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Bump dependency versions #92

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merged 5 commits into from
Feb 22, 2024
Merged

Bump dependency versions #92

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1cfef0d
build(deps): bump actions/checkout from v3 to v4
chasemc Feb 22, 2024
7bc7fd8
refactor: remove unused nf-core GH actions
chasemc Feb 22, 2024
cc61326
build(deps): bump micromamba docker from 1.1.0 to 1.5.0
chasemc Feb 22, 2024
702054f
build(deps): bump Neo4j from 5.7.0 to 5.16.0
chasemc Feb 22, 2024
d312744
Merge branch 'update_versions' into dev
chasemc Feb 22, 2024
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39 changes: 0 additions & 39 deletions .github/workflows/awsfulltest.yml
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33 changes: 0 additions & 33 deletions .github/workflows/awstest.yml
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
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8 changes: 4 additions & 4 deletions .github/workflows/docker.yml
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Expand Up @@ -17,9 +17,9 @@ jobs:
env: [["sgpy-base", "dockerfiles/sgpy/sgpy_base"]]
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Check out the repo
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Log in to Docker Hub
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
with:
Expand Down Expand Up @@ -73,9 +73,9 @@ jobs:
]
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Check out the repo
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Log in to Docker Hub
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
with:
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10 changes: 5 additions & 5 deletions .github/workflows/linting.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3

Expand All @@ -27,7 +27,7 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: actions/setup-node@v3

Expand All @@ -41,15 +41,15 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: black
uses: psf/black@stable

nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
Expand Down Expand Up @@ -77,7 +77,7 @@ jobs:

# - name: Upload linting log file artifact
# if: ${{ always() }}
# uses: actions/upload-artifact@v3
# uses: actions/upload-artifact@v4
# with:
# name: linting-logs
# path: |
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2 changes: 1 addition & 1 deletion dockerfiles/hmmer/Dockerfile
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@@ -1,4 +1,4 @@
FROM mambaorg/micromamba:1.1.0
FROM mambaorg/micromamba:1.5.0

COPY environment.yaml /tmp/env.yaml

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2 changes: 1 addition & 1 deletion dockerfiles/hmmer_plus/Dockerfile
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@@ -1,4 +1,4 @@
FROM mambaorg/micromamba:1.1.0
FROM mambaorg/micromamba:1.5.0

COPY environment.yaml /tmp/env.yaml

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2 changes: 1 addition & 1 deletion dockerfiles/minimal/Dockerfile
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@@ -1,4 +1,4 @@
FROM mambaorg/micromamba:1.1.0
FROM mambaorg/micromamba:1.5.0

COPY environment.yaml /tmp/env.yaml

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4 changes: 2 additions & 2 deletions dockerfiles/sgpy/sgpy_base/Dockerfile
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@@ -1,4 +1,4 @@
FROM mambaorg/micromamba:1.1.0
FROM mambaorg/micromamba:1.5.0

COPY environment.yaml /tmp/env.yaml

Expand All @@ -7,7 +7,7 @@ RUN micromamba install -y -n base -f /tmp/env.yaml && \

### Add Neo4j, remove then re-add the needed directories/files to avoid any potential permission issues
# https://neo4j.com/docs/operations-manual/current/configuration/file-locations/
RUN /opt/conda/bin/wget -q https://neo4j.com/artifact.php?name=neo4j-community-5.7.0-unix.tar.gz -O neo4j.tar.gz \
RUN /opt/conda/bin/wget -q https://neo4j.com/artifact.php?name=neo4j-community-5.16.0-unix.tar.gz -O neo4j.tar.gz \
&& tar -xf neo4j.tar.gz \
&& rm neo4j.tar.gz \
&& mv neo4j* neo4j \
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