build: modernize build configs (#533)

* Use the "src" layout instead of a "flat" layout * Move build settings into pyproject.toml
cancervariants · Feb 13, 2024 · c73d476 · c73d476
1 parent 415b735
commit c73d476
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Showing 128 changed files with 74 additions and 78 deletions.
diff --git a/.gitignore b/.gitignore
@@ -16,10 +16,7 @@ dist/
 
 .mypy_cache/
 
-variation/data/seqrepo/
-variation/data/uta_20180821
-variation/data/notebooks
-variation/data/*.txt
+src/variation/data
 
 Pipfile.lock
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,8 +1,77 @@
+[project]
+name = "variation-normalizer"
+authors = [
+ {name = "Alex Wagner"},
+ {name = "Kori Kuzma"},
+ {name = "James Stevenson"}
+]
+readme = "README.md"
+classifiers = [
+ "Development Status :: 3 - Alpha",
+ "Framework :: FastAPI",
+ "Framework :: Pydantic",
+ "Framework :: Pydantic :: 2",
+ "Intended Audience :: Science/Research",
+ "Intended Audience :: Developers",
+ "Topic :: Scientific/Engineering :: Bio-Informatics",
+ "License :: OSI Approved :: MIT License",
+ "Programming Language :: Python :: 3",
+ "Programming Language :: Python :: 3.8",
+ "Programming Language :: Python :: 3.9",
+ "Programming Language :: Python :: 3.10",
+ "Programming Language :: Python :: 3.11",
+]
+requires-python = ">=3.8"
+description = "VICC normalization routine for variations"
+license = {file = "LICENSE"}
+dependencies = [
+ "biocommons.seqrepo",
+ "fastapi",
+ "uvicorn",
+ "pydantic ==2.*",
+ "ga4gh.vrs[extras] ~= 2.0.0a2",
+ "gene-normalizer ~=0.3.0.dev1",
+ "boto3",
+ "cool-seq-tool ~=0.4.0.dev1",
+ "bioutils"
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+test = ["pytest>=6.0", "pytest-cov", "pytest-asyncio"]
+dev = ["pre-commit", "ruff==0.2.0", "psycopg2-binary", "jupyter", "ipykernel"]
+
+[project.urls]
+Homepage = "https://github.com/cancervariants/variation-normalization"
+Documentation = "https://github.com/cancervariants/variation-normalization"
+Changelog = "https://github.com/cancervariants/variation-normalization/releases"
+Source = "https://github.com/cancervariants/variation-normalization"
+"Bug Tracker" = "https://github.com/cancervariants/variation-normalization/issues"
+
 [build-system]
-requires = ["setuptools", "wheel"]
-build-backend = "setuptools.build_meta:__legacy__"
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = {attr = "variation.version.__version__"}
+
+# Scanning for namespace packages in the ``src`` directory is true by
+# default in pyproject.toml, so you do NOT need to include the
+# `tool.setuptools.packages.find` if it looks like the following:
+# [tool.setuptools.packages.find]
+# namespaces = true
+# where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=src --cov-report term-missing"
+testpaths = ["tests"]
+
+[tool.coverage.run]
+branch = true
 
 [tool.ruff]
+src = ["src"]
+
 lint.select = [
  "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
  "E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
@@ -72,10 +141,6 @@ lint.ignore = [
  "S321",
 ]
 
-exclude = [
- "setup.py"
-]
-
 [tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
@@ -86,7 +151,7 @@ exclude = [
 # B011 - assert-false
 # RUF001 - ambiguous-unicode-character-string
 "tests/*" = ["ANN001", "ANN102", "ANN2", "S101", "B011"]
-"variation/schemas/*" = ["ANN001", "ANN201", "N805", "S101"]
+"src/variation/schemas/*" = ["ANN001", "ANN201", "N805", "S101"]
 "codebuild/*" = ["T201"]
 
 [tool.ruff.lint.flake8-bugbear]

diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/variation/__init__.py → src/variation/__init__.py b/variation/__init__.py → src/variation/__init__.py
diff --git a/variation/classifiers/__init__.py → src/variation/classifiers/__init__.py b/variation/classifiers/__init__.py → src/variation/classifiers/__init__.py
