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Comment: add '-' to placeholder args
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← Revision 36 as of 2020-12-03 07:13:54 ⇥
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<<TableOfContents()>> == 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. {{{#!highlight bash 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> }}} 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'''. {{{#!highlight bash 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. First, create the cache directory, if it doesn't exist. {{{#!highlight bash 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)''' {{{#!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 }}} == 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 == == 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. {{{#!highlight bash 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. {{{#!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-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. {{{#!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-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. {{{#!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 }}} |