1368
Comment: Initial setup and usage of python 3 environments
|
4070
Some improvements
|
Deletions are marked like this. | Additions are marked like this. |
Line 1: | Line 1: |
== Setup Python 3 Environment == | = Under Construction = |
Line 3: | Line 3: |
=== Existing Miniconda/Anaconda Installations === | |
Line 5: | Line 4: |
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 |
== 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> |
Line 8: | Line 15: |
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> |
Line 13: | Line 20: |
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. 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 }}} 1. Configure conda. a. Do not update conda automatically. '''(Strongly recommended.)''' {{{ conda config --set auto_update_conda False }}} a. If you don't want conda's base environment to be activated automatically. '''(Optional)''' {{{ 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 |
Line 20: | Line 51: |
=== New Miniconda Installations === | |
Line 22: | Line 52: |
1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]]. 1. Add the new installation to PATH.{{{ export PATH=<new miniconda path>/bin:$PATH |
== Development Environments == 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 |
Line 26: | Line 60: |
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 |
Line 29: | Line 64: |
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 |
Line 32: | Line 68: |
== 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 |
Line 43: | Line 72: |
1. Build and install {{{ | 1. Navigate to your source directory. Checkout a branch and pull updates from the remote. {{{ cd <source directory> git checkout <branch> git pull --rebase }}} 1. Navigate to your build directory, build and install. {{{ cd <build directory> |
Line 48: | Line 85: |
== Python 3 Transition Environments == == Upgrade CMake to 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 }}} == Test 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 }}} == Test 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. 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