diff --git a/...n/classifiers/amplification_classifier.py → ...n/classifiers/amplification_classifier.py b/...n/classifiers/amplification_classifier.py → ...n/classifiers/amplification_classifier.py
diff --git a/...n/classifiers/cdna_deletion_classifier.py → ...n/classifiers/cdna_deletion_classifier.py b/...n/classifiers/cdna_deletion_classifier.py → ...n/classifiers/cdna_deletion_classifier.py
diff --git a/...ion/classifiers/cdna_delins_classifier.py → ...ion/classifiers/cdna_delins_classifier.py b/...ion/classifiers/cdna_delins_classifier.py → ...ion/classifiers/cdna_delins_classifier.py
diff --git a/.../classifiers/cdna_insertion_classifier.py → .../classifiers/cdna_insertion_classifier.py b/.../classifiers/cdna_insertion_classifier.py → .../classifiers/cdna_insertion_classifier.py
diff --git a/...ifiers/cdna_reference_agree_classifier.py → ...ifiers/cdna_reference_agree_classifier.py b/...ifiers/cdna_reference_agree_classifier.py → ...ifiers/cdna_reference_agree_classifier.py
diff --git a/...assifiers/cdna_substitution_classifier.py → ...assifiers/cdna_substitution_classifier.py b/...assifiers/cdna_substitution_classifier.py → ...assifiers/cdna_substitution_classifier.py
diff --git a/variation/classifiers/classifier.py → src/variation/classifiers/classifier.py b/variation/classifiers/classifier.py → src/variation/classifiers/classifier.py
diff --git a/...classifiers/genomic_deletion_ambiguous.py → ...classifiers/genomic_deletion_ambiguous.py b/...classifiers/genomic_deletion_ambiguous.py → ...classifiers/genomic_deletion_ambiguous.py
diff --git a/...lassifiers/genomic_deletion_classifier.py → ...lassifiers/genomic_deletion_classifier.py b/...lassifiers/genomic_deletion_classifier.py → ...lassifiers/genomic_deletion_classifier.py
diff --git a/.../classifiers/genomic_delins_classifier.py → .../classifiers/genomic_delins_classifier.py b/.../classifiers/genomic_delins_classifier.py → .../classifiers/genomic_delins_classifier.py
diff --git a/...ssifiers/genomic_duplication_ambiguous.py → ...ssifiers/genomic_duplication_ambiguous.py b/...ssifiers/genomic_duplication_ambiguous.py → ...ssifiers/genomic_duplication_ambiguous.py
diff --git a/...sifiers/genomic_duplication_classifier.py → ...sifiers/genomic_duplication_classifier.py b/...sifiers/genomic_duplication_classifier.py → ...sifiers/genomic_duplication_classifier.py
diff --git a/...assifiers/genomic_insertion_classifier.py → ...assifiers/genomic_insertion_classifier.py b/...assifiers/genomic_insertion_classifier.py → ...assifiers/genomic_insertion_classifier.py
diff --git a/...ers/genomic_reference_agree_classifier.py → ...ers/genomic_reference_agree_classifier.py b/...ers/genomic_reference_agree_classifier.py → ...ers/genomic_reference_agree_classifier.py
diff --git a/...ifiers/genomic_substitution_classifier.py → ...ifiers/genomic_substitution_classifier.py b/...ifiers/genomic_substitution_classifier.py → ...ifiers/genomic_substitution_classifier.py
diff --git a/...tion/classifiers/gnomad_vcf_classifier.py → ...tion/classifiers/gnomad_vcf_classifier.py b/...tion/classifiers/gnomad_vcf_classifier.py → ...tion/classifiers/gnomad_vcf_classifier.py
diff --git a/variation/classifiers/hgvs_classifier.py → src/variation/classifiers/hgvs_classifier.py b/variation/classifiers/hgvs_classifier.py → src/variation/classifiers/hgvs_classifier.py
diff --git a/...lassifiers/protein_deletion_classifier.py → ...lassifiers/protein_deletion_classifier.py b/...lassifiers/protein_deletion_classifier.py → ...lassifiers/protein_deletion_classifier.py
diff --git a/.../classifiers/protein_delins_classifier.py → .../classifiers/protein_delins_classifier.py b/.../classifiers/protein_delins_classifier.py → .../classifiers/protein_delins_classifier.py
