1368
Comment: Initial setup and usage of python 3 environments
|
6582
todo admonitions
|
Deletions are marked like this. | Additions are marked like this. |
Line 1: | Line 1: |
== Setup Python 3 Environment == | <<TableOfContents()>> |
Line 3: | Line 3: |
=== Existing Miniconda/Anaconda Installations === | == Setup Development Environment with Conda == {{{#!wiki caution '''TODO''' 1. For difference between login- and non-login shells on Mac OSX, https://www.anintegratedworld.com/basics-of-osx-bashrc-v-profile-v-bash_profile/ 1. Review how to install new vs existing installations. How do you use conda-init, if conda is not on PATH? a. The installer seems to take care of it, if it is not used in batch mode. a. How do we handle it manually, if the installation was done in batch mode. }}} |
Line 5: | Line 12: |
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 |
1. If you have an existing '''Miniconda2/Anaconda2''' installation, a. '''Remove miniconda/anaconda 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. {{{#!highlight bash mkdir -p <path-to-conda-cache-directory> # mkdir -p ~/conda-global-cache mv <path-to-current-miniconda2-installation>/pkgs <path-to-conda-cache-directory> mv <path-to-current-miniconda2-installation>/envs <path-to-conda-cache-directory> |
Line 8: | Line 22: |
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'''. {{{#!highlight bash bash <Miniconda3-installer> |
Line 13: | Line 27: |
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 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. {{{#!highlight bash mkdir -p <path-to-conda-cache-directory> # mkdir -p ~/conda-global-cache conda config --add pkgs_dirs <path-to-conda-cache-directory>/pkgs # conda config --add pkgs_dirs ~/conda-global-cache/pkgs conda config --add envs_dirs <path-to-conda-cache-directory>/envs # conda config --add pkgs_dirs ~/conda-global-cache/envs }}} 1. Configure conda. a. Do not update conda automatically. '''(Strongly recommended)''' {{{#!highlight bash conda config --set auto_update_conda False }}} a. If you don't want conda's base environment to be activated automatically. '''(Optional)''' {{{#!highlight bash conda config --set auto_activate_base False }}} 1. Install '''conda 4.6.14'''. {{{#!highlight bash conda install conda=4.6.14 -c defaults }}} 1. Initialize conda for shell interaction. {{{#!highlight bash conda init bash # See command help for supported shells conda init --help |
Line 20: | Line 61: |
=== New Miniconda Installations === | |
Line 22: | Line 62: |
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. {{{#!highlight bash conda create -n eman-deps-14.1 eman-deps=14.1 -c cryoem -c defaults -c conda-forge |
Line 26: | Line 70: |
1. Update conda {{{ conda update conda -c defaults |
OR choose a simpler name for the environment, '''eman-env''' or '''eman'''. {{{#!highlight bash conda create -n eman-env eman-deps=14.1 -c cryoem -c defaults -c conda-forge |
Line 29: | Line 74: |
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. {{{#!highlight bash conda activate eman-deps-14.1 }}} OR {{{#!highlight bash conda activate eman-env }}} 1. Navigate to your source directory. Checkout a branch and pull updates from the remote. {{{#!highlight bash cd <source-directory> git checkout <branch> git pull --rebase }}} 1. Navigate to your build directory, build and install. {{{#!highlight bash cd <build-directory> cmake <eman-source-directory> make make install |
Line 34: | Line 97: |
== 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> |
== Python 3 Transition Environments == {{{#!wiki comment '''TODO''' 1. Fix eman-deps versions in the PR envs. 1. Add new env for new compilers, maybe, for boost 1.67 and update eman-deps-feedstock. |
Line 43: | Line 105: |
1. Build and install {{{ cmake <eman2 source directory> |
=== Phase 1: 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. {{{#!highlight bash 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. Navigate to your source directory. Checkout branch '''cmake-upgrade''' and pull updates from the remote. {{{#!highlight bash cd <source-directory> git checkout cmake-upgrade git pull --rebase }}} 1. Navigate to your build directory, build and install. {{{#!highlight bash cd <build-directory> cmake <eman2-source-directory> |
Line 48: | Line 127: |
1. To switch to another conda environment, first deactivate your current environment. {{{#!highlight bash conda deactivate }}} === Phase 2: 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. {{{#!highlight bash 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. Navigate to your source directory. Checkout branch '''py2-boost-164''' and pull updates from the remote. {{{#!highlight bash cd <source-directory> git checkout py2-boost-164 git pull --rebase }}} 1. Navigate to your build directory, build and install. {{{#!highlight bash cd <build-directory> cmake <eman2-source-directory> make make install }}} 1. To switch to another conda environment, first deactivate your current environment. {{{#!highlight bash conda deactivate }}} === Phase 3: 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. {{{#!highlight bash 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. Navigate to your source directory. Checkout branch '''py2-boost-166''' and pull updates from the remote. {{{#!highlight bash cd <source-directory> git checkout py2-boost-166 git pull --rebase }}} 1. Navigate to your build directory, build and install. {{{#!highlight bash cd <build-directory> cmake <eman2-source-directory> make make install }}} 1. To switch to another conda environment, first deactivate your current environment. {{{#!highlight bash conda deactivate }}} == Python 3 Environments (Coming Soon!) == Coming soon! |
Contents
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?
- The installer seems to take care of it, if it is not used in batch mode.
- How do we handle it manually, if the installation was done in batch mode.
If you have an existing Miniconda2/Anaconda2 installation,
Remove miniconda/anaconda 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 --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.
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
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
Python 3 Environments (Coming Soon!)
Coming soon!