The previous section outlined how to get pandas installed as part of theAnaconda distribution.However this approach means you will install well over one hundred packagesand involves downloading the installer which is a few hundred megabytes in size.
I would say that the recommended way to install anaconda is to use the official anaconda installer, which can be downloaded from the link I just posted. I've done it several times, never had a problem, and it walks you through it (including an option to automatically add it to your PATH).
I don't know about other people but I've had issue downloading conda/miniconda etc for a few hours now. For some reason it decided to install at ~/opt when using the graphical installer (i.e. the .dmg file). I've been through the uninstall here How to uninstall Anaconda completely from macOS and additionall did an rm -rf ~/opt command. Seems that without this its not actually uninstalled (you might also have to change your PATH or .bash_profile or .bashrc until your path is virigin again before you start your re-installation installation). Seems that using the command line installer is what works:
If conda is installed and its system path is registered in the PATHenvironmental variable, conda help contents should appear in theterminal. If the help contents appear, skip to theInstall API section. If conda is not recognized, theresult will read something like:conda not found or not recognized as a command. It is possible that theprogram exists on your system but is not registered in the PATHenvironmental variable. Even if this is the case, for consistency, pleasecontinue with the Install conda section, as it isdifficult to address all possible system configurations. As long as thefolder 'miniconda3' does not exist in your Home folder, the followingconda install instructions should succeed. For more information on condainstall location and registration, please see theMiniconda Installationand Anaconda Installationpages.
In this section you will download and install Miniconda, which will serveas the Python platform to access the Earth Engine API. Asdescribed above, you may use Miniconda or Anaconda, but tominimize impact to your system, this guide will describe aMiniconda installation with no alteration to your system'senvironmental variables. If you prefer Anaconda, please see theinstallation instructions providedhere and then skip to theInstall API section.
Complete these steps by copying and pasting the following lines into theappropriate command line interface for your system. Installationresults in a folder named 'miniconda3' added to your Home directory.
You will be asked to confirm the installation of the API and itsdependencies. After confirming, conda will download and install thedependencies. If all goes well, you will now have a conda environmentcalled 'ee' with all the requirements for accessing the API, as well asthe earthengine command line tool.
NCL can be installed on Mac and Linux systemsvia conda. Conda is a packagemanagement system that enables you to easily install software from theUNIX command line via the "conda" command: conda install package_nameYou must download and install conda first, eithervia minicondaor Anaconda. If disk spaceis an issue (Anaconda is quite large), we recommendminiconda as this is a more minimal system that requires less diskspace.Keep reading for information on how to install conda, and then how touse it to install NCL.If you already have conda but haven't updated it in awhile, you mightwant update it by typing the following from a UNIX terminal window: conda update -n root --allInstalling minicondaIf you don't already have conda installed on your system, then goto: select the appropriate 64-bit bash installer for whatever MacOSXor Linux system you have. (We do not have a pure Windows version ofNCL.)Follow the instructions for installing miniconda. When theinstallation is finished, you can test it quickly by typing thefollowing from a UNIX terminal window: conda -VThis should echo something like "conda 4.6.2".Note: you can also get the conda command by downloading andinstalling Anaconda.Create a conda environment and install NCLWe recommend that you install NCL under aconda environment,which will be called ncl_stable in the examples below. You cancall it whatever you want.From a UNIX terminal window in sh/bash mode, type: conda create -n ncl_stable -c conda-forge ncl source activate ncl_stableYou will need to run the "source activate ncl_stable" commandevery time you log out and log back in.Installing a NCL 'development' versionOccasionally we provide a development version of NCL that provides bugfixes and/or new functionality that you can't get from the current version.We don't currently have an NCL development version available, but check backhere later.Test NCLFrom a UNIX terminal window, type: ncl -V ncl $NCARG_ROOT/lib/ncarg/nclex/gsun/gsun02n.ncl ncl $NCARG_ROOT/lib/ncarg/nclex/nug/NUG_multi_timeseries.nclThe first command should echo "6.6.2".The second command should pop up an "x11" window with a simple linecontour plot. Click on this window to advance to the next plot (thereare five plots total). If the x11 windows don't come up, thensomething may be wrong with your DISPLAY environment variable. Seethe install frombinary instruction page for details about setting DISPLAY.The third command should produce a PNG file called"NUG_multi_timeseries.png" (click on image for larger view):TroubleshootingIf NCL is not working after you installed conda, then you may want toforce your NCL conda environment to recalculate all dependencies,which sometimes fixes the broken environment. Type the following froma UNIX terminal window, where ncl_stable should be replace withwhatever your NCL conda environment is called: conda update -n ncl_stable -c conda-forge --allIf you continue to have problems, then see the next section.Send questions or problems to ncl-install email listIf you are having problems installing NCL using conda or NCL doesn'tappear to be working, then subscribeto ncl-install and email your issue firstname.lastname@example.org.Please include the exact error message and what you were typing thatcaused the error. Also include the output from typing the followingcommands from a UNIX terminal window: conda list -n ncl_stable conda --version which ncl ncl -V env | grep NCARG
Miniconda is a Python distribution, package manager, and virtual environment solution. While QIIME 1 is Python 2 software, we recommend installingMiniconda with Python 3 (miniconda3), as many bioinformatics packagesare now transitioning to Python 3. You can still install Python 2software with miniconda3 by passing the python=2.7 flag when you createa new environment; otherwise the default Python version will be Python3.
As noted above, we will be using the mamba package installer to manage the installation of Python packages in Miniconda.To do this, we must first install mamba and then download some Python environment files that contain the list of packages used in the Geo-Python course.This will ensure the Python environment on your computer is the same as that used in the cloud computing system for the course.The steps for installing the Geo-Python packages are below.
If you are not familiar with git, you can visit the GitHub repository with the environment files, click on the green Code button, and select Download ZIP to download a copy of the files.
Once you have obtained the code (either by cloning with git or downloading otherwise) can return to your terminal window, change to the directory where you have downloaded the files and create the environment as shown below.For example, on macOS or Linux you would do the following.
In order to be able to follow the course lessons it may also be helpful to have a copy of the course notebooks.You can download a copy of the course notebooks from -python/notebooks.git by clicking on the Code button and then selecting Download ZIP.Alternatively, once you are familiar with git, you can clone the course notebook repository by typing
You can install new packages using the mamba install command.The basic syntax for installing packages is mamba install package-name.In addition, we also want to specify the channel from where the package is downloaded using the parameter -c.
Conda channels used by mamba and are remote locations where packages are stored.During this course (and in general when installing packages for scientific computing and GIS analysis) we download most packages from the conda-forge channel.
The location where Miniconda is (or should be) installed. Notethat the Miniconda installer does not support paths containing spaces. Seeminiconda_path for more details on the default path used by reticulate.
Note that miniconda is a SUBSTITUTE for a tool like pyenv / venv that may be suggested in some other courses (like our MIDS NLP class). Do NOT install pyenv / venv and miniconda, just install miniconda. (This is the coordinated recommendation of myself and the Duke MIDS NLP Professor Patrick Wang!)
To download the supported Spyder installer for your platform, simply click the appropriate link below (for Linux, see the Conda-based distributions section).Then, double-click the downloaded file to open the installer.If a security warning pops up, you may need to click Yes, OK, Open, Allow or similar.
You can install Spyder with the pip package manager, which is included by default with most Python installations.Before installing Spyder itself by this method, you need to download the Python programming language. 2b1af7f3a8