PR: package rename bluenamer -> openclatura

[r-fedorov]

Summary by Sourcery

Rename the core SMILES-to-IUPAC naming package and all public-facing surfaces from bluenamer to openclatura.

Enhancements:

• Update all Python package modules, imports, and namespaces from bluenamer to openclatura while preserving functionality.
• Adjust CLI entry points, FastAPI app metadata, and Docker runtime commands to use the new openclatura name.
• Refresh documentation, examples, and testing guides to reference the openclatura package and commands instead of bluenamer.
• Rename environment variables and internal identifiers related to datasets and fuzzing to the new OPENCLATURA prefix.

Build:

• Change project metadata, script entry points, and wheel packaging configuration to publish the package as openclatura and relocate sources under src/openclatura.

CI:

• Update CI and Docker GitHub workflows to build, lint, test, and tag Docker images under the openclatura name instead of bluenamer.

Deployment:

• Retarget Dockerfile and compose configuration to run the HTTP service and images under the openclatura user, image name, and module entrypoint.

Tests:

• Move and update tests and round-trip suites to import openclatura and adjust snapshots and prefixes that encoded the old name.

[sourcery-ai]

Reviewer's Guide

Renames the core Python package, CLI, and Docker image from bluenamer to openclatura, updating imports, module paths, configuration, docs, tests, datasets, and CI tooling accordingly while preserving behavior.

File-Level Changes

Change	Details	Files
Rename the library package namespace and public API from bluenamer to openclatura while keeping runtime behavior stable.	Move all source modules from src/bluenamer/ to src/openclatura/ and update intra-package imports to the new namespace. Update docstrings and module-level comments to reference openclatura instead of bluenamer, including Sphinx/reST-style cross-references. Adjust data file paths and embedded identifiers (e.g., parser grammar snapshot metadata) to live under the openclatura package.	src/openclatura/__init__.py src/openclatura/engine.py src/openclatura/namer.py src/openclatura/opsin_verify.py src/openclatura/human_descriptor.py src/openclatura/namer_config.py src/openclatura/naming_data.py src/openclatura/overview_namer.md src/openclatura/rules/*.py src/openclatura/data/parser_grammar_snapshot.json src/openclatura/data/parser_xml_resources/*.json
Rename the CLI surface and HTTP service entrypoints from bluenamer to openclatura, including scripts, help text, and Docker wiring.	Change CLI program name, help descriptions, and version banner to openclatura, and update all usage examples accordingly. Update FastAPI app title and import paths for the web service, along with the python -m entrypoint module path. Adjust Dockerfile user, workdir, CMD, and docker-compose service/image names to openclatura, plus CI smoke-test commands and tags.	src/openclatura/cli.py src/openclatura/web/__init__.py src/openclatura/web/app.py src/openclatura/web/__main__.py pyproject.toml Dockerfile docker/compose.yaml .github/workflows/ci.yml .github/workflows/docker-image.yml
Update documentation, examples, and testing guides to use the new openclatura name and installation instructions.	Rewrite README branding and quickstart examples to import and invoke openclatura instead of bluenamer, including pip install commands and CLI examples. Adjust testing guide environment variables and command snippets to use OPENCLATURA_* names and new paths. Ensure narrative docs (overview, descriptions) consistently use the openclatura project name.	README.md testing_guide.md src/openclatura/overview_namer.md
Update tests, fuzzing, and dataset pipelines to import openclatura and to use new env var names and identifiers.	Relocate test packages from src/bluenamer/tests* to src/openclatura/tests* and update all imports of the library to the new namespace. Update integration tests and fuzz tests that shell out to the CLI or python -m modules to use openclatura commands. Rename dataset-related environment variables from BLUENAMER_* to OPENCLATURA_* and adjust references in dataset tests and docs. Update roundtrip tests and temporary file prefixes to use openclatura-prefixed names.	src/openclatura/tests/test_analysis.py src/openclatura/tests/test_public_api.py src/openclatura/tests_roundtrip/*.py tests/fuzz/test_smiles_strategies.py tests/datasets/test_pubchem_sample.py tests/datasets/test_qm9_sample.py tests/integration/test_describer.py tests/integration/test_corpus_golden.py tests/integration/test_human_descriptor.py tests/integration/test_diverse_corpus.py tests/integration/test_web_app.py testing_guide.md
Update examples and scripts to import and run openclatura instead of bluenamer.	Replace all example imports of bluenamer.* with openclatura.* across evaluation, sanity, and OPSIN-related scripts. Keep behavior of examples intact while ensuring they exercise the new package name and CLI. Align script-level comments and configuration hints with the new branding.	examples/find_small_failures.py examples/opsin_eval_ZINC22.py examples/opsin_eval_pubchem.py examples/test_opsin_mac.py examples/test_opsin_mac_ZINC22.py examples/test_opsin_mac_ZINC22_light.py examples/eval_via_opsin.py examples/qm9_iupac_collect_token_confidence.py examples/random_sanity.py examples/sanity_examples.py examples/test_opsin_mac_ZINC.py examples/test_qm9_opsin_batch.py scripts/regenerate_goldens.py

