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⇤ ← Revision 1 as of 2019-05-18 10:42:26 →
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Editor: TunayDurmaz
Comment: Initial setup and usage of python 3 environments
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Editor: TunayDurmaz
Comment: typos, build updates
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== Setup Python 3 Environment == = Under Construction =
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=== Existing Miniconda/Anaconda Installations ===
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 1. Create a new environment with python 3{{{
conda create -n eman-deps-15 eman-deps=15 -c cryoem/label/py3 -c cryoem -c defaults -c conda-forge		 == 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-cache-directory>
# mkdir -p ~/conda-global-cache

mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>
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 1. Use the activation command printed at the end of the previous command's run to activate the new conda environment {{{
conda activate eman-deps-15
or
source activate eman-deps-15		  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>
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 1. To switch to another conda environment, first deactivate your current environment{{{
conda deactivate
or
source deactivate		  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. First, create the cache directory, if it doesn't exist.
 {{{
  mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache

  conda config --set pkgs_dirs <path-to-conda-cache-directory>/pkgs
# conda config --set pkgs_dirs ~/conda-global-cache/pkgs

  conda config --set envs_dirs <path-to-conda-cache-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
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=== New Miniconda Installations ===
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 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]].
 1. Add the new installation to PATH.{{{
export PATH=<new miniconda path>/bin:$PATH		 == 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
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 1. Update conda {{{
conda update conda -c defaults		  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
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 1. Install eman-deps with python 3{{{
conda install eman-deps=15 -c cryoem/label/py3 -c cryoem -c defaults -c conda-forge		  1. Activate the environment.
 {{{
conda activate eman-deps-14.1
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== Build ==
 1. Activate the python 3 environment, if it is a conda environment{{{
conda activate eman-deps-15
or
source activate eman-deps-15
}}} or edit PATH to have the miniconda installation with python 3 as the first entry.
 1. Move into your build directory {{{
cd <python 3 build directory>		  OR
 {{{
conda activate eman-env
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 1. Build and install {{{  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>
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== Python 3 Transition Environments ==

== 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.
'''END TODO'''

== 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.
 {{{
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. Navigate to your source directory. Checkout branch '''cmake-upgrade''' and pull updates from the remote.
 {{{
cd <source directory>
git checkout cmake-upgrade
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
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.
 {{{
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. Navigate to your source directory. Checkout branch '''py2-boost-164''' and pull updates from the remote.
 {{{
cd <source directory>
git checkout py2-boost-164
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
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.
 {{{
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. Navigate to your source directory. Checkout branch '''py2-boost-166''' and pull updates from the remote.
 {{{
cd <source directory>
git checkout py2-boost-166
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{
cd <build directory>
cmake <eman2 source directory>
make
make install
}}}
 1. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
}}}

Under Construction

Setup Development Environment with Conda

  1. If you have an existing Miniconda2 installation,

    1. Remove miniconda entries from PATH.

    2. 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-cache-directory>
# mkdir -p ~/conda-global-cache

mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>

  2. Download Miniconda3 for Linux or MacOSX.

  3. Install Miniconda3. 

    bash <Miniconda3-installer>
    and follow the prompts.

  4. 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. First, create the cache directory, if it doesn't exist. 

      mkdir -p <path-to-conda-cache-directory>
# mkdir -p ~/conda-global-cache

  conda config --set pkgs_dirs <path-to-conda-cache-directory>/pkgs
# conda config --set pkgs_dirs ~/conda-global-cache/pkgs

  conda config --set envs_dirs <path-to-conda-cache-directory>/envs
# conda config --set pkgs_dirs ~/conda-global-cache/envs
  5. Configure conda.

    1. Do not update conda automatically. (Strongly recommended) 

      conda config --set auto_update_conda False

    2. If you don't want conda's base environment to be activated automatically. (Optional) 

      conda config --set auto_activate_base False

  6. Install conda 4.6.14. 

    conda install conda=4.6.14 -c defaults
  7. 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
  2. Activate the environment. 
    conda activate eman-deps-14.1
    OR 
    conda activate eman-env
  3. Navigate to your source directory. Checkout a branch and pull updates from the remote. 
    cd <source directory>
git checkout <branch>
git pull --rebase
  4. Navigate to your build directory, build and install. 
    cd <build directory>
cmake <eman2 source directory>
make
make install

Python 3 Transition Environments

TODO

  1. Fix eman-deps versions in the PR envs.
  2. Add new env for new compilers, maybe, for boost 1.67 and update eman-deps-feedstock.

END TODO

Phase 1: Upgrade CMake to 3.14

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

  2. Navigate to your source directory. Checkout branch cmake-upgrade and pull updates from the remote. 

    cd <source directory>
git checkout cmake-upgrade
git pull --rebase
  3. Navigate to your build directory, build and install. 
    cd <build directory>
cmake <eman2 source directory>
make
make install
  4. To switch to another conda environment, first deactivate your current environment. 
    conda deactivate

Phase 2: Test Boost 1.64

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

  2. Navigate to your source directory. Checkout branch py2-boost-164 and pull updates from the remote. 

    cd <source directory>
git checkout py2-boost-164
git pull --rebase
  3. Navigate to your build directory, build and install. 
    cd <build directory>
cmake <eman2 source directory>
make
make install
  4. To switch to another conda environment, first deactivate your current environment. 
    conda deactivate

Phase 3: Test Boost 1.66

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

  2. Navigate to your source directory. Checkout branch py2-boost-166 and pull updates from the remote. 

    cd <source directory>
git checkout py2-boost-166
git pull --rebase
  3. Navigate to your build directory, build and install. 
    cd <build directory>
cmake <eman2 source directory>
make
make install
  4. To switch to another conda environment, first deactivate your current environment. 
    conda deactivate