Merge pull request #33 from elephant-track/v0.6

ELEPHANT server v0.5.6 -> v0.6.0

.github/workflows/python-app.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 name: Test
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   build:
@@ -10,35 +10,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/cache@v3
-      id: cache
-      with:
-        path: ~/miniconda
-        key: ubuntu-conda-${{ hashFiles('environment.yml') }}
-    - name: Install Conda
-      if: steps.cache.outputs.cache-hit != 'true'
+    - name: Test with pytest in 
       run: |
-        wget https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh
-        bash Miniconda3-py37_4.11.0-Linux-x86_64.sh -bfp ~/miniconda
-        rm Miniconda3-py37_4.11.0-Linux-x86_64.sh
-        source ~/miniconda/etc/profile.d/conda.sh
-        conda init
-        conda install -c conda-forge -y mamba
-        mamba clean -qafy
-        mamba env update -f environment.yml
-    - name: Install dependencies
-      run: |
-        ~/miniconda/bin/python -m pip install --upgrade pip
-        ~/miniconda/bin/python -m pip install flake8 pytest
-    - name: Install package
-      run: |
-        ~/miniconda/bin/python -m pip install ./elephant-core
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        ~/miniconda/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        ~/miniconda/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        ~/miniconda/bin/pytest
+        make build
+        make test

Dockerfile

@@ -1,4 +1,4 @@
-FROM nvidia/cuda:11.3.1-runtime-ubuntu20.04
+FROM pytorch/pytorch:2.3.1-cuda12.1-cudnn8-runtime
 # Modified from https://github.com/tiangolo/uwsgi-nginx-flask-docker (Apache license)
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
@@ -21,23 +21,6 @@ RUN set -x \
 ENV PATH /opt/conda/bin:$PATH
 SHELL ["/bin/bash", "-c"]
 
-# Install Python modules
-COPY ./environment.yml /tmp/environment.yml
-RUN sed -i '/.\/elephant-core/d' /tmp/environment.yml \
-    && curl -OL https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh \
-    && bash Miniconda3-py37_4.11.0-Linux-x86_64.sh -bfp /opt/conda \
-    && rm Miniconda3-py37_4.11.0-Linux-x86_64.sh \
-    && . /opt/conda/etc/profile.d/conda.sh \
-    && conda init \
-    && echo "conda activate base" >> ~/.bashrc \
-    && conda install -c conda-forge -y mamba=0.19.1 \
-    && mamba clean -qafy \
-    && mamba env update -f /tmp/environment.yml \
-    && mamba clean -qafy \
-    && rm -rf /tmp/elephant-core \
-    && rm /tmp/environment.yml
-RUN mamba install jupyter
-
 # Install and set up RabbbitMQ
 COPY docker/install-rabbitmq.sh /tmp/install-rabbitmq.sh
 RUN chmod +x /tmp/install-rabbitmq.sh && /tmp/install-rabbitmq.sh && rm /tmp/install-rabbitmq.sh
@@ -56,6 +39,9 @@ RUN groupadd -r nginx && useradd -r -g nginx nginx
 RUN ln -sf /dev/stdout /var/log/nginx/access.log \
     && ln -sf /dev/stderr /var/log/nginx/error.log
 
+# install pypi packages
+COPY requirements.txt /tmp/requirements.txt
+RUN python -m pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
 # RUN pip install memory_profiler line_profiler
 # RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
 

Dockerfile-test

@@ -1,4 +1,4 @@
-FROM elephant-server:0.5.6
+FROM elephant-server:0.6.0
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
 

Makefile

@@ -5,7 +5,7 @@ help:
 
