Rename main module from curate_gpt to curategpt

monarch-initiative · Oct 3, 2024 · 82e15d5 · 82e15d5
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diff --git a/src/curate_gpt/__init__.py → src/curategpt/__init__.py b/src/curate_gpt/__init__.py → src/curategpt/__init__.py
diff --git a/src/curate_gpt/adhoc/__init__.py → src/curategpt/adhoc/__init__.py b/src/curate_gpt/adhoc/__init__.py → src/curategpt/adhoc/__init__.py
diff --git a/src/curate_gpt/adhoc/gocam_predictor.py → src/curategpt/adhoc/gocam_predictor.py b/src/curate_gpt/adhoc/gocam_predictor.py → src/curategpt/adhoc/gocam_predictor.py
diff --git a/src/curate_gpt/agents/__init__.py → src/curategpt/agents/__init__.py b/src/curate_gpt/agents/__init__.py → src/curategpt/agents/__init__.py
diff --git a/src/curate_gpt/agents/agent_utils.py → src/curategpt/agents/agent_utils.py b/src/curate_gpt/agents/agent_utils.py → src/curategpt/agents/agent_utils.py
diff --git a/src/curate_gpt/agents/base_agent.py → src/curategpt/agents/base_agent.py b/src/curate_gpt/agents/base_agent.py → src/curategpt/agents/base_agent.py
diff --git a/src/curate_gpt/agents/bootstrap_agent.py → src/curategpt/agents/bootstrap_agent.py b/src/curate_gpt/agents/bootstrap_agent.py → src/curategpt/agents/bootstrap_agent.py
diff --git a/src/curate_gpt/agents/chat_agent.py → src/curategpt/agents/chat_agent.py b/src/curate_gpt/agents/chat_agent.py → src/curategpt/agents/chat_agent.py
diff --git a/...e_gpt/agents/concept_recognition_agent.py → ...tegpt/agents/concept_recognition_agent.py b/...e_gpt/agents/concept_recognition_agent.py → ...tegpt/agents/concept_recognition_agent.py
diff --git a/src/curate_gpt/agents/dase_agent.py → src/curategpt/agents/dase_agent.py b/src/curate_gpt/agents/dase_agent.py → src/curategpt/agents/dase_agent.py
diff --git a/src/curate_gpt/agents/dragon_agent.py → src/curategpt/agents/dragon_agent.py b/src/curate_gpt/agents/dragon_agent.py → src/curategpt/agents/dragon_agent.py
diff --git a/src/curate_gpt/agents/evidence_agent.py → src/curategpt/agents/evidence_agent.py b/src/curate_gpt/agents/evidence_agent.py → src/curategpt/agents/evidence_agent.py
diff --git a/src/curate_gpt/agents/huggingface_agent.py → src/curategpt/agents/huggingface_agent.py b/src/curate_gpt/agents/huggingface_agent.py → src/curategpt/agents/huggingface_agent.py
diff --git a/src/curate_gpt/agents/mapping_agent.py → src/curategpt/agents/mapping_agent.py b/src/curate_gpt/agents/mapping_agent.py → src/curategpt/agents/mapping_agent.py
diff --git a/src/curate_gpt/agents/summarization_agent.py → src/curategpt/agents/summarization_agent.py b/src/curate_gpt/agents/summarization_agent.py → src/curategpt/agents/summarization_agent.py
diff --git a/src/curate_gpt/app/__init__.py → src/curategpt/app/__init__.py b/src/curate_gpt/app/__init__.py → src/curategpt/app/__init__.py
diff --git a/src/curate_gpt/app/app.py → src/curategpt/app/app.py b/src/curate_gpt/app/app.py → src/curategpt/app/app.py
diff --git a/src/curate_gpt/app/cart.py → src/curategpt/app/cart.py b/src/curate_gpt/app/cart.py → src/curategpt/app/cart.py
diff --git a/src/curate_gpt/app/components.py → src/curategpt/app/components.py b/src/curate_gpt/app/components.py → src/curategpt/app/components.py
