From 9e03fc7a4b768c18cb6b9b672f0ab5bc51774fbf Mon Sep 17 00:00:00 2001
From: Tony Tung <ttung@chanzuckerberg.com>
Date: Wed, 13 Nov 2019 00:49:51 -0600
Subject: [PATCH] Simplify Dockerfile (#1642)

It simply overlays a python image 3.6 image with a starfish install.  No weird conda bugs.  It will be fantastic.

Changed the entry point so that it's just a bash shell.

Depends on #1641

Test plan: `make docker`
---
 .dockerignore          | 19 ++++++++++++++++++-
 Makefile               |  2 +-
 docker/Dockerfile      | 25 ++++++++++---------------
 docker/condarc         |  2 --
 docker/environment.yml | 13 -------------
 docker/pip-config      |  2 --
 6 files changed, 29 insertions(+), 34 deletions(-)
 delete mode 100644 docker/condarc
 delete mode 100644 docker/environment.yml
 delete mode 100644 docker/pip-config

diff --git a/.dockerignore b/.dockerignore
index 6b8710a71..1aaebe24d 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1 +1,18 @@
-.git
+.DS_Store
+*.pyc
+starfish.egg-info/
+*.ipynb_checkpoints
+.coverage
+.coverage.*
+.mypy_cache/
+.pytest_cache/
+build/
+dist/
+.venv/
+.eggs/
+docs/source/usage/data_formatting_examples/
+docs/source/usage/data_processing_examples/
+docs/source/creating_an_image_processing_pipeline/tutorials/
+.idea/
+.git/
+.hg/
diff --git a/Makefile b/Makefile
index 24daca43a..af2013843 100644
--- a/Makefile
+++ b/Makefile
@@ -121,7 +121,7 @@ slow: fast run-notebooks test-examples docker
 
 docker:
 	docker build -f docker/Dockerfile -t $(DOCKER_IMAGE) .
-	docker run -ti --rm $(DOCKER_IMAGE) --help
+	docker run -ti --rm $(DOCKER_IMAGE) starfish --help
 
 
 help-integration:
diff --git a/docker/Dockerfile b/docker/Dockerfile
index a3a02ceb6..2b4e7e4e8 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -36,27 +36,22 @@
 ##
 ##   $ docker run -e TEST_ISS_KEEP_DATA=true --entrypoint=pytest spacetx/starfish -vsxk TestWithIssData
 ##
-FROM continuumio/miniconda3
+FROM python:3.6-slim-stretch
+
 RUN useradd -m starfish
 USER starfish
+WORKDIR /home/starfish/
 
-# Set up the initial conda environment
-COPY --chown=starfish:starfish docker/environment.yml /src/docker/environment.yml
-COPY --chown=starfish:starfish docker/pip-config /src/
-COPY --chown=starfish:starfish docker/condarc /home/starfish/.condarc
-COPY --chown=starfish:starfish REQUIREMENTS* /src/
-WORKDIR /src
-ENV PIP_CONFIG_FILE=/src/pip-config
-RUN conda env create -f docker/environment.yml \
-    && conda clean -tipsy
+# create a virtual environment
+RUN python -m venv .venv
+ENV PATH /home/starfish/.venv/bin/:$PATH
 
 # Prepare for build
-COPY --chown=starfish:starfish . /src
-RUN echo "source activate starfish" >> ~/.bashrc
-ENV PATH /home/starfish/.conda/envs/starfish/bin:$PATH
+COPY --chown=starfish:starfish . /home/starfish/src
 
 # Build and configure for running
-RUN pip install -e . --ignore-installed --no-cache-dir
+RUN pip install -e src --ignore-installed --no-cache-dir
 
 env MPLBACKEND Agg
-ENTRYPOINT ["starfish"]
+
+CMD ["bash"]
diff --git a/docker/condarc b/docker/condarc
deleted file mode 100644
index c862506c9..000000000
--- a/docker/condarc
+++ /dev/null
@@ -1,2 +0,0 @@
-pkgs_dirs:
- - /home/starfish/.conda/pkgs
diff --git a/docker/environment.yml b/docker/environment.yml
deleted file mode 100644
index 378c92588..000000000
--- a/docker/environment.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-name: starfish
-channels:
-- defaults
-- bioconda
-- conda-forge
-dependencies:
-- python>=3.6
-- pip
-- matplotlib==2.1.2
-- numpy==1.16.1
-- pip:
-  - -r ../REQUIREMENTS-STRICT.txt
-  - jsonpath-rw
diff --git a/docker/pip-config b/docker/pip-config
deleted file mode 100644
index 5ec564090..000000000
--- a/docker/pip-config
+++ /dev/null
@@ -1,2 +0,0 @@
-[install]
-ignore-installed = true