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| <<TableOfContents()>> == Setup Development Environment with Conda == {{{#!wiki caution '''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'''. 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 --add pkgs_dirs <path-to-conda-cache-directory>/pkgs # conda config --add pkgs_dirs ~/conda-global-cache/pkgs conda config --add envs_dirs <path-to-conda-cache-directory>/envs # conda config --add 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 == {{{#!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! |
- Diff for "EMAN2/Python3"