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Comment: Initial setup and usage of python 3 environments
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Python 3 Transition Environments
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== Setup Python 3 Environment == === Existing Miniconda/Anaconda Installations === 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 |
= Under Construction = == 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-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> |
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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. {{{ 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 |
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== 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. |
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=== 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. 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. Checkout a branch. 1. Update eman2 source. {{{ 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 == == CMake 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. To switch to another conda environment, first deactivate your current environment. {{{ conda deactivate }}} == 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. To switch to another conda environment, first deactivate your current environment. {{{ conda deactivate }}} == 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. To switch to another conda environment, first deactivate your current environment. {{{ conda deactivate }}} |
Under Construction
Setup Development Environment with Conda
If you have an existing Miniconda2 installation,
Remove miniconda entries from PATH.
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-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>
Install Miniconda3.
bash <Miniconda3-installer>
- and follow the prompts.
- 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
- Configure conda.
- Do not update conda automatically.
conda config --set auto_update_conda False
- If you don't want conda's base environment to be activated automatically.
conda config --set auto_activate_base False
- Do not update conda automatically.
Install conda 4.6.14.
conda install conda=4.6.14 -c defaults
- 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.
- 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
- Activate the environment.
conda activate eman-deps-14.1
ORconda activate eman-env
- Checkout a branch.
- Update eman2 source.
cd <source directory> git checkout <branch> git pull --rebase
- Navigate to your build directory, build and install.
cd <build directory> cmake <eman2 source directory> make make install
Python 3 Transition Environments
CMake 3.14
- 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
- To switch to another conda environment, first deactivate your current environment.
conda deactivate
Boost 1.64
- 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
- To switch to another conda environment, first deactivate your current environment.
conda deactivate
Boost 1.66
PR: Build with Boost versions 1.65-1.66
- 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
- To switch to another conda environment, first deactivate your current environment.
conda deactivate