Update some requirements to their latest versions (#1309)

This replaces the recent Dependabot PRs

* #1305
* #1303
* #1302

with a single PR that also updates all the transitive dependencies by
running the re-pip-compile script.

Author: mhucka

dev_tools/requirements/deps/runtime.txt

@@ -4,7 +4,7 @@ h5py>=3.10.0
 networkx
 numpy>=1.26
 pubchempy
-requests~=2.33.1
+requests~=2.34.0
 
 scipy~=1.15
 

dev_tools/requirements/envs/dev.env.txt

@@ -6,6 +6,8 @@
 #
 ase==3.28.0
     # via -r deps/resource_estimates_runtime.txt
+ast-serialize==0.5.0
+    # via mypy
 astroid==3.3.11
     # via pylint
 attrs==26.1.0
@@ -17,25 +19,25 @@ backports-asyncio-runner==1.2.0 ; python_full_version < "3.11"
     # via
     #   -r deps/runtime.txt
     #   pytest-asyncio
-black==26.3.1
+black==26.5.1
     # via -r deps/format.txt
-build==1.4.4
+build==1.5.0
     # via pip-tools
-certifi==2026.4.22
+certifi==2026.5.20
     # via requests
 charset-normalizer==3.4.7
     # via requests
 cirq-core==1.5.0
     # via -r deps/runtime.txt
-click==8.3.3
+click==8.4.1
     # via
     #   black
     #   pip-tools
 contourpy==1.3.2
     # via
     #   -r deps/runtime.txt
     #   matplotlib
-coverage[toml]==7.13.5
+coverage[toml]==7.14.1
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
@@ -51,13 +53,13 @@ execnet==2.1.2
     # via pytest-xdist
 fastjsonschema==2.21.2
     # via nbformat
-fonttools==4.62.1
+fonttools==4.63.0
     # via matplotlib
 h5py==3.16.0
     # via
     #   -r deps/runtime.txt
     #   pyscf
-idna==3.13
+idna==3.17
     # via requests
 iniconfig==2.3.0
     # via pytest
@@ -77,7 +79,7 @@ jupyter-core==5.9.1
     # via nbformat
 kiwisolver==1.5.0
     # via matplotlib
-librt==0.9.0
+librt==0.11.0
     # via mypy
 matplotlib==3.10.9
     # via
@@ -91,7 +93,7 @@ ml-dtypes==0.5.4
     #   jaxlib
 mpmath==1.3.0
     # via sympy
-mypy==1.20.2
+mypy==2.1.0
     # via -r deps/mypy.txt
 mypy-extensions==1.1.0
     # via
@@ -141,7 +143,7 @@ pillow==12.2.0
     # via matplotlib
 pip-tools==7.5.3
     # via -r deps/pip-tools.txt
-platformdirs==4.9.6
+platformdirs==4.10.0
     # via
     #   black
     #   jupyter-core
@@ -172,7 +174,7 @@ pytest==9.0.3
     #   pytest-randomly
     #   pytest-retry
     #   pytest-xdist
-pytest-asyncio==1.3.0
+pytest-asyncio==1.4.0
     # via -r deps/pytest.txt
 pytest-cov==7.1.0
     # via -r deps/pytest.txt
@@ -188,13 +190,13 @@ python-dateutil==2.9.0.post0
     #   pandas
 pytokens==0.4.1
     # via black
-pytz==2026.1.post1
+pytz==2026.2
     # via pandas
 referencing==0.37.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.33.1
+requests==2.34.2
     # via -r deps/runtime.txt
 rpds-py==0.30.0
     # via
@@ -225,21 +227,21 @@ tomli==2.4.1
     #   pip-tools
     #   pylint
     #   pytest
-tomlkit==0.14.0
+tomlkit==0.15.0
     # via pylint
 tqdm==4.67.3
     # via cirq-core
-traitlets==5.14.3
+traitlets==5.15.0
     # via
     #   jupyter-core
     #   nbformat
-types-networkx==3.6.1.20260408
+types-networkx==3.6.1.20260518
     # via -r deps/mypy.txt
-types-pytz==2026.1.1.20260408
+types-pytz==2026.2.0.20260518
     # via pandas-stubs
-types-requests==2.33.0.20260408
+types-requests==2.33.0.20260518
     # via -r deps/mypy.txt
-types-setuptools==82.0.0.20260408
+types-setuptools==82.0.0.20260518
     # via -r deps/mypy.txt
 typing-extensions==4.15.0
     # via
@@ -252,7 +254,7 @@ typing-extensions==4.15.0
     #   referencing
 tzdata==2026.2
     # via pandas
-urllib3==2.6.3
+urllib3==2.7.0
     # via
     #   requests
     #   types-requests

