python3Packages.python-lsp-server: fix test issues from 1.5.0 upgrade

[lilyinstarlight]

Description of changes

Fixes issues building python-lsp-server since it was bumped to 1.5.0 in #181620 (see hydra build 185438708)

Changes:

• The test_numpy_completion test is currently broken - see Autocompletion not working for numpy >= 1.22 davidhalter/jedi#1864
• The test flags were moved from setup.cfg to pyproject.toml - see Move the project metadata into PEP 621-compliant pyproject.toml python-lsp/python-lsp-server#207
• A dependency on whatthepatch was added for yapf - see Parse YAPF diffs into TextEdits (instead of sending the full doc) python-lsp/python-lsp-server#136

The package python3Packages.spyder (which depends on this package) is still failing due to the python3Packages.qdarkstyle update, but that's unrelated to this PR (I might open another PR to fix that one, but I don't personally use it, unlike this one)

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/)
• 22.11 Release Notes (or backporting 22.05 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.

nixpkgs-review

Result of nixpkgs-review run on x86_64-linux 1

2 packages failed to build:

• spyder (python310Packages.spyder)
• python39Packages.spyder

14 packages built:

• python310Packages.pyls-flake8
• python310Packages.pyls-isort
• python310Packages.pyls-spyder
• python310Packages.pylsp-mypy
• python310Packages.python-lsp-black
• python310Packages.python-lsp-server
• python310Packages.whatthepatch
• python39Packages.pyls-flake8
• python39Packages.pyls-isort
• python39Packages.pyls-spyder
• python39Packages.pylsp-mypy
• python39Packages.python-lsp-black
• python39Packages.python-lsp-server
• python39Packages.whatthepatch

[lilyinstarlight]

Oops I swear I searched this, but I missed #183862 somehow. Closing this PR in favor of that one (sorry about the extra noise)