diff --git a/README.md b/README.md index a4242d7a064a7634f27cb73ab41b2e334abbee75..d2c53d7542946ed46adcb5124e748cc27cfa2bef 100644 --- a/README.md +++ b/README.md @@ -40,64 +40,70 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ ### ISIS Installation With Conda -1. Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html) -2. If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment. - - chmod +x Anaconda3-5.3.0-Linux-x86_64.sh - ./Anaconda3-5.3.0-Linux-x86_64.sh - - +1. Download either the Anaconda or Miniconda installation script for your OS platform. Anaconda is a much larger distribtion of packages supporting scientific python, while Miniconda is a minimal installation and not as large: [Anaconda installer](https://www.anaconda.com/download), [Miniconda installer](https://conda.io/miniconda.html) +1. If you are running on some variant of Linux, open a terminal window in the directory where you downloaded the script, and run the following commands. In this example, we chose to do a full install of Anaconda, and our OS is Linux-based. Your file name may be different depending on your environment. + + ```bash + chmod +x Anaconda3-5.3.0-Linux-x86_64.sh + ./Anaconda3-5.3.0-Linux-x86_64.sh + ``` This will start the Anaconda installer which will guide you through the installation process. -3. If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process. -4. After the installation has finished, open up a bash prompt in your terminal window. -5. Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands: - - #Create a new conda environment to install ISIS in - conda create -n isis python=3.6 - - #Activate the environment - #Depending on your version of Anaconda use one of the following: +1. If you are running Mac OS X, a pkg file (which looks similar to Anaconda3-5.3.0-MacOSX-x86\_64.pkg) will be downloaded. Double-click on the file to start the installation process. +1. After the installation has finished, open up a bash prompt in your terminal window. +1. Next setup your Anaconda environment for ISIS. In the bash prompt, run the following commands: - #Anaconda 3.4 and up: - conda activate isis - - #Prior to Anaconda 3.4: - source activate isis - - #Add the following channels to the environment - conda config --env --add channels conda-forge - conda config --env --add channels usgs-astrogeology + ```bash + #Create a new conda environment to install ISIS in + conda create -n isis python=3.6 - #Verify you have the correct channels: - conda config --show channels + #Activate the environment + #Depending on your version of Anaconda use one of the following: - #You should see: + #Anaconda 3.4 and up: + conda activate isis - channels: - - usgs-astrogeology - - conda-forge - - defaults + #Prior to Anaconda 3.4: + source activate isis - #The order is important. If conda-forge is before usgs-astrogeology, you will need to run: + #Add the following channels to the environment + conda config --env --add channels conda-forge + conda config --env --add channels usgs-astrogeology - conda config --env --add channels usgs-astrogeology + #Verify you have the correct channels: + conda config --show channels -6. Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver: + #You should see: - conda install -n base -c conda-forge mamba + channels: + - usgs-astrogeology + - conda-forge + - defaults -7. The environment is now ready to download ISIS and its dependencies: + #The order is important. If conda-forge is before usgs-astrogeology, you will need to run: - mamba install -c usgs-astrogeology isis + conda config --env --add channels usgs-astrogeology + ``` + +1. Download [Mamba](https://github.com/mamba-org/mamba). The ISIS environment is quite large and the Conda solver can take hours to resolve it. Instead, we recommend you use the much faster [Mamba](https://github.com/mamba-org/mamba) solver: + + ```bash + conda install -n base -c conda-forge mamba + ``` +1. The environment is now ready to download ISIS and its dependencies: + ```bash + mamba install -c usgs-astrogeology isis + ``` + If you would like to work with our latest ISIS version 3, rather than updating to ISIS 4, instead run: - mamba install -c usgs-astrogeology isis=3.10.0 + ```bash + mamba install -c usgs-astrogeology isis=3.10.0 + ``` - -8. Finally, setup the environment variables: +1. Finally, setup the environment variables: ISIS requires several environment variables to be set in order to run correctly. The variables include: ISISROOT and ISISDATA. @@ -109,55 +115,54 @@ This installation guide is for ISIS users interested in installing ISIS (3.6.0)+ There are two methods to configure the environment variables for ISIS: - 7.1 Using `conda env config vars` *preferred* - - Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8. - This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed. + 1. Using `conda env config vars` *preferred* - To determine if your version of conda is recent enough run: + Conda has a built in method for configuring environment variables that are specific to a conda environment since version 4.8. + This version number applies only to the conda package, not to the version of miniconda or anaconda that was installed. - conda --version + To determine if your version of conda is recent enough run: - If the version number is less than 4.8, update conda to a newer version by running: + conda --version - conda update -n base conda + If the version number is less than 4.8, update conda to a newer version by running: - The version number should now be greater than 4.8. + conda update -n base conda - To use the built in environment variable configuration feature, first activate the environment by first running: + The version number should now be greater than 4.8. - conda activate isis + To use the built in environment variable configuration feature, first activate the environment by first running: - After activation, the environment variables can be set using the syntax: `conda config vars set KEY=VALUE`. - To set all the environment variables ISIS requires, run the following command, updating the path to `ISISDATA` as needed: + conda activate isis - conda env config vars set ISISROOT=$CONDA_PREFIX ISISDATA=[path to data directory] + After activation, the environment variables can be set using the syntax: `conda config vars set KEY=VALUE`. + To set all the environment variables ISIS requires, run the following command, updating the path to `ISISDATA` as needed: - To make these changes take effect, re-activate the isis environment by running: + conda env config vars set ISISROOT=$CONDA_PREFIX ISISDATA=[path to data directory] - conda activate isis + To make these changes take effect, re-activate the isis environment by running: - The environment variables are now set and ISIS is ready for use every time the isis environment is activated. + conda activate isis - **Note** This method will not enable tab completion for arguments in C-Shell. + The environment variables are now set and ISIS is ready for use every time the isis environment is activated. + **Note** This method will not enable tab completion for arguments in C-Shell. - 7.2 Using the provided isisVarInit.py script: - To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments: + 1. Using the provided isisVarInit.py script: - python $CONDA_PREFIX/scripts/isisVarInit.py + To use the default values for: `$ISISROOT` and `$ISISDATA`, run the ISIS variable initialization script with default arguments: - Executing this script with no arguments will result in $ISISROOT=$CONDA\_PREFIX and $ISISDATA=$CONDA\_PREFIX/data. The user can specify different directories for `$ISISDATA` using the optional value: + python $CONDA_PREFIX/scripts/isisVarInit.py - python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory] + Executing this script with no arguments will result in $ISISROOT=$CONDA\_PREFIX and $ISISDATA=$CONDA\_PREFIX/data. The user can specify different directories for `$ISISDATA` using the optional value: - Now every time the isis environment is activated, $ISISROOT and $ISISDATA will be set to the values passed to isisVarInit.py. - This does not happen retroactively, so re-activate the isis environment with one of the following commands: + python $CONDA_PREFIX/scripts/isisVarInit.py --data-dir=[path to data directory] - for Anaconda 3.4 and up - conda activate isis - prior to Anaconda 3.4 - source activate isis + Now every time the isis environment is activated, $ISISROOT and $ISISDATA will be set to the values passed to isisVarInit.py. + This does not happen retroactively, so re-activate the isis environment with one of the following commands: + for Anaconda 3.4 and up - conda activate isis + prior to Anaconda 3.4 - source activate isis ### Installation with Docker