diff --git a/src/curate_gpt/app/helper.py → src/curategpt/app/helper.py b/src/curate_gpt/app/helper.py → src/curategpt/app/helper.py
diff --git a/src/curate_gpt/app/state.py → src/curategpt/app/state.py b/src/curate_gpt/app/state.py → src/curategpt/app/state.py
diff --git a/src/curate_gpt/cli.py → src/curategpt/cli.py b/src/curate_gpt/cli.py → src/curategpt/cli.py
diff --git a/src/curate_gpt/conf/__init__.py → src/curategpt/conf/__init__.py b/src/curate_gpt/conf/__init__.py → src/curategpt/conf/__init__.py
diff --git a/src/curate_gpt/conf/examples/bio.yaml → src/curategpt/conf/examples/bio.yaml b/src/curate_gpt/conf/examples/bio.yaml → src/curategpt/conf/examples/bio.yaml
diff --git a/src/curate_gpt/conf/examples/rdp.yaml → src/curategpt/conf/examples/rdp.yaml b/src/curate_gpt/conf/examples/rdp.yaml → src/curategpt/conf/examples/rdp.yaml
diff --git a/src/curate_gpt/conf/prompts/__init__.py → src/curategpt/conf/prompts/__init__.py b/src/curate_gpt/conf/prompts/__init__.py → src/curategpt/conf/prompts/__init__.py
diff --git a/...rate_gpt/conf/prompts/bootstrap-schema.j2 → ...urategpt/conf/prompts/bootstrap-schema.j2 b/...rate_gpt/conf/prompts/bootstrap-schema.j2 → ...urategpt/conf/prompts/bootstrap-schema.j2
diff --git a/src/curate_gpt/evaluation/__init__.py → src/curategpt/evaluation/__init__.py b/src/curate_gpt/evaluation/__init__.py → src/curategpt/evaluation/__init__.py
diff --git a/src/curate_gpt/evaluation/base_evaluator.py → src/curategpt/evaluation/base_evaluator.py b/src/curate_gpt/evaluation/base_evaluator.py → src/curategpt/evaluation/base_evaluator.py
diff --git a/src/curate_gpt/evaluation/calc_statistics.py → src/curategpt/evaluation/calc_statistics.py b/src/curate_gpt/evaluation/calc_statistics.py → src/curategpt/evaluation/calc_statistics.py
diff --git a/src/curate_gpt/evaluation/dae_evaluator.py → src/curategpt/evaluation/dae_evaluator.py b/src/curate_gpt/evaluation/dae_evaluator.py → src/curategpt/evaluation/dae_evaluator.py
diff --git a/...te_gpt/evaluation/evaluation_datamodel.py → ...ategpt/evaluation/evaluation_datamodel.py b/...te_gpt/evaluation/evaluation_datamodel.py → ...ategpt/evaluation/evaluation_datamodel.py
diff --git a/src/curate_gpt/evaluation/runner.py → src/curategpt/evaluation/runner.py b/src/curate_gpt/evaluation/runner.py → src/curategpt/evaluation/runner.py
diff --git a/src/curate_gpt/evaluation/splitter.py → src/curategpt/evaluation/splitter.py b/src/curate_gpt/evaluation/splitter.py → src/curategpt/evaluation/splitter.py
diff --git a/src/curate_gpt/extract/__init__.py → src/curategpt/extract/__init__.py b/src/curate_gpt/extract/__init__.py → src/curategpt/extract/__init__.py
diff --git a/src/curate_gpt/extract/basic_extractor.py → src/curategpt/extract/basic_extractor.py b/src/curate_gpt/extract/basic_extractor.py → src/curategpt/extract/basic_extractor.py
diff --git a/src/curate_gpt/extract/extractor.py → src/curategpt/extract/extractor.py b/src/curate_gpt/extract/extractor.py → src/curategpt/extract/extractor.py
diff --git a/src/curate_gpt/extract/openai_extractor.py → src/curategpt/extract/openai_extractor.py b/src/curate_gpt/extract/openai_extractor.py → src/curategpt/extract/openai_extractor.py
