Merge pull request #37 from broadinstitute/dp-scaffold

build and dependency updates

.github/workflows/build.yml

@@ -2,14 +2,13 @@ name: "viral-assemble CI"
 
 on:
   push:
+  merge_group:
   pull_request:
     branches:
       - master
   release:
     types:
       - created
-  schedule:
-    - cron: '0 18 * * 1' # weekly at 18:00 on Mondays
 
 env:
   HOME: "${{ github.workspace }}"
@@ -45,9 +44,9 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       # fetch git tags (tagged releases) because
-      # actions/checkout@v3 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -75,15 +74,15 @@ jobs:
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
 
       - name: Login to docker registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.DOCKER_REGISTRY }}
           username: ${{ secrets.QUAY_USERNAME }}
           password: ${{ secrets.QUAY_ROBOT_TOKEN }}
       # cache; see: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows
       - name: setup cache
         id: docker_cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: old-docker-tag
         with:
@@ -143,9 +142,9 @@ jobs:
       PYTEST_ADDOPTS: "-rsxX -n 2 --durations=25 --fixture-durations=10 --junit-xml=pytest.xml --cov-report= --cov assembly --cov assemble"
     steps:
       - name: checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v3 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -172,11 +171,11 @@ jobs:
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
       - name: install python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "${{ env.GITHUB_ACTIONS_PYTHON_VERSION }}"
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       - name: pull docker image
         run: |
           set -e -x
@@ -202,9 +201,9 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - name: checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       # fetch git tags (tagged releases) because 
-      # actions/checkout@v3 does either a full checkout or a shallow checkout without tags
+      # actions/checkout@v4 does either a full checkout or a shallow checkout without tags
       - name: fetch tags
         run: git fetch --prune --unshallow --tags
       - name: Programmatic environment setup
@@ -231,7 +230,7 @@ jobs:
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH"
           echo "GITHUB_ACTIONS_BRANCH=$GITHUB_ACTIONS_BRANCH" >> $GITHUB_ENV
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
       - name: pull docker image
         run: |
           set -e -x

.readthedocs.yml

@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the version of Python
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
@@ -19,6 +25,6 @@ formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.8
+  version: 3.10
   install:
     - requirements: docs/requirements.txt

Dockerfile

@@ -1,11 +1,11 @@
-FROM quay.io/broadinstitute/viral-core:2.2.4
+FROM quay.io/broadinstitute/viral-core:2.3.0
 
 LABEL maintainer "viral-ngs@broadinstitute.org"
 
 ENV VIRAL_ASSEMBLE_PATH=$INSTALL_PATH/viral-assemble
 
 COPY requirements-conda.txt $VIRAL_ASSEMBLE_PATH/
-RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_ASSEMBLE_PATH/requirements-conda.txt
+RUN $VIRAL_NGS_PATH/docker/install-conda-dependencies.sh $VIRAL_ASSEMBLE_PATH/requirements-conda.txt $VIRAL_NGS_PATH/requirements-conda.txt
 
 # Copy all source code into the base repo
 # (this probably changes all the time, so all downstream build

requirements-conda.txt

@@ -1,6 +1,12 @@
 gap2seq=3.1.1a
-mafft>=7.508
+mafft>=7.520
 mummer4>=4.0.0rc1
 muscle=3.8.1551
 spades>=3.15.5
+fastani>=1.34
+mashtree>=1.4.6
+#sourmash-minimal>=4.8.6 ## see below
+#sourmash_plugin_branchwater>=0.9.1  ## running into resolver problems at least with our current version of python
+skani>=0.2.1
+kwip>=0.2.0
 # Python packages below