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= Under Construction =


== Setup Development Environment with Conda ==
 1. If you have an existing '''Miniconda2''' installation,
  a. '''Remove miniconda entries from PATH'''.
  a. If you want to make use of your cached packages, move your '''pkgs/''' and '''envs/''' folders out of your current installation to another location.
  {{{
  mkdir -p <path-to-conda-cahe-directory>
# mkdir -p ~/conda-global-cache

mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cahe-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cahe-directory>
}}}
 1. Download '''Miniconda3''' for [[https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh|Linux]] or [[https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh|MacOSX]].
 1. Install '''Miniconda3'''.
 {{{
bash <Miniconda3-installer>
}}}
 and follow the prompts.
 1. Specify package and environment directories outside of the miniconda installation. These are the directories where conda environments and extracted packages will live. If you need to reinstall miniconda, you won't have to re-create your environments and re-download and re-extract all the packages. Reinstallation will only reset the '''base''' environment.
 {{{
  conda config --set pkgs_dirs <path-to-conda-cahe-directory>/pkgs
# conda config --set pkgs_dirs ~/conda-global-cache/pkgs

  conda config --set envs_dirs <path-to-conda-cahe-directory>/envs
# conda config --set pkgs_dirs ~/conda-global-cache/envs
}}}
 1. Configure conda.
  a. Do not update conda automatically. '''(Strongly recommended)'''
  {{{
conda config --set auto_update_conda False
}}}
  a. If you don't want conda's base environment to be activated automatically. '''(Optional)'''
  {{{
conda config --set auto_activate_base False
}}}
 1. Install '''conda 4.6.14'''.
 {{{
conda install conda=4.6.14 -c defaults
}}}
 1. Initialize conda for shell interaction.
 {{{
conda init bash

# See command help for supported shells
conda init --help
}}}



== Development Environments ==

Do not install anything into the '''base''' environment, do not use the '''base''' environment for development, use '''non-base''' environments.

 1. Create a new environment.
 {{{
conda create -n eman-deps-14.1 eman-deps=14.1 -c cryoem -c defaults -c conda-forge
}}}
 OR choose a simpler name for the environment, '''eman-env''' or '''eman'''.
 {{{
conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge
}}}
 1. Activate the environment.
 {{{
conda activate eman-deps-14.1
}}}
 OR
 {{{
conda activate eman-env
}}}
 1. Navigate to your source directory. Checkout a branch and pull updates from the remote.
 {{{
cd <source directory>
git checkout <branch>
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}



== Python 3 Transition Environments ==

== TODO ==
 1. Add mkdir build-eman-deps-14 steps, maybe, after activation.
 1. Fix eman-deps versions in the PR envs.
 1. Add new env for new compilers, maybe, for boost 1.67 and update eman-deps-feedstock.

== Upgrade CMake to 3.14 ==
[[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]]

 1. Create a new environment and activate it.
 {{{
conda create -n eman-deps-14.2 eman-deps=14.2 cmake=3.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge
conda activate eman-deps-14.2
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
}}}

== Test Boost 1.64 ==
[[https://github.com/cryoem/eman2/pull/408|PR: Upgrade Boost to 1.64]]

 1. Create a new environment and activate it.
 {{{
conda create -n eman-deps-14.2 eman-deps=14.3 cmake=3.14 boost=1.64 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
conda activate eman-deps-14.3
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
}}}


== Test Boost 1.66 ==
[[https://github.com/cryoem/eman2/pull/410|PR: Build with Boost versions 1.65-1.66]]

 1. Create a new environment and activate it.
 {{{
conda create -n eman-deps-14.2 eman-deps=14.3 cmake=3.14 boost=1.66 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge
conda activate eman-deps-14.3
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
}}}