move stuff

cancervariants · Mar 29, 2024 · 3dfee5f · 3dfee5f
1 parent 69c0a2c
commit 3dfee5f
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Showing 26 changed files with 6 additions and 8 deletions.
diff --git a/.gitignore b/.gitignore
@@ -124,7 +124,7 @@ pytest.ini
 .DS_Store
 
 # data files
-metakb/data/*
+src/metakb/data/*
 analysis/graph/*.json
 analysis/graph/*.ipynb
 

diff --git a/Pipfile b/Pipfile
@@ -11,7 +11,6 @@ disease-normalizer = {version = "~=0.4.0.dev3", extras = ["etl"]}
 thera-py = {version = "~=0.5.0.dev3", extras = ["etl"]}
 civicpy = "~=3.0.0"
 requests = "*"
-jsondiff = "*"
 pydantic = "==2.*"
 requests-cache = "*"
 neo4j = "==5.*"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,5 @@
 [project]
-name = metakb
+name = "metakb"
 authors = [
     {name = "Alex H Wagner"},
     {name = "Kori Kuzma"},
@@ -32,7 +32,6 @@ dependencies = [
     "disease-normalizer[etl]~=0.4.0.dev0",
     "thera-py[etl]~=0.5.0.dev1",
     "requests",
-    "jsondiff",
     "pydantic~=2.1",
     "requests-cache",
     "neo4j",
@@ -46,7 +45,7 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 tests = ["pytest", "pytest-cov", "mock", "pytest-asyncio"]
-dev = ["pre-commit", "flake8", "flake8-docstrings", "ipykernel"]
+dev = ["pre-commit", "flake8", "flake8-docstrings"]
 
 [project.urls]
 Homepage = "https://github.com/cancervariants/metakb"
@@ -68,7 +67,7 @@ version = {attr = "metakb.version.__version__"}
 where = ["src"]
 
 [tool.pytest.ini_options]
-addopts = "--cov=src --cov-report term-missing"
+addopts = "--cov=src --cov-report term-missing --ignore=codebuild/"
 testpaths = ["tests"]
 
 [tool.coverage.run]

diff --git a/metakb/__init__.py → src/metakb/__init__.py b/metakb/__init__.py → src/metakb/__init__.py
diff --git a/metakb/cli.py → src/metakb/cli.py b/metakb/cli.py → src/metakb/cli.py
@@ -182,7 +182,7 @@ async def update_metakb_db(
         g.close()
         end = timer()
         echo_info(
-            f"Successfully loaded neo4j database in {(end-start):.5f} s\n"
+            f"Successfully loaded neo4j database in {(end - start):.5f} s\n"
         )
 
     s3_cdm_pattern = re.compile(
@@ -288,7 +288,7 @@ async def _transform_sources() -> None:
         total_end = timer()
         echo_info(
             f"Successfully transformed all sources to CDM in "
-            f"{(total_end-total_start):.5f} s\n"
+            f"{(total_end - total_start):.5f} s\n"
         )
 
     def _load_normalizers_db(self, load_normalizer_db):

diff --git a/metakb/database.py → src/metakb/database.py b/metakb/database.py → src/metakb/database.py
diff --git a/metakb/exceptions.py → src/metakb/exceptions.py b/metakb/exceptions.py → src/metakb/exceptions.py
diff --git a/metakb/harvesters/__init__.py → src/metakb/harvesters/__init__.py b/metakb/harvesters/__init__.py → src/metakb/harvesters/__init__.py
diff --git a/metakb/harvesters/base.py → src/metakb/harvesters/base.py b/metakb/harvesters/base.py → src/metakb/harvesters/base.py
diff --git a/metakb/harvesters/civic.py → src/metakb/harvesters/civic.py b/metakb/harvesters/civic.py → src/metakb/harvesters/civic.py
diff --git a/metakb/harvesters/moa.py → src/metakb/harvesters/moa.py b/metakb/harvesters/moa.py → src/metakb/harvesters/moa.py
diff --git a/metakb/main.py → src/metakb/main.py b/metakb/main.py → src/metakb/main.py
diff --git a/metakb/normalizers.py → src/metakb/normalizers.py b/metakb/normalizers.py → src/metakb/normalizers.py
diff --git a/metakb/query.py → src/metakb/query.py b/metakb/query.py → src/metakb/query.py
diff --git a/metakb/schemas/__init__.py → src/metakb/schemas/__init__.py b/metakb/schemas/__init__.py → src/metakb/schemas/__init__.py
diff --git a/metakb/schemas/annotation.py → src/metakb/schemas/annotation.py b/metakb/schemas/annotation.py → src/metakb/schemas/annotation.py
diff --git a/metakb/schemas/api.py → src/metakb/schemas/api.py b/metakb/schemas/api.py → src/metakb/schemas/api.py
diff --git a/metakb/schemas/app.py → src/metakb/schemas/app.py b/metakb/schemas/app.py → src/metakb/schemas/app.py
diff --git a/metakb/schemas/categorical_variation.py → src/metakb/schemas/categorical_variation.py b/metakb/schemas/categorical_variation.py → src/metakb/schemas/categorical_variation.py
diff --git a/metakb/schemas/variation_statement.py → src/metakb/schemas/variation_statement.py b/metakb/schemas/variation_statement.py → src/metakb/schemas/variation_statement.py
diff --git a/metakb/transform/README.md → src/metakb/transform/README.md b/metakb/transform/README.md → src/metakb/transform/README.md
diff --git a/metakb/transform/__init__.py → src/metakb/transform/__init__.py b/metakb/transform/__init__.py → src/metakb/transform/__init__.py
diff --git a/metakb/transform/base.py → src/metakb/transform/base.py b/metakb/transform/base.py → src/metakb/transform/base.py
diff --git a/metakb/transform/civic.py → src/metakb/transform/civic.py b/metakb/transform/civic.py → src/metakb/transform/civic.py
diff --git a/metakb/transform/moa.py → src/metakb/transform/moa.py b/metakb/transform/moa.py → src/metakb/transform/moa.py
diff --git a/metakb/version.py → src/metakb/version.py b/metakb/version.py → src/metakb/version.py