From ec0cdbe8ca28bcf2e6699c41691b7c5f41fe00e3 Mon Sep 17 00:00:00 2001
From: Kalin Nonchev <50597791+KalinNonchev@users.noreply.github.com>
Date: Sat, 4 Nov 2023 10:36:28 +0100
Subject: [PATCH 1/3] Update python-publish.yml

---
 .github/workflows/python-publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 542e83e..a8edd9a 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -24,8 +24,8 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/*

From 01ef68aa848b14a52c9148923b295bae6f5fd122 Mon Sep 17 00:00:00 2001
From: Kalin Nonchev <50597791+KalinNonchev@users.noreply.github.com>
Date: Sat, 4 Nov 2023 10:38:48 +0100
Subject: [PATCH 2/3] Update setup.py (#25)

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 7f9f885..b525f74 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 setup(name='gnomad_db',
-      version='0.1.3',
+      version='0.1.4',
       description='This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.',
       author='KalinNonchev',
       author_email='boo@foo.com',

From f8a5b593f5d2c2237a15572ad3ebbba0c5cbbd96 Mon Sep 17 00:00:00 2001
From: Kalin Nonchev <50597791+KalinNonchev@users.noreply.github.com>
Date: Sat, 4 Nov 2023 11:02:25 +0100
Subject: [PATCH 3/3] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 70b464a..15587e4 100644
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@
 
 [The Genome Aggregation Database (gnomAD)](https://gnomad.broadinstitute.org) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
 
-This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 34G for WGS v2.1.1 (261.942.336 variants) and 98G for WGS v3.1.2 (about 759.302.267 variants), and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - [here](https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml) you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)
+This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - [here](https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml) you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)
 
 It extracts from a gnomAD vcf about 23 variant annotations. You can find further information about the exact fields [here](https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml).