Migrate provision-with-micromamba to setup-micromamba by weiji14 · Pull Request #2536 · GenericMappingTools/pygmt

weiji14 · 2023-05-11T04:32:41Z

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

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 paramete with create-args instead.

Xref https://github.com/mamba-org/setup-micromamba/tree/v1.2.1#caching

Xref https://github.com/mamba-org/setup-micromamba/tree/v1.2.1#custom-condarc-file

Xref https://stackoverflow.com/questions/3790454/how-do-i-break-a-string-in-yaml-over-multiple-lines/21699210#21699210

pavelzw · 2023-05-11T13:16:24Z

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.

Xref #2536 (comment)

Forgot that we don't use the environment.yml file

This reverts commit 31b775f.

Need to format the blank spaces a bit more carefully.

weiji14 · 2023-05-11T21:09:51Z

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!

This reverts commit a6b19f7.

.github/workflows/cache_data.yaml

Co-Authored-By: Dongdong Tian <seisman.info@gmail.com>

seisman · 2023-05-12T06:25:21Z

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.

Reverts 69bb40d in #2435.

weiji14 · 2023-05-12T07:10:45Z

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 · 2023-05-12T07:33:24Z

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 · 2023-05-12T07:59:40Z

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 · 2023-05-12T08:15:47Z

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.

weiji14 self-assigned this May 11, 2023

weiji14 marked this pull request as draft May 11, 2023 04:34

weiji14 added 6 commits May 11, 2023 16:36

Rename cache-env to cache-environment

1866c97

Xref https://github.com/mamba-org/setup-micromamba/tree/v1.2.1#caching

Replace channels with condarc

565f9ad

Xref https://github.com/mamba-org/setup-micromamba/tree/v1.2.1#custom-condarc-file

Temporarily disable cache

a6b19f7

Set environment-file to environment.yml

06445fd

Replace YAML linebreak | with >-

c53ddec

Xref https://stackoverflow.com/questions/3790454/how-do-i-break-a-string-in-yaml-over-multiple-lines/21699210#21699210

Try removing environment-name parameter

3e2d136

weiji14 added 6 commits May 12, 2023 08:28

Add extra space before optional contextily package

31b775f

Xref #2536 (comment)

Use environment-name instead of environment-file

38a0b17

Forgot that we don't use the environment.yml file

Revert "Add extra space before optional contextily package"

448494e

This reverts commit 31b775f.

Put optional-packages with space after python-version

9932847

Need to format the blank spaces a bit more carefully.

More whitespace tweaks

58c807c

Try formatting as a single line with a leading space

b5cc1c7

Revert "Temporarily disable cache"

0e0c866

This reverts commit a6b19f7.

weiji14 marked this pull request as ready for review May 11, 2023 21:12

weiji14 added maintenance Boring but important stuff for the core devs needs review This PR has higher priority and needs review. labels May 11, 2023

seisman reviewed May 12, 2023

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.github/workflows/cache_data.yaml Outdated Show resolved Hide resolved

seisman added this to the 0.10.0 milestone May 12, 2023

Bump mamba-org/setup-micromamba from 1.2.1 to 1.3.0

06c89e4

Co-Authored-By: Dongdong Tian <seisman.info@gmail.com>

weiji14 added 2 commits May 12, 2023 19:08

List installed packages from micromamba

9808f18

Reverts 69bb40d in #2435.

Use micromamba list, not mamba list

ea3afa9

seisman approved these changes May 12, 2023

View reviewed changes

seisman removed the needs review This PR has higher priority and needs review. label May 12, 2023

michaelgrund approved these changes May 12, 2023

View reviewed changes

Bump to mamba-org/setup-micromamba 1.4.0 and remove micromamba list

2ca451f

weiji14 merged commit c443374 into main May 12, 2023

weiji14 deleted the setup-micromamba branch May 12, 2023 08:42

seisman mentioned this pull request May 26, 2023

CI: Do not use geopandas 0.13.0 in docs #2545

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Migrate provision-with-micromamba to setup-micromamba#2536

Migrate provision-with-micromamba to setup-micromamba#2536
weiji14 merged 18 commits intomainfrom
setup-micromamba

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