diff --git a/...assifiers/protein_insertion_classifier.py → ...assifiers/protein_insertion_classifier.py b/...assifiers/protein_insertion_classifier.py → ...assifiers/protein_insertion_classifier.py
diff --git a/...on/classifiers/protein_reference_agree.py → ...on/classifiers/protein_reference_agree.py b/...on/classifiers/protein_reference_agree.py → ...on/classifiers/protein_reference_agree.py
diff --git a/...assifiers/protein_stop_gain_classifier.py → ...assifiers/protein_stop_gain_classifier.py b/...assifiers/protein_stop_gain_classifier.py → ...assifiers/protein_stop_gain_classifier.py
diff --git a/...ifiers/protein_substitution_classifier.py → ...ifiers/protein_substitution_classifier.py b/...ifiers/protein_substitution_classifier.py → ...ifiers/protein_substitution_classifier.py
diff --git a/variation/classify.py → src/variation/classify.py b/variation/classify.py → src/variation/classify.py
diff --git a/variation/gnomad_vcf_to_protein_variation.py → ...iation/gnomad_vcf_to_protein_variation.py b/variation/gnomad_vcf_to_protein_variation.py → ...iation/gnomad_vcf_to_protein_variation.py
diff --git a/variation/hgvs_dup_del_mode.py → src/variation/hgvs_dup_del_mode.py b/variation/hgvs_dup_del_mode.py → src/variation/hgvs_dup_del_mode.py
diff --git a/variation/main.py → src/variation/main.py b/variation/main.py → src/variation/main.py
diff --git a/variation/normalize.py → src/variation/normalize.py b/variation/normalize.py → src/variation/normalize.py
diff --git a/variation/query.py → src/variation/query.py b/variation/query.py → src/variation/query.py
diff --git a/variation/regex.py → src/variation/regex.py b/variation/regex.py → src/variation/regex.py
diff --git a/variation/schemas/__init__.py → src/variation/schemas/__init__.py b/variation/schemas/__init__.py → src/variation/schemas/__init__.py
diff --git a/variation/schemas/app_schemas.py → src/variation/schemas/app_schemas.py b/variation/schemas/app_schemas.py → src/variation/schemas/app_schemas.py
diff --git a/...schemas/classification_response_schema.py → ...schemas/classification_response_schema.py b/...schemas/classification_response_schema.py → ...schemas/classification_response_schema.py
diff --git a/variation/schemas/copy_number_schema.py → src/variation/schemas/copy_number_schema.py b/variation/schemas/copy_number_schema.py → src/variation/schemas/copy_number_schema.py
diff --git a/...n/schemas/gnomad_vcf_to_protein_schema.py → ...n/schemas/gnomad_vcf_to_protein_schema.py b/...n/schemas/gnomad_vcf_to_protein_schema.py → ...n/schemas/gnomad_vcf_to_protein_schema.py
diff --git a/...ion/schemas/hgvs_to_copy_number_schema.py → ...ion/schemas/hgvs_to_copy_number_schema.py b/...ion/schemas/hgvs_to_copy_number_schema.py → ...ion/schemas/hgvs_to_copy_number_schema.py
diff --git a/...tion/schemas/normalize_response_schema.py → ...tion/schemas/normalize_response_schema.py b/...tion/schemas/normalize_response_schema.py → ...tion/schemas/normalize_response_schema.py
diff --git a/variation/schemas/service_schema.py → src/variation/schemas/service_schema.py b/variation/schemas/service_schema.py → src/variation/schemas/service_schema.py
diff --git a/variation/schemas/to_vrs_response_schema.py → ...riation/schemas/to_vrs_response_schema.py b/variation/schemas/to_vrs_response_schema.py → ...riation/schemas/to_vrs_response_schema.py
diff --git a/variation/schemas/token_response_schema.py → ...ariation/schemas/token_response_schema.py b/variation/schemas/token_response_schema.py → ...ariation/schemas/token_response_schema.py
diff --git a/...on/schemas/translation_response_schema.py → ...on/schemas/translation_response_schema.py b/...on/schemas/translation_response_schema.py → ...on/schemas/translation_response_schema.py
