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💚 Fix CI build: Upgrade miniconda (4.8.2 → 4.12.0) (#1803)
2 parents 4bb27d6 + f3c5a60 commit 3615688

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‎.github/Dockerfiles/Ubuntu.bionic-non-free.Dockerfile‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -107,9 +107,9 @@ RUN groupadd -r c-pac && \
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libxp-dev && \
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add-apt-repository --remove --yes ppa:zeehio/libxp && \
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apt-get update && \
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curl -sO https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh && \
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bash Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-py37_4.8.2-Linux-x86_64.sh && chmod -R 777 /usr/local/miniconda && \
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curl -sO https://repo.anaconda.com/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh && \
111+
bash Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -p /usr/local/miniconda && \
112+
rm Miniconda3-py37_4.12.0-Linux-x86_64.sh && chmod -R 777 /usr/local/miniconda && \
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ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
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echo $TZ > /etc/timezone && \
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sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && \

‎.github/Dockerfiles/Ubuntu.xenial-20200114.Dockerfile‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -120,9 +120,9 @@ RUN apt-get update && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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# Installing and setting up miniconda
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RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
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bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
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rm Miniconda3-4.5.11-Linux-x86_64.sh && chmod -R 777 /usr/local/miniconda
123+
RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py37_4.12.0-Linux-x86_64.sh && \
124+
bash Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -p /usr/local/miniconda && \
125+
rm Miniconda3-py37_4.12.0-Linux-x86_64.sh && chmod -R 777 /usr/local/miniconda
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# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
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ENV PATH="/usr/local/miniconda/bin:$PATH" \

‎.github/scripts/get_package_id.py‎

Lines changed: 16 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -11,18 +11,18 @@
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def get_packages(owner, tag, api_token=None):
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"""Function to collect GHCR packages for a given owner & tag
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Parameters
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----------
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owner : str
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username or org name
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tag : str
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image tag (part left of the colon)
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api_token : str or None
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GitHub API personal access token with read.packages permission
25-
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Returns
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-------
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list
@@ -32,11 +32,11 @@ def get_packages(owner, tag, api_token=None):
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3333
def fetch(url):
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"""Method to make API call and return response, given a URL
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Parameters
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----------
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url : str
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Returns
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-------
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dict or list
@@ -59,34 +59,36 @@ def fetch(url):
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'$VERSION_TAG $GITHUB_TOKEN`'
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]))
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return response
62-
packages = fetch(
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_packages = fetch(
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f'https://api.github.com/orgs/{owner}/packages/container/'
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f'{tag}/versions')
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if packages.get('message', 'Not Found') == 'Not Found':
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packages = fetch(
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f'https://api.github.com/users/{owner}/packages/container/'
68-
f'{tag}/versions')
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packages = []
66+
for _package in _packages:
67+
if _package.get('message', 'Not Found') == 'Not Found':
68+
packages += fetch(
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f'https://api.github.com/users/{owner}/packages/container/'
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f'{tag}/versions')
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return packages
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7173

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def id_from_tag(owner, image, tag, api_token=None):
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"""Function to return a package ID given an image version tag
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Parameters
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----------
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owner : str
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GitHub username or org name
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image : str
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Image tag (the part to the left of the colon)
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tag : str
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Image version tag (the part to the right of the colon)
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api_token: str or None
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GitHub API personal access token with read.packages permission
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"""
89-
packages = get_packages(owner, image)
91+
packages = get_packages(owner, image, api_token)
9092
versions = [image['id'] for image in packages if tag in image.get(
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'metadata', {}
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).get('container', {}).get('tags', [])]

‎.github/workflows/build_stages.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ jobs:
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DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
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echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
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docker manifest inspect $DOCKER_TAG >/dev/null
69-
echo "::set-output name=not_yet_exists::$?"
69+
echo "not_yet_exists=$?" >> $GITHUB_OUTPUT
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- name: Set up Docker Buildx
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uses: docker/[email protected]
7272
if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
@@ -156,7 +156,7 @@ jobs:
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DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
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echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
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docker manifest inspect $DOCKER_TAG >/dev/null
159-
echo "::set-output name=not_yet_exists::$?"
159+
echo "not_yet_exists=$?" >> $GITHUB_OUTPUT
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if: contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
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- name: Prep Dockerfiles for forked repository
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if: github.repository_owner != 'FCP-INDI' && contains(steps.changed-files-base.outputs.all_changed_files, matrix.Dockerfile) || contains(steps.changed-files.outputs.all_changed_files, matrix.Dockerfile)
@@ -230,7 +230,7 @@ jobs:
230230
DOCKER_TAG=$(echo "ghcr.io/${{ github.repository }}/$TAG" | tr '[:upper:]' '[:lower:]')
231231
echo DOCKER_TAG=$DOCKER_TAG >> $GITHUB_ENV
232232
docker manifest inspect $DOCKER_TAG >/dev/null
233-
echo "::set-output name=not_yet_exists::$?"
233+
echo "not_yet_exists=$?" >> $GITHUB_OUTPUT
234234
id: docker_tag
235235
- name: Clear up some space on runner
236236
if: always() && steps.changed-files-base.outputs.any_changed == 'true' || steps.changed-files.outputs.any_changed == 'true' || steps.docker_tag.not_yet_exists == 1

‎CPAC/info.py‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -177,6 +177,7 @@ def get_cpac_gitversion():
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"future",
178178
"INDI-Tools",
179179
"lockfile==0.12.2",
180+
"joblib==1.0.1",
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"matplotlib==3.1.3",
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"networkx==2.4",
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"nibabel==2.3.3",

‎requirements.txt‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@ click==6.7
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configparser==3.7.4
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future==0.16.0
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git+https://[email protected]/FCP-INDI/INDI-Tools.git#egg=INDI-Tools
6+
joblib==1.0.1
67
lockfile==0.12.2
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matplotlib==3.1.3
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networkx==2.4

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