diff --git a/...curate_gpt/extract/recursive_extractor.py → src/curategpt/extract/recursive_extractor.py b/...curate_gpt/extract/recursive_extractor.py → src/curategpt/extract/recursive_extractor.py
diff --git a/src/curate_gpt/formatters/__init__.py → src/curategpt/formatters/__init__.py b/src/curate_gpt/formatters/__init__.py → src/curategpt/formatters/__init__.py
diff --git a/src/curate_gpt/formatters/format_utils.py → src/curategpt/formatters/format_utils.py b/src/curate_gpt/formatters/format_utils.py → src/curategpt/formatters/format_utils.py
diff --git a/src/curate_gpt/store/__init__.py → src/curategpt/store/__init__.py b/src/curate_gpt/store/__init__.py → src/curategpt/store/__init__.py
diff --git a/src/curate_gpt/store/chromadb_adapter.py → src/curategpt/store/chromadb_adapter.py b/src/curate_gpt/store/chromadb_adapter.py → src/curategpt/store/chromadb_adapter.py
diff --git a/src/curate_gpt/store/db_adapter.py → src/curategpt/store/db_adapter.py b/src/curate_gpt/store/db_adapter.py → src/curategpt/store/db_adapter.py
diff --git a/src/curate_gpt/store/db_metadata.py → src/curategpt/store/db_metadata.py b/src/curate_gpt/store/db_metadata.py → src/curategpt/store/db_metadata.py
diff --git a/src/curate_gpt/store/duckdb_adapter.py → src/curategpt/store/duckdb_adapter.py b/src/curate_gpt/store/duckdb_adapter.py → src/curategpt/store/duckdb_adapter.py
diff --git a/src/curate_gpt/store/duckdb_result.py → src/curategpt/store/duckdb_result.py b/src/curate_gpt/store/duckdb_result.py → src/curategpt/store/duckdb_result.py
diff --git a/src/curate_gpt/store/in_memory_adapter.py → src/curategpt/store/in_memory_adapter.py b/src/curate_gpt/store/in_memory_adapter.py → src/curategpt/store/in_memory_adapter.py
diff --git a/src/curate_gpt/store/metadata.py → src/curategpt/store/metadata.py b/src/curate_gpt/store/metadata.py → src/curategpt/store/metadata.py
diff --git a/src/curate_gpt/store/schema_proxy.py → src/curategpt/store/schema_proxy.py b/src/curate_gpt/store/schema_proxy.py → src/curategpt/store/schema_proxy.py
diff --git a/src/curate_gpt/store/vocab.py → src/curategpt/store/vocab.py b/src/curate_gpt/store/vocab.py → src/curategpt/store/vocab.py
diff --git a/src/curate_gpt/utils/__init__.py → src/curategpt/utils/__init__.py b/src/curate_gpt/utils/__init__.py → src/curategpt/utils/__init__.py
diff --git a/src/curate_gpt/utils/eval_utils.py → src/curategpt/utils/eval_utils.py b/src/curate_gpt/utils/eval_utils.py → src/curategpt/utils/eval_utils.py
diff --git a/src/curate_gpt/utils/llm_utils.py → src/curategpt/utils/llm_utils.py b/src/curate_gpt/utils/llm_utils.py → src/curategpt/utils/llm_utils.py
diff --git a/src/curate_gpt/utils/patch_utils.py → src/curategpt/utils/patch_utils.py b/src/curate_gpt/utils/patch_utils.py → src/curategpt/utils/patch_utils.py
diff --git a/src/curate_gpt/utils/search.py → src/curategpt/utils/search.py b/src/curate_gpt/utils/search.py → src/curategpt/utils/search.py
diff --git a/src/curate_gpt/utils/tokens.py → src/curategpt/utils/tokens.py b/src/curate_gpt/utils/tokens.py → src/curategpt/utils/tokens.py
