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Merged
mhucka merged 15 commits into from
Mar 26, 2026
Merged

Fix #481: make tests of Pubchem more robust #1219

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c94825f
Fix #481: add mocking of Pubchem network calls
mhucka Mar 12, 2026
3e44144
Many fixes
mhucka Mar 14, 2026
1b8114b
chore: merge branch
mhucka Mar 14, 2026
5941b88
Merge branch 'main' into mh-revised-fix-481
mhucka Mar 14, 2026
63ddd11
Define pytest marker "integration"
mhucka Mar 14, 2026
89d7c69
Remove unnecessary try-except
mhucka Mar 14, 2026
95558d6
Add pragma no cover for 2 lines
mhucka Mar 14, 2026
707a4d4
Merge branch 'main' into mh-revised-fix-481
mhucka Mar 16, 2026
2afe215
Merge branch 'main' into mh-revised-fix-481
mhucka Mar 26, 2026
e8a796f
Use Python `match` statement instead of many `if`
mhucka Mar 26, 2026
552ab23
Add pytest-retry package to pytest requirements
mhucka Mar 26, 2026
5bafc2e
Remove no-longer-used integration marker
mhucka Mar 26, 2026
b8ccb5f
Remove the pubchem retry code
mhucka Mar 26, 2026
e3ad6e7
Regenerate requirements files
mhucka Mar 26, 2026
dae2e59
Merge branch 'main' into mh-revised-fix-481
mhucka Mar 26, 2026
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1 change: 1 addition & 0 deletions dev_tools/requirements/deps/pytest.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
pytest
pytest-asyncio
pytest-cov
pytest-retry
pytest-xdist

nbformat
23 changes: 13 additions & 10 deletions dev_tools/requirements/envs/dev.env.txt
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Expand Up @@ -4,11 +4,11 @@
#
# pip-compile --output-file=envs/dev.env.txt deps/format.txt deps/mypy.txt deps/pip-tools.txt deps/pylint.txt deps/pytest.txt deps/resource_estimates_runtime.txt deps/runtime.txt
#
ase==3.27.0
ase==3.28.0
# via -r deps/resource_estimates_runtime.txt
astroid==3.3.11
# via pylint
attrs==25.4.0
attrs==26.1.0
# via
# cirq-core
# jsonschema
Expand All @@ -19,11 +19,11 @@ backports-asyncio-runner==1.2.0 ; python_full_version < "3.11"
# pytest-asyncio
black==26.3.1
# via -r deps/format.txt
build==1.4.0
build==1.4.2
# via pip-tools
certifi==2026.2.25
# via requests
charset-normalizer==3.4.5
charset-normalizer==3.4.6
# via requests
cirq-core==1.5.0
# via -r deps/runtime.txt
Expand All @@ -35,7 +35,7 @@ contourpy==1.3.2
# via
# -r deps/runtime.txt
# matplotlib
coverage[toml]==7.13.4
coverage[toml]==7.13.5
# via pytest-cov
cycler==0.12.1
# via matplotlib
Expand All @@ -51,7 +51,7 @@ execnet==2.1.2
# via pytest-xdist
fastjsonschema==2.21.2
# via nbformat
fonttools==4.62.0
fonttools==4.62.1
# via matplotlib
h5py==3.16.0
# via
Expand Down Expand Up @@ -169,10 +169,13 @@ pytest==9.0.2
# -r deps/pytest.txt
# pytest-asyncio
# pytest-cov
# pytest-retry
# pytest-xdist
pytest-asyncio==1.3.0
# via -r deps/pytest.txt
pytest-cov==7.0.0
pytest-cov==7.1.0
# via -r deps/pytest.txt
pytest-retry==1.7.0
# via -r deps/pytest.txt
pytest-xdist==3.8.0
# via -r deps/pytest.txt
Expand Down Expand Up @@ -210,7 +213,7 @@ sympy==1.14.0
# via
# -r deps/runtime.txt
# cirq-core
tomli==2.4.0
tomli==2.4.1
# via
# black
# build
Expand All @@ -227,11 +230,11 @@ traitlets==5.14.3
# via
# jupyter-core
# nbformat
types-networkx==3.6.1.20260303
types-networkx==3.6.1.20260321
# via -r deps/mypy.txt
types-pytz==2026.1.1.20260304
# via pandas-stubs
types-requests==2.32.4.20260107
types-requests==2.32.4.20260324
# via -r deps/mypy.txt
types-setuptools==82.0.0.20260210
# via -r deps/mypy.txt
Expand Down
8 changes: 4 additions & 4 deletions dev_tools/requirements/envs/format.env.txt
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Expand Up @@ -4,7 +4,7 @@
#
# pip-compile --constraint=envs/dev.env.txt --output-file=envs/format.env.txt deps/format.txt deps/runtime.txt
#
attrs==25.4.0
attrs==26.1.0
# via
# -c envs/dev.env.txt
# cirq-core
Expand All @@ -20,7 +20,7 @@ certifi==2026.2.25
# via
# -c envs/dev.env.txt
# requests
charset-normalizer==3.4.5
charset-normalizer==3.4.6
# via
# -c envs/dev.env.txt
# requests
Expand Down Expand Up @@ -49,7 +49,7 @@ duet==0.2.9
# via
# -c envs/dev.env.txt
# cirq-core
fonttools==4.62.0
fonttools==4.62.1
# via
# -c envs/dev.env.txt
# matplotlib
Expand Down Expand Up @@ -157,7 +157,7 @@ sympy==1.14.0
# -c envs/dev.env.txt
# -r deps/runtime.txt
# cirq-core
tomli==2.4.0
tomli==2.4.1
# via
# -c envs/dev.env.txt
# black
Expand Down
12 changes: 6 additions & 6 deletions dev_tools/requirements/envs/mypy.env.txt
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Expand Up @@ -4,7 +4,7 @@
#
# pip-compile --constraint=envs/dev.env.txt --output-file=envs/mypy.env.txt deps/mypy.txt deps/runtime.txt
#
attrs==25.4.0
attrs==26.1.0
# via
# -c envs/dev.env.txt
# cirq-core
Expand All @@ -16,7 +16,7 @@ certifi==2026.2.25
# via
# -c envs/dev.env.txt
# requests
charset-normalizer==3.4.5
charset-normalizer==3.4.6
# via
# -c envs/dev.env.txt
# requests
Expand All @@ -41,7 +41,7 @@ duet==0.2.9
# via
# -c envs/dev.env.txt
# cirq-core
fonttools==4.62.0
fonttools==4.62.1
# via
# -c