diff --git a/...ion/schemas/validation_response_schema.py → ...ion/schemas/validation_response_schema.py b/...ion/schemas/validation_response_schema.py → ...ion/schemas/validation_response_schema.py
diff --git a/variation/schemas/variation_schema.py → src/variation/schemas/variation_schema.py b/variation/schemas/variation_schema.py → src/variation/schemas/variation_schema.py
diff --git a/...n/schemas/vrs_python_translator_schema.py → ...n/schemas/vrs_python_translator_schema.py b/...n/schemas/vrs_python_translator_schema.py → ...n/schemas/vrs_python_translator_schema.py
diff --git a/variation/to_copy_number_variation.py → src/variation/to_copy_number_variation.py b/variation/to_copy_number_variation.py → src/variation/to_copy_number_variation.py
diff --git a/variation/to_vrs.py → src/variation/to_vrs.py b/variation/to_vrs.py → src/variation/to_vrs.py
diff --git a/variation/tokenize.py → src/variation/tokenize.py b/variation/tokenize.py → src/variation/tokenize.py
diff --git a/variation/tokenizers/__init__.py → src/variation/tokenizers/__init__.py b/variation/tokenizers/__init__.py → src/variation/tokenizers/__init__.py
diff --git a/...izers/cdna_and_genomic_reference_agree.py → ...izers/cdna_and_genomic_reference_agree.py b/...izers/cdna_and_genomic_reference_agree.py → ...izers/cdna_and_genomic_reference_agree.py
diff --git a/variation/tokenizers/cdna_deletion.py → src/variation/tokenizers/cdna_deletion.py b/variation/tokenizers/cdna_deletion.py → src/variation/tokenizers/cdna_deletion.py
diff --git a/variation/tokenizers/cdna_delins.py → src/variation/tokenizers/cdna_delins.py b/variation/tokenizers/cdna_delins.py → src/variation/tokenizers/cdna_delins.py
diff --git a/variation/tokenizers/cdna_insertion.py → src/variation/tokenizers/cdna_insertion.py b/variation/tokenizers/cdna_insertion.py → src/variation/tokenizers/cdna_insertion.py
diff --git a/variation/tokenizers/cdna_substitution.py → ...variation/tokenizers/cdna_substitution.py b/variation/tokenizers/cdna_substitution.py → ...variation/tokenizers/cdna_substitution.py
diff --git a/...ation/tokenizers/free_text_categorical.py → ...ation/tokenizers/free_text_categorical.py b/...ation/tokenizers/free_text_categorical.py → ...ation/tokenizers/free_text_categorical.py
diff --git a/variation/tokenizers/gene_symbol.py → src/variation/tokenizers/gene_symbol.py b/variation/tokenizers/gene_symbol.py → src/variation/tokenizers/gene_symbol.py
diff --git a/variation/tokenizers/genomic_deletion.py → src/variation/tokenizers/genomic_deletion.py b/variation/tokenizers/genomic_deletion.py → src/variation/tokenizers/genomic_deletion.py
diff --git a/variation/tokenizers/genomic_delins.py → src/variation/tokenizers/genomic_delins.py b/variation/tokenizers/genomic_delins.py → src/variation/tokenizers/genomic_delins.py
diff --git a/variation/tokenizers/genomic_duplication.py → ...riation/tokenizers/genomic_duplication.py b/variation/tokenizers/genomic_duplication.py → ...riation/tokenizers/genomic_duplication.py
diff --git a/variation/tokenizers/genomic_insertion.py → ...variation/tokenizers/genomic_insertion.py b/variation/tokenizers/genomic_insertion.py → ...variation/tokenizers/genomic_insertion.py
diff --git a/variation/tokenizers/genomic_substitution.py → ...iation/tokenizers/genomic_substitution.py b/variation/tokenizers/genomic_substitution.py → ...iation/tokenizers/genomic_substitution.py
diff --git a/variation/tokenizers/gnomad_vcf.py → src/variation/tokenizers/gnomad_vcf.py b/variation/tokenizers/gnomad_vcf.py → src/variation/tokenizers/gnomad_vcf.py
diff --git a/variation/tokenizers/hgvs.py → src/variation/tokenizers/hgvs.py b/variation/tokenizers/hgvs.py → src/variation/tokenizers/hgvs.py
