I've updated the following packages:


- ~~chore: update lxml to 4.8.0~~
- chore: update MarkupSafe to 2.1.0
- chore: update astropy to 5.0.1
- chore: update logbook to 1.5.3
- chore: update regex to 2022.1.18
- chore: update sqlalchemy to 1.4.31
- chore: updated cffi to 1.15.0
- chore: updated imageio to 2.16.1
- chore: updated setuptools to 60.9.3
- chore: updated pytest to 7.0.1
- chore: updated typing-extensions to 4.1.1
- chore: updated pyrsistent to 0.18.1
- chore: updated threadpoolctl to 3.1.0

I wasn't sure how caching was done (if I update numpy, etc. all at once will
that blow up the CI build time?), and I'm hoping to avoid failures, so I left
the big or patched ones alone. Was after lxml (see #2225), but thought I'd get a couple other ones while at it. Removed it, having an issue so will be bumped separately.

* matplotlib 3.3.3 ❌ -> 3.5.1
* nltk 3.6.7 ❌ -> 3.7
* numpy 1.21.4 ❌ -> 1.22.2
* pandas 1.3.5 ❌ -> 1.4.1
* pillow 9.0.0 ❌ -> 9.0.1
* pyrsistent 0.18.0 ❌ -> 0.18.1
* python-sat 0.1.7.dev15 ❌ -> 0.1.7.dev16
* scikit-image 0.19.1 ❌ -> 0.19.2
* scipy 1.7.3 ❌ -> 1.8.0
* statsmodels 0.13.1 ❌ -> 0.13.2
* swiglpk 5.0.3 ❌ -> 5.0.4
* yt 3.6.1 ❌ -> 4.0.2
* zarr 2.10.3 ❌ -> 2.11.0

chore: some package updates. I've updated the following packages:


- ~~chore: update lxml to 4.8.0~~
- chore: update MarkupSafe to 2.1.0
- chore: update astropy to 5.0.1
- chore: update logbook to 1.5.3
- chore: update regex to 2022.1.18
- chore: update sqlalchemy to 1.4.31
- chore: updated cffi to 1.15.0
- chore: updated imageio to 2.16.1
- chore: updated setuptools to 60.9.3
- chore: updated pytest to 7.0.1
- chore: updated typing-extensions to 4.1.1
- chore: updated pyrsistent to 0.18.1
- chore: updated threadpoolctl to 3.1.0

I wasn't sure how caching was done (if I update numpy, etc. all at once will
that blow up the CI build time?), and I'm hoping to avoid failures, so I left
the big or patched ones alone. Was after lxml (see #2225), but thought I'd get a couple other ones while at it. Removed it, having an issue so will be bumped separately.

* matplotlib 3.3.3 ❌ -> 3.5.1
* nltk 3.6.7 ❌ -> 3.7
* numpy 1.21.4 ❌ -> 1.22.2
* pandas 1.3.5 ❌ -> 1.4.1
* pillow 9.0.0 ❌ -> 9.0.1
* pyrsistent 0.18.0 ❌ -> 0.18.1
* python-sat 0.1.7.dev15 ❌ -> 0.1.7.dev16
* scikit-image 0.19.1 ❌ -> 0.19.2
* scipy 1.7.3 ❌ -> 1.8.0
* statsmodels 0.13.1 ❌ -> 0.13.2
* swiglpk 5.0.3 ❌ -> 5.0.4
* yt 3.6.1 ❌ -> 4.0.2
* zarr 2.10.3 ❌ -> 2.11.0

exclude: (^.*patches|.*\.cgi$|^packages/micropip/src/micropip/externals|^src/py/lib/pystone.py$)
default_language_version:
  python: "3.9"
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: "v4.1.0"
    hooks:
      - id: check-yaml
        exclude: .clang-format
      - id: end-of-file-fixer
      - id: trailing-whitespace

  - repo: https://github.com/PyCQA/isort
    rev: "5.10.1"
    hooks:
      - id: isort

  - repo: https://github.com/asottile/pyupgrade
    rev: "v2.31.0"
    hooks:
      - id: pyupgrade
        args: ["--py39-plus"]

  - repo: https://github.com/hadialqattan/pycln
    rev: "v1.2.0"
    hooks:
      - id: pycln
        args: [--config=pyproject.toml]
        stages: [manual]

  - repo: https://github.com/psf/black
    rev: "22.1.0"
    hooks:
      - id: black

  - repo: https://gitlab.com/pycqa/flake8
    rev: "4.0.1"
    hooks:
      - id: flake8
        additional_dependencies: [flake8-bugbear]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v0.931
    hooks:
      - id: mypy
        args:
          - --show-error-codes
          - --ignore-missing-imports
        files: ^(src/|packages/.*/test|conftest.py|docs/)
        additional_dependencies: &mypy-deps
          - packaging
          - types-docutils
          - types-pyyaml
          - types-setuptools
      - id: mypy
        name: mypy-micropip
        files: ^packages/micropip/src/
        args: &mypy-args
          - --show-error-codes
        additional_dependencies: *mypy-deps
      - id: mypy
        name: mypy-pyodide-build
        files: ^pyodide-build/pyodide_build/
        args: *mypy-args
        additional_dependencies: *mypy-deps

  - repo: https://github.com/pre-commit/mirrors-clang-format
    rev: "v13.0.1"
    hooks:
      - id: clang-format
        types_or: [c++, c, cuda]

  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v2.5.1"
    hooks:
      - id: prettier

exclude: (^.*patches|.*\.cgi$|^packages/micropip/src/micropip/externals|^src/py/lib/pystone.py$)
default_language_version:
  python: "3.9"
repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: "v4.1.0"
    hooks:
      - id: check-yaml
        exclude: .clang-format
      - id: end-of-file-fixer
      - id: trailing-whitespace

  - repo: https://github.com/PyCQA/isort
    rev: "5.10.1"
    hooks:
      - id: isort

  - repo: https://github.com/asottile/pyupgrade
    rev: "v2.31.0"
    hooks:
      - id: pyupgrade
        args: ["--py39-plus"]

  - repo: https://github.com/hadialqattan/pycln
    rev: "v1.2.0"
    hooks:
      - id: pycln
        args: [--config=pyproject.toml]
        stages: [manual]

  - repo: https://github.com/psf/black
    rev: "22.1.0"
    hooks:
      - id: black

  - repo: https://gitlab.com/pycqa/flake8
    rev: "4.0.1"
    hooks:
      - id: flake8
        additional_dependencies: [flake8-bugbear]

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v0.931
    hooks:
      - id: mypy
        args:
          - --show-error-codes
          - --ignore-missing-imports
        files: ^(src/|packages/.*/test|conftest.py|docs/)
        additional_dependencies: &mypy-deps
          - packaging
          - types-docutils
          - types-pyyaml
          - types-setuptools
      - id: mypy
        name: mypy-micropip
        files: ^packages/micropip/src/
        args: &mypy-args
          - --show-error-codes
        additional_dependencies: *mypy-deps
      - id: mypy
        name: mypy-pyodide-build
        files: ^pyodide-build/pyodide_build/
        args: *mypy-args
        additional_dependencies: *mypy-deps

  - repo: https://github.com/pre-commit/mirrors-clang-format
    rev: "v13.0.1"
    hooks:
      - id: clang-format
        types_or: [c++, c, cuda]

  - repo: https://github.com/pre-commit/mirrors-prettier
    rev: "v2.5.1"
    hooks:
      - id: prettier
