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GettingStarted.md

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Installation

  • To develop and contribute new code, see below on Sharing Your Work. If you only want to run a copy of the site, move into a new directory and type

    git clone https://github.com/LMFDB/lmfdb.git lmfdb

    and follow these instructions.

  • Make sure you have a recent version of Sage installed (at least running on Python 3) and that sage is available from the commandline. In particular see Sage installation. Also check that your version of Sage has ssl available by checking that import ssl works on its command line. If not, then the pip install commands below will fail. To remedy this, either install SSL globally on your system or have Sage build its own local version, as mentioned here and here, respectively.

  • Install dependencies. This requires you to have write access to the Sage installation directory, so should be no problem on a personal machine, but if you are using a system-wide Sage install on a shared machine, you will need ask a system administrator to do this step.

    sage -i gap_packages
sage -i database_gap # only needed if sage version < 8.6
sage -i pip
sage -b
# in the 'lmfdb/' directory:
sage -pip install -r requirements.txt

    Troubleshooting with packages.

    • If you have not run the site for a while you might get an error with packages like

      ImportError: cannot import name monitoring

      In this case or if you need to upgrade for any reason run

      sage -pip install -r requirements.txt --upgrade

    • For versions of macOSX after 10.15 (Catalina), Sage 9.2 is unable to insall gap_packages (see this post for some documentation on that). This problem does seem to be resolved for Sage 9.3beta, and it is currently unclear if the problem exists for Sage 9.0 or 9.1.

    • In case the last step fails by is Mac OSX with the error

      Error: pg_config executable not found.

      we recommend to installing PostgreSQL by doing

      brew install postgresql

      and performing the last step again.

    • In case the last step fails due to some missing SSL library, (this may be the case on osX) follow these steps

      sage -i openssl
sage -f python2 # takes some time
sage -i pyopenssl
sage -pip install --upgrade pip
sage -pip install -r requirements.txt

    • [optional] Memcache. This step is not at all necessary and can safely be ignored! Memcache speeds up recompilation of python modules during development. Using it requires both installing the appropriate package for your Operating System and installing an additional python module. The first line below needs to be run in a Sage shell, and the for second you need to be a super-user to install memcached if your machine does not have it.

      • easy_install -U python-memcached

      or even better and only possible if you have the dev headers:

      • easy_install -U pylibmc

      • install memcached (e.g. apt-get install memcached) and run the service at 127.0.0.1:11211

Running

  • A read-only copy of the database is hosted at devmirror.lmfdb.xyz. This is what is used by default. You can launch the webserver directly like this:

    sage -python start-lmfdb.py --debug

  • The effect of the (optional) --debug is that you will be running with the beta flag switched on as at dev.lmfdb.org, and also that if code fails your browser will show useful debugging information. Without --debug what you see will be more like www.lmfdb.org.

  • Once the server is running, visit http://localhost:37777/

    You should now have a fully functional LMFDB site through this server.

  • When running with --debug, whenever a python (*.py) file changes the server will reload automatically. If you save while editing at a point where such a file is not syntactically correct, the server will crash and you will need to start_lmfdb again. Any changes to html files will not cause the server to restart, so you will need to reload the pages in your browser. Changes in the yaml files which are read only once at startup will require you to manually stop the server and restart it.

  • You may have to suppress loading of your local python libraries: sage -python -s start-lmfdb.py

  • If several people are running their own version of the webserver on the same machine, they cannot all use port 37777 -- if they try, they can get very confused. In such a scenario, all involved should agree to using a sequence of port numbers from 37700 upwards and allocate one such number to each user, editing their config.ini file with their personal port number.

  • It is possible to use a different instance of the database. For many uses, using the default configuration (which uses a read-only database on devmirror.lmfdb.xyz) is sufficient, and this step is not necessary. If you do plan on using a different database instance, you can do so by changing config.ini in the root of the lmfdb directory.

CoCalc

  • You can run the LMFDB inside a CoCalc project by doing following the above installation instructions on a terminal in your project (you may want to install the requirements using the --user flag). Explicitly,

    cd ~
git clone https://github.com/LMFDB/lmfdb.git lmfdb
cd lmfdb
sage -pip install --user -r requirements.txt
sage -python start-lmfdb.py --debug

    On the last step, when you start the server running, LMFDB will detect that it is running inside CoCalc and provide a URL through which the site can be accessed.