diff --git a/variation/tokenizers/protein_deletion.py → src/variation/tokenizers/protein_deletion.py b/variation/tokenizers/protein_deletion.py → src/variation/tokenizers/protein_deletion.py
diff --git a/variation/tokenizers/protein_delins.py → src/variation/tokenizers/protein_delins.py b/variation/tokenizers/protein_delins.py → src/variation/tokenizers/protein_delins.py
diff --git a/variation/tokenizers/protein_insertion.py → ...variation/tokenizers/protein_insertion.py b/variation/tokenizers/protein_insertion.py → ...variation/tokenizers/protein_insertion.py
diff --git a/...ion/tokenizers/protein_reference_agree.py → ...ion/tokenizers/protein_reference_agree.py b/...ion/tokenizers/protein_reference_agree.py → ...ion/tokenizers/protein_reference_agree.py
diff --git a/variation/tokenizers/protein_substitution.py → ...iation/tokenizers/protein_substitution.py b/variation/tokenizers/protein_substitution.py → ...iation/tokenizers/protein_substitution.py
diff --git a/variation/tokenizers/tokenizer.py → src/variation/tokenizers/tokenizer.py b/variation/tokenizers/tokenizer.py → src/variation/tokenizers/tokenizer.py
diff --git a/variation/translate.py → src/variation/translate.py b/variation/translate.py → src/variation/translate.py
diff --git a/variation/translators/__init__.py → src/variation/translators/__init__.py b/variation/translators/__init__.py → src/variation/translators/__init__.py
diff --git a/.../translators/ambiguous_translator_base.py → .../translators/ambiguous_translator_base.py b/.../translators/ambiguous_translator_base.py → .../translators/ambiguous_translator_base.py
diff --git a/variation/translators/amplification.py → src/variation/translators/amplification.py b/variation/translators/amplification.py → src/variation/translators/amplification.py
diff --git a/variation/translators/cdna_deletion.py → src/variation/translators/cdna_deletion.py b/variation/translators/cdna_deletion.py → src/variation/translators/cdna_deletion.py
diff --git a/variation/translators/cdna_delins.py → src/variation/translators/cdna_delins.py b/variation/translators/cdna_delins.py → src/variation/translators/cdna_delins.py
diff --git a/variation/translators/cdna_insertion.py → src/variation/translators/cdna_insertion.py b/variation/translators/cdna_insertion.py → src/variation/translators/cdna_insertion.py
diff --git a/...ation/translators/cdna_reference_agree.py → ...ation/translators/cdna_reference_agree.py b/...ation/translators/cdna_reference_agree.py → ...ation/translators/cdna_reference_agree.py
diff --git a/variation/translators/cdna_substitution.py → ...ariation/translators/cdna_substitution.py b/variation/translators/cdna_substitution.py → ...ariation/translators/cdna_substitution.py
diff --git a/...ation/translators/genomic_del_dup_base.py → ...ation/translators/genomic_del_dup_base.py b/...ation/translators/genomic_del_dup_base.py → ...ation/translators/genomic_del_dup_base.py
diff --git a/variation/translators/genomic_deletion.py → ...variation/translators/genomic_deletion.py b/variation/translators/genomic_deletion.py → ...variation/translators/genomic_deletion.py
diff --git a/...translators/genomic_deletion_ambiguous.py → ...translators/genomic_deletion_ambiguous.py b/...translators/genomic_deletion_ambiguous.py → ...translators/genomic_deletion_ambiguous.py
diff --git a/variation/translators/genomic_delins.py → src/variation/translators/genomic_delins.py b/variation/translators/genomic_delins.py → src/variation/translators/genomic_delins.py
diff --git a/variation/translators/genomic_duplication.py → ...iation/translators/genomic_duplication.py b/variation/translators/genomic_duplication.py → ...iation/translators/genomic_duplication.py
