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>

  2. Download Miniconda3 for Linux or MacOSX.

  3. Install Miniconda3.

    bash <Miniconda3-installer>
    and follow the prompts.

  4. 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
  5. Configure conda.

    1. Do not update conda automatically.

      conda config --set auto_update_conda False

    2. If you don't want conda's base environment to be activated automatically.

      conda config --set auto_activate_base False

  6. Install conda 4.6.14.

    conda install conda=4.6.14 -c defaults

  7. 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

  2. Activate the environment.

    conda activate eman-deps-14.1

    OR

    conda activate eman-env

Setup Python 2 Environment With CMake 3.14

PR: Upgrade CMake to 3.14

New Miniconda Installations

  1. Download and install Miniconda.

  2. Add the new installation to PATH.

    export PATH=<new miniconda path>/bin:$PATH

  3. 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

  2. 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

  3. 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

  4. To switch to another conda environment, first deactivate your current environment.

    conda deactivate
or
source deactivate

Setup Python 2 Environment with Boost 1.64

PR: Upgrade Boost to 1.64

New Miniconda Installations

  1. Download and install Miniconda.

  2. Add the new installation to PATH.

    export PATH=<new miniconda path>/bin:$PATH

  3. 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

  2. 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

  3. 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

  4. To switch to another conda environment, first deactivate your current environment.

    conda deactivate
or
source deactivate

Setup Python 2 Environment with Boost 1.66

PR: Build with Boost versions 1.65-1.66

New Miniconda Installations

  1. Download and install Miniconda.

  2. Add the new installation to PATH.

    export PATH=<new miniconda path>/bin:$PATH

  3. 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

  2. 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

  3. 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

  4. 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

  2. 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.

  3. Move into your build directory.

    cd <build directory>

  4. Build and install.

    cmake <eman2 source directory>
make
make install