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📥 Commits

Reviewing files that changed from the base of the PR and between b55ae25 and 78c77e2.

📒 Files selected for processing (206)

• .github/workflows/ci.yml
• .github/workflows/docker-image.yml
• Dockerfile
• README.md
• docker/compose.yaml
• examples/eval_via_opsin.py
• examples/find_small_failures.py
• examples/opsin_eval_ZINC22.py
• examples/opsin_eval_pubchem.py
• examples/qm9_iupac_collect_token_confidence.py
• examples/random_sanity.py
• examples/sanity_examples.py
• examples/test_opsin_mac.py
• examples/test_opsin_mac_ZINC.py
• examples/test_opsin_mac_ZINC22.py
• examples/test_opsin_mac_ZINC22_light.py
• examples/test_qm9_opsin_batch.py
• pyproject.toml
• scripts/regenerate_goldens.py
• src/openclatura/__init__.py
• src/openclatura/additive.py
• src/openclatura/assembler.py
• src/openclatura/assembly_charge.py
• src/openclatura/assembly_parent.py
• src/openclatura/assembly_parts.py
• src/openclatura/assembly_prefixes.py
• src/openclatura/assembly_spiro.py
• src/openclatura/assembly_utils.py
• src/openclatura/chains.py
• src/openclatura/charge_pair_roles.py
• src/openclatura/charge_specs.py
• src/openclatura/cli.py
• src/openclatura/component_group_rules.py
• src/openclatura/component_modifiers.py
• src/openclatura/component_namer.py
• src/openclatura/data/fused_emission_examples.json
• src/openclatura/data/fused_ion_templates.json
• src/openclatura/data/heteroatom_substituents.json
• src/openclatura/data/namer_rules.json
• src/openclatura/data/parser_grammar_snapshot.json
• src/openclatura/data/parser_xml_resources/alkanes.json
• src/openclatura/data/parser_xml_resources/aminoAcids.json
• src/openclatura/data/parser_xml_resources/arylGroups.json
• src/openclatura/data/parser_xml_resources/arylSubstituents.json
• src/openclatura/data/parser_xml_resources/atomHydrides.json
• src/openclatura/data/parser_xml_resources/carbohydrates.json
• src/openclatura/data/parser_xml_resources/carboxylicAcids.json
• src/openclatura/data/parser_xml_resources/chargeAndOxidationNumberSpecifiers.json
• src/openclatura/data/parser_xml_resources/cyclicUnsaturableHydrocarbon.json
• src/openclatura/data/parser_xml_resources/elementaryAtoms.json
• src/openclatura/data/parser_xml_resources/fragments.json
• src/openclatura/data/parser_xml_resources/functionalTerms.json
• src/openclatura/data/parser_xml_resources/fusionComponents.json
• src/openclatura/data/parser_xml_resources/germanTokens.json
• src/openclatura/data/parser_xml_resources/groupStemsAllowingAllSuffixes.json
• src/openclatura/data/parser_xml_resources/groupStemsAllowingInlineSuffixes.json
• src/openclatura/data/parser_xml_resources/heteroAtoms.json
• src/openclatura/data/parser_xml_resources/hwHeteroAtoms.json
• src/openclatura/data/parser_xml_resources/hwSuffixes.json
• src/openclatura/data/parser_xml_resources/infixes.json
• src/openclatura/data/parser_xml_resources/inlineChargeSuffixes.json
• src/openclatura/data/parser_xml_resources/inlineSuffixes.json
• src/openclatura/data/parser_xml_resources/miscTokens.json
• src/openclatura/data/parser_xml_resources/multiRadicalSubstituents.json
