Fixing Builds and Automation

.github/workflows/build.yml

@@ -0,0 +1,29 @@
+name: Docker Build Test
+
+on:
+  push:
+    branches:
+      master
+  pull_request:
+    branches:
+      master
+  schedule:
+      - cron:  '0 0 * * 1'
+
+jobs:
+  build-test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.8]
+# TODO: We probably should switch to using the Docker version.
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Build Docker
+      run: |
+        cd basic && docker build . 

Dockerfile

@@ -1,14 +1,15 @@
-FROM continuumio/miniconda3:4.8.2
+FROM continuumio/miniconda3:4.10.3
 MAINTAINER Mingxun Wang "[email protected]"
 
 WORKDIR /app
 RUN apt-get update -y && \
         apt-get install -y libxrender-dev && \
         apt-get install -y git-core
-RUN conda create -y -n usi -c conda-forge -c bioconda -c defaults celery \
+RUN conda install -c conda-forge mamba
+RUN mamba create -y -n usi -c conda-forge -c bioconda -c defaults celery \
         dash=1.20.0 dash-bootstrap-components=0.9.2 flask gunicorn \
         joblib matplotlib numba numpy openssl qrcode rdkit requests \
-        requests-cache scipy spectrum_utils werkzeug
+        requests-cache scipy spectrum_utils==0.3.5 werkzeug==2.0.0
 RUN /bin/bash -c 'source activate usi && pip install "git+https://github.com/berlinguyinca/spectra-hash.git#subdirectory=python" && pip install celery-once'
 
 RUN echo "source activate usi" > ~/.bashrc

Makefile

@@ -23,19 +23,19 @@ clear-cache:
 
 #Docker Compose
 server-compose-interactive:
-	docker-compose build
-	docker-compose up
+	docker-compose --compatibility build
+	docker-compose --compatibility up
 
 server-compose:
-	docker-compose build
-	docker-compose up -d
+	docker-compose --compatibility build
+	docker-compose --compatibility up -d
 
 server-compose-production-interactive:
-	docker-compose build
+	docker-compose --compatibility build
 	docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up
 
 server-compose-production:
-	docker-compose build
+	docker-compose --compatibility build
 	docker-compose -f docker-compose.yml -f docker-compose-production.yml --compatibility up -d
 
 attach:

docker-compose-production.yml

@@ -5,9 +5,11 @@ services:
       - default
       - nginx-net
     environment:
-      VIRTUAL_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
-      VIRTUAL_PORT: 5087
-      LETSENCRYPT_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
+      #VIRTUAL_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
+      VIRTUAL_HOST: metabolomics-usi.gnps2.org
+      VIRTUAL_PORT: 5000
+      #LETSENCRYPT_HOST: metabolomics-usi.ucsd.edu,metabolomics-usi.gnps2.org
+      LETSENCRYPT_HOST: metabolomics-usi.gnps2.org
       LETSENCRYPT_EMAIL: [email protected]
     command: /app/run_server.sh
     deploy:

requirements.txt

@@ -19,5 +19,5 @@ requests
 requests_cache
 scipy
 spectrum_utils
-werkzeug
-git+https://github.com/berlinguyinca/spectra-hash.git#subdirectory=python
+werkzeug==2.0.0
+git+https://github.com/berlinguyinca/spectra-hash.git#subdirectory=python