From 25099696807e9a6a8c038dabca756188224c9fbc Mon Sep 17 00:00:00 2001 From: mwang87 Date: Wed, 25 Feb 2026 13:55:21 -0800 Subject: [PATCH] updating --- Dockerfile | 7 ++++++- Makefile | 28 ++++++++++++---------------- 2 files changed, 18 insertions(+), 17 deletions(-) diff --git a/Dockerfile b/Dockerfile index 88326a9..64cc0d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 \ diff --git a/Makefile b/Makefile index f6723a8..f8d40dc 100644 --- a/Makefile +++ b/Makefile @@ -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 \ No newline at end of file