Reinstall optional geopandas dependency on CI tests

[weiji14]

Description of proposed changes

Add geopandas as a dependency again on the latest NEP29 Python 3.9/NumPy 1.20 tests. Also unpin gdal version on ci_tests.yaml so that tests run on gdal>=3.3, and include geopandas in the conda environment.yml file.

This reverts the workaround in #1290 (comment) since conda-forge/fiona-feedstock#179 has been merged (so geopandas/fiona with gdal 3.3 can be installed from conda-forge). Note: Merge this after conda-forge/gmt-feedstock#154

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If adding new functionality, add an example to docstrings or tutorials.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash commands are:

• /format: automatically format and lint the code
• /test-gmt-dev: run full tests on the latest GMT development version

[weiji14]

Unpinning gdal here should fix the failing GMT Dev Tests on Windows (that have been failing for months now, e.g. at https://github.com/GenericMappingTools/pygmt/runs/2811637685?check_suite_focus=true#step:16:18) by installing the GMT 6.3.0 dev version. However, this will need to wait until conda-forge/gmt-feedstock#154 is merged.

[weiji14]

Seems like geopandas on conda-forge split into two packages in conda-forge/geopandas-feedstock#90. There is geopandas-base (light version) and geopandas (full version). An option might be to install geopandas-base and fiona (needed for doing I/O, c.f. #1000) instead of the full geopandas package (which brings in stuff like rtree and mapclassify that we probably don't need). Or we could keep things as is and just install geopandas since that's what most users would do.

[weiji14]

There are still some package conflicts...

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - codecov -> python[version='2.7.*|3.5.*|3.6.*']
  - pytest-mpl -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package six conflicts for:
pytest-cov -> pytest[version='>=4.6'] -> six[version='>=1.10.0']
numpy=1.20 -> mkl-service[version='>=2.3.0,<3.0a0'] -> six
sphinx-gallery -> sphinx[version='>=1.8.3'] -> six[version='>=1.5']
pytest-mpl -> pytest -> six[version='>=1.10.0']
ipython -> prompt-toolkit[version='>=2.0.0,!=3.0.0,!=3.0.1,<3.1.0'] -> six[version='>=1.9.0']
pandas -> python-dateutil[version='>=2.7.3'] -> six[version='>=1.5']
packaging -> six
pytest -> more-itertools[version='>=4.0.0'] -> six[version='>=1.0.0,<2.0.0']
geopandas -> six
dvc -> configobj[version='>=5.0.6'] -> six[version='>=1.12,<2.0|>=1.13.0|>=1.5|>=1.13.0,<2dev|>=1.6.1,<2dev|>=1.6.1,<2']
geopandas -> fiona -> six[version='>=1.7']
pytest -> six[version='>=1.10.0']


Package pandas conflicts for:
geopandas -> mapclassify[version='>=2.2.0'] -> pandas[version='>=1.0']
geopandas -> pandas[version='>=0.23|>=0.24']
dvc -> pyarrow[version='>=0.17.1'] -> pandas
xarray -> dask[version='>=0.9'] -> pandas[version='>=0.19.0|>=0.21.0|>=0.23.0|>=0.25.0']
xarray -> pandas[version='>=0.18.0|>=0.18|>=0.19.2|>=0.24|>=0.25|>=1.0']

Package typing conflicts for:
dvc -> ruamel.yaml[version='>=0.16.1'] -> typing[version='>=3.7.4']
sphinx-gallery -> sphinx[version='>=1.8.3'] -> typing

Package libedit conflicts for:
python=3.9 -> sqlite[version='>=3.33.0,<4.0a0'] -> libedit[version='>=3.1.20191231,<3.2.0a0']
netcdf4 -> openssh -> libedit[version='>=3.1.20191231,<3.2.0a0']

Package freetype conflicts for:
geopandas -> matplotlib-base -> freetype[version='2.6.*|>=2.10.2,<3.0a0|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8,<2.9.0a0']
pytest-mpl -> matplotlib-base -> freetype[version='2.5.*|2.6.*|2.7|2.7.*|2.7|2.8.*|2.8.1|2.8.1.*|>=2.10.2,<3.0a0|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8.1,<2.9.0a0|>=2.10.3,<3.0a0|>=2.8,<2.9.0a0']
sphinx-gallery -> matplotlib-base -> freetype[version='2.5.*|2.6.*|2.7|2.7.*|2.7|2.8.*|2.8.1|2.8.1.*|>=2.10.2,<3.0a0|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8.1,<2.9.0a0|>=2.10.3,<3.0a0|>=2.8,<2.9.0a0']
gmt=6.2.0 -> ffmpeg -> freetype[version='2.8.1|2.8.1.*|>=2.10.4,<3.0a0|>=2.9.1,<3.0a0|>=2.8.1,<2.9.0a0|>=2.8.1,<2.8.2.0a0|>=2.8,<2.9.0a0']