 ELEPHANT_GPU?=all
 ELEPHANT_WORKSPACE?=${PWD}/workspace
-ELEPHANT_IMAGE_NAME?=elephant-server:0.5.6
+ELEPHANT_IMAGE_NAME?=elephant-server:0.6.0
 ELEPHANT_NVIDIA_GID?=$$(ls -n /dev/nvidia0 2>/dev/null | awk '{print $$4}')
 ELEPHANT_DOCKER?=docker
 ELEPHANT_RABBITMQ_NODENAME?=rabbit@localhost
@@ -82,7 +82,7 @@ notebook: warmup
 
 test:
 	$(ELEPHANT_DOCKER) build -t $(ELEPHANT_IMAGE_NAME)-test -f Dockerfile-test . && $(ELEPHANT_DOCKER) image prune -f 
-	$(ELEPHANT_DOCKER) run -it --rm $(ELEPHANT_IMAGE_NAME)-test
+	$(ELEPHANT_DOCKER) run --rm $(ELEPHANT_IMAGE_NAME)-test
 
 apptainer-build:
 	apptainer build --fakeroot elephant.sif elephant.def

docker/supervisord.conf

@@ -5,7 +5,7 @@ file=/var/run/supervisor%(ENV_ELEPHANT_BATCH_ID)s.sock
 nodaemon=true
 
 [program:uwsgi]
-command=/opt/conda/bin/uwsgi --ini /etc/uwsgi/uwsgi.ini
+command=uwsgi --ini /etc/uwsgi/uwsgi.ini
 stdout_logfile=/dev/stdout
 stdout_logfile_maxbytes=0
 stderr_logfile=/dev/stderr

elephant-core/elephant/version.py

@@ -24,4 +24,4 @@
 # ==============================================================================
 """Version definition."""
 
-__version__ = "0.5.6"
+__version__ = "0.6.0"

elephant.def

@@ -1,12 +1,12 @@
 Bootstrap: docker
-From: nvidia/cuda:11.3.1-runtime-ubuntu20.04
+From: pytorch/pytorch:2.3.1-cuda12.1-cudnn8-runtime
 
 %files
     ./docker /docker
     ./script /opt/elephant/script
     ./app /app
     ./elephant-core /src/elephant-core
-    ./environment.yml /src/environment.yml
+    ./requirements.txt /src/requirements.txt
 
 %environment
     export UWSGI_UID=$(id -u)
@@ -38,22 +38,13 @@ From: nvidia/cuda:11.3.1-runtime-ubuntu20.04
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
-    # Install Python modules
-    sed -i 's/.\/elephant-core/\/src\/elephant-core/g' /src/environment.yml \
-    && curl -OL https://repo.continuum.io/miniconda/Miniconda3-py37_4.11.0-Linux-x86_64.sh \
-    && bash Miniconda3-py37_4.11.0-Linux-x86_64.sh -bfp /opt/conda \
-    && rm Miniconda3-py37_4.11.0-Linux-x86_64.sh \
-    && . /opt/conda/etc/profile.d/conda.sh \
-    && conda init \
-    && echo "conda activate base" >> ~/.bashrc \
-    && conda install -c conda-forge -y mamba==0.19.1 \
-    && mamba clean -qafy \
-    && mamba env update -f /src/environment.yml \
-    && mamba clean -qafy \
-    && rm -rf /src/elephant-core \
-    && rm /src/environment.yml
+    # install pypi packages
+    python -m pip install -r /src/requirements.txt && rm /src/requirements.txt
+    python -m pip install /src/elephant-core && rm -r /src/elephant-core
 
     # Install and set up RabbbitMQ
+        # Install Python modules
+    sed -i 's/sudo //g' /docker/install-rabbitmq.sh
     chmod +x /docker/install-rabbitmq.sh && /docker/install-rabbitmq.sh
     echo "rabbitmq-server \$@" > /rabbitmq.sh
     chmod +x /rabbitmq.sh

elephant_server.ipynb

@@ -39,7 +39,7 @@
       },
       "outputs": [],
       "source": [
-        "%env ELEPHANT_SERVER_VERSION = v0.5.6"
+        "%env ELEPHANT_SERVER_VERSION = v0.6.0"
       ]
     },
     {