diff --git a/src/curate_gpt/utils/vector_algorithms.py → src/curategpt/utils/vector_algorithms.py b/src/curate_gpt/utils/vector_algorithms.py → src/curategpt/utils/vector_algorithms.py
diff --git a/src/curate_gpt/utils/vectordb_operations.py → src/curategpt/utils/vectordb_operations.py b/src/curate_gpt/utils/vectordb_operations.py → src/curategpt/utils/vectordb_operations.py
diff --git a/src/curate_gpt/views/__init__.py → src/curategpt/views/__init__.py b/src/curate_gpt/views/__init__.py → src/curategpt/views/__init__.py
diff --git a/src/curate_gpt/views/namer.py → src/curategpt/views/namer.py b/src/curate_gpt/views/namer.py → src/curategpt/views/namer.py
diff --git a/src/curate_gpt/wrappers/__init__.py → src/curategpt/wrappers/__init__.py b/src/curate_gpt/wrappers/__init__.py → src/curategpt/wrappers/__init__.py
diff --git a/src/curate_gpt/wrappers/base_wrapper.py → src/curategpt/wrappers/base_wrapper.py b/src/curate_gpt/wrappers/base_wrapper.py → src/curategpt/wrappers/base_wrapper.py
diff --git a/src/curate_gpt/wrappers/bio/__init__.py → src/curategpt/wrappers/bio/__init__.py b/src/curate_gpt/wrappers/bio/__init__.py → src/curategpt/wrappers/bio/__init__.py
diff --git a/...gpt/wrappers/bio/alliance_gene_wrapper.py → ...gpt/wrappers/bio/alliance_gene_wrapper.py b/...gpt/wrappers/bio/alliance_gene_wrapper.py → ...gpt/wrappers/bio/alliance_gene_wrapper.py
diff --git a/...urate_gpt/wrappers/bio/bacdive_wrapper.py → ...curategpt/wrappers/bio/bacdive_wrapper.py b/...urate_gpt/wrappers/bio/bacdive_wrapper.py → ...curategpt/wrappers/bio/bacdive_wrapper.py
diff --git a/src/curate_gpt/wrappers/bio/gocam_wrapper.py → src/curategpt/wrappers/bio/gocam_wrapper.py b/src/curate_gpt/wrappers/bio/gocam_wrapper.py → src/curategpt/wrappers/bio/gocam_wrapper.py
diff --git a/...ate_gpt/wrappers/bio/mediadive_wrapper.py → ...rategpt/wrappers/bio/mediadive_wrapper.py b/...ate_gpt/wrappers/bio/mediadive_wrapper.py → ...rategpt/wrappers/bio/mediadive_wrapper.py
diff --git a/...urate_gpt/wrappers/bio/omicsdi_wrapper.py → ...curategpt/wrappers/bio/omicsdi_wrapper.py b/...urate_gpt/wrappers/bio/omicsdi_wrapper.py → ...curategpt/wrappers/bio/omicsdi_wrapper.py
diff --git a/...rate_gpt/wrappers/bio/reactome_wrapper.py → ...urategpt/wrappers/bio/reactome_wrapper.py b/...rate_gpt/wrappers/bio/reactome_wrapper.py → ...urategpt/wrappers/bio/reactome_wrapper.py
diff --git a/...urate_gpt/wrappers/bio/uniprot_wrapper.py → ...curategpt/wrappers/bio/uniprot_wrapper.py b/...urate_gpt/wrappers/bio/uniprot_wrapper.py → ...curategpt/wrappers/bio/uniprot_wrapper.py
diff --git a/src/curate_gpt/wrappers/clinical/__init__.py → src/curategpt/wrappers/clinical/__init__.py b/src/curate_gpt/wrappers/clinical/__init__.py → src/curategpt/wrappers/clinical/__init__.py
diff --git a/..._gpt/wrappers/clinical/clinvar_wrapper.py → ...egpt/wrappers/clinical/clinvar_wrapper.py b/..._gpt/wrappers/clinical/clinvar_wrapper.py → ...egpt/wrappers/clinical/clinvar_wrapper.py
diff --git a/...te_gpt/wrappers/clinical/ctgov_wrapper.py → ...ategpt/wrappers/clinical/ctgov_wrapper.py b/...te_gpt/wrappers/clinical/ctgov_wrapper.py → ...ategpt/wrappers/clinical/ctgov_wrapper.py
