Fix dependencies with deptry

[fpgmaas]

The project seems to contain some issues with the dependencies. These can be detected by running deptry.

• matplotlib, pandas and pyarrow are transitive dependencies. It would be a good idea to specify those as dependencies explicitly, to prevent the project from unexpectedly breaking in the future when one of the transitive dependencies is dropped.
• umap is missing from the project's dependencies.
• numba, fastparquet, scipy, swifter and textual are specified as dependencies, but they don't seem to be used in the codebase.

The detailed log of running deptry can be found below.

This PR aims to solve the issues with the project's dependencies. In a future PR we could consider adding it to the CI/CD pipeline to make sure the dependencies stay up-to-date.

deptry .
Scanning 417 files...

examples/custom_input/run.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
examples/custom_set_of_available_verbs/run.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
examples/custom_set_of_available_workflows/run.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
examples/interdependent_workflows/run.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
examples/single_verb/run.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
examples_notebooks/global_search.ipynb:5:8: DEP003 'pandas' imported but it is a transitive dependency
examples_notebooks/local_search.ipynb:5:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/emit/csv_table_emitter.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/emit/json_table_emitter.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/emit/parquet_table_emitter.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/emit/parquet_table_emitter.py:10:1: DEP003 'pyarrow' imported but it is a transitive dependency
graphrag/index/emit/table_emitter.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/graph/extractors/community_reports/build_mixed_context.py:5:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/graph/extractors/community_reports/prep_community_report_context.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/graph/extractors/community_reports/sort_context.py:5:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/graph/extractors/community_reports/utils.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/graph/visualization/compute_umap_positions.py:7:8: DEP003 'matplotlib' imported but it is a transitive dependency
graphrag/index/graph/visualization/compute_umap_positions.py:10:8: DEP001 'umap' imported but missing from the dependency definitions
graphrag/index/input/csv.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/input/load_input.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/input/text.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/run.py:18:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/text_splitting/text_splitting.py:14:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/typing.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/utils/dataframes.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/utils/dataframes.py:10:1: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/covariates/extract_covariates/extract_covariates.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/entities/extraction/entity_extract.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/entities/summarize/description_summarize.py:12:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/genid.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/clustering/cluster_graph.py:12:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/compute_edge_combined_degree.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/create.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/embed/embed_graph.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/layout/layout_graph.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/merge/merge_graphs.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/create_community_reports.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/prepare_community_reports.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/prepare_community_reports_claims.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/prepare_community_reports_edges.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/prepare_community_reports_nodes.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/report/restore_community_hierarchy.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/graph/unpack.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/overrides/aggregate.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/overrides/concat.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/overrides/merge.py:12:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/spread_json.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/text/chunk/text_chunk.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/text/embed/text_embed.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/text/replace/replace.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/text/split.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/text/translate/text_translate.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/unzip.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/index/verbs/zip.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/prompt_tune/loader/input.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/cli.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/context_builder/builders.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/context_builder/community_context.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/context_builder/conversation_history.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/context_builder/local_context.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/context_builder/source_context.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/indexer_adapters.py:11:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/loaders/dfs.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/loaders/utils.py:7:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/retrieval/community_reports.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/retrieval/covariates.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/retrieval/entities.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/retrieval/relationships.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/input/retrieval/text_units.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/structured_search/base.py:10:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/structured_search/global_search/community_context.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/structured_search/global_search/search.py:13:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/query/structured_search/local_search/mixed_context.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
graphrag/vector_stores/lancedb.py:12:8: DEP003 'pyarrow' imported but it is a transitive dependency
pyproject.toml: DEP002 'numba' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'fastparquet' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'scipy' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'swifter' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'textual' defined as a dependency but not used in the codebase
Found 79 dependency issues.

For more information, see the documentation: https://deptry.com/

Disclaimer: I am the author of deptry.

[fpgmaas]

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[fpgmaas]

Hi @AlonsoGuevara, did you maybe have the time to look into this? Could you approve the workflows to verify that the unit tests still pass? I understand that you may be quite busy with maintaining this new repo, so no rush. Thanks!