Drop support for Python 3.9; eliminate duplicate run of test-mindeps CI

[mfisher87]

Following SPEC0, we can stop supporting Python 3.9. We can also stop supporting 3.10, but we decided to give 3.10 a little more time before dropping. Resolves #836.

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📚 Documentation preview 📚: https://earthaccess--876.org.readthedocs.build/en/876/

[github-actions]

👈 Launch a binder notebook on this branch for commit c782c52

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[mfisher87]

  Caused by: Failed to download and build `h5py==3.0.0`
  <...>
  Caused by: Failed to download and build `numpy==1.19.3`

?? Our minimum supported version of numpy is 1.24.0. Is uv failing to understand our conditional numpy dependency?

[mfisher87]

Removed the numpy conditional dependency after upgrading h5py to a version that supports Python 3.10. Still getting the same error. When I lock the environment locally with lowest-direct resolution, I get: Updated numpy v2.0.2 -> v1.26.4. I don't understand where numpy==1.19.3 is coming from!

[mfisher87]

It looks to me like a bug in uv's lowest-direct resolution algorithm. It's pulling in the lowest version for numpy as an indirect dependency of h5py (https://github.com/h5py/h5py/blob/3.4.0/setup.py#L32) and ignoring our direct specification of the lowest numpy version.

[jhkennedy]

@mfisher87 this is dumb, but might just work -- can you try putting numpy at the top of the dependencies list so it's before h5py?

[mfisher87]

@jhkennedy great idea, but no change :(

[jhkennedy]

OK, rats. I was hoping dumb but easy would work. 🤣

@mfisher87 in #872, when I pulled the min-deps test into nox, I changed:

uv sync --resolution lowest-direct --extra test
uv pip install --no-deps .

to

uv pip install --resolution lowest-direct --editable .[test]

https://github.com/nsidc/earthaccess/pull/872/files#diff-f7a16a65f061822bcc73b8296f4dc837353d379d8d9cc5307982cb6941442835R38

It sounds like from your comments the uv sync step first might actually be necessary, so adding that back into the session might be the way to go.

[jhkennedy]

recipe here:
https://nox.thea.codes/en/stable/cookbook.html#using-a-lockfile

[mfisher87]

The uv sync command fails with the exact same error output :(

[jhkennedy]

(╯°□°)╯︵ ┻━┻

[mfisher87]

I'm thinking open an issue on the uv repo for this. What do you think?

[jhkennedy]

I'm thinking open an issue on the uv repo for this. What do you think?

Makes sense -- there's a couple that look like they might be related already open. E.g.,
astral-sh/uv#5492

But I'm in a meeting so haven't ready them closely (I'm all booked today 😭 )

[mfisher87]

I never did figure out the underlying cause. pip install h5py==3.4.0 doesn't work in a Python 3.10 environment either; it attempts to build the wheel, and pulls in the lowest supported version of numpy and fails with the same message as we receive in CI. I expected it would pull in a version of numpy which supported Python 3.10.

Either way, we can avoid building the wheel by upgrading h5py >=3.6.0, which has a pre-built wheel for Python 3.10, and that fixes the error!

[jhkennedy]

The 3.10 and 3.11 integration tests failed because 6 tests failed, while in 3.12 and 3.13 only 5 failed, which is below our threshold. The additional failure is just a flakey failure, so I think were g2g.

[mfisher87]

🤣

[github-actions]

User ayushnag does not have permission to run integration tests. A maintainer must perform a security review of the code changes in this pull request and re-run the failed integration tests jobs, if the code is deemed safe.