diff --git a/.../wrappers/clinical/hpoa_by_pub_wrapper.py → .../wrappers/clinical/hpoa_by_pub_wrapper.py b/.../wrappers/clinical/hpoa_by_pub_wrapper.py → .../wrappers/clinical/hpoa_by_pub_wrapper.py
diff --git a/...ate_gpt/wrappers/clinical/hpoa_wrapper.py → ...rategpt/wrappers/clinical/hpoa_wrapper.py b/...ate_gpt/wrappers/clinical/hpoa_wrapper.py → ...rategpt/wrappers/clinical/hpoa_wrapper.py
diff --git a/...te_gpt/wrappers/clinical/maxoa_wrapper.py → ...ategpt/wrappers/clinical/maxoa_wrapper.py b/...te_gpt/wrappers/clinical/maxoa_wrapper.py → ...ategpt/wrappers/clinical/maxoa_wrapper.py
diff --git a/src/curate_gpt/wrappers/general/__init__.py → src/curategpt/wrappers/general/__init__.py b/src/curate_gpt/wrappers/general/__init__.py → src/curategpt/wrappers/general/__init__.py
diff --git a/...pt/wrappers/general/filesystem_wrapper.py → ...pt/wrappers/general/filesystem_wrapper.py b/...pt/wrappers/general/filesystem_wrapper.py → ...pt/wrappers/general/filesystem_wrapper.py
diff --git a/...te_gpt/wrappers/general/github_wrapper.py → ...ategpt/wrappers/general/github_wrapper.py b/...te_gpt/wrappers/general/github_wrapper.py → ...ategpt/wrappers/general/github_wrapper.py
diff --git a/.../wrappers/general/google_drive_wrapper.py → .../wrappers/general/google_drive_wrapper.py b/.../wrappers/general/google_drive_wrapper.py → .../wrappers/general/google_drive_wrapper.py
diff --git a/...e_gpt/wrappers/general/gspread_wrapper.py → ...tegpt/wrappers/general/gspread_wrapper.py b/...e_gpt/wrappers/general/gspread_wrapper.py → ...tegpt/wrappers/general/gspread_wrapper.py
diff --git a/...rate_gpt/wrappers/general/json_wrapper.py → ...urategpt/wrappers/general/json_wrapper.py b/...rate_gpt/wrappers/general/json_wrapper.py → ...urategpt/wrappers/general/json_wrapper.py
diff --git a/...wrappers/general/linkml_schema_wrapper.py → ...wrappers/general/linkml_schema_wrapper.py b/...wrappers/general/linkml_schema_wrapper.py → ...wrappers/general/linkml_schema_wrapper.py
diff --git a/...te_gpt/wrappers/investigation/__init__.py → ...ategpt/wrappers/investigation/__init__.py b/...te_gpt/wrappers/investigation/__init__.py → ...ategpt/wrappers/investigation/__init__.py
diff --git a/...ers/investigation/ess_deepdive_wrapper.py → ...ers/investigation/ess_deepdive_wrapper.py b/...ers/investigation/ess_deepdive_wrapper.py → ...ers/investigation/ess_deepdive_wrapper.py
diff --git a/...pers/investigation/fairsharing_wrapper.py → ...pers/investigation/fairsharing_wrapper.py b/...pers/investigation/fairsharing_wrapper.py → ...pers/investigation/fairsharing_wrapper.py
diff --git a/...gpt/wrappers/investigation/jgi_wrapper.py → ...gpt/wrappers/investigation/jgi_wrapper.py b/...gpt/wrappers/investigation/jgi_wrapper.py → ...gpt/wrappers/investigation/jgi_wrapper.py
diff --git a/.../investigation/ncbi_bioproject_wrapper.py → .../investigation/ncbi_bioproject_wrapper.py b/.../investigation/ncbi_bioproject_wrapper.py → .../investigation/ncbi_bioproject_wrapper.py
diff --git a/...s/investigation/ncbi_biosample_wrapper.py → ...s/investigation/ncbi_biosample_wrapper.py b/...s/investigation/ncbi_biosample_wrapper.py → ...s/investigation/ncbi_biosample_wrapper.py
