Keep Landlab Updated#
To take advantage of new features and new library additions, we recommend you update Landlab fairly frequently. From time to time you should fetch commits to the “trunk” version of Landlab that you don’t have in your forked working copy. This is also important to keep your branch up to date with improvements/bug elimination happening as part of core Landlab development.
Before you begin, we recommend you review this GitHub page describing syncing a fork.
Through the command line, you should be able to update your Landlab repository from master using the following command
$ git fetch upstream
A common reason why this might not work is if you haven’t set the remotes correctly. This GitHub page on managing remotes might be helpful.
If we have added a dependency, you may see an import error. Similarly, if we have added a dependency, you may see some tests break. A likely fix is to ensure you have all the requirements specified in the Landlab development environment described by the environment-dev.yml file
$ conda env update landlab_dev --file environment-dev.yml $ conda activate landlab_dev $ pip install -e .
The first of these installs any new requirements for development. The second line activates the environment (called “landlab_dev”). The third will verify that all requirements are met and recompile Landlab.
If the Cython code has changed since you last updated, you will probably see errors associated with files named cfuncs.pyx (or similar). These changes require that you recompile your code. This can be done by executing the following from within the top level landlab folder (which contains the setup.py file)
$ pip install -e .
If none of these options work, please make an issue.
If you have been developing code and making commits to the
master branch on
your fork, this may not work. It is for this reason that we highly recommend
you develop on a development branch.
Still having problems? This probably means that some time early in our development cycle you installed Landlab with one of our old procedures. The clue will be that you still have a (very out of date!) copy of the Landlab code base somewhere on your machine. Another possibility is that you’ve previously tried a developer install. This procedure will also work in this case.
In a terminal, navigate to the top level directory of that old code, the one that contains the file setup.py. This is likely to be your_home_dir/landlab, if you installed with git and left all the defaults as is. Then
$ pip uninstall landlab #just to be on the safe side, may get errors again $ python setup.py develop -u
This should remove the install, if you installed as a developer.
Still getting error messages? This means we’re going to have to excise the old Landlab install “by hand”. You’re looking to remove any reference to Landlab that lives inside your_python_install/lib/python2.7/site-packages. Do this only after you’ve exhausted other possibilities, above, as packages like pip will get annoyed with you if you start manually deleting their files if they installed them in the first place. To minimize the risk, once again make sure you have just run
$ pip uninstall landlab
Then find your Python directory with
$ which python
Find that folder, ignoring everything after and including the subfolder bin. Instead, go to your_install/lib/python2.7/site-packages. In here, you should find one (or more) folders referring to Landlab, e.g., landlab or landlab.egg-link, or some other reference to landlab.egg. Delete these. Leave everything else as it is!
If you are running an Anaconda distribution, we now recommend you replace your pip install with a conda install. Simply do this
$ pip uninstall landlab $ conda install landlab -c landlab
You will then be able to update Landlab along with the rest of your conda packages
$ conda update --all -c landlab
If you prefer to remain with pip, try another pip install
$ pip install landlab
This should now take.
Still having problems? There are probably multiple versions of Python on your machine interfering with each other. Solve that problem first (see here for some help), then return to trying to install Landlab.
Without using command line:
You can’t do the equivalent in the GitHub app, but you can do it through the website—though it is a bit more involved. Navigate to the master Landlab fork. Hit the big green “new pull request” button. Hit the “compare across forks” hyperlink. You now want to set the base fork dropdown menu to your local Landlab (UserName/landlab), and leave the head fork as it is (landlab/landlab). Leave both the base and compare boxes set to master, as they should already be. The site will then have a think, then report back to you whether it can perform an automatic merge (in green or yellow, just below the dropdown boxes), and also what the differences between these two versions are (scroll down).
Take a quick look at the commits list to reassure yourself you got the “base” and “head” versions the right way round (DH struggles with this every time…). Presuming you got the green “able to merge” dialogue, now just fill in the pull request box with a title (e.g., “updating local Landlab fork from master”) and hit “Create pull request.” This will take you to a page showing the open request. Confirm it and actually perform the code update in your fork by scrolling down and hitting the green “Merge pull request” button. You’ll then need to sync your local version with the fork that just updated on the Github servers—easiest through the app, using the “Sync” button in the top right (make sure you’re in the local master branch).
If you didn’t get the green “able to merge” button, it means some of your local changes conflict with what’s in the main Landlab repo. Don’t panic! This is fine. Just follow the instructions to press ahead. Conflicts can be resolved manually later in the process—conflicting sections of the code will be tagged with a distinctive >>>>>>> symbology, and you can find and modify them by hand. See here for more documentation on this.