Update dockerfile

.github/workflows/build_docker.yml

@@ -2,7 +2,7 @@
 name: Build and Push Docker Image
 on:
   push:
-    branches: [main]
+    branches: [main, 'djay/pin-python-dockerfile']
   workflow_dispatch:
 jobs:
   build-and-push:

Dockerfile

@@ -1,33 +1,42 @@
-FROM --platform=linux/amd64 condaforge/miniforge3:latest
+# --- Stage 1: Build & Environment Prep ---
+FROM ghcr.io/prefix-dev/pixi:latest AS build
 
-WORKDIR /src/
+WORKDIR /src
+COPY . /src
 
-# Copy your code
-COPY . /src/
+# Install git so pip can clone remote repository dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgomp1 git wget unzip \
+    && rm -rf /var/lib/apt/lists/*
 
-# Disable user site packages
-ENV PYTHONNOUSERSITE=1
+# Create the environment based on your lockfile and install dependencies
+# This creates an isolated, self-contained environment in /src/.pixi/envs/default
+RUN pixi install --locked
 
-# Use bash for the following RUNs
-SHELL ["/bin/bash", "-c"]
-
-# ---- ONE SINGLE RUN ----
-RUN set -e && \
-    conda install -n base -c conda-forge mamba -y && \
-    mamba create -y -n snakebids-env -c conda-forge -c bioconda python=3.11 snakebids appdirs unzip && \
-    source /opt/conda/etc/profile.d/conda.sh && \
-    conda activate snakebids-env && \
-    ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
-    ./autoafids/run.py test_data/bids_T2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
-    ./autoafids/run.py test_data/bids_ct test_out participant --modality ct --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
-    ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --stereotaxy STN --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
-    ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --fidqc --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
-    conda clean --all -y && \
-    rm -rf /opt/conda/pkgs /root/.caches
-
-# Set snakemake profile
-ENV SNAKEMAKE_PROFILE=/src/autoafids/workflow/profiles/docker-conda
+# Run your autoafids pre-caching tasks inside the pixi environment
+RUN pixi run ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
+    pixi run ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs --detect_with_nnlm && \
+    pixi run ./autoafids/run.py test_data/bids_T2w test_out participant --modality T2w --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
+    pixi run ./autoafids/run.py test_data/bids_ct test_out participant --modality ct --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
+    pixi run ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --stereotaxy STN --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs && \
+    pixi run ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --fidqc --use-conda --conda-create-envs-only --cores all --conda-prefix /src/conda-envs
+
+# --- Stage 2: Tiny Production Image ---
+# Use a lightweight glibc base image instead of a heavy Conda/Miniforge image
+FROM ubuntu:24.04 AS production
+
+WORKDIR /src
 
-# Set entrypoint
-ENTRYPOINT ["/src/entrypoint.sh"]
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgomp1 wget unzip \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy your source code, pre-cached conda environments, and the built Pixi environment
+COPY --from=build /src /src
+
+# Add the pixi environment binaries straight to the PATH so you don't have to "activate" it
+ENV PATH="/src/.pixi/envs/default/bin:$PATH"
+ENV SNAKEMAKE_PROFILE=/src/autoafids/workflow/profiles/docker-conda
+ENV PYTHONNOUSERSITE=1
 
+ENTRYPOINT ["/src/entrypoint.sh"]

autoafids/workflow/rules/nnlm.smk

@@ -123,7 +123,7 @@ rule run_nnlm:
         cp $TMPDIR/output_dir/{wildcards.subject}.json    {output.coords_json}
 
         # Cleanup temp dir
-        rm -rf $TMPDIR
+        # rm -rf $TMPDIR
         """
 
 

entrypoint.sh

@@ -1,4 +1,2 @@
 #!/bin/bash
-source /opt/conda/etc/profile.d/conda.sh
-conda activate snakebids-env
 exec /src/autoafids/run.py "$@"