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Use official Miniforge image, remove redundant apt bootstrap step, and fix Python 3.13 environment pin compatibility #66

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Merged
espenhgn merged 8 commits into from
Apr 21, 2026
Merged

Use official Miniforge image, remove redundant apt bootstrap step, and fix Python 3.13 environment pin compatibility #66

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0a17290
Initial plan
Copilot Apr 21, 2026
e670bc0
feat: use miniforge base image and remove installer step
Copilot Apr 21, 2026
3ac8795
test: centralize expected miniforge base image string
Copilot Apr 21, 2026
38fb622
test: focus Dockerfile check on desired configuration
Copilot Apr 21, 2026
729242a
refactor: remove apt_get_essential bootstrap step
Copilot Apr 21, 2026
6905637
fix: bump pandas pin for python 3.13 compatibility
Copilot Apr 21, 2026
9150d38
Update Anchore scan action to version 7
espenhgn Apr 21, 2026
84a5f97
Change Anchore scan settings to not fail build
espenhgn Apr 21, 2026
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6 changes: 3 additions & 3 deletions .github/workflows/container_build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,12 +66,12 @@ jobs:

- name: Scan image
id: anchor_scan
uses: anchore/scan-action@v3
uses: anchore/scan-action@v7
with:
image: ${{ env.LATEST_TAG }}
fail-build: true
fail-build: false
output-format: table
severity-cutoff: high
severity-cutoff: critical

# - name: Inspect scan action table report
# run: cat ${{ steps.anchor_scan.outputs.sarif }}
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10 changes: 1 addition & 9 deletions docker/dockerfiles/container_template/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,17 +1,9 @@
FROM ubuntu:24.04
FROM quay.io/condaforge/miniforge3:26.1.1-3

ENV TZ=Europe
ENV DEBIAN_FRONTEND=noninteractive

WORKDIR /tmp
COPY /scripts/apt_get_essential.sh .
RUN bash apt_get_essential.sh && \
rm apt_get_essential.sh


WORKDIR /tmp
COPY /scripts/install_miniforge3.sh .
RUN bash install_miniforge3.sh
COPY /scripts/environment.yml .
RUN mamba env update --name base --file environment.yml && \
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@espenhgn espenhgn Apr 21, 2026

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@copilot update version pins in environment.yml file to versions compatible with Python=3.13, fixing failing build:

#6 [4/5] RUN mamba env update --name base --file environment.yml &&     conda clean --all --yes &&     rm -rf /tmp/*
#6 11.77 
#6 11.77 Pinned packages:
#6 11.77 
#6 11.77   - python=3.13
#6 11.77 
#6 13.53 error    libmamba Could not solve for environment specs
#6 13.53     The following packages are incompatible
#6 13.53     ├─ pandas =2.2.2 * is installable with the potential options
#6 13.53     │  ├─ pandas 2.2.2 would require
#6 13.53     │  │  └─ python >=3.10,<3.11.0a0 *, which can be installed;
#6 13.53     │  ├─ pandas 2.2.2 would require
#6 13.53     │  │  └─ python >=3.11,<3.12.0a0 *, which can be installed;
#6 13.53     │  ├─ pandas 2.2.2 would require
#6 13.53     │  │  └─ python >=3.12,<3.13.0a0 *, which can be installed;
#6 13.53     │  └─ pandas 2.2.2 would require
#6 13.53     │     └─ python >=3.9,<3.10.0a0 *, which can be installed;
#6 13.53     └─ pin on python =3.13 * is not installable because it requires
#6 13.53        └─ python =3.13 *, which conflicts with any installable versions previously reported.
#6 13.55 critical libmamba Could not solve for environment specs
#6 ERROR: process "/bin/sh -c mamba env update --name base --file environment.yml &&     conda clean --all --yes &&     rm -rf /tmp/*" did not complete successfully: exit code: 1
------
 > [4/5] RUN mamba env update --name base --file environment.yml &&     conda clean --all --yes &&     rm -rf /tmp/*:
13.53     │  │  └─ python >=3.10,<3.11.0a0 *, which can be installed;
13.53     │  ├─ pandas 2.2.2 would require
13.53     │  │  └─ python >=3.11,<3.12.0a0 *, which can be installed;
13.53     │  ├─ pandas 2.2.2 would require
13.53     │  │  └─ python >=3.12,<3.13.0a0 *, which can be installed;
13.53     │  └─ pandas 2.2.2 would require
13.53     │     └─ python >=3.9,<3.10.0a0 *, which can be installed;
13.53     └─ pin on python =3.13 * is not installable because it requires
13.53        └─ python =3.13 *, which conflicts with any installable versions previously reported.
13.55 critical libmamba Could not solve for environment specs
------

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Copilot AI Apr 21, 2026

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Fixed in 6905637: updated /docker/scripts/environment.yml pin from pandas=2.2.2 to pandas=2.2.3, which is compatible with python=3.13 and resolves the CI solver failure you reported.

conda clean --all --yes && \
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11 changes: 0 additions & 11 deletions docker/scripts/apt_get_essential.sh
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2 changes: 1 addition & 1 deletion docker/scripts/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ dependencies:
- jupyterlab=4.2.5
- matplotlib=3.9.2
- numpy=2.1.1
- pandas=2.2.2
- pandas=2.2.3
- scikit-learn=1.5.2
- scipy=1.14.1
- seaborn=0.13.2
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13 changes: 13 additions & 0 deletions tests/test_container_template.py
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Expand Up @@ -19,6 +19,7 @@
# This may be useful for testing on a local machine, but should
# be revised for the particular usecase.
cwd = os.getcwd()
EXPECTED_CONTAINER_BASE_IMAGE = 'quay.io/condaforge/miniforge3:26.1.1-3'
try:
pth = os.path.join('containers', 'container_template.sif')
try:
Expand Down Expand Up @@ -77,6 +78,18 @@ def test_container_template_python_script():
assert out.returncode == 0


def test_container_template_dockerfile_base_image_and_env_install():
"""test that Dockerfile uses miniforge base image and environment.yml"""
dockerfile = os.path.join(
cwd, 'docker', 'dockerfiles', 'container_template', 'Dockerfile'
)
with open(dockerfile, 'r', encoding='utf-8') as f:
content = f.read()

assert f'FROM {EXPECTED_CONTAINER_BASE_IMAGE}' in content
assert 'mamba env update --name base --file environment.yml' in content


def test_container_template_python_script_from_tempdir():
'''test that the tempdir is working'''
with tempfile.TemporaryDirectory() as d:
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