Merge pull request #242 from BU-ISCIII/develop

Release 3.0.0

.github/workflows/python_lint.yml

@@ -0,0 +1,36 @@
+name: python_lint
+
+on:
+  push:
+    paths:
+      - '**.py'
+  pull_request:
+    paths:
+      - '**.py'
+
+jobs:
+  flake8_py3:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.9.x
+          architecture: x64
+      - name: Checkout PyTorch
+        uses: actions/checkout@master
+      - name: Install flake8
+        run: pip install flake8
+      - name: Run flake8
+        run: flake8 --ignore E501,W503,E203,W605
+
+  black_lint:
+    runs-on: ubuntu-latest
+    steps:
+        - name: Setup
+          uses: actions/checkout@v2
+        - name: Install black in jupyter
+          run: pip install black[jupyter]
+        - name: Check code lints with Black
+          uses: psf/black@stable
+

.gitignore

@@ -2,18 +2,21 @@
 *.xml
 *.bin
 *.gz
-*.csv
+*_BAK
 migrations/
 tmp/
 logs/
-static/
+/static/
+install_settings.txt
+wetlab/logging_config.ini
 #--- updates introduced for iSkyLIMS in submodules packaging ---
 virtualenv/
 iSkyLIMS/
 *iskylims/
 documents/
 manage.py
 logs/
+logs
 
 
 # Byte-compiled / optimized / DLL files

Dockerfile

@@ -1,56 +1,30 @@
-FROM ubuntu:20.04
-# ENV PYTHONUNBUFFERED 1
+FROM ubuntu:22.04
 ENV TZ=Europe/Madrid
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
 # Updates
 ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get update && apt-get upgrade -y
 
 # Essential software
 RUN apt-get install -y \
-    lightdm git apt-utils libcairo2 libcairo2-dev  wget gnuplot python3-pip \
-    libmysqlclient-dev apache2 apache2-dev vim 
-
-RUN mkdir /opt/interop
-WORKDIR /opt/interop
-
-RUN wget https://github.com/Illumina/interop/releases/download/v1.1.15/InterOp-1.1.15-Linux-GNU.tar.gz
-RUN tar -xvf  InterOp-1.1.15-Linux-GNU.tar.gz
-RUN ln -s InterOp-1.1.15-Linux-GNU interop
-RUN rm InterOp-1.1.15-Linux-GNU.tar.gz
-
-
-RUN mkdir /opt/iSkyLIMS
-WORKDIR /opt/iSkyLIMS
-
-RUN git clone https://github.com/BU-ISCIII/iSkyLIMS.git .
-
-# RUN git submodule init
+    git wget lsb-core lsb-release \
+    libmysqlclient-dev \
+    python3-pip libpq-dev \
+    python3-wheel apache2-dev \
+    gnuplot
+
+RUN git clone https://github.com/bu-isciii/iskylims.git /srv/iskylims
+WORKDIR /srv/iskylims
 RUN git checkout develop
-# RUN git submodule init
-# RUN git submodule update --checkout
-RUN cd iSkyLIMS_wetlab git 
-
-
-
-RUN mkdir -p /opt/iSkyLIMS/documents/wetlab/tmp
-RUN mkdir -p /opt/iSkyLIMS/documents/drylab
-RUN mkdir -p /opt/iSkyLIMS/logs
-
-
 
-# Starting iSkyLIMS
-RUN python3 -m pip install -r conf/pythonPackagesRequired.txt
-RUN django-admin startproject iSkyLIMS .
-RUN /bin/bash -c 'grep ^SECRET iSkyLIMS/settings.py > ~/.secret'
+RUN pip install -r conf/requirements.txt 
 
+RUN bash install.sh --install app --dev --conf conf/docker_install_settings.txt --docker
 
-# Copying config files and script
-RUN cp conf/docker_settings.py /opt/iSkyLIMS/iSkyLIMS/settings.py
-RUN cp conf/urls.py /opt/iSkyLIMS/iSkyLIMS/
+WORKDIR /opt/iskylims
 
-RUN sed -i "/^SECRET/c\\$(cat ~/.secret)" iSkyLIMS/settings.py
-ENV PATH="usr/bin:$PATH"
-# Expose and run
-EXPOSE 8000
-CMD python3 manage.py runserver 0:8000
+# Expose
+EXPOSE 8001
+# Start the application
+CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"]