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cd <source directory> | cd <source-directory> |
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cd <build directory> cmake <eman2 source directory> |
cd <build-directory> cmake <eman-source-directory> |
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cd <build directory> cmake <eman2 source directory> |
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cd <build directory> cmake <eman2 source directory> |
cd <build-directory> cmake <eman2-source-directory> |
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Contents
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.
Install Miniconda3.
and follow the prompts.1 bash <Miniconda3-installer>
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.
1 mkdir -p <path-to-conda-cache-directory> 2 # mkdir -p ~/conda-global-cache 3 4 conda config --set pkgs_dirs <path-to-conda-cache-directory>/pkgs 5 # conda config --set pkgs_dirs ~/conda-global-cache/pkgs 6 7 conda config --set envs_dirs <path-to-conda-cache-directory>/envs 8 # conda config --set pkgs_dirs ~/conda-global-cache/envs 9
- Configure conda.
Install conda 4.6.14.
1 conda install conda=4.6.14 -c defaults
- Initialize conda for shell interaction.
Development Environments
Do not install anything into the base environment, do not use the base environment for development, use non-base environments.
- Create a new environment.
1 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.
1 conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge
- Activate the environment. OR
1 conda activate eman-deps-14.1
1 conda activate eman-env
- Navigate to your source directory. Checkout a branch and pull updates from the remote.
- Navigate to your build directory, build and install.
Python 3 Transition Environments
TODO
- Fix eman-deps versions in the PR envs.
- 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
- Create a new environment and activate it.
Navigate to your source directory. Checkout branch cmake-upgrade and pull updates from the remote.
- Navigate to your build directory, build and install.
- To switch to another conda environment, first deactivate your current environment.
1 conda deactivate
Phase 2: Test Boost 1.64
- Create a new environment and activate it.
Navigate to your source directory. Checkout branch py2-boost-164 and pull updates from the remote.
- Navigate to your build directory, build and install.
- To switch to another conda environment, first deactivate your current environment.
1 conda deactivate
Phase 3: Test Boost 1.66
PR: Build with Boost versions 1.65-1.66
- Create a new environment and activate it.
Navigate to your source directory. Checkout branch py2-boost-166 and pull updates from the remote.
- Navigate to your build directory, build and install.
- To switch to another conda environment, first deactivate your current environment.
1 conda deactivate