  • If you've changed static files, you will have to run LMFDB on a different port in order for the files to update. For instance, to run LMFDB on port 37778:

    sage -python start-lmfdb.py --debug --port=37778

Troubleshooting

[warning] Recently on some linux machines, users have had to install the contents of requirements.txt by manually. If the above instructions do not work, un-install the above packages and re-install them one at a time, including those in requirements.txt.

Code development and sharing your work

  • Get a (free) github account if you do not have one already.

  • Login to github

  • If you don't already have an SSH key, you must generate a new SSH key. Once you have an SSH key you must add it to your GitHub account, if it isn't already added. This documentation explains how to do that.

  • Go to https://github.com/LMFDB/lmfdb and click on Fork in the upper right corner.

  • On your machine, create a new directory and type

    git init
git clone [email protected]:YourGithubUserId/lmfdb.git

    using your own github user id. Your github repository will be known to git as a remote called origin.

  • Add the (official) LMFDB repository as a remote called upstream.

    git remote add upstream [email protected]:LMFDB/lmfdb.git

  • To run LMFDB, go through the rest of the instructions in Installation and Running.

  • You should make a new branch if you want to work on a new feature. The following command creates a new branch named new_feature and switches to that branch, after first switching to the main branch and making sure that it is up-to-date:

    git checkout main
git pull upstream main
git checkout -b new_feature

  • After making your local changes, testing them and committing the changes, push your branch to your own github fork:

    git push -u origin new_feature

    Here, the option -u tells git to set up the remote branch origin/new_feature to be the corresponding upstream branch you push to.

  • You should make sure from time to time that you pull the latest changes from the official LMFDB repository. There are three branches upstream to be aware of: web, dev and main:

    • web is changed rarely and contains the code currently running at www.lmfdb.org

    • dev is changed more often and contains the code currently running at beta.lmfdb.org

    • main is the development branch.

    Normal developers only need to be aware of the main (=development) branch.

  • To pull in the most recent changes there to your own main branch locally and update your github repository too:

    git checkout main
git pull upstream main
git push origin main

  • To rebase your current working branch on the latest main:

    git pull --rebase upstream main

  • Tell the lmdb mailing list that you have some new code! You should also issue a pull request at github (from your feature branch new_feature) at the same time. Make sure that your pull request is to the lmfdb main branch, whatever your own development or feature branch is called. Others will review your code, and release managers will (eventually, if all is well) merge it into the main branch.

LMFDB On Windows

We do not recommend attempting to run LMFDB from within the Sage virtual image. For anyone who would like to attempt it, the following steps should theoretically work.

  • Download VirtualBox and the Sage appliance, following the instructions here.

  • The default Sage appliance does not have enough space to install LMFDB's prerequisites. Moreover, the default file type (vmdk) installed by VirtualBox does not support resizing. You will need to increase the available space by cloning into a vdi file, increasing the space and cloning back, following the instructions here and here. We had trouble at this stage: make sure to keep the .ova file in case you screw up your virtual image.

  • The resulting disk image needs to be repartitioned to make the space available. Unfortunately, the Sage appliance does not include gparted, the linux partition editor. So, you'll need to install gparted into the appliance (perhaps following instructions here) and use it to repartition.

  • You now need to set up port forwarding so that the sage appliance can use the ports 37777 and 37010 used by lmfdb. See Section 6.3.1 here.

  • Clone the LMFDB git repository into your host OS, and set up shared folders so that you can access the LMFDB code from within the Sage appliance. See the Sage instructions for how to share folders.

  • Now you need to run ssh-keygen within the Sage appliance and e-mail the result to Harald Schilly, Jonathan Bober or John Cremona (see above). Since copy-and-paste can be tricky from inside the virtual image, we suggest writing to a file shared by the host OS.

  • The instructions for Linux/OS X should now work. You should be able to forward the mongo database and run sage -python start-lmfdb.py within the Sage appliance, and access the resulting website from your host OS' web browser.