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Comment: general environment setup
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| = Under Construction = == Setup Development Environment with Conda == 1. If you have an existing '''Miniconda2''' installation and 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.{{{ 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.{{{ conda config --set auto_update_conda False }}} a. If you don't want conda's base environment to be activated automatically.{{{ 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 }}} == Use Conda Environments for Development == 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 }}} == Setup Python 2 Environment With CMake 3.14 == [[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]] === New Miniconda Installations === 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]]. 1. Add the new installation to PATH.{{{ export PATH=<new miniconda path>/bin:$PATH }}} 1. Install eman-deps with cmake 3.14.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 conda install eman-deps=14.2 cmake=3.14 conda=4.6.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge }}} === Existing Miniconda/Anaconda Installations === 1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 }}} 1. Create a new environment.{{{ conda create -n eman-deps-14.2 eman-deps=14.2 cmake=3.14 -c cryoem/label/dev -c cryoem -c defaults -c conda-forge }}} 1. Use the activation command printed at the end of the previous command's run to activate the new conda environment.{{{ conda activate eman-deps-14.2 or source activate eman-deps-14.2 }}} 1. To switch to another conda environment, first deactivate your current environment.{{{ conda deactivate or source deactivate }}} == Setup Python 2 Environment with Boost 1.64 == [[https://github.com/cryoem/eman2/pull/408|PR: Upgrade Boost to 1.64]] === New Miniconda Installations === 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]]. 1. Add the new installation to PATH.{{{ export PATH=<new miniconda path>/bin:$PATH }}} 1. Install eman-deps with cmake 3.14.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 conda install eman-deps=14.3 cmake=3.14 boost=1.64 conda=4.6.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge }}} === Existing Miniconda/Anaconda Installations === 1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 }}} 1. Create a new environment.{{{ 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 }}} 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-14.3 or source activate eman-deps-14.3 }}} 1. To switch to another conda environment, first deactivate your current environment.{{{ conda deactivate or source deactivate }}} == Setup Python 2 Environment with Boost 1.66 == [[https://github.com/cryoem/eman2/pull/410|PR: Build with Boost versions 1.65-1.66]] === New Miniconda Installations === 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]]. 1. Add the new installation to PATH.{{{ export PATH=<new miniconda path>/bin:$PATH }}} 1. Install eman-deps with cmake 3.14.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 conda install eman-deps=14.3 cmake=3.14 boost=1.66 conda=4.6.14 -c cryoem/label/boost -c cryoem -c defaults -c conda-forge }}} === Existing Miniconda/Anaconda Installations === 1. Pin your conda, you need to do this only once. Skip this step, if you have already done it.{{{ conda config --set auto_update_conda False conda install conda=4.6.14 }}} 1. Create a new environment.{{{ 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 }}} 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-14.3 or source activate eman-deps-14.3 }}} 1. To switch to another conda environment, first deactivate your current environment.{{{ conda deactivate or source deactivate }}} == Build == Checkout a branch and build as usual. 1. Update eman2 source.{{{ cd <source directory> git checkout <branch> git pull --rebase }}} 1. Activate conda environment, if it is a conda environment.{{{ conda activate <env-name> or source activate <env-name> }}} or edit PATH to have the miniconda installation as the first entry. 1. Move into your build directory.{{{ cd <build directory> }}} 1. Build and install.{{{ cmake <eman2 source directory> make make install }}} |
- Diff for "EMAN2/Python3"