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Refactoring without anaconda #222

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Merged
mwang87 merged 1 commit into from
Feb 25, 2026
Merged

Refactoring without anaconda #222

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7 changes: 6 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,12 @@ RUN wget https://github.com/conda-forge/miniforge/releases/latest/download/Minif
ENV PATH=$CONDA_DIR/bin:$PATH
RUN echo "export PATH=$CONDA_DIR:$PATH" >> ~/.bashrc

RUN mamba create -y -n usi -c conda-forge -c bioconda -c defaults celery==5.3.6 \
# Ensure packages resolve only from conda-forge/bioconda (no defaults/anaconda).
RUN mamba config --system --set channel_priority strict && \
mamba config --system --set show_channel_urls true && \
mamba config --system --remove channels defaults || true

RUN mamba create -y -n usi -c conda-forge -c bioconda celery==5.3.6 \
dash=1.20.0 dash-bootstrap-components=0.9.2 flask gunicorn \
joblib matplotlib==3.6.3 numba numpy openssl qrcode rdkit requests \
requests-cache scipy setuptools spectrum_utils==0.3.5 werkzeug==2.0.0 \
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28 changes: 12 additions & 16 deletions Makefile
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Expand Up @@ -23,31 +23,27 @@ clear-cache:

#Docker Compose
server-compose-interactive:
docker-compose --compatibility build
docker-compose --compatibility up
docker compose --compatibility build
docker compose --compatibility up

server-compose-autotest-interactive:
docker-compose --compatibility build
docker-compose -f docker-compose.yml -f docker-compose-autotest.yml --compatibility up
docker compose --compatibility build
docker compose -f docker-compose.yml -f docker-compose-autotest.yml --compatibility up

server-compose:
docker-compose --compatibility build
docker-compose --compatibility up -d
docker compose --compatibility build
docker compose --compatibility up -d

server-compose-production-interactive:
docker-compose --compatibility build
docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up
docker compose --compatibility build
docker compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up

server-compose-production:
docker-compose --compatibility build
docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up -d
docker compose --compatibility build
docker compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up -d

attach:
docker exec -i -t metabolomicsusi-web /bin/bash

# Github Testing with Act
test-actions-unit:
act -j unit-test -P ubuntu-latest=nektos/act-environments-ubuntu:18.04

test-actions-locust:
act -j load-test -P ubuntu-latest=nektos/act-environments-ubuntu:18.04
submodule_init:
git submodule update --init --recursive
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