Installation

Installing python dependencies with Conda

Modflow-setup depends on a number of python packages, many of which have external C library dependencies. The easiest way to install most of these is through a Conda environment, using Mamba as the package manager. A few packages are not available via Conda, and must be installed with pip. If you are on the USGS internal network, see the Considerations for USGS Users section below first.

Download and install a python distribution and Conda-like package installer

There are many ways to do this:

  • The Anaconda python distribution comes with a large selection of popular data science and scientific packages pre-installed.

  • Miniconda is a minimal installer with a much smaller footprint, making it ideal for creating python environments dedicated to specific tasks (a recommended practice).

  • Mambaforge is like Miniconda, but pre-configured to use the Mamba installer, and only the conda-forge channel for getting packages (more below). If the above two options don’t work (for example, the Conda installer fails or gets stuck on the “solve” step), this may be your best option.

Make sure to install Anaconda or Miniconda to your username (not at the system level). More often than not, installing at the system level (for all users) seems to result in issues with library dependencies (for example, import of fiona or rasterio failing because gdal isn’t found). It is also good practice to periodically do a clean uninstall of Anaconda, which at the system level requires admin. privileges.

  • In the installer, at the “Destination Select” step, select “Install for me only.” It should say something about how the software will be installed to your home folder.

  • If your installer skips the “Destination Select” step, when you get to “Installation Type”, click “Change Install Location” and then “Install for me only.”

Download an environment file

  • requirements.yml for a Conda environment with the minimum packages required to run Modflow-setup, or

  • gis.yml for a more full set of packages in the python geospatial stack, including Jupyter Notebooks and packages needed for testing, documentation and packaging. Note that the environment described by requirements.yml is called mfsetup, while the environment in gis.yml is called gis.

    Note

    To download the above YAML files, simply follow the links to get the raw text and then go to File > Save within your web browser, and save the text as a YAML file (with the .yaml or .yml extension).

  • Alternatively, clone (using git) or download the modflow-setup repository, which includes the two environment files at the root level.

  • Note that both of these environment files contain a pip section of packages that will be installed with pip, after the Conda packages are installed.

Creating a Conda environment using Mamba

If you are on the USGS internal network, see the Considerations for USGS Users section below first.

Before using Mamba, you will need to install it first.

Python packages are available from conda via channels. Conda comes preconfigured to install packages from the default channel, which is maintained by Anaconda, Inc. In general, you may have better luck exclusively using the conda-forge channel instead, which is community-based and intended to provide a single location to get any package, with a minimum of hassle. In general, it is bad practice to mix package channels within a single environment. You can read more here, but to set conda-forge as the default:

conda config --add channels conda-forge

Note

If you are having trouble installing Mamba (for example, the conda package solver fails when you try to install it, or takes an excessively long time), you may have better luck uninstalling Anaconda completely and installing Mambaforge instead, as directed in the Mamba install instructions. Mambaforge solves both of the above problems by providing a minimal python distribution and conda-style package installer that is preconfigured to use both conda-forge and Mamba.

Once you have a python distribution and mamba installed, to create the conda environment, open a new Anaconda Command Prompt on Windows or a new terminal window on OSX and point it to the location of requirements.yml or gis.yml and enter:

mamba env create -f requirements.yml

Building the environment will probably take a while. If the build fails because of an SSL error, fix the problem (see Considerations for USGS Users below) and either:

Note

Creating the requirements.yml environment (or any environment with git+https: ... installs) requires Git to be installed and visible in the system path where env create is being run. If Git is installed and somehow not in the system path, it can be added to the system path on Windows 10 without admin. rights via the “environment variables” editor under User Accounts in the Control Panel (Google it).

  1. Update the environment

    mamba env update -f requirements.yml

  2. or remove and reinstall it:

    mamba env remove -n mfsetup
mamba env create -f requirements.yml

Keeping the Conda environment up to date

The python packages and other open source software libraries that Modflow-setup depends on are continually changing. Modflow-setup aims to mostly follow the Numpy guidelines for package support, which effectively means that the two latest minor versions of Python (e.g. 3.11 and 3.10) and their associated Numpy versions will be supported. However, occasionally backwards compatability with a particular package may be broken in a shorter timeframe, in which case the minimum required version of that package will be specified in the requirements.yml file. All of this to say that your Conda environment will eventually get out of date. The Conda documentation has instructions for updating packages within a Conda environment, but at some point (perhaps a few times a year) it is good practice to simply delete the environment and rebuild it from the .yml file. Every so often, you may also want to reinstall Anaconda after a clean uninstall.

Installing Modflow-setup

There are several ways to install Modflow-setup. Regardless of the method, the installation must be performed in a python environment with the required dependencies. In the case of the Conda environment created above, the environment must be activated, so that right version of python is called when python is entered at the command line:

conda activate mfsetup

(note that even with Mamba, conda activate/deactivate are still used)

Installing and updating Modflow-setup from PyPI

Once a suitable conda environment (that contains ALL of the dependencies) is made and activated, the simplest way to install Modflow-setup is from the Python Package Index using pip.

pip install modflow-setup

Subsequent releases of Modflow-setup to PyPI can then be installed with

pip install --upgrade modflow-setup

Note that in some situations you may have to pip uninstall modflow-setup and then pip install modflow-setup. You can always check what version of Modflow-setup you have within a python session with

import mfsetup
mfsetup.__version__

Or if you are using Conda, at the command line with

conda list

Installing the latest develop version of Modflow-setup

In some situations you may want the bleeding-edge version of Modflow-setup that is being actively developed on GitHub. For example, to incorporate a bug fix that was made after the latest release. Pip can also be used to fetch Modflow-setup directly from GitHub:

pip install git+https://github.com/aleaf/modflow-setup@develop

(for the develop branch). Subsequent updates can then be made with

pip uninstall modflow-setup
pip install git+https://github.com/aleaf/modflow-setup@develop

Installing the Modflow-setup source code in-place

Alternatively, if you intend to contribute to Modflow-setup (please do!) or update your install frequently, the best route is probably to clone the source code from git and install it in place.

git clone https://github.com/aleaf/modflow-setup.git
cd modflow-setup
pip install -e .

