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Merged
xraymemory merged 5 commits into from
Jun 3, 2026
Merged

fix(docker): set sampleworks workspace home #253

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6050e1a
fix(docker): set sampleworks workspace home
xraymemory Jun 2, 2026
08bad74
test(runs): isolate runner tests from ACTL workspace
xraymemory Jun 2, 2026
77ea7c7
fix(docker): install workspace bashrc snippet
xraymemory Jun 2, 2026
ef36b68
Merge branch 'main' into fix/sampleworks-home-env
xraymemory Jun 2, 2026
35f4d7f
Merge branch 'main' into fix/sampleworks-home-env
xraymemory Jun 2, 2026
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14 changes: 12 additions & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,8 @@ RUN rm -rf /app/src /app/scripts /app/experiments /app/analyses \
&& mkdir -p /home/dev/workspace

COPY --chmod=755 run_experiments run_experiments.sh run_all_models.sh run_analysis run_analysis.sh /usr/local/bin/
RUN printf '\n# ACTL scientist workflow: land in the synced Sampleworks checkout.\nif [[ $- == *i* ]] && [ -z "${SAMPLEWORKS_NO_AUTO_CD:-}" ] && [ -d /home/dev/workspace ]; then\n cd /home/dev/workspace\nfi\n' >> /root/.bashrc
RUN printf '\n# ACTL scientist workflow: land in the synced Sampleworks checkout.\nif [[ $- == *i* ]] && [ -z "${SAMPLEWORKS_NO_AUTO_CD:-}" ] && [ -d /home/dev/workspace ]; then\n cd /home/dev/workspace\nfi\n' \
| tee -a /root/.bashrc /home/dev/.bashrc >/dev/null

# ============================================================================
# Public runtime: regular Sampleworks image for the public registry
Expand All @@ -134,7 +135,16 @@ ENV BOLTZ1_CHECKPOINT=/checkpoints/boltz1_conf.ckpt \
BOLTZ2_CHECKPOINT=/checkpoints/boltz2_conf.ckpt \
CCD_PATH=/checkpoints/ccd.pkl \
RF3_CHECKPOINT=/checkpoints/rf3_foundry_01_24_latest.ckpt \
PROTENIX_CHECKPOINT=/checkpoints/protenix_base_default_v0.5.0.pt
PROTENIX_CHECKPOINT=/checkpoints/protenix_base_default_v0.5.0.pt \
HOME=/home/dev \
XDG_CONFIG_HOME=/home/dev/.config \
XDG_CACHE_HOME=/home/dev/.cache \
XDG_DATA_HOME=/home/dev/.local/share \
SHELL=/bin/bash

RUN mkdir -p /home/dev/.config /home/dev/.cache /home/dev/.local/share /home/dev/workspace

@manzuoni-astera manzuoni-astera Jun 2, 2026

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Addressed in 77ea7c7 by installing the ACTL auto-cd snippet into both /root/.bashrc and /home/dev/.bashrc. Keeping /root/.bashrc preserves the prior root-user behavior, and /home/dev/.bashrc matches the new HOME=/home/dev runtime environment.


WORKDIR /home/dev
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ENTRYPOINT ["entrypoint.sh"]
CMD ["--help"]
2 changes: 2 additions & 0 deletions Dockerfile.astera
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Expand Up @@ -45,6 +45,8 @@ COPY --from=ext-cli /ext /usr/local/bin/ext

RUN chmod 0755 /usr/local/bin/ext

WORKDIR /home/dev

# ACTL workspace pods intentionally keep the inherited root runtime user: the
# prebuilt /app/.pixi environments and shared PVC workflows are currently
# root-oriented, and switching USER here would break existing scientist runs.
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