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<<TableOfContents()>>
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=== Phase 4: Decide Boost Version ===
[[https://github.com/cryoem/eman2/pull/409|PR: Build with Boost versions 1.67-1.69]]
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== Python 3 Environments (Coming Soon!) ==

Coming soon!

---------

The following sections were written with conda environments in mind, but will not be used. Keeping here for future reference.

---------

== Setup Development Environment with Conda ==
{{{#!wiki comment
'''TODO'''
 1. For difference between login- and non-login shells on Mac OSX, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/
 1. Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH?
  a. The installer seems to take care of it, if it is not used in batch mode.
  a. How do we handle it manually, if the installation was done in batch mode.
 1. Activation, conda init ... https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment
}}}

 1. If you have an existing '''Miniconda2/Anaconda2''' installation,
  a. '''Remove miniconda/anaconda entries from PATH'''.

 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'''.
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bash <Miniconda3-installer>
}}}
 and follow the prompts.

 1. Configure conda.
  a. Do not update conda automatically. '''(Strongly recommended)'''
  {{{#!highlight bash
conda config --set auto_update_conda False
}}}
  a. If you don't want conda's base environment to be activated automatically. '''(Optional)'''
  {{{#!highlight bash
conda config --set auto_activate_base False
}}}
 1. Install '''conda 4.6.14'''.
 {{{#!highlight bash
conda install conda=4.6.14 -c defaults
}}}
 1. Initialize conda for shell interaction.
 {{{#!highlight bash
conda init bash

# See command help for supported shells
conda init --help		 conda install eman-deps=16.1 cmake=3.14 boost=1.67 -c cryoem -c defaults -c conda-forge
conda install eman-deps=16.1 cmake=3.14 boost=1.68 -c cryoem -c defaults -c conda-forge
conda install eman-deps=16.1 cmake=3.14 boost=1.69 -c cryoem -c defaults -c conda-forge
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== Python 3 Environments ==
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== 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.
 {{{#!highlight bash
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'''.
 {{{#!highlight bash
conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge
}}}
 1. Activate the environment.
 {{{#!highlight bash
conda activate eman-deps-14.1
}}}
 OR
 {{{#!highlight bash
conda activate eman-env
}}}
 1. Navigate to your source directory. Checkout a branch and pull updates from the remote.
 {{{#!highlight bash
cd <source-directory>
git checkout <branch>
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build-directory>
cmake <eman-source-directory>
make
make install
}}}



== Python 3 Transition Environments ==

{{{#!wiki comment
'''TODO'''
 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.
}}}

=== Phase 1: 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.
 {{{#!highlight bash
conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
conda activate eman-deps-15.1
}}}
 1. Navigate to your source directory. Checkout branch '''cmake-upgrade''' and pull updates from the remote.
 {{{#!highlight bash
cd <source-directory>
git checkout cmake-upgrade
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build-directory>
cmake <eman2-source-directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{#!highlight bash
conda deactivate
}}}

=== Phase 2: 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.
 {{{#!highlight bash
conda create -n eman-deps-16.1 eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge
conda activate eman-deps-16.1
}}}
 1. Navigate to your source directory. Checkout branch '''py2-boost-164''' and pull updates from the remote.
 {{{#!highlight bash
cd <source-directory>
git checkout py2-boost-164
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build-directory>
cmake <eman2-source-directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{#!highlight bash
conda deactivate
}}}


=== Phase 3: 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.
 {{{#!highlight bash
conda create -n eman-deps-16.1 eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge
conda activate eman-deps-16.1
}}}
 1. Navigate to your source directory. Checkout branch '''py2-boost-166''' and pull updates from the remote.
 {{{#!highlight bash
cd <source-directory>
git checkout py2-boost-166
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{#!highlight bash
cd <build-directory>
cmake <eman2-source-directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{#!highlight bash
conda deactivate
}}}


== Python 3 Environments (Coming Soon!) ==

Coming soon!		 No python 3 environments yet.

Contents

  1. Python 3 Transition Environments
    1. Phase 1: Upgrade CMake to 3.14
    2. Phase 2: Test Boost 1.64
    3. Phase 3: Test Boost 1.66
    4. Phase 4: Decide Boost Version
  2. Python 3 Environments

Python 3 Transition Environments

Phase 1: Upgrade CMake to 3.14

PR: Upgrade CMake to 3.14

Install cmake=3.14 and eman-deps=15.1. 

  •    1 conda install eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge

Phase 2: Test Boost 1.64

PR: Upgrade Boost to 1.64 

  •    1 conda install eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge

Phase 3: Test Boost 1.66

PR: Build with Boost versions 1.65-1.66 

  •    1 conda install eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge

Phase 4: Decide Boost Version

PR: Build with Boost versions 1.67-1.69 

  •    1 conda install eman-deps=16.1 cmake=3.14 boost=1.67 -c cryoem -c defaults -c conda-forge
   2 conda install eman-deps=16.1 cmake=3.14 boost=1.68 -c cryoem -c defaults -c conda-forge
   3 conda install eman-deps=16.1 cmake=3.14 boost=1.69 -c cryoem -c defaults -c conda-forge

Python 3 Environments

No python 3 environments yet.