chore: update dependencies, base img, codecov

fix: issue with fasta-checksum-utils w/o circular contig flag
bento-platform · Feb 13, 2024 · 808006d · 808006d
1 parent f9d3bbc
commit 808006d
Show file tree

Hide file tree

Showing 6 changed files with 457 additions and 449 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -33,4 +33,6 @@ jobs:
       - name: Test
         run: mkdir -p tmp && poetry run pytest -svv --cov=bento_wes --cov-branch
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 AS base-deps
 
 SHELL ["/bin/bash", "-c"]
 

diff --git a/container.requirements.txt b/container.requirements.txt
@@ -1,4 +1,4 @@
 gunicorn==21.2.0
 gevent==23.9.1
 pysam>=0.22.0,<0.23.0
-fasta-checksum-utils>=0.4.0,<0.5
+fasta-checksum-utils>=0.4.1,<0.5
diff --git a/dev.Dockerfile b/dev.Dockerfile
@@ -1,4 +1,4 @@
-FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 AS base-deps
+FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.02.01 AS base-deps
 
 LABEL org.opencontainers.image.description="Local development image for Bento WES."
 LABEL devcontainer.metadata='[{ \