Fix scipy sqrtm precision issue (#864)

* Use eigendecomposition inplace of la.sqrtm.

* Update envs.

* Upper limit on cirq due to gate equality failure.

* Update dependencies.

* Fix comment typo about sqrt.

dev_tools/requirements/deps/runtime.txt

@@ -1,12 +1,11 @@
-cirq-core~=1.0
+cirq-core~=1.0,<1.3.0
 deprecation
 h5py>=2.8
 networkx
 numpy>=1.11.0
 pubchempy
 requests>=2.18
 
-# https://github.com/scipy/scipy/issues/18250
-scipy>=1.1.0,<1.10.0
+scipy>=1.1.0
 
 sympy

dev_tools/requirements/envs/dev.env.txt

@@ -8,15 +8,15 @@ ase==3.22.1
     # via -r deps/resource_estimates_runtime.txt
 astroid==2.13.5
     # via pylint
-attrs==23.1.0
+attrs==23.2.0
     # via
     #   jsonschema
     #   referencing
 black==23.3.0
     # via -r deps/format.txt
 build==1.0.3
     # via pip-tools
-certifi==2023.7.22
+certifi==2023.11.17
     # via requests
 charset-normalizer==3.3.2
     # via requests
@@ -28,7 +28,7 @@ click==8.1.7
     #   pip-tools
 contourpy==1.2.0
     # via matplotlib
-coverage[toml]==7.3.2
+coverage[toml]==7.4.0
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
@@ -38,45 +38,45 @@ dill==0.3.7
     # via pylint
 duet==0.2.9
     # via cirq-core
-exceptiongroup==1.1.3
+exceptiongroup==1.2.0
     # via pytest
 execnet==2.0.2
     # via pytest-xdist
-fastjsonschema==2.18.1
+fastjsonschema==2.19.1
     # via nbformat
-fonttools==4.43.0
+fonttools==4.47.2
     # via matplotlib
 h5py==3.10.0
     # via
     #   -r deps/runtime.txt
     #   pyscf
-idna==3.4
+idna==3.6
     # via requests
 iniconfig==2.0.0
     # via pytest
-isort==5.12.0
+isort==5.13.2
     # via pylint
-jax==0.4.20
+jax==0.4.23
     # via -r deps/resource_estimates_runtime.txt
-jaxlib==0.4.20
+jaxlib==0.4.23
     # via -r deps/resource_estimates_runtime.txt
-jsonschema==4.19.2
+jsonschema==4.21.0
     # via nbformat
-jsonschema-specifications==2023.7.1
+jsonschema-specifications==2023.12.1
     # via jsonschema
-jupyter-core==5.5.0
+jupyter-core==5.7.1
     # via nbformat
 kiwisolver==1.4.5
     # via matplotlib
-lazy-object-proxy==1.9.0
+lazy-object-proxy==1.10.0
     # via astroid
-matplotlib==3.8.1
+matplotlib==3.8.2
     # via
     #   ase
     #   cirq-core
 mccabe==0.7.0
     # via pylint
-ml-dtypes==0.3.1
+ml-dtypes==0.3.2
     # via
     #   jax
     #   jaxlib
@@ -94,7 +94,7 @@ networkx==3.2.1
     # via
     #   -r deps/runtime.txt
     #   cirq-core
-numpy==1.25.2
+numpy==1.26.3
     # via
     #   -r deps/runtime.txt
     #   ase
@@ -118,15 +118,15 @@ packaging==23.2
     #   deprecation
     #   matplotlib
     #   pytest
-pandas==2.1.2
+pandas==2.1.4
     # via cirq-core
-pathspec==0.11.2
+pathspec==0.12.1
     # via black
-pillow==10.1.0
+pillow==10.2.0
     # via matplotlib
 pip-tools==7.3.0
     # via -r deps/pip-tools.txt
-platformdirs==3.11.0
+platformdirs==4.1.0
     # via
     #   black
     #   jupyter-core
@@ -143,35 +143,35 @@ pyproject-hooks==1.0.0
     # via build
 pyscf==2.4.0
     # via -r deps/resource_estimates_runtime.txt
-pytest==7.4.3
+pytest==7.4.4
     # via
     #   -r deps/pytest.txt
     #   pytest-asyncio
     #   pytest-cov
     #   pytest-xdist
-pytest-asyncio==0.21.1
+pytest-asyncio==0.23.3
     # via -r deps/pytest.txt
 pytest-cov==4.1.0
     # via -r deps/pytest.txt
-pytest-xdist==3.3.1
+pytest-xdist==3.5.0
     # via -r deps/pytest.txt
 python-dateutil==2.8.2
     # via
     #   matplotlib
     #   pandas
 pytz==2023.3.post1
     # via pandas
-referencing==0.30.2
+referencing==0.32.1
     # via
     #   jsonschema
     #   jsonschema-specifications
 requests==2.31.0
     # via -r deps/runtime.txt
-rpds-py==0.10.6
+rpds-py==0.17.1
     # via
     #   jsonschema
     #   referencing
-scipy==1.9.3
+scipy==1.11.4
     # via
     #   -r deps/runtime.txt
     #   ase
@@ -196,28 +196,28 @@ tomli==2.0.1
     #   pylint
     #   pyproject-hooks
     #   pytest
-tomlkit==0.12.2
+tomlkit==0.12.3
     # via pylint
 tqdm==4.66.1
     # via cirq-core
-traitlets==5.13.0
+traitlets==5.14.1
     # via
     #   jupyter-core
     #   nbformat
 typed-ast==1.4.3
     # via mypy
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   astroid
     #   cirq-core
     #   mypy
-tzdata==2023.3
+tzdata==2023.4
     # via pandas
-urllib3==2.0.7
+urllib3==2.1.0
     # via requests
-wheel==0.41.3
+wheel==0.42.0
     # via pip-tools
-wrapt==1.15.0
+wrapt==1.16.0
     # via astroid
 
