Migrate provision-with-micromamba to setup-micromamba

[weiji14]

Description of proposed changes

The mamba-org/provision-with-micromamba GitHub Action is about to be deprecated in favour of https://github.com/mamba-org/setup-micromamba, see mamba-org/provision-with-micromamba#122. Also replaced the extra-specs parameter with create-args instead.

Migration reference: mamba-org/provision-with-micromamba#114

Supersedes #2435

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 wrapping a new module, open a 'Wrap new GMT module' issue and submit reasonably-sized PRs.
• If adding new functionality, add an example to docstrings or tutorials.
• Use underscores (not hyphens) in names of Python files and directories.

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

[pavelzw]

In ci_tests.yaml, you need to switch from

        include:
          - python-version: '3.9'
            numpy-version: '1.21'
            optional-packages: ''
          - python-version: '3.11'
            numpy-version: '1.24'
            optional-packages: |
              contextily
              geopandas
              ipython
              rioxarray
              sphinx-gallery
[...]
            packaging
            ${{ matrix.optional-packages }}
            build

to

        include:
          - python-version: '3.9'
            numpy-version: '1.21'
            optional-packages: ''
          - python-version: '3.11'
            numpy-version: '1.24'
            optional-packages: >-
               contextily
              geopandas
              ipython
              rioxarray
              sphinx-gallery
[...]
            packaging${{ matrix.optional-packages }}
            build

(beware the extra space at contextily) since the new action expects all dependencies to be separated by spaces.
The | YAML block scalar doesn't convert new lines to spaces but leaves them as newlines.

[weiji14]

In ci_tests.yaml, you need to switch
to

        include:
          - python-version: '3.9'
            numpy-version: '1.21'
            optional-packages: ''
          - python-version: '3.11'
            numpy-version: '1.24'
            optional-packages: >-
               contextily
              geopandas
              ipython
              rioxarray
              sphinx-gallery
[...]
            packaging${{ matrix.optional-packages }}
            build

(beware the extra space at contextily) since the new action expects all dependencies to be separated by spaces. The | YAML block scalar doesn't convert new lines to spaces but leaves them as newlines.

Thanks for the tip @pavelzw! I was wondering why the error for the CI test with optional dependencies was different to the one without. The single space before contextily didn't work at 58c807c, something about a YAML lint error. I just changed everything to a single line instead of multi-line at b5cc1c7 and now it runs!

[seisman]

In PR #2435, I removed the mamba list step because the old mamba-org/provision-with-micromamba action already did it (https://github.com/GenericMappingTools/pygmt/pull/2435/files#r1173833125).

I don't find the package list in the new action output. I think we should add micromamba list back.

[weiji14]

In PR #2435, I removed the mamba list step because the old mamba-org/provision-with-micromamba action already did it (https://github.com/GenericMappingTools/pygmt/pull/2435/files#r1173833125).

I don't find the package list in the new action output. I think we should add micromamba list back.

Good catch. done in 9808f18 and ea3afa9 (need to use micromamba list).

[seisman]

Looks good.

[weiji14]

Hmm, the readthedocs build is failing with an unrelated fiona.errors.DriverError: '/vsizip/vsicurl/ error. Might be due to changes with the geopandas 0.13.0 release (see geopandas/geopandas#2796 (comment)).

[pavelzw]

I don't find the package list in the new action output. I think we should add micromamba list back.

I wanted to add this in setup-micromamba but forgot until now, thanks for reminding me :)

[pavelzw]

If you update to v1.4.0 (or use @v1 to always get the most recent vx.y.z), you can remove the micromamba list again.