initial commit

Author: mattcieslak

Dockerfile

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+FROM ubuntu:22.04
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    ca-certificates \
+                    bzip2 \
+                    curl \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users babs
+WORKDIR /home/babs
+ENV HOME="/home/babs"
+
+WORKDIR /
+RUN echo "2024.04.11"
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+
+COPY docker/environment.yml /tmp/environment.yml
+ENV MAMBA_ROOT_PREFIX="/opt/conda" \
+    MAMBA_NO_LOW_SPEED_LIMIT=1 \
+    PIP_DEFAULT_TIMEOUT=100
+
+RUN micromamba config set extract_threads 1 \
+    && micromamba create -vv -y -f /tmp/environment.yml \
+    && micromamba clean -y -a
+
+ENV PATH=/opt/conda/envs/babs/bin:$PATH
+
+# Configure the git user name and email
+RUN git config --global user.name "CircleCI" \
+    && git config --global user.email "circleci@example.com"
+
+# install BABS
+COPY . $HOME/babs
+WORKDIR $HOME/babs
+RUN pip install .[tests]
+
+# # pytest BABS
+# RUN pytest ~/babs

docker/environment.yml

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+name: babs
+channels:
+  - conda-forge
+dependencies:
+  - apptainer
+  - git
+  - git-annex
+  - pip
+  - python=3.11
+  - pip:
+      - backoff
+      - coverage
+      - datalad >= 0.17.2
+      - datalad_container >= 1.1.6
+      - filelock >= 3.8.0
+      - jinja2
+      - nibabel
+      - numpy
+      - pandas
+      - pyyaml >= 6.0
+      - qstat >= 0.0.5
+      - regex
+      - tqdm
+      - pytest
+      - pytest-cov==5.0.0
+      - pytest-env==1.1.3