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chore: update dependencies
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@markwoon
markwoon committed Apr 16, 2024
1 parent a280021 commit 1c55b41
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Showing 6 changed files with 165 additions and 45 deletions.
43 changes: 36 additions & 7 deletions .github/workflows/ci-pharmcat.yml
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Expand Up @@ -25,10 +25,10 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set up JDK
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-version: |
Expand Down Expand Up @@ -78,10 +78,39 @@ jobs:

- name: Send Slack notification on failure
if: failure()
uses: slackapi/slack-github-action@v1
with:
channel-id: 'dev'
payload: |
{
"attachments": [{
"color": "#ff0000",
"blocks": [
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
}
},
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
}
},
{
"type": "context",
"elements": [
{
"type": "mrkdwn",
"text": "Last commit:\n${{ github.event.head_commit.message }}"
}
]
}
]
}]
}
env:
SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}
uses: voxmedia/github-action-slack-notify-build@v1
with:
channel: dev
status: FAILED
color: danger
55 changes: 42 additions & 13 deletions .github/workflows/ci-preprocessor.yml
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Expand Up @@ -17,8 +17,8 @@ concurrency:
cancel-in-progress: true

env:
BCFTOOLS_VERSION: 1.18
HTSLIB_VERSION: 1.18
BCFTOOLS_VERSION: 1.20
HTSLIB_VERSION: 1.20
REFERENCE_FASTA_ZENODO_ID: 7288118
TOOLS_DIR: /home/runner/work/PharmCAT/PharmCAT/tools

Expand All @@ -29,11 +29,11 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Cache bcftools
id: cache-bcftools
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.TOOLS_DIR }}/bcftools
key: bcftools-${{ env.BCFTOOLS_VERSION }}
Expand All @@ -50,7 +50,7 @@ jobs:
- name: Cache htslib
id: cache-htslib
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.TOOLS_DIR }}/htslib
key: htslib-${{ env.HTSLIB_VERSION }}
Expand All @@ -70,13 +70,13 @@ jobs:

# need JDK present for tests
- name: Set up JDK
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-version: '17'

- name: Set up python
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: '3.10'
cache: 'pip'
Expand All @@ -89,7 +89,7 @@ jobs:

- name: Cache reference FASTA
id: cache-ref-fasta
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: |
reference.fna.bgz
Expand All @@ -116,10 +116,39 @@ jobs:

- name: Send Slack notification on failure
if: failure()
uses: slackapi/slack-github-action@v1
with:
channel-id: 'dev'
payload: |
{
"attachments": [{
"color": "#ff0000",
"blocks": [
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
}
},
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
}
},
{
"type": "context",
"elements": [
{
"type": "mrkdwn",
"text": "Last commit:\n${{ github.event.head_commit.message }}"
}
]
}
]
}]
}
env:
SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}
uses: voxmedia/github-action-slack-notify-build@v1
with:
channel: dev
status: FAILED
color: danger
8 changes: 4 additions & 4 deletions .github/workflows/pages-upload.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Setup Ruby
uses: ruby/setup-ruby@v1
Expand All @@ -37,7 +37,7 @@ jobs:

- name: Setup Pages
id: pages
uses: actions/configure-pages@v2
uses: actions/configure-pages@v5

- name: Build with search index
run: bundle exec just-the-docs rake search:init
Expand All @@ -51,7 +51,7 @@ jobs:

- name: Upload artifact
# Automatically uploads an artifact from the './_site' directory by default
uses: actions/upload-pages-artifact@v1
uses: actions/upload-pages-artifact@v3
with:
path: docs/_site

Expand All @@ -65,4 +65,4 @@ jobs:
steps:
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v1
uses: actions/deploy-pages@v4
53 changes: 43 additions & 10 deletions .github/workflows/release-docker.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set appVersion
uses: bhowell2/github-substring-action@v1
Expand All @@ -23,7 +23,7 @@ jobs:
- run: echo "Version = ${{steps.appVersion.outputs.substring}}"

- name: Set up JDK
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: temurin
java-version: 17
Expand All @@ -35,30 +35,63 @@ jobs:
mv build/libs/pharmcat-${{steps.appVersion.outputs.substring}}-all.jar build/pharmcat.jar
- name: Set up QEMU
uses: docker/setup-qemu-action@v3

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3

- name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}

- name: Build and push
id: docker_build
uses: docker/build-push-action@v3
uses: docker/build-push-action@v5
with:
context: .
platforms: linux/amd64,linux/arm64
push: true
tags: pgkb/pharmcat:latest,pgkb/pharmcat:${{steps.appVersion.outputs.substring}}


- name: Send Slack notification on failure
if: failure()
uses: slackapi/slack-github-action@v1
with:
channel-id: 'dev'
payload: |
{
"attachments": [{
"color": "#ff0000",
"blocks": [
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
}
},
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
}
},
{
"type": "context",
"elements": [
{
"type": "mrkdwn",
"text": "Last commit:\n${{ github.event.head_commit.message }}"
}
]
}
]
}]
}
env:
SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}
uses: voxmedia/github-action-slack-notify-build@v1
with:
channel: dev
status: FAILED
color: danger
43 changes: 36 additions & 7 deletions .github/workflows/release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ jobs:

steps:
- name: Checkout code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Set appVersion
uses: bhowell2/github-substring-action@v1
Expand All @@ -23,7 +23,7 @@ jobs:
- run: echo "Version = ${{steps.appVersion.outputs.substring}}"

- name: Set up JDK
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
distribution: temurin
java-version: 17
Expand Down Expand Up @@ -100,10 +100,39 @@ jobs:

- name: Send Slack notification on failure
if: failure()
uses: slackapi/slack-github-action@v1
with:
channel-id: 'dev'
payload: |
{
"attachments": [{
"color": "#ff0000",
"blocks": [
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": ":stop: <https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}|FAILED ${{ github.workflow }}!>"
}
},
{
"type": "section",
"text": {
"type": "mrkdwn",
"text": "Triggered by ${{ github.event_name }} on <${{ github.event.pull_request.html_url || github.event.head_commit.url }}|${{ github.ref_name }}> by ${{ github.actor }}."
}
},
{
"type": "context",
"elements": [
{
"type": "mrkdwn",
"text": "Last commit:\n${{ github.event.head_commit.message }}"
}
]
}
]
}]
}
env:
SLACK_BOT_TOKEN: ${{ secrets.SLACK_NOTIFICATIONS_BOT_TOKEN }}
uses: voxmedia/github-action-slack-notify-build@v1
with:
channel: dev
status: FAILED
color: danger
8 changes: 4 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
#
# Base Dockerfile for PharmCAT
#
FROM python:3.10
FROM python:3.12

# apt-utils line due to https://github.com/phusion/baseimage-docker/issues/319
RUN apt-get update && \
Expand All @@ -26,9 +26,9 @@ RUN wget https://zenodo.org/record/7288118/files/GRCh38_reference_fasta.tar && \
rm -f GRCh38_reference_fasta.tar


ENV BCFTOOLS_VERSION 1.18
ENV HTSLIB_VERSION 1.18
ENV SAMTOOLS_VERSION 1.18
ENV BCFTOOLS_VERSION 1.20
ENV HTSLIB_VERSION 1.20
ENV SAMTOOLS_VERSION 1.20

# download the suite of tools
WORKDIR /usr/local/bin/
Expand Down

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