Package blas conflicts for:
numpy=1.20 -> mkl_fft -> blas=[build=mkl]
numpy=1.20 -> blas[version='*|1.0',build='mkl|openblas']

Package urllib3 conflicts for:
dvc -> dulwich[version='>=0.20.23'] -> urllib3[version='>=1.21.1,<1.25|>=1.21.1,<1.26,!=1.25.0,!=1.25.1|>=1.21.1,<1.27']
codecov -> requests[version='>=2.7.9'] -> urllib3[version='>=1.21.1,<1.22|>=1.21.1,<1.23|>=1.21.1,<1.24|>=1.21.1,<1.25|>=1.21.1,<1.26,!=1.25.0,!=1.25.1|>=1.21.1,<1.27']
geopandas -> pysal -> urllib3[version='<1.25|<1.26']

Package numpy-base conflicts for:
numpy=1.20 -> numpy-base[version='1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.1|1.20.2',build='py39h34387ca_0|py38h7d8b39e_0|py39h7d8b39e_0|py38he2ba247_0|py37he2ba247_0|py39hfae3a4d_0|py37hfae3a4d_0|py39he2ba247_0|py38hfae3a4d_0|py38h34387ca_0|py37h7d8b39e_0|py37h34387ca_0']
numpy=1.20 -> mkl_fft -> numpy-base[version='>=1.0.14,<2.0a0|>=1.0.6,<2.0a0|>=1.0.2,<2.0a0|>=1.0.4,<2.0a0']

Package configparser conflicts for:
dvc -> configparser[version='>=3.5.0']
dvc -> importlib-metadata -> configparser[version='>=3.5']

Package mpich conflicts for:
netcdf4 -> hdf5=[build=mpi_mpich_*] -> mpich[version='3.2.*|>=3.2,<3.3.0a0|>=3.3,<3.4.0a0']
netcdf4 -> mpich[version='>=3.3,<4.0.0a0|>=3.4,<4.0.0a0']

Package blis conflicts for:
gmt=6.2.0 -> libblas[version='>=3.8.0,<4.0a0'] -> blis[version='0.5.1.*|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0']
numpy=1.20 -> libblas[version='>=3.8.0,<4.0a0'] -> blis[version='0.5.1.*|>=0.5.2,<0.5.3.0a0|>=0.6.0,<0.6.1.0a0|>=0.6.1,<0.6.2.0a0|>=0.7.0,<0.7.1.0a0|>=0.8.0,<0.8.1.0a0|>=0.8.1,<0.8.2.0a0']

Package hdf5 conflicts for:
netcdf4 -> libnetcdf=4.4 -> hdf5=1.8.17
netcdf4 -> hdf5[version='*|*|*|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.6,<1.10.7.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.5,<1.10.6.0a0|>=1.10.4,<1.10.5.0a0|>=1.10.3,<1.10.4.0a0|1.10.2.*|>=1.10.2,<1.10.3.0a0|1.10.1.*|1.10.1|1.8.18|1.8.18.*|1.8.17|1.8.17.*|1.8.15.*|>=1.8.20,<1.9.0a0|>=1.8.18,<1.8.19.0a0|>=1.10.1,<1.10.2.0a0',build='mpi_mpich_*|mpi_openmpi_*|mpi_openmpi_*|nompi_*|mpi_openmpi_*|mpi_mpich_*']

Package enum34 conflicts for:
ipython -> traitlets[version='>=4.2'] -> enum34
geopandas -> fiona -> enum34

Error: Process completed with exit code 1.

[weiji14]

Looks like the package conflicts magically resolved itself 🙌 PyGMT and geopandas installation using conda should now work!

[maxrjones]

Why is geopandas included for the CI tests but not for the development dependencies in environment.yml?

[weiji14]

Why is geopandas included for the CI tests but not for the development dependencies in environment.yml?

Good question. Geopandas is an optional dependency, and isn't required for development. But I could add it to the environment.yml file if developers prefer to have it in their conda env? Or they could install it using conda install geopandas afterwards themselves.

[maxrjones]

Why is geopandas included for the CI tests but not for the development dependencies in environment.yml?

Good question. Geopandas is an optional dependency, and isn't required for development. But I could add it to the environment.yml file if developers prefer to have it in their conda env? Or they could install it using conda install geopandas afterwards themselves.

I think if geopandas gallery examples will be suggested as good first issues for the upcoming sprint, it would be better to include it so that setup is as simple as possible for new contributors.

[weiji14]

I think if geopandas gallery examples will be suggested as good first issues for the upcoming sprint, it would be better to include it so that setup is as simple as possible for new contributors.

Makes sense, I'll add it in then. The Vercel continuous documentation actually installs from the environment.yml too (see package.json) so we'll need it for the gallery examples in the future. Edit: done at 35562cd