EMAN2/Python3 - EMAN Wiki

Contents

Setup Development Environment with Conda
Development Environments
Python 3 Transition Environments
Python 3 Environments (Coming Soon!)

Setup Development Environment with Conda

TODO

For difference between login- and non-login shells on Mac OSX, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/
Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH?
1. The installer seems to take care of it, if it is not used in batch mode.
2. How do we handle it manually, if the installation was done in batch mode.
Activation, conda init ... https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment

If you have an existing Miniconda2/Anaconda2 installation,
1. Remove miniconda/anaconda entries from PATH.
2. If you want to make use of your cached packages, move your pkgs/ and envs/ folders out of your current installation to another location.
```
   1   mkdir -p <path-to-conda-cache-directory>
   2 # mkdir -p ~/conda-global-cache
   3 
   4 mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory>
   5 mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory>
```
Download Miniconda3 for Linux or MacOSX.
Install Miniconda3.
```
   1 bash <Miniconda3-installer>
```
and follow the prompts.
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 --add pkgs_dirs <path-to-conda-cache-directory>/pkgs
   5 # conda config --add pkgs_dirs ~/conda-global-cache/pkgs
   6 
   7   conda config --add envs_dirs <path-to-conda-cache-directory>/envs
   8 # conda config --add pkgs_dirs ~/conda-global-cache/envs
   9 
```
Configure conda.
1. Do not update conda automatically. (Strongly recommended)
```
   1 conda config --set auto_update_conda False
```
2. If you don't want conda's base environment to be activated automatically. (Optional)
```
   1 conda config --set auto_activate_base False
```
Install conda 4.6.14.
```
   1 conda install conda=4.6.14 -c defaults
```
Initialize conda for shell interaction.
```
   1 conda init bash
   2 
   3 # See command help for supported shells
   4 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.
```
   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.
```
   1 conda activate eman-deps-14.1
```
OR
```
   1 conda activate eman-env
```
Navigate to your source directory. Checkout a branch and pull updates from the remote.
```
   1 cd <source-directory>
   2 git checkout <branch>
   3 git pull --rebase
```
Navigate to your build directory, build and install.
```
   1 cd <build-directory>
   2 cmake <eman-source-directory>
   3 make
   4 make install
```

Python 3 Transition Environments

Phase 1: Upgrade CMake to 3.14

PR: Upgrade CMake to 3.14

Create a new environment and activate it.
```
   1 conda create -n eman-deps-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
   2 conda activate eman-deps-15.1
```
Navigate to your source directory. Checkout branch cmake-upgrade and pull updates from the remote.
```
   1 cd <source-directory>
   2 git checkout cmake-upgrade
   3 git pull --rebase
```
Navigate to your build directory, build and install.
```
   1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make install
```
To switch to another conda environment, first deactivate your current environment.
```
   1 conda deactivate
```

Phase 2: Test Boost 1.64

PR: Upgrade Boost to 1.64

Create a new environment and activate it.
```
   1 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
   2 conda activate eman-deps-14.3
```
Navigate to your source directory. Checkout branch py2-boost-164 and pull updates from the remote.
```
   1 cd <source-directory>
   2 git checkout py2-boost-164
   3 git pull --rebase
```
Navigate to your build directory, build and install.
```
   1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make 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.
```
   1 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
   2 conda activate eman-deps-14.3
```
Navigate to your source directory. Checkout branch py2-boost-166 and pull updates from the remote.
```
   1 cd <source-directory>
   2 git checkout py2-boost-166
   3 git pull --rebase
```
Navigate to your build directory, build and install.
```
   1 cd <build-directory>
   2 cmake <eman2-source-directory>
   3 make
   4 make install
```
To switch to another conda environment, first deactivate your current environment.
```
   1 conda deactivate
```

Python 3 Environments (Coming Soon!)

Coming soon!