rEpiabm data extraction fail

[anitaapplegarth]

rEpiabm is a new repository which is a R-wrapper around Epiabm. The first step is to extract data using EpiGeoPop but this was not possible without making some changes to both prep.sh and snakefile (see rEpiabm-usage branch).

There are two further issues:

1. error when running pip install -r requirements.txt:
This is the end of the warning message:
'''
:78: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead
WARNING:root:Failed to get options via gdal-config: [Errno 2] No such file or directory: 'gdal-config'
CRITICAL:root:A GDAL API version must be specified. Provide a path to gdal-config using a GDAL_CONFIG environment variable or use a GDAL_VERSION environment variable.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
'''

FIX:
This is because Fiona, which is a Python package for reading and writing spatial data, requires GDAL (Geospatial Data Abstraction Library) to be installed on your system first.
On a mac, you can install as follows:

1. brew install gdal
2. export GDAL_CONFIG=/usr/local/bin/gdal-config
3. export GDAL_VERSION=$(gdal-config --version)

2. Downloading files from Natural Earth website
We commented out the lines to extract data from Natural Earth as we could not get them to work and used the following workaround:

FIX:

• Go here https://www.naturalearthdata.com/downloads/10m-cultural-vectors/
• Click on the link: Download without boundary lakes
  https://www.naturalearthdata.com/http//www.naturalearthdata.com/download/10m/cultural/ne_10m_admin_0_countries_lakes.zip
• Save in the folder: (data/raw)

Also as a note, the user needs to set their environment to Python 3.11.

[anitaapplegarth]

The new branch includes an important couple of changes to prep.sh.

1. The link to extract the main 2019 data file has been updated to 2023.
2. The last extract we couldn't get to work, so we commented it out as we didn't need it. We also commented out the corresponding rule in snakefile, make_pop_dist.

Hope this makes sense.

[Ellmen]

Thanks for raising these issues @anitaapplegarth. The data links have been updated and the Python dependencies have been updated so it should work for Python 3.12 now. I haven't been able to reproduce the Fiona issue - it's possible that the GDAL version which comes with Fiona doesn't work on an M1 chip. Have you tried updating Fiona?