Add pyright/pytest config

.github/workflows/data-pipeline-ci.yml

@@ -34,3 +34,5 @@ jobs:
         run: black --check data-pipeline/src/data_pipeline
       - name: Run Ruff
         run: ruff data-pipeline/src/data_pipeline
+      - name: Run Pyright
+        run: pyright 

data-pipeline/check.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+echo "┏━━━ Running pyright ━━━━━━━━━━━━━━━━━━━"
+pyright
+
+echo "┏━━━ Running black ━━━━━━━━━━━━━━━━━━━"
+black src/data_pipeline
+black tests
+
+echo "┏━━━ Running ruff ━━━━━━━━━━━━━━━━━━━"
+ruff src/data_pipeline
+ruff tests --fix
+
+echo "┏━━━ Running pytest ━━━━━━━━━━━━━━━━━━━"
+pytest -m only

data-pipeline/pyproject.toml

@@ -19,6 +19,7 @@ pytest = "^7.4.2"
 ipython = "^8.15.0"
 ruff = "^0.0.290"
 black = "^23.9.1"
+pyright = "^1.1.327"
 
 [build-system]
 requires = ["poetry-core"]
@@ -30,3 +31,19 @@ line-length = 120
 [tool.ruff]
 line-length = 120
 
+[tool.pyright]
+include = [ 
+"src/data_pipeline/pipeline.py",
+"src/data_pipeline/config.py",
+"src/data_pipeline/helpers/write_schemas.py",
+"src/data_pipeline/helpers/logging.py",
+"src/data_pipeline/pipelines/gnomad_v4_variants.py",
+"src/data_pipeline/pipelines/gnomad_v4_coverage.py",
+# "src/data_pipeline/datasets/gnomad_v4",
+"tests"
+]
+reportMissingImports = true
+reportMissingTypeStubs = false
+typeCheckingMode = "basic"
+pythonVersion = "3.9"
+

data-pipeline/pytest.ini

@@ -0,0 +1,8 @@
+[pytest]
+testpaths =
+    tests
+addopts = --strict -W ignore -v -s --durations=0
+markers =
+    only: marked with "only"
+    long: takes a long time
+    broken: test is broken

data-pipeline/requirements.txt

@@ -790,6 +790,9 @@ mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "4.0" \
 nest-asyncio==1.5.8 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:25aa2ca0d2a5b5531956b9e273b45cf664cae2b145101d73b86b199978d48fdb \
     --hash=sha256:accda7a339a70599cb08f9dd09a67e0c2ef8d8d6f4c07f96ab203f2ae254e48d
+nodeenv==1.8.0 ; python_version >= "3.9" and python_version < "4.0" \
+    --hash=sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2 \
+    --hash=sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec
 numpy==1.25.2 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:0d60fbae8e0019865fc4784745814cff1c421df5afee233db6d88ab4f14655a2 \
     --hash=sha256:1a1329e26f46230bf77b02cc19e900db9b52f398d6722ca853349a782d4cff55 \
@@ -1113,6 +1116,9 @@ pygments==2.16.1 ; python_version >= "3.9" and python_version < "4.0" \
 pyjwt[crypto]==2.8.0 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de \
     --hash=sha256:59127c392cc44c2da5bb3192169a91f429924e17aff6534d70fdc02ab3e04320
+pyright==1.1.327 ; python_version >= "3.9" and python_version < "4.0" \
+    --hash=sha256:3462cda239e9140276238bbdbd0b59d77406f1c2e14d8cb8c20c8e25639c6b3c \
+    --hash=sha256:ba74148ad64f22020dbbed6781c4bdb38ecb8a7ca90dc3c87a4f08d1c0e11592
 pyspark==3.3.3 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:384d2ad7090cd1db5b2d2ac497bda409d86ab3a27272833e1a27efadf45e4d2f
 pytest==7.4.2 ; python_version >= "3.9" and python_version < "4.0" \
@@ -1337,6 +1343,9 @@ scipy==1.9.3 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:d644a64e174c16cb4b2e41dfea6af722053e83d066da7343f333a54dae9bc31c \
     --hash=sha256:da8245491d73ed0a994ed9c2e380fd058ce2fa8a18da204681f2fe1f57f98f95 \
     --hash=sha256:fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027
+setuptools==68.2.2 ; python_version >= "3.9" and python_version < "4.0" \
+    --hash=sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87 \
+    --hash=sha256:b454a35605876da60632df1a60f736524eb73cc47bbc9f3f1ef1b644de74fd2a
 six==1.16.0 ; python_version >= "3.9" and python_version < "4.0" \
     --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254