python3Packages.tensorflow-probability: 0.8.0 -> 0.15.0

[simeoncarstens]

Motivation for this change

python3Packages.tensorflow-probability was outdated and marked as broken because of an unpackaged dependency (python3Packages.dm-tree). dm-tree is now packaged (#152971), so I updated tensorflow-probability to the most current version.
Several python3Packages depend on tensorflow-probability, namely dm-sonnet, arviz, and pymc3 and fixing tensorflow-probability thus potentially "unbreaks" them. Turns out that

• arviz tests require an older version of tensorflow-probability,
• pymc3 now is broken for a different reason (missing dependencies),
• dm-sonnet is broken for a different reason (requires an older tensorflow version than the one currently packaged).

So I disabled the arviz tests requiring tensorflow-probability and marked pymc3 and dm-sonnet as broken.
Furthermore, tensorflow-tensorboard is a dependency of tensorflow-probability, but is currently incompatible with Python 3.10. I thus disabled tensorflow-tensorboard for Python 3.10.
I also took the liberty to add the numba-related tests to the list of tests run for arviz.

Finally, unfortunately tensorflow-probability is maintainerless. I would love to get engaged and maintain it, but I feel I don't have the necessary Nix skills quite yet to do / review more difficult changes , especially with regards to the Bazel tooling or the hacking likely required to run the unit tests.

This is my first PR here, so please let me know in case I am breaking any protocols or how to improve / do better next time.

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• 22.05 Release Notes (or backporting 21.11 Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
  • (Release notes changes) Ran nixos/doc/manual/md-to-db.sh to update generated release notes
• Fits CONTRIBUTING.md.

[GuillaumeDesforges]

Is it required? Broken?

[simeoncarstens]

I added / cleaned up some of the comments. Hope it's all clearer now.

[SuperSandro2000]

This is a semi-automatic executed nixpkgs-review with nixpkgs-review-checks extension. It is checked by a human on a best effort basis and does not build all packages (e.g. lumo, tensorflow or pytorch).

Result of nixpkgs-review pr 156027 run on x86_64-linux 1

3 packages marked as broken and skipped:

• python39Packages.dm-sonnet
• python39Packages.graph_nets
• python39Packages.pymc3

1 package failed to build and are new build failure:

• python39Packages.arviz: plain log | pretty log

[simeoncarstens]

Since the merging of #154708, building arviz fails, via #152660. Looks like I should have used NixOS:staging as the base branch, right?
Anyways, arviz 0.11.4 pins typing_extensions>=3.7.4.3,<4. In the next release, this is not the case anymore (arviz-devs/arviz#1948). I'm not sure what the protocol is - a simple

patchPhase = ''
  sed -i "s#typing_extensions>=3.7.4.3,<4#typing_extensions>=3.7.4.3#" requirements.txt
'';

makes it build (and pass the activated tests) perfectly fine, but it's probably out of scope for this PR, so I'll mark arviz as broken.

[SuperSandro2000]

Looks like I should have used NixOS:staging as the base branch, right?

No, this PR rebuilds under 10 packages which means it goes to master.

makes it build (and pass the activated tests) perfectly fine, but it's probably out of scope for this PR, so I'll mark arviz as broken.

If the fix is as simple as that and you only need to commit it, it is a waste of time to mark it broken now and unmark it later and then fix it. We can also throw that into this PR.

Also you want to to use postPatch to not break patches and substituteInPlace because it logs if there is no match.

postPhase = ''
  substituteInPlace requirements.txt \
    --replace- "typing_extensions>=3.7.4.3,<4" "typing_extensions>=3.7.4.3"
'';

[simeoncarstens]

Thanks for the helpful comments! I am now patching arviz instead of marking it as broken.