Add gnomad_gks() and get_gks() for extracting gks information for a specified variant

.github/workflows/ci.yml

@@ -10,13 +10,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/checkout@v3
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Use pip cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-${{ hashFiles('**/requirements*.txt') }}
@@ -44,13 +44,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v1
+        uses: actions/checkout@v3
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Use pip cache
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-${{ hashFiles('**/requirements*.txt') }}
@@ -98,21 +98,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gnomad_methods
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: gnomad_methods
       - name: Checkout gnomad_qc
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           submodules: recursive
           repository: broadinstitute/gnomad_qc
           path: gnomad_qc
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Use pip cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-${{ hashFiles('gnomad_methods/**/requirements*.txt') }}

.github/workflows/publish.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Validate version
         run: |
           package_version=$(grep 'version' setup.py | sed -E 's|.*([0-9]+\.[0-9]+\.[0-9]+).*|\1|')
@@ -19,12 +19,12 @@ jobs:
             echo "Tag version (${tag_version}) does not match package version (${package_version})"
             exit 1
           fi
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
       - name: Use pip cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: pip-${{ hashFiles('**/requirements*.txt') }}

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/psf/black
-    rev: 22.10.0 # This should be kept in sync with the version in requirements-dev.in
+    rev: 23.7.0 # This should be kept in sync with the version in requirements-dev.in
     hooks:
       - id: black
         language_version: python3

docs/requirements.docs.in

@@ -1,6 +1,6 @@
-myst-parser==0.14.0
+myst-parser
 requests
-Sphinx>=2.1,<3
-sphinx-autodoc-typehints==1.10.3
+Sphinx>=4.2.0,<7.0.0
+sphinx-autodoc-typehints
 sphinx-rtd-theme
-Jinja2==3.0.3
+Jinja2

docs/requirements.docs.txt

@@ -1,20 +1,18 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
 #
 #    pip-compile docs/requirements.docs.in
 #
 alabaster==0.7.13
     # via sphinx
-attrs==21.4.0
-    # via markdown-it-py
 babel==2.12.1
     # via sphinx
-certifi==2022.12.7
+certifi==2023.7.22
     # via requests
-charset-normalizer==3.1.0
+charset-normalizer==3.2.0
     # via requests
-docutils==0.17.1
+docutils==0.18.1
     # via
     #   myst-parser
     #   sphinx
@@ -23,62 +21,64 @@ idna==3.4
     # via requests
 imagesize==1.4.1
     # via sphinx
-jinja2==3.0.3
+jinja2==3.1.2
     # via
     #   -r docs/requirements.docs.in
     #   myst-parser
     #   sphinx
-markdown-it-py==1.1.0
+markdown-it-py==3.0.0
     # via
     #   mdit-py-plugins
     #   myst-parser
-markupsafe==2.1.2
+markupsafe==2.1.3
     # via jinja2
-mdit-py-plugins==0.2.8
+mdit-py-plugins==0.4.0
     # via myst-parser
-myst-parser==0.14.0
+mdurl==0.1.2
+    # via markdown-it-py
+myst-parser==2.0.0
     # via -r docs/requirements.docs.in
-packaging==23.0
+packaging==23.1
     # via sphinx
-pygments==2.14.0
+pygments==2.16.1
     # via sphinx
-pytz==2023.3
-    # via babel
-pyyaml==6.0
+pyyaml==6.0.1
     # via myst-parser
 requests==2.31.0
     # via
     #   -r docs/requirements.docs.in
     #   sphinx
 snowballstemmer==2.2.0
     # via sphinx
-sphinx==2.4.5
+sphinx==6.2.1
     # via
     #   -r docs/requirements.docs.in
     #   myst-parser
     #   sphinx-autodoc-typehints
     #   sphinx-rtd-theme
+    #   sphinxcontrib-applehelp
+    #   sphinxcontrib-devhelp
+    #   sphinxcontrib-htmlhelp
     #   sphinxcontrib-jquery
-sphinx-autodoc-typehints==1.10.3
+    #   sphinxcontrib-qthelp
+    #   sphinxcontrib-serializinghtml
+sphinx-autodoc-typehints==1.23.0
     # via -r docs/requirements.docs.in
-sphinx-rtd-theme==1.2.0
+sphinx-rtd-theme==1.2.2
     # via -r docs/requirements.docs.in
-sphinxcontrib-applehelp==1.0.4
+sphinxcontrib-applehelp==1.0.7
     # via sphinx
-sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-devhelp==1.0.5
     # via sphinx
-sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-htmlhelp==2.0.4
     # via sphinx
 sphinxcontrib-jquery==4.1
     # via sphinx-rtd-theme
 sphinxcontrib-jsmath==1.0.1
     # via sphinx
-sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-qthelp==1.0.6
     # via sphinx
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-serializinghtml==1.1.8
     # via sphinx
-urllib3==1.26.15
+urllib3==2.0.4
     # via requests
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools

gnomad/assessment/validity_checks.py

@@ -180,9 +180,9 @@ def make_group_sum_expr_dict(
             else:
                 logger.warning("%s is not in table's info field", field)
 
-        annot_dict[
-            f"sum{delimiter}{field_prefix}{group}{delimiter}{sum_group}"
-        ] = hl.sum(sum_group_exprs)
+        annot_dict[f"sum{delimiter}{field_prefix}{group}{delimiter}{sum_group}"] = (
+            hl.sum(sum_group_exprs)
+        )
 
     # If metric_first_field is True, metric is AC, subset is tgp, sum_group is pop, and group is adj, then the values below are:
     # check_field_left = "AC-tgp-adj"