 # The following packages are considered to be unsafe in a requirements file:

dev_tools/requirements/envs/format.env.txt

@@ -8,7 +8,7 @@ black==23.3.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/format.txt
-certifi==2023.7.22
+certifi==2023.11.17
     # via
     #   -c envs/dev.env.txt
     #   requests
@@ -40,23 +40,23 @@ duet==0.2.9
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-fonttools==4.43.0
+fonttools==4.47.2
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
 h5py==3.10.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-idna==3.4
+idna==3.6
     # via
     #   -c envs/dev.env.txt
     #   requests
 kiwisolver==1.4.5
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
-matplotlib==3.8.1
+matplotlib==3.8.2
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
@@ -73,7 +73,7 @@ networkx==3.2.1
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
     #   cirq-core
-numpy==1.25.2
+numpy==1.26.3
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -89,19 +89,19 @@ packaging==23.2
     #   black
     #   deprecation
     #   matplotlib
-pandas==2.1.2
+pandas==2.1.4
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-pathspec==0.11.2
+pathspec==0.12.1
     # via
     #   -c envs/dev.env.txt
     #   black
-pillow==10.1.0
+pillow==10.2.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
-platformdirs==3.11.0
+platformdirs==4.1.0
     # via
     #   -c envs/dev.env.txt
     #   black
@@ -126,7 +126,7 @@ requests==2.31.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-scipy==1.9.3
+scipy==1.11.4
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -152,15 +152,15 @@ tqdm==4.66.1
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-tzdata==2023.3
+tzdata==2023.4
     # via
     #   -c envs/dev.env.txt
     #   pandas
-urllib3==2.0.7
+urllib3==2.1.0
     # via
     #   -c envs/dev.env.txt
     #   requests

dev_tools/requirements/envs/mypy.env.txt

@@ -4,7 +4,7 @@
 #
 #    pip-compile --constraint=envs/dev.env.txt --output-file=envs/mypy.env.txt deps/mypy.txt deps/runtime.txt
 #
-certifi==2023.7.22
+certifi==2023.11.17
     # via
     #   -c envs/dev.env.txt
     #   requests
@@ -32,23 +32,23 @@ duet==0.2.9
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-fonttools==4.43.0
+fonttools==4.47.2
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
 h5py==3.10.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-idna==3.4
+idna==3.6
     # via
     #   -c envs/dev.env.txt
     #   requests
 kiwisolver==1.4.5
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
-matplotlib==3.8.1
+matplotlib==3.8.2
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
@@ -69,7 +69,7 @@ networkx==3.2.1
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
     #   cirq-core
-numpy==1.25.2
+numpy==1.26.3
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -84,11 +84,11 @@ packaging==23.2
     #   -c envs/dev.env.txt
     #   deprecation
     #   matplotlib
-pandas==2.1.2
+pandas==2.1.4
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-pillow==10.1.0
+pillow==10.2.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
@@ -113,7 +113,7 @@ requests==2.31.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-scipy==1.9.3
+scipy==1.11.4
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -139,16 +139,16 @@ typed-ast==1.4.3
     # via
     #   -c envs/dev.env.txt
     #   mypy
-typing-extensions==4.8.0
+typing-extensions==4.9.0
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
     #   mypy
-tzdata==2023.3
+tzdata==2023.4
     # via
     #   -c envs/dev.env.txt
     #   pandas
-urllib3==2.0.7
+urllib3==2.1.0
     # via
     #   -c envs/dev.env.txt
     #   requests