• src/openclatura/data/parser_xml_resources/multipliers.json
• src/openclatura/data/parser_xml_resources/naturalProducts.json
• src/openclatura/data/parser_xml_resources/nonCarboxylicAcids.json
• src/openclatura/data/parser_xml_resources/regexTokens.json
• src/openclatura/data/parser_xml_resources/regexes.json
• src/openclatura/data/parser_xml_resources/simpleCyclicGroups.json
• src/openclatura/data/parser_xml_resources/simpleGroups.json
• src/openclatura/data/parser_xml_resources/simpleSubstituents.json
• src/openclatura/data/parser_xml_resources/substituents.json
• src/openclatura/data/parser_xml_resources/suffixApplicability.json
• src/openclatura/data/parser_xml_resources/suffixPrefix.json
• src/openclatura/data/parser_xml_resources/suffixRules.json
• src/openclatura/data/parser_xml_resources/suffixes.json
• src/openclatura/data/parser_xml_resources/unsaturators.json
• src/openclatura/data/parser_xml_resources/wordRules.json
• src/openclatura/data/retained_fused_graph_templates.json
• src/openclatura/describer.py
• src/openclatura/engine.py
• src/openclatura/formatting.py
• src/openclatura/functional_groups.py
• src/openclatura/functional_prefixes.py
• src/openclatura/fused_ion_templates.py
• src/openclatura/fused_topology.py
• src/openclatura/grammar_snapshot_data.py
• src/openclatura/graph_io.py
• src/openclatura/group_atom_roles.py
• src/openclatura/heteroatom_subgraphs.py
• src/openclatura/heteroatom_substituent_specs.py
• src/openclatura/heterocumulene_roles.py
• src/openclatura/human_descriptor.py
• src/openclatura/hypervalent_roles.py
• src/openclatura/ionic_naming.py
• src/openclatura/locants.py
• src/openclatura/map_namer.md
• src/openclatura/molecule.py
• src/openclatura/name_assembly.py
• src/openclatura/name_bindings.py
• src/openclatura/name_operations.py
• src/openclatura/name_postprocessing.py
• src/openclatura/namer.py
• src/openclatura/namer_config.py
• src/openclatura/naming_audit.py
• src/openclatura/naming_context.py
• src/openclatura/naming_data.py
• src/openclatura/nitrogen_roles.py
• src/openclatura/nomenclature.py
• src/openclatura/numbering.py
• src/openclatura/operations.py
• src/openclatura/opsin_verify.py
• src/openclatura/overview_namer.md
• src/openclatura/oxoacid_roles.py
• src/openclatura/oxoacid_templates.py
• src/openclatura/parent_pipeline.py
• src/openclatura/parent_selection.py
• src/openclatura/perception.py
• src/openclatura/peroxy_carbonyl_roles.py
• src/openclatura/polycycle_topology.py
• src/openclatura/principal_groups.py
• src/openclatura/principal_suffixes.py
• src/openclatura/resonance_compare.py
• src/openclatura/retained_fused_production.py
• src/openclatura/retained_fused_templates.py
• src/openclatura/retained_specs.py
• src/openclatura/ring_parent.py
• src/openclatura/ring_renderer.py
• src/openclatura/ring_systems.py
• src/openclatura/role_certificate.py
• src/openclatura/rule_layout.py
• src/openclatura/rules/__init__.py
• src/openclatura/rules/bonds.py
• src/openclatura/rules/elements.py
• src/openclatura/rules/elision.py
• src/openclatura/rules/locants.py
• src/openclatura/rules/multipliers.py
• src/openclatura/rules/retained.py
• src/openclatura/rules/stems.py