dev_tools/requirements/envs/format.env.txt

@@ -12,11 +12,11 @@ backports-asyncio-runner==1.2.0 ; python_full_version < "3.11"
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-black==26.3.1
+black==26.5.1
     # via
     #   -c envs/dev.env.txt
     #   -r deps/format.txt
-certifi==2026.4.22
+certifi==2026.5.20
     # via
     #   -c envs/dev.env.txt
     #   requests
@@ -28,7 +28,7 @@ cirq-core==1.5.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-click==8.3.3
+click==8.4.1
     # via
     #   -c envs/dev.env.txt
     #   black
@@ -49,15 +49,15 @@ duet==0.2.9
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-fonttools==4.62.1
+fonttools==4.63.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
 h5py==3.16.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-idna==3.13
+idna==3.17
     # via
     #   -c envs/dev.env.txt
     #   requests
@@ -110,7 +110,7 @@ pillow==12.2.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
-platformdirs==4.9.6
+platformdirs==4.10.0
     # via
     #   -c envs/dev.env.txt
     #   black
@@ -131,11 +131,11 @@ pytokens==0.4.1
     # via
     #   -c envs/dev.env.txt
     #   black
-pytz==2026.1.post1
+pytz==2026.2
     # via
     #   -c envs/dev.env.txt
     #   pandas
-requests==2.33.1
+requests==2.34.2
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -174,7 +174,7 @@ tzdata==2026.2
     # via
     #   -c envs/dev.env.txt
     #   pandas
-urllib3==2.6.3
+urllib3==2.7.0
     # via
     #   -c envs/dev.env.txt
     #   requests

dev_tools/requirements/envs/mypy.env.txt

@@ -4,6 +4,10 @@
 #
 #    pip-compile --constraint=envs/dev.env.txt --output-file=envs/mypy.env.txt deps/mypy.txt deps/runtime.txt
 #
+ast-serialize==0.5.0
+    # via
+    #   -c envs/dev.env.txt
+    #   mypy
 attrs==26.1.0
     # via
     #   -c envs/dev.env.txt
@@ -12,7 +16,7 @@ backports-asyncio-runner==1.2.0 ; python_full_version < "3.11"
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-certifi==2026.4.22
+certifi==2026.5.20
     # via
     #   -c envs/dev.env.txt
     #   requests
@@ -41,23 +45,23 @@ duet==0.2.9
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-fonttools==4.62.1
+fonttools==4.63.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
 h5py==3.16.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
-idna==3.13
+idna==3.17
     # via
     #   -c envs/dev.env.txt
     #   requests
 kiwisolver==1.5.0
     # via
     #   -c envs/dev.env.txt
     #   matplotlib
-librt==0.9.0
+librt==0.11.0
     # via
     #   -c envs/dev.env.txt
     #   mypy
@@ -69,7 +73,7 @@ mpmath==1.3.0
     # via
     #   -c envs/dev.env.txt
     #   sympy
-mypy==1.20.2
+mypy==2.1.0
     # via
     #   -c envs/dev.env.txt
     #   -r deps/mypy.txt
@@ -128,11 +132,11 @@ python-dateutil==2.9.0.post0
     #   -c envs/dev.env.txt
     #   matplotlib
     #   pandas
-pytz==2026.1.post1
+pytz==2026.2
     # via
     #   -c envs/dev.env.txt
     #   pandas
-requests==2.33.1
+requests==2.34.2
     # via
     #   -c envs/dev.env.txt
     #   -r deps/runtime.txt
@@ -162,19 +166,19 @@ tqdm==4.67.3
     # via
     #   -c envs/dev.env.txt
     #   cirq-core
-types-networkx==3.6.1.20260408
+types-networkx==3.6.1.20260518
     # via
     #   -c envs/dev.env.txt
     #   -r deps/mypy.txt
-types-pytz==2026.1.1.20260408
+types-pytz==2026.2.0.20260518
     # via
     #   -c envs/dev.env.txt
     #   pandas-stubs
-types-requests==2.33.0.20260408
+types-requests==2.33.0.20260518
     # via
     #   -c envs/dev.env.txt
     #   -r deps/mypy.txt
-types-setuptools==82.0.0.20260408
+types-setuptools==82.0.0.20260518
     # via
     #   -c envs/dev.env.txt
     #   -r deps/mypy.txt
@@ -187,7 +191,7 @@ tzdata==2026.2
     # via
     #   -c envs/dev.env.txt
     #   pandas
-urllib3==2.6.3
+urllib3==2.7.0
     # via
     #   -c envs/dev.env.txt
     #   requests

dev_tools/requirements/envs/pip-tools.env.txt

@@ -4,11 +4,11 @@
 #
 #    pip-compile --constraint=envs/dev.env.txt --output-file=envs/pip-tools.env.txt deps/pip-tools.txt
 #
-build==1.4.4
+build==1.5.0
     # via
     #   -c envs/dev.env.txt
     #   pip-tools
-click==8.3.3
+click==8.4.1
     # via
     #   -c envs/dev.env.txt
     #   pip-tools