EMAN2 is built with `conda-build` using binaries from https://anaconda.org, packaged into an installer with constructor as of v2.2.

1. conda is the package manager. 2. https://anaconda.org is the online repository of binaries. 3. conda-build is the tool to build from source. 4. constructor is the tool to package eman2 and dependency binaries into a single installer file.

EMAN2 is distributed as a single installer which includes all its dependencies. However, EMAN2 is not available as a conda-package on https://anaconda.org. In other words it is not possible to install EMAN2 by typing

conda install eman2

.

Packages that are available on https://anaconda.org can be installed into any conda environment by issuing the command

conda install <package>

. Conda installs the package along with its dependencies. In order for packages to benefit from this automation, they need to be packaged in a specific way. That can be done with

conda-build

.

conda-build

builds packages according to instructions provided in a

recipe

. A recipe consists of a file with package metadata,

meta.yaml

, and any other necessary resources like build scripts, (

build.sh

,

bld.bat

), patches and so on.

Most of EMAN2 dependencies can be found on anaconda's channels,

defaults

and

conda-forge

. A few that do not exist or need to be customized have been built and uploaded to channel cryoem. The recipes are hosted in separate repositories on GitHub. Every recipe repository follows the feedstock approach of conda-forge. See here for a complete list.

It is possible to utilize conda for building and installing EMAN2 in a few ways. One way is to just install binaries with conda and point to the right locations of dependencies during cmake configuration. Another way is to make use of the newly added features in EMAN2's cmake which find the dependencies automatically. These features are activated only when the build is performed by

conda-build

. CMake knows the build is a

conda-build

build only through an environment variable. So, it is possible to set the specific environment variable manually and still activate those features without actually using

conda-build

. Third way is to use a recipe to run

conda-build

. Basic instructions for all three strategies follow.

5. Install dependencies

  a. Manually with <code>

conda install <package> </code>

  a. Or with a single command<code>

conda install eman-deps -c cryoem -c defaults -c conda-forge </code>

2. Build and install EMAN2 manually into home directory with

cmake

,

make

and

make install

.

3. Resulting installation is under $HOME/EMAN2 by default.

This is detailed on EMAN WIKI. Also, see build_no_envars.sh.

6. Install dependencies

  a. Manually with <code>

conda install <package> </code>

  a. Or with a single command<code>

conda install eman-deps -c cryoem -c defaults -c conda-forge </code>

2. Set environment variables.

export CONDA_BUILD_STATE=BUILD
export PREFIX=<path-to-anaconda-installation-directory> # $HOME/miniconda2/ or $HOME/anaconda2/
export SP_DIR=$PREFIX/lib/python2.7/site-packages

3. Build and install EMAN2 manually into conda environment with

cmake

,

make

and

make install

. See build_with_envars.sh.

4. Resulting installation is under Anaconda/Miniconda installation, $HOME/anaconda2/ or $HOME/miniconda2/ by default.

conda build <path-to-eman-recipe-directory>
conda install eman2 --use-local -c cryoem -c defaults -c conda-forge

Resulting installation is under Anaconda/Miniconda installation, $HOME/anaconda2/ or $HOME/miniconda2/ by default.

:TODO: Advantages/disadvantages/comparison of the strategies.

The build strategies described in section Build Strategies are tested on CI (Continuous Integration) servers for MacOSX (TravisCI) and Linux (CircleCI). For Windows (Appveyor), only the recipe strategy is tested. The tests are triggered for every commit that is pushed to GitHub.

:TODO: Jenkins.

Packaging is done with

constructor

, a tool for making installers from conda packages. In order to slightly customize the installers the project was forked. The customized project is at https://github.com/cryoem/constructor. The input files for

constructor

are maintained at –(https://github.com/cryoem/docker-images )– https://github.com/cryoem/build-scripts.

The installer has additional tools like

conda

,

conda-build

,

pip

bundled. The installer is setup so that the packages are kept in the installed EMAN2 conda environment cache for convenience.

The binary packages are built on three physical machines. The operating systems are Mac OSX 10.10, CentOS 7 and Windows 10. CentOS 6 binaries are built in a CentOS 6 docker container on the CentOS 7 machine. Various build related scripts are on https://github.com/cryoem/build-scripts.

:TODO:

[Windows]

Docker images and helper scripts are at –(https://github.com/cryoem/docker-images )– https://github.com/cryoem/build-scripts.

Command to run docker with GUI support, CentOS7:

xhost + local:root

docker run -it -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$DISPLAY cryoem/eman-nvidia-cuda8-centos7

# When done with eman
xhost - local:root

:: Runs as root on Linux. `chown` doesn't work, the resulting installer has root ownership.