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. These are the directories where conda environments and extracted packages will live.
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. (Strongly recommended.)
conda config --set auto_update_conda False
If you don't want conda's base environment to be activated automatically. (Optional)
conda config --set auto_activate_base False
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
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.
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
- Navigate to your source directory. Checkout a branch and pull updates from the remote.
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
Upgrade CMake to 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
Test 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
Test 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