Merge branch 'release/1.3.0'

.github/workflows/docker-publish.yml

@@ -9,18 +9,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       - name: Prepare
         # In this preparation step, a few configurations are made
         # according to tags that will be used to export the image
         # for Docker Hub, as well as the name of the image itself
         id: prep
         run: |
-          DOCKER_IMAGE=ghcr.io/rhshah/iAnnotateSV
+          DOCKER_IMAGE=ghcr.io/rhshah/iannotatesv
           VERSION=noop
           if [ "${{ github.event_name }}" = "schedule" ]; then
             VERSION=nightly
@@ -44,13 +44,13 @@ jobs:
           echo ::set-output name=tags::${TAGS}
       - name: Login to GitHub Container Registry
         #if: github.event_name != 'pull_request'
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.RS_PAT }}
       - name: Push to GitHub Packages
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v6
         with:
           context: .
           file: ./Dockerfile

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.10]
+        python-version: ['3.8', '3.9', '3.10']
 
     steps:
     - name: Checkout github repo (+ download lfs dependencies)

pyproject.toml

@@ -3,7 +3,7 @@ name = "iAnnotateSV"
 version = "1.3.0"
 description = "iAnnotateSV is a Python library and command-line software toolkit to annotate and visualize structural variants detected from Next Generation DNA sequencing data."
 authors = ["Ronak Shah <[email protected]>"]
-readme = "README.rst"
+readme = "See README"
 packages = [{include = "iAnnotateSV"}]
 include = [
     "iAnnotateSV/data/*",

setup.cfg

@@ -31,7 +31,7 @@ exclude = docs
 
 [aliases]
 # Define setup.py command aliases here
-test = nosetests
+test = poetry
 
-[tool:nosetests]
+[tool:poetry]
 collect_ignore = ['setup.py']