Differences between revisions 4 and 6 (spanning 2 versions)

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>

Download Miniconda3 for Linux or MacOSX.
Install Miniconda3.
```
bash <Miniconda3-installer>
```
- and follow the prompts.

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

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
```
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

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.

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

conda activate eman-env

Checkout a branch.

Update eman2 source.

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

CMake 3.14

PR: 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
```

Boost 1.64

PR: Upgrade Boost to 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
```

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
```

-  ⇤ ← Revision 4 as of 2019-07-09 05:14:25 → 
  Size: 4447
  Editor: TunayDurmaz
  Comment: boost 1.64
+   ← Revision 6 as of 2019-07-11 05:39:40 → ⇥
  Size: 3845
  Editor: TunayDurmaz
  Comment: Python 3 Transition Environments
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-== Setup Python 2 Environment With CMake 3.14 ==
+= Under Construction =
== 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>
}}}
 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>
}}}
  and follow the prompts.
 1. 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
}}}
 1. Configure conda.
  a. Do not update conda automatically.
  {{{
conda config --set auto_update_conda False
}}}
  a. If you don't want conda's base environment to be activated automatically.
  {{{
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 3:
+Line 45:
-[[https://github.com/cryoem/eman2/pull/407|PR: Upgrade CMake to 3.14]]
+== 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.
-Line 5:
+Line 48:
-=== 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
+. Create a new environment.
 {{{
conda create -n eman-deps-14.1 eman-deps=14.1 -c cryoem -c defaults -c conda-forge
-Line 11:
+Line 52:
-. 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
+ 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
}}}
 1. Activate the environment.
 {{{
conda activate eman-deps-14.1
}}}
 OR
 {{{
conda activate eman-env
}}}
 1. Checkout a branch.
 1. Update eman2 source.
 {{{
cd <source directory>
git checkout <branch>
git pull --rebase
}}}
 1. Navigate to your build directory, build and install.
 {{{
cd <build directory>
cmake <eman2 source directory>
make
make install
-Line 19:
+Line 81:
-=== Existing Miniconda/Anaconda Installations ===
+== Python 3 Transition Environments ==
-Line 21:
+Line 83:
-. 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
+== CMake 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
-Line 25:
+Line 91:
-. 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
}}}
 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-14.2
or
source activate eman-deps-14.2
}}}
 1. To switch to another conda environment, first deactivate your current environment.{{{
+. To switch to another conda environment, first deactivate your current environment.
 {{{
-Line 35:
+Line 94:
-or
source deactivate
-Line 39:
+Line 96:
-== Setup Python 2 Environment with Boost 1.64 ==
+== Boost 1.64 ==
-Line 45:
+Line 99:
-=== 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
+. 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
-Line 51:
+Line 104:
-. 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
+. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
-Line 57:
+Line 109:
-=== 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
}}}
 1. 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
}}}
 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-14.3
or
source activate eman-deps-14.3
}}}
 1. To switch to another conda environment, first deactivate your current environment.{{{
conda deactivate
or
source deactivate
}}}




== Setup Python 2 Environment with Boost 1.66 ==
+== Boost 1.66 ==
-Line 86:
+Line 112:
-=== 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
+. 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
-Line 92:
+Line 117:
-. 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
+. To switch to another conda environment, first deactivate your current environment.
 {{{
conda deactivate
-Line 97:
+Line 121:
-=== 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
}}}
 1. 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
}}}
 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-14.3
or
source activate eman-deps-14.3
}}}
 1. 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
}}}
 1. 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.
 1. Move into your build directory.{{{
cd <build directory>
}}}
 1. Build and install.{{{
cmake <eman2 source directory>
make
make install
}}}