diff --git a/...pt/wrappers/investigation/nmdc_wrapper.py → ...pt/wrappers/investigation/nmdc_wrapper.py b/...pt/wrappers/investigation/nmdc_wrapper.py → ...pt/wrappers/investigation/nmdc_wrapper.py
diff --git a/src/curate_gpt/wrappers/legal/__init__.py → src/curategpt/wrappers/legal/__init__.py b/src/curate_gpt/wrappers/legal/__init__.py → src/curategpt/wrappers/legal/__init__.py
diff --git a/...pt/wrappers/legal/reusabledata_wrapper.py → ...pt/wrappers/legal/reusabledata_wrapper.py b/...pt/wrappers/legal/reusabledata_wrapper.py → ...pt/wrappers/legal/reusabledata_wrapper.py
diff --git a/...urate_gpt/wrappers/literature/__init__.py → ...curategpt/wrappers/literature/__init__.py b/...urate_gpt/wrappers/literature/__init__.py → ...curategpt/wrappers/literature/__init__.py
diff --git a/...e_gpt/wrappers/literature/bioc_wrapper.py → ...tegpt/wrappers/literature/bioc_wrapper.py b/...e_gpt/wrappers/literature/bioc_wrapper.py → ...tegpt/wrappers/literature/bioc_wrapper.py
diff --git a/...gpt/wrappers/literature/eutils_wrapper.py → ...gpt/wrappers/literature/eutils_wrapper.py b/...gpt/wrappers/literature/eutils_wrapper.py → ...gpt/wrappers/literature/eutils_wrapper.py
diff --git a/...te_gpt/wrappers/literature/pmc_wrapper.py → ...ategpt/wrappers/literature/pmc_wrapper.py b/...te_gpt/wrappers/literature/pmc_wrapper.py → ...ategpt/wrappers/literature/pmc_wrapper.py
diff --git a/...gpt/wrappers/literature/pubmed_wrapper.py → ...gpt/wrappers/literature/pubmed_wrapper.py b/...gpt/wrappers/literature/pubmed_wrapper.py → ...gpt/wrappers/literature/pubmed_wrapper.py
diff --git a/.../wrappers/literature/wikipedia_wrapper.py → .../wrappers/literature/wikipedia_wrapper.py b/.../wrappers/literature/wikipedia_wrapper.py → .../wrappers/literature/wikipedia_wrapper.py
diff --git a/src/curate_gpt/wrappers/ontology/__init__.py → src/curategpt/wrappers/ontology/__init__.py b/src/curate_gpt/wrappers/ontology/__init__.py → src/curategpt/wrappers/ontology/__init__.py
diff --git a/...pt/wrappers/ontology/bioportal_wrapper.py → ...pt/wrappers/ontology/bioportal_wrapper.py b/...pt/wrappers/ontology/bioportal_wrapper.py → ...pt/wrappers/ontology/bioportal_wrapper.py
diff --git a/...rate_gpt/wrappers/ontology/cell_type.yaml → ...urategpt/wrappers/ontology/cell_type.yaml b/...rate_gpt/wrappers/ontology/cell_type.yaml → ...urategpt/wrappers/ontology/cell_type.yaml
diff --git a/...pt/wrappers/ontology/oboformat_wrapper.py → ...pt/wrappers/ontology/oboformat_wrapper.py b/...pt/wrappers/ontology/oboformat_wrapper.py → ...pt/wrappers/ontology/oboformat_wrapper.py
diff --git a/src/curate_gpt/wrappers/ontology/ontology.py → src/curategpt/wrappers/ontology/ontology.py b/src/curate_gpt/wrappers/ontology/ontology.py → src/curategpt/wrappers/ontology/ontology.py
diff --git a/...urate_gpt/wrappers/ontology/ontology.yaml → ...curategpt/wrappers/ontology/ontology.yaml b/...urate_gpt/wrappers/ontology/ontology.yaml → ...curategpt/wrappers/ontology/ontology.yaml
diff --git a/...gpt/wrappers/ontology/ontology_wrapper.py → ...gpt/wrappers/ontology/ontology_wrapper.py b/...gpt/wrappers/ontology/ontology_wrapper.py → ...gpt/wrappers/ontology/ontology_wrapper.py