Note

Don’t forget the . after pip install -e!

Your local copy of the Modflow-setup repository can then be subsequently updated with

git pull origin master

Note

If you are making local changes to Modflow-setup that you want to contribute, the workflow is slightly different. See the Contributing to modflow-setup page for more details.

The advantage of installing the source code in-place is that any changes you make are automatically incorporated into your python environment, without any additional install commands. When debugging in an interactive development environment (IDE) such as Pycharm or VS Code, error tracebacks and inspection features go to the actual source code, not the version installed in the site-packages folder. Additionally, since this install is done through pip, pip uninstall will work to remove the package, and the current version of the package (including the latest commit information) will be visible with conda list.

Installing the IPython kernel to use Modflow-setup in Jupyter Notebooks

This step may not be needed if you already have an existing Python environment with the packages required by Modflow-setup and Jupyter Notebook installed. However, if you’d like to use Modflow-setup in a Jupyter Notebook with the included mfsetup environment (specified in requirements.yml), you’ll most likely need to install the IPython kernel in that environment. You can do this at the command line or terminal window (with mfsetup activated):

python -m ipykernel install --user --name mfsetup --display-name "mfsetup"

The first instance of mfsetup in this command is the environment to install the kernel to, and the second instance (in quotes) is the name that will appear in the Kernel menu within Jupyter Notebook. To use the kernel, simply select it from the Kernel > Change kernel menu within Jupyter Notebook.

Best practices

  • Install the *conda distribution of your choice to your user account, NOT at the system level. Installing to your user means you have rights to delete and reinstall Anaconda as-needed, as well as to edit any configuration files for pip, Conda, etc. Installing at the system level also just seems to lead to more confusing problems with dependencies, at least in the USGS.

  • Periodically (maybe a few times a year?) fully remove your *conda distribution and reinstall it. If you just can’t get things to work (packages won’t import or produce DLL errors on import, adding or upgrading a package takes a very long time or results in excessive upgrades or downgrades of other packages, etc.), fully removing and reinstalling *conda just may resolve your issues.

  • Don’t use your base environment; create and delete environments as needed. Conda is generally pretty good about managing packages between environments without wasting a lot of disk space.

  • Use an environment file (as above) to create a conda environment, instead of installing packages ad-hoc.

  • Use Mamba instead of Conda; it just works better for environments with a lot of packages.

  • After setting up the above conda environment, scan the screen output to make sure that everything installed correctly, especially the packages installed through pip.

  • Avoid mixing package channels within a Conda environment. Strictly sticking to conda-forge may yield the best results.

  • Use conda-pack, rather than an overly-detailed environment file, to guarantee reproducibility.

Considerations for USGS Users

Using conda or pip on the USGS network requires SSL verification, which can cause a number of issues. If you are encountering persistant issues with creating the conda environment, you may have better luck trying the install off of the USGS network (e.g. at home). See here for more information about SSL verification on the USGS network, and to download the DOI SSL certificate.

Installing the DOI SSL certificate for use with pip

  1. Download the DOI SSL certificate

  2. Create a pip configuration file, which may be specified at the user, environment, or system level. At the user level:

    • On Windows: %APPDATA%\pip\pip.ini or %APPDATA%\Roaming\pip\pip.ini, where %APPDATA% is most likely C:\Users\<your username>\AppData

    • On OSX, create $HOME/Library/Application Support/pip/pip.conf if directory $HOME/Library/Application Support/pip exists else $HOME/.config/pip/pip.conf., where $HOME is most likely /Users/<your username>.

    • On Linux: $HOME/.config/pip/pip.conf

For more details about the configuration file, see the pip documentation.

Include the following in this file:

[global]
cert = <path to DOI certificate file (e.g. DOIRootCA2.cer)>

Note that when you are off the USGS network, you may have to comment out the cert= line in the above pip configuration file to get pip to work.

Installing the DOI SSL certificate for use with conda

See these instructions. This may or may not work. Basically, ssl_verify: needs to be set in your condarc file to point to a valid SSL certificate, which may be different from the basic DOIRootCA2.cer file.

You can find the location of your condarc file with:

conda info -a

which displays information about how Conda is configured. Note that you may have multiple condarc files at the system, user and possibly project levels.

Common issues:

  • Conda Install fails on the USGS network without a certificate, or with an incorrectly formatted certificate. Possible solutions are to either get a correctly formatted SSL certificate from your IT person, or try installing off the network.

  • Conda Install fails off the USGS network with a certificate (may or may not be correctly formatted). Solution: open your condarc file and comment out the SSL certificate file, if it is specified. E.g.:

    ssl_verify: #D:\certificates\DOIRootCA2.cer

Troubleshooting issues with the USGS network

If you are on the USGS network, using Windows, and you get this error message:

CondaHTTPError: HTTP 500 INTERNAL ERROR for url <https://repo.anaconda.com/pkgs/msys2/win-64/m2w64-gettext-0.19.7-2.tar.bz2> Elapsed: 00:30.647993

An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way.

Adding the following line to environment.yml should work:

- msys2::m2w64-gettext

This tells conda to fetch m2w64-gettext from the msys2 channel instead. Note that this is only a dependency on Windows, so it needs to be commented out on other operating systems (normally it wouldn’t need to be listed, but the above HTTP 500 error indicates that installation from the default source location failed.)