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== Setup Python 3 Environment == === Existing Miniconda/Anaconda Installations === 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. 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. To switch to another conda environment, first deactivate your current environment{{{ |
== Python 3 Transition Environments == === Phase 1: Upgrade CMake to 3.14 === [[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]] Install cmake=3.24 and eman-deps=15.1. {{{#!highlight bash conda install eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge }}} === Phase 2: Test Boost 1.64 === [[https://github.com/cryoem/eman2/pull/408|PR: Upgrade Boost to 1.64]] {{{#!highlight bash conda install eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge }}} === Phase 3: Test Boost 1.66 === [[https://github.com/cryoem/eman2/pull/410|PR: Build with Boost versions 1.65-1.66]] {{{#!highlight bash conda install eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge }}} == Python 3 Environments (Coming Soon!) == Coming soon! --------- The following sections were written with conda environments in mind, but will not be used. Keeping here for future reference. --------- == Setup Development Environment with Conda == {{{#!wiki comment '''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. 1. Activation, conda init ... https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#activating-an-environment }}} 1. If you have an existing '''Miniconda2/Anaconda2''' installation, a. '''Remove miniconda/anaconda entries from PATH'''. 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> }}} and follow the prompts. 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 }}} == 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 }}} 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 }}} 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 }}} == 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. }}} === 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-15.1 eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge conda activate eman-deps-15.1 }}} 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> make make install }}} 1. To switch to another conda environment, first deactivate your current environment. {{{#!highlight bash |
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or source deactivate }}} === New Miniconda Installations === 1. Download and install [[https://repo.continuum.io/miniconda/|Miniconda]]. 1. Add the new installation to PATH.{{{ export PATH=<new miniconda path>/bin:$PATH }}} 1. Update conda {{{ conda update conda -c defaults }}} 1. Install eman-deps with python 3{{{ conda install eman-deps=15 -c cryoem/label/py3 -c cryoem -c defaults -c conda-forge }}} == 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> }}} 1. Build and install {{{ cmake <eman2 source directory> make make install }}} |
}}} === 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-16.1 eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge conda activate eman-deps-16.1 }}} 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-16.1 eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge conda activate eman-deps-16.1 }}} 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! |
Python 3 Transition Environments
Phase 1: Upgrade CMake to 3.14
Install cmake=3.24 and eman-deps=15.1.
1 conda install eman-deps=15.1 cmake=3.14 -c cryoem -c defaults -c conda-forge
Phase 2: Test Boost 1.64
1 conda install eman-deps=16.1 cmake=3.14 boost=1.64 -c cryoem -c defaults -c conda-forge
Phase 3: Test Boost 1.66
PR: Build with Boost versions 1.65-1.66
1 conda install eman-deps=16.1 cmake=3.14 boost=1.66 -c cryoem -c defaults -c conda-forge
Python 3 Environments (Coming Soon!)
Coming soon!
The following sections were written with conda environments in mind, but will not be used. Keeping here for future reference.
Setup Development Environment with Conda
If you have an existing Miniconda2/Anaconda2 installation,
Remove miniconda/anaconda entries from PATH.
Install Miniconda3.
and follow the prompts.1 bash <Miniconda3-installer>
- 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!