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

package:
  name: numpy
  version: 1.21.4

source:
  url: https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip
  sha256: e6c76a87633aa3fa16614b61ccedfae45b91df2767cf097aa9c933932a7ed1e0

  patches:
    - patches/segfault-PyArray_Broadcast.patch
    - patches/segfault-PyArray_PyIntAsIntp.patch
    - patches/disable-maybe-uninitialized.patch
    - patches/dont-include-execinfo.patch
    - patches/fix-longdouble.patch
    - patches/fix-static-init-of-nditer-pywrap.patch
    - patches/init-alloc-cache.patch
    - patches/use-local-blas-lapack.patch
    - patches/fix-install-with-skip-build.patch
    - patches/make-int-return-values.patch
    - patches/fix-ieee754.patch
    - patches/disable-optimization.patch
    - patches/not-build-lapack-lite-as-64-bit.patch
    - patches/fix-invalid-asm-instruction.patch
    - patches/fix-removed-decorators-module.patch
    - patches/fix-comparator-function-signatures.patch
    - patches/fix-random_float_fill-return-type.patch

build:
  skip_host: False
  # set linker and C flags to error on anything to do with function declarations being wrong.
  # In webassembly, any conflicts mean that a randomly selected 50% of calls to the function
  # will fail. Better to fail at compile or link time.
  cflags: |
    -include math.h
    -I $(PYODIDE_ROOT)/packages/numpy/config
    -Werror=implicit-function-declaration
    -Werror=mismatched-parameter-types
    -Werror=mismatched-return-types
  ldflags: |
    -Wl,--fatal-warnings
  post: |
    # copy the correct numpy config into the build artifacts. Otherwise scipy will try to build with the config
    # from the build computer and bad things will happen
    cp config/* $PKGDIR/../.artifacts/lib/python/numpy-1.21.4-py3.9-emscripten_wasm32.egg/numpy/core/include/numpy
    cp -r $PKGDIR/../.artifacts/lib/python/numpy-1.21.4-py3.9-emscripten_wasm32.egg/numpy $PKGDIR/../.artifacts/lib/python

test:
  imports:
    - numpy

package:
  name: numpy
  version: 1.21.4

source:
  url: https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip
  sha256: e6c76a87633aa3fa16614b61ccedfae45b91df2767cf097aa9c933932a7ed1e0

  patches:
    - patches/segfault-PyArray_Broadcast.patch
    - patches/segfault-PyArray_PyIntAsIntp.patch
    - patches/disable-maybe-uninitialized.patch
    - patches/dont-include-execinfo.patch
    - patches/fix-longdouble.patch
    - patches/fix-static-init-of-nditer-pywrap.patch
    - patches/init-alloc-cache.patch
    - patches/use-local-blas-lapack.patch
    - patches/fix-install-with-skip-build.patch
    - patches/make-int-return-values.patch
    - patches/fix-ieee754.patch
    - patches/disable-optimization.patch
    - patches/not-build-lapack-lite-as-64-bit.patch
    - patches/fix-invalid-asm-instruction.patch
    - patches/fix-removed-decorators-module.patch
    - patches/fix-comparator-function-signatures.patch
    - patches/fix-random_float_fill-return-type.patch

build:
  skip_host: False
  # set linker and C flags to error on anything to do with function declarations being wrong.
  # In webassembly, any conflicts mean that a randomly selected 50% of calls to the function
  # will fail. Better to fail at compile or link time.
  cflags: |
    -include math.h
    -I $(PYODIDE_ROOT)/packages/numpy/config
    -Werror=implicit-function-declaration
    -Werror=mismatched-parameter-types
    -Werror=mismatched-return-types
  ldflags: |
    -Wl,--fatal-warnings
  post: |
    # copy the correct numpy config into the build artifacts. Otherwise scipy will try to build with the config
    # from the build computer and bad things will happen
    cp config/* $PKGDIR/../.artifacts/lib/python/numpy-1.21.4-py3.9-emscripten_wasm32.egg/numpy/core/include/numpy
    cp -r $PKGDIR/../.artifacts/lib/python/numpy-1.21.4-py3.9-emscripten_wasm32.egg/numpy $PKGDIR/../.artifacts/lib/python

test:
  imports:
    - numpy
