract_domain_from_template.py
src/entropy_table/commands/freeze_guard.py
src/entropy_table/commands/ingest.py
src/entropy_table/commands/manage_cases.py
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src/entropy_table/commands/query.py
src/entropy_table/commands/query_claims.py
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src/entropy_table/commands/report_claims.py
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src/entropy_table/commands/snapshot.py
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src/entropy_table/commands/validate_bibliography.py
src/entropy_table/commands/validate_claims.py
src/entropy_table/commands/validate_composition.py
src/entropy_table/commands/validate_math.py
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src/entropy_table/compute/__init__.py
src/entropy_table/compute/case_runner.py
src/entropy_table/compute/cli.py
src/entropy_table/compute/ctmc_ep.py
src/entropy_table/compute/diffusion_ep_1d.py
src/entropy_table/compute/report.py
src/entropy_table/core/__init__.py
src/entropy_table/core/bindings.py
src/entropy_table/core/common.py
staging/README.md
staging/intake/README.md
staging/intake/drafts/README.md
staging/intake/raw/README.md
templates/case_template.yaml
templates/domain_template.yaml
tests/test_analyze_health.py
tests/test_bibliography.py
tests/test_build_index.py
tests/test_case_runner.py
tests/test_claim_case_binding.py
tests/test_compute_ctmc.py
tests/test_compute_diffusion.py
tests/test_contract.py
tests/test_extract_template.py
tests/test_ingest.py
tests/test_manage_cases.py
tests/test_metrics.py
tests/test_query.py
tests/test_relation_schema_pr14.py
tests/test_release.py
tests/test_report_scan.py
tests/test_schema_version.py
tests/test_snapshot_determinism.py
tests/test_validate_claims.py
tests/test_validate_composition.py
tests/test_validate_composition_pr14.py
tests/test_visualize.py
tests/fixtures/fail/domain_invalid_enum.yaml
tests/fixtures/fail/domain_missing_closure_notes.yaml
tests/fixtures/fail/domain_missing_must_fail_tests.yaml
tests/fixtures/fail/relation_dangling_endpoint.yaml
tests/fixtures/fail/transitive_channels/domains/atom.yaml
tests/fixtures/fail/transitive_channels/domains/molecule.yaml
tests/fixtures/fail/transitive_channels/relations/comp.yaml
tests/fixtures/pass/domain_valid.yaml
tests/fixtures/pass/relation_valid.yaml
tools/__init__.py
tools/analyze_health.py
tools/build_index.py
tools/extract_domain_from_template.py
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tools/validate.py
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tools/validate_claims.py
tools/validate_composition.py
tools/visualize.py