• src/openclatura/rules/substituents.py
• src/openclatura/rules/suffixes.py
• src/openclatura/small_ring_stereo.py
• src/openclatura/special_cases.py
• src/openclatura/spiro_assembly.py
• src/openclatura/stereo_audit.py
• src/openclatura/stereo_descriptors.py
• src/openclatura/subgraph_tools.py
• src/openclatura/substituent_tokens.py
• src/openclatura/subtractive.py
• src/openclatura/suffix_stack.py
• src/openclatura/tests/test_analysis.py
• src/openclatura/tests/test_public_api.py
• src/openclatura/tests_roundtrip/__init__.py
• src/openclatura/tests_roundtrip/roundtrip_helpers.py
• src/openclatura/tests_roundtrip/test_acids.py
• src/openclatura/tests_roundtrip/test_alcohols.py
• src/openclatura/tests_roundtrip/test_alkanes.py
• src/openclatura/tests_roundtrip/test_alkenes_alkynes.py
• src/openclatura/tests_roundtrip/test_api.py
• src/openclatura/tests_roundtrip/test_bridges.py
• src/openclatura/tests_roundtrip/test_charged_fused_heteroaromatics.py
• src/openclatura/tests_roundtrip/test_composite_bridges.py
• src/openclatura/tests_roundtrip/test_fused_multiplicity.py
• src/openclatura/tests_roundtrip/test_fused_parents.py
• src/openclatura/tests_roundtrip/test_haloalkanes.py
• src/openclatura/tests_roundtrip/test_heteroatom_substituents.py
• src/openclatura/tests_roundtrip/test_heterocycles.py
• src/openclatura/tests_roundtrip/test_imines.py
• src/openclatura/tests_roundtrip/test_ketones.py
• src/openclatura/tests_roundtrip/test_locant_display.py
• src/openclatura/tests_roundtrip/test_nitro.py
• src/openclatura/tests_roundtrip/test_numbering.py
• src/openclatura/tests_roundtrip/test_oxyacids.py
• src/openclatura/tests_roundtrip/test_p13_additive.py
• src/openclatura/tests_roundtrip/test_p13_conjunctive.py
• src/openclatura/tests_roundtrip/test_p13_fusion.py
• src/openclatura/tests_roundtrip/test_p13_multiplicative.py
• src/openclatura/tests_roundtrip/test_p13_operations.py
• src/openclatura/tests_roundtrip/test_p13_replacement.py
• src/openclatura/tests_roundtrip/test_p13_substitutive.py
• src/openclatura/tests_roundtrip/test_p13_subtractive.py
• src/openclatura/tests_roundtrip/test_polycycles.py
• src/openclatura/tests_roundtrip/test_polycyclic_descriptors.py
• src/openclatura/tests_roundtrip/test_polyfunctional_fragments.py
• src/openclatura/tests_roundtrip/test_principal_group_breadth.py
• src/openclatura/tests_roundtrip/test_replacement_parents.py
• src/openclatura/tests_roundtrip/test_role_models.py
• src/openclatura/tests_roundtrip/test_stereo.py
• src/openclatura/tests_roundtrip/test_substituents.py
• src/openclatura/token_grammar.py
• src/openclatura/trace_helpers.py
• src/openclatura/utils.py
• src/openclatura/von_baeyer.py
• src/openclatura/web/__init__.py
• src/openclatura/web/__main__.py
• src/openclatura/web/app.py
• testing_guide.md
• tests/datasets/test_pubchem_sample.py
• tests/datasets/test_qm9_sample.py
• tests/fuzz/test_smiles_strategies.py
• tests/integration/test_corpus_golden.py
• tests/integration/test_describer.py
• tests/integration/test_diverse_corpus.py
• tests/integration/test_human_descriptor.py
• tests/integration/test_web_app.py

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