diff --git a/...nslators/genomic_duplication_ambiguous.py → ...nslators/genomic_duplication_ambiguous.py b/...nslators/genomic_duplication_ambiguous.py → ...nslators/genomic_duplication_ambiguous.py
diff --git a/variation/translators/genomic_insertion.py → ...ariation/translators/genomic_insertion.py b/variation/translators/genomic_insertion.py → ...ariation/translators/genomic_insertion.py
diff --git a/...on/translators/genomic_reference_agree.py → ...on/translators/genomic_reference_agree.py b/...on/translators/genomic_reference_agree.py → ...on/translators/genomic_reference_agree.py
diff --git a/...ation/translators/genomic_substitution.py → ...ation/translators/genomic_substitution.py b/...ation/translators/genomic_substitution.py → ...ation/translators/genomic_substitution.py
diff --git a/variation/translators/protein_deletion.py → ...variation/translators/protein_deletion.py b/variation/translators/protein_deletion.py → ...variation/translators/protein_deletion.py
diff --git a/variation/translators/protein_delins.py → src/variation/translators/protein_delins.py b/variation/translators/protein_delins.py → src/variation/translators/protein_delins.py
diff --git a/variation/translators/protein_insertion.py → ...ariation/translators/protein_insertion.py b/variation/translators/protein_insertion.py → ...ariation/translators/protein_insertion.py
diff --git a/...on/translators/protein_reference_agree.py → ...on/translators/protein_reference_agree.py b/...on/translators/protein_reference_agree.py → ...on/translators/protein_reference_agree.py
diff --git a/variation/translators/protein_stop_gain.py → ...ariation/translators/protein_stop_gain.py b/variation/translators/protein_stop_gain.py → ...ariation/translators/protein_stop_gain.py
diff --git a/...ation/translators/protein_substitution.py → ...ation/translators/protein_substitution.py b/...ation/translators/protein_substitution.py → ...ation/translators/protein_substitution.py
diff --git a/variation/translators/translator.py → src/variation/translators/translator.py b/variation/translators/translator.py → src/variation/translators/translator.py
diff --git a/variation/utils.py → src/variation/utils.py b/variation/utils.py → src/variation/utils.py
diff --git a/variation/validate.py → src/variation/validate.py b/variation/validate.py → src/variation/validate.py
diff --git a/variation/validators/__init__.py → src/variation/validators/__init__.py b/variation/validators/__init__.py → src/variation/validators/__init__.py
diff --git a/variation/validators/amplification.py → src/variation/validators/amplification.py b/variation/validators/amplification.py → src/variation/validators/amplification.py
diff --git a/variation/validators/cdna_deletion.py → src/variation/validators/cdna_deletion.py b/variation/validators/cdna_deletion.py → src/variation/validators/cdna_deletion.py
diff --git a/variation/validators/cdna_delins.py → src/variation/validators/cdna_delins.py b/variation/validators/cdna_delins.py → src/variation/validators/cdna_delins.py
diff --git a/variation/validators/cdna_insertion.py → src/variation/validators/cdna_insertion.py b/variation/validators/cdna_insertion.py → src/variation/validators/cdna_insertion.py
diff --git a/variation/validators/cdna_reference_agree.py → ...iation/validators/cdna_reference_agree.py b/variation/validators/cdna_reference_agree.py → ...iation/validators/cdna_reference_agree.py
diff --git a/variation/validators/cdna_substitution.py → ...variation/validators/cdna_substitution.py b/variation/validators/cdna_substitution.py → ...variation/validators/cdna_substitution.py
diff --git a/variation/validators/genomic_base.py → src/variation/validators/genomic_base.py b/variation/validators/genomic_base.py → src/variation/validators/genomic_base.py
