Merge pull request #205 from NIEHS/stable

Stable

.gitignore

@@ -31,4 +31,7 @@ docker-compose.yml.bak
 .config
 .python_history
 MyDocker/*
-
+.ipython
+.mysql_history
+.gitignore
+.ipython/profile_default/history.sqlite

.ipython/profile_default/startup/README

@@ -0,0 +1,11 @@
+This is the IPython startup directory
+
+.py and .ipy files in this directory will be run *prior* to any code or files specified
+via the exec_lines or exec_files configurables whenever you load this profile.
+
+Files will be run in lexicographical order, so you can control the execution order of files
+with a prefix, e.g.::
+
+    00-first.py
+    50-middle.py
+    99-last.ipy

Docker/Dockerfile-base

@@ -1,50 +1,37 @@
-FROM nvidia/cuda:10.1-base-ubuntu18.04
-
+FROM nvidia/cuda:12.1.0-base-ubuntu20.04
 
 ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && apt-get install -y \
-	python3-dev default-libmysqlclient-dev build-essential wget libglib2.0-0 ffmpeg libsm6 libxext6 curl mariadb-server && \
+	python3-dev default-libmysqlclient-dev build-essential wget libglib2.0-0 ffmpeg libsm6 libxext6 curl mariadb-server git && \
 	apt-get clean && rm -rf /var/cache/apt/lists
 
-# RUN service mariadb stop && service mariadb disable
-
 RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
 	bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3 && \
 	rm Miniconda3-latest-Linux-x86_64.sh
 
-RUN wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.11.15_RHEL7-64_CUDA10.1.sh && \
-	yes | bash imod_4.11.15_RHEL7-64_CUDA10.1.sh -name IMOD && \
-	rm imod_4.11.15_RHEL7-64_CUDA10.1.sh
+RUN wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.11.24_RHEL7-64_CUDA10.1.sh && ls && \
+	yes | bash imod_4.11.24_RHEL7-64_CUDA10.1.sh -name IMOD && \
+	rm imod_4.11.24_RHEL7-64_CUDA10.1.sh
 
 ADD config/singularity/ctffind /usr/local/
 
 ADD config/docker/requirements.txt .
 
-# RUN	mkdir /opt/logs/ /mnt/fake_scope/ /mnt/fake_scope/raw/ /opt/nginx-mount/
-
-
-
-ENV PATH=$PATH:/opt/smartscope/Smartscope/bin:/opt/miniconda3/bin:$IMOD_DIR/bin
+ENV PATH=$PATH:/opt/miniconda3/bin
 
 RUN conda update -y conda && \
-	yes | conda install python=3.9 cudatoolkit=10.2 cudnn=7.6 && \
-	yes | pip install numpy==1.21.0 && \
-	yes | pip install torch==1.8.2 torchvision==0.9.2 torchaudio==0.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu102 && \
-	yes | pip install -r requirements.txt && \
-	yes | pip install ipython && \
-	yes | pip install sphinx-multiversion && \
+	yes | conda install python=3.9 && \
+	yes | conda install cudatoolkit=11.1 cudnn -c nvidia 
+RUN	yes | conda install pytorch torchvision -c pytorch-lts -c nvidia && \
 	conda clean --all
 
-# RUN wget docs.smartscope.org/downloads/Smartscope0.6.tar.gz --no-check-certificate &&\
-# 	tar -xvf Smartscope0.6.tar.gz -C /opt/ &&\
-# 	rm Smartscope0.6.tar.gz
+RUN	yes | pip install numpy==1.21.0 && \
+	# yes | pip install torch==1.8.2 torchvision==0.9.2 torchaudio==0.8.2 --extra-index-url https://download.pytorch.org/whl/lts/1.8/cu111 && \
+	yes | pip install -r requirements.txt
+
 
 # create a non-root user
 ARG USER_ID=9999
 
-RUN	useradd -m --no-log-init --system  --uid $USER_ID smartscope_user
-
-# RUN chmod 777 -R /mnt/ && \
-# 	chmod 777 /opt/logs/ && \
-# 	chmod 777 /opt/nginx-mount/
+RUN	useradd -m --no-log-init --system  --uid $USER_ID smartscope_user

Docker/Dockerfile-smartscope

@@ -35,13 +35,15 @@ ENV	ALLOWED_HOSTS=localhost \
 	MYSQL_HOST=db \
 	MYSQL_PORT=3306 \
 	MYSQL_USERNAME=root \
-	MYSQL_ROOT_PASSWORD=pass \ 
+	MYSQL_PASSWORD=pass \ 
 	DB_NAME=smartscope \
 	REDIS_HOST=cache \
 	REDIS_PORT=6379 \
 	USE_AWS=False \
 	FORCE_CPU=False
 
+ENV PATH=$PATH:/opt/smartscope/Smartscope/bin:/usr/local/IMOD/bin
+
 ADD . /opt/smartscope/
 
 RUN wget docs.smartscope.org/downloads/Smartscope0.6.tar.gz --no-check-certificate && \

Docker/SmartScope/database.conf

@@ -1,3 +1,6 @@
 MYSQL_USER=root
-MYSQL_ROOT_PASSWORD=pass
-MYSQL_DATABASE=smartscope
+MYSQL_PASSWORD=pass
+MYSQL_DATABASE=smartscope
+MYSQL_HOST=db
+MYSQL_PORT=3306
+MYSQL_SSL=False

Docker/SmartScope/smartscope.conf

@@ -3,12 +3,10 @@ ALLOWED_HOSTS=localhost
 AUTO_MIGRATION=true
 USE_SSL=false
 USE_LONGTERMSTORAGE=False
+TIMEZONE=America/New_York
 
 ### EXPERT SETTINGS ###
 ### EVERYTHING BELOW SHOULD NOT NEED TO BE CHANGED###
-#Other database settings
-# MYSQL_HOST=db
-# MYSQL_PORT=3306
 
 # #Executables
 # IMOD_DIR=/usr/local/IMOD	

Smartscope/bin/smartscope.py

@@ -10,6 +10,7 @@
 import logging
 from Smartscope.core.main_commands import main
 
+
 logger = logging.getLogger(__name__)
 
 

Smartscope/bin/smartscope.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+smartscope.py $@ &