groom dependencies

[turbomam]

poetry add --group dev deptry
poetry run deptry .

[turbomam]

nmdc_schema/anyuri_strings_to_iris.py:4:8: DEP003 'curies' imported but it is a transitive dependency
nmdc_schema/dump_single_modality.py:7:8: DEP003 'requests' imported but it is a transitive dependency
nmdc_schema/nmdc.py:17:1: DEP003 'jsonasobj2' imported but it is a transitive dependency
nmdc_schema/nmdc_schema_accepting_legacy_ids.py:17:1: DEP003 'jsonasobj2' imported but it is a transitive dependency
nmdc_schema/validate_nmdc_json.py:12:14: DEP003 'jsonschema' imported but it is a transitive dependency
nmdc_schema/validate_nmdc_json.py:14:1: DEP003 'deprecated' imported but it is a transitive dependency
notebooks/find-ControlledTermValue-usages.ipynb:7:8: DEP003 'requests' imported but it is a transitive dependency
notebooks/find-ControlledTermValue-usages.ipynb:8:8: DEP003 'pandas' imported but it is a transitive dependency
notebooks/nist_bioeconomy_lexicon_scraper.ipynb:3:8: DEP003 'requests' imported but it is a transitive dependency
notebooks/nist_bioeconomy_lexicon_scraper.ipynb:5:1: DEP003 'tabulate' imported but it is a transitive dependency
src/scripts/experimental/class_sparql.py:11:1: DEP003 'SPARQLWrapper' imported but it is a transitive dependency
src/scripts/experimental/class_sparql.py:8:8: DEP003 'curies' imported but it is a transitive dependency
src/scripts/experimental/class_sparql.py:9:8: DEP003 'pandas' imported but it is a transitive dependency
src/scripts/ncbi_nmdc_exact_term_matching.py:7:8: DEP003 'requests' imported but it is a transitive dependency
src/scripts/ncbi_nmdc_exact_term_matching.py:8:8: DEP003 'pandas' imported but it is a transitive dependency
src/scripts/ncbi_postgres_nmdc_exact_term_matching.py:5:8: DEP003 'requests' imported but it is a transitive dependency
src/scripts/ncbi_postgres_nmdc_exact_term_matching.py:6:8: DEP003 'pandas' imported but it is a transitive dependency
src/scripts/nmdc_database_tools.py:13:8: DEP003 'requests' imported but it is a transitive dependency
src/scripts/report_biosamples_per_study.py:3:8: DEP003 'requests' imported but it is a transitive dependency
src/scripts/task_specific_code/insert_many_pymongo.py:7:8: DEP003 'requests' imported but it is a transitive dependency

[turbomam]

nmdc_schema/anyuri_strings_to_iris.py:3:8: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/anyuri_strings_to_iris.py:5:8: DEP004 'rdflib' imported but declared as a dev dependency
nmdc_schema/anyuri_strings_to_iris.py:6:1: DEP004 'rdflib' imported but declared as a dev dependency
nmdc_schema/dump_single_modality.py:3:8: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/dump_single_modality.py:4:8: DEP004 'click_log' imported but declared as a dev dependency
nmdc_schema/dump_single_modality.py:8:1: DEP004 'dotenv' imported but declared as a dev dependency
nmdc_schema/migration_recursion.py:7:8: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/migration_recursion.py:8:8: DEP004 'click_log' imported but declared as a dev dependency
nmdc_schema/migrators/cli/create_migrator.py:6:8: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/nmdc_data.py:12:8: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/nmdc.py:29:1: DEP004 'rdflib' imported but declared as a dev dependency
nmdc_schema/nmdc_schema_accepting_legacy_ids.py:29:1: DEP004 'rdflib' imported but declared as a dev dependency
nmdc_schema/nmdc_version.py:5:23: DEP004 'click' imported but declared as a dev dependency
nmdc_schema/validate_nmdc_json.py:12:26: DEP004 'click' imported but declared as a dev dependency
notebooks/mongo_doc_top_slot_usage_counts.ipynb:4:1: DEP004 'dotenv' imported but declared as a dev dependency
src/scripts/analyze_mentions_of_ids.py:5:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/check_examples_class_coverage.py:3:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/class_instantiation_counts.py:2:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/database_to_json_list_files.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/date_created_blank_node.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/experimental/class_sparql.py:14:1: DEP004 'SPARQLBurger' imported but declared as a dev dependency
src/scripts/experimental/class_sparql.py:7:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/interleave_yaml.py:2:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/ncbi_nmdc_exact_term_matching.py:6:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/ncbi_postgres_nmdc_exact_term_matching.py:8:1: DEP004 'dotenv' imported but declared as a dev dependency
src/scripts/nmdc_database_tools.py:10:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/report_biosamples_per_study.py:2:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/report_usages.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/schema_pattern_linting.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/schema_view_relation_graph.py:4:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/schema_view_relation_graph.py:6:1: DEP004 'rdflib' imported but declared as a dev dependency
src/scripts/scrutinize_elements.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/slot_range_type_reporter.py:1:8: DEP004 'click' imported but declared as a dev dependency
src/scripts/task_specific_code/insert_many_pymongo.py:4:8: DEP004 'click_log' imported but declared as a dev dependency
src/scripts/task_specific_code/insert_many_pymongo.py:5:8: DEP004 'click' imported but declared as a dev dependency

[turbomam]

nmdc_schema/migration_recursion.py:9:8: DEP001 'yaml' imported but missing from the dependency definitions
nmdc_schema/migrators/helpers.py:5:8: DEP001 'yaml' imported but missing from the dependency definitions
nmdc_schema/nmdc_data.py:13:8: DEP001 'yaml' imported but missing from the dependency definitions
nmdc_schema/nmdc_version.py:5:8: DEP001 'pkg_resources' imported but missing from the dependency definitions
notebooks/nist_bioeconomy_lexicon_scraper.ipynb:4:1: DEP001 'bs4' imported but missing from the dependency definitions
src/scripts/check_examples_class_coverage.py:4:8: DEP001 'yaml' imported but missing from the dependency definitions
src/scripts/database_to_json_list_files.py:2:8: DEP001 'yaml' imported but missing from the dependency definitions
src/scripts/experimental/partial_imports_graph.py:4:8: DEP001 'networkx' imported but missing from the dependency definitions
src/scripts/experimental/partial_imports_graph.py:5:8: DEP001 'plotly' imported but missing from the dependency definitions
src/scripts/interleave_yaml.py:5:8: DEP001 'yaml' imported but missing from the dependency definitions
src/scripts/ncbi_nmdc_exact_term_matching.py:2:1: DEP001 'bs4' imported but missing from the dependency definitions
src/scripts/ncbi_postgres_nmdc_exact_term_matching.py:7:8: DEP001 'psycopg2' imported but missing from the dependency definitions
src/scripts/nmdc_database_tools.py:15:8: DEP001 'yaml' imported but missing from the dependency definitions

[turbomam]

pyproject.toml: DEP002 'mkdocs' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'mkdocs-material' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'mkdocs-mermaid2-plugin' defined as a dependency but not used in the codebase
pyproject.toml: DEP002 'mkdocs-redirects' defined as a dependency but not used in the codebase

[eecavanna]

pyproject.toml: DEP002 'mkdocs-redirects' defined as a dependency but not used in the codebase

The mkdocs-redirects package underlies the redirects configured in mkdocs.yml:

plugins:
  - search
  - mermaid2:
      version: 10.9.0
  - redirects: # reference: https://github.com/mkdocs/mkdocs-redirects
      redirect_maps:
        'home.md': 'index.md'  # redirects "/home" to "/"