diff --git a/variation/validators/genomic_deletion.py → src/variation/validators/genomic_deletion.py b/variation/validators/genomic_deletion.py → src/variation/validators/genomic_deletion.py
diff --git a/.../validators/genomic_deletion_ambiguous.py → .../validators/genomic_deletion_ambiguous.py b/.../validators/genomic_deletion_ambiguous.py → .../validators/genomic_deletion_ambiguous.py
diff --git a/variation/validators/genomic_delins.py → src/variation/validators/genomic_delins.py b/variation/validators/genomic_delins.py → src/variation/validators/genomic_delins.py
diff --git a/variation/validators/genomic_duplication.py → ...riation/validators/genomic_duplication.py b/variation/validators/genomic_duplication.py → ...riation/validators/genomic_duplication.py
diff --git a/...lidators/genomic_duplication_ambiguous.py → ...lidators/genomic_duplication_ambiguous.py b/...lidators/genomic_duplication_ambiguous.py → ...lidators/genomic_duplication_ambiguous.py
diff --git a/variation/validators/genomic_insertion.py → ...variation/validators/genomic_insertion.py b/variation/validators/genomic_insertion.py → ...variation/validators/genomic_insertion.py
diff --git a/...ion/validators/genomic_reference_agree.py → ...ion/validators/genomic_reference_agree.py b/...ion/validators/genomic_reference_agree.py → ...ion/validators/genomic_reference_agree.py
diff --git a/variation/validators/genomic_substitution.py → ...iation/validators/genomic_substitution.py b/variation/validators/genomic_substitution.py → ...iation/validators/genomic_substitution.py
diff --git a/variation/validators/protein_deletion.py → src/variation/validators/protein_deletion.py b/variation/validators/protein_deletion.py → src/variation/validators/protein_deletion.py
diff --git a/variation/validators/protein_delins.py → src/variation/validators/protein_delins.py b/variation/validators/protein_delins.py → src/variation/validators/protein_delins.py
diff --git a/variation/validators/protein_insertion.py → ...variation/validators/protein_insertion.py b/variation/validators/protein_insertion.py → ...variation/validators/protein_insertion.py
diff --git a/...ion/validators/protein_reference_agree.py → ...ion/validators/protein_reference_agree.py b/...ion/validators/protein_reference_agree.py → ...ion/validators/protein_reference_agree.py
diff --git a/variation/validators/protein_stop_gain.py → ...variation/validators/protein_stop_gain.py b/variation/validators/protein_stop_gain.py → ...variation/validators/protein_stop_gain.py
diff --git a/variation/validators/protein_substitution.py → ...iation/validators/protein_substitution.py b/variation/validators/protein_substitution.py → ...iation/validators/protein_substitution.py
diff --git a/variation/validators/validator.py → src/variation/validators/validator.py b/variation/validators/validator.py → src/variation/validators/validator.py
diff --git a/variation/version.py → src/variation/version.py b/variation/version.py → src/variation/version.py
diff --git a/variation/vrs_representation.py → src/variation/vrs_representation.py b/variation/vrs_representation.py → src/variation/vrs_representation.py
diff --git a/tests/to_copy_number_variation/test_hgvs_to_copy_number.py b/tests/to_copy_number_variation/test_hgvs_to_copy_number.py
@@ -3,7 +3,6 @@
 
 import pytest
 from ga4gh.vrs import models
-
 from tests.conftest import cnv_assertion_checks
 
 

diff --git a/tests/to_copy_number_variation/test_parsed_to_copy_number.py b/tests/to_copy_number_variation/test_parsed_to_copy_number.py
@@ -4,8 +4,8 @@
 import pytest
 from ga4gh.vrs import models
 from pydantic import ValidationError
-
 from tests.conftest import cnv_assertion_checks
+
 from variation.schemas.copy_number_schema import (
  ClinVarAssembly,
  Comparator,