From 629e2ecc71f5892181893b22beaa64de117a501e Mon Sep 17 00:00:00 2001
From: Pat Gunn <pgunn01@gmail.com>
Date: Tue, 12 Feb 2019 14:54:50 -0500
Subject: [PATCH 1/4] Provide a modern Dockerfile

---
 Dockerfile | 40 +++-------------------------------------
 1 file changed, 3 insertions(+), 37 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 842c1769d..30fb4f28d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,41 +1,7 @@
-FROM ubuntu
+FROM continuumio/anaconda3
 
-RUN apt-get update
-RUN apt-get install -y libglib2.0-0
-RUN apt-get install -y git wget
-RUN apt-get install bzip2
-RUN apt-get install -y gcc
-RUN apt-get install -y g++
-RUN apt-get install -y libgtk2.0-0
-RUN apt-get install -y xvfb
-RUN export MINICONDA=$HOME/miniconda
-RUN export PATH="$MINICONDA/bin:$PATH"
-RUN hash -r
-RUN wget -q https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda2-2.5.0-Linux-x86_64.sh -O anaconda.sh
-# RUN bash anaconda.sh -b -p $ANACONDA
-RUN bash anaconda.sh -p /anaconda -b
-ENV PATH=/anaconda/bin:${PATH}
 RUN conda config --set always_yes yes
 RUN conda update --yes conda
-RUN conda info -a
-RUN CONDA_SSL_VERIFY=false conda update pyopenssl
-# RUN conda install -c menpo opencv3=3.1.0
-# RUN conda install -c cvxgrp cvxpy
-# RUN conda install -c https://conda.anaconda.org/conda-forge tifffile
-# RUN git clone --recursive -b agiovann-master https://github.com/valentina-s/Constrained_NMF.git
-# RUN git clone --recursive https://github.com/agiovann/Constrained_NMF.git
-# RUN git clone --recursive -b dev https://github.com/agiovann/Constrained_NMF.git
-ADD . /CaImAn
-WORKDIR /CaImAn/
-RUN conda env update -f environment.yml -n root
-#RUN conda install --file requirements_conda.txt
-#RUN pip install -r requirements_pip.txt
-RUN apt-get install libc6-i386
-RUN apt-get install -y libsm6 libxrender1
-RUN conda install pyqt=4.11.4
-RUN python setup.py install
-RUN python setup.py build_ext -i
+RUN mkdir src && cd src && git clone -b dev git@github.com:flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda activate caiman && pip install .
+RUN conda activate caiman && caimanmanager.py install
 
-# RUN nosetests
-
-EXPOSE 8080

From b03c77b759bc4caea6b9b08a41664ba67300ebdb Mon Sep 17 00:00:00 2001
From: Pat Gunn <pgunn01@gmail.com>
Date: Tue, 12 Feb 2019 17:29:36 -0500
Subject: [PATCH 2/4] Inside docker, must not rely on git credentials.

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 30fb4f28d..3a7edcc5f 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,6 +2,6 @@ FROM continuumio/anaconda3
 
 RUN conda config --set always_yes yes
 RUN conda update --yes conda
-RUN mkdir src && cd src && git clone -b dev git@github.com:flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda activate caiman && pip install .
+RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda activate caiman && pip install .
 RUN conda activate caiman && caimanmanager.py install
 

From b10d147d23866ba4c10bd7b3d91760d31566620f Mon Sep 17 00:00:00 2001
From: Pat Gunn <pgunn01@gmail.com>
Date: Tue, 12 Feb 2019 17:35:14 -0500
Subject: [PATCH 3/4] Dockerfile: continuumio/anaconda3 is not installed in a
 modern way; adapt

---
 Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3a7edcc5f..1ce0e669d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,6 +2,6 @@ FROM continuumio/anaconda3
 
 RUN conda config --set always_yes yes
 RUN conda update --yes conda
-RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda activate caiman && pip install .
-RUN conda activate caiman && caimanmanager.py install
+RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && source activate caiman && pip install .
+RUN source activate caiman && caimanmanager.py install
 

From 0c3b07d694229056ef6f26a70f840821280d1ab9 Mon Sep 17 00:00:00 2001
From: Pat Gunn <pgunn01@gmail.com>
Date: Tue, 12 Feb 2019 18:55:43 -0500
Subject: [PATCH 4/4] This dockerfile finally builds correctly.

---
 Dockerfile | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 1ce0e669d..473576ad4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,6 +2,8 @@ FROM continuumio/anaconda3
 
 RUN conda config --set always_yes yes
 RUN conda update --yes conda
-RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && source activate caiman && pip install .
-RUN source activate caiman && caimanmanager.py install
+RUN apt-get install -y gcc g++ libgl1
+RUN mkdir src && cd src && git clone -b dev https://github.com/flatironinstitute/CaImAn.git && cd CaImAn && conda env create -n caiman -f environment.yml && conda install --override-channels -c conda-forge -n caiman pip
+RUN /bin/bash -c "cd src/CaImAn && source activate caiman && /opt/conda/envs/caiman/bin/pip install ."
+RUN /bin/bash -c "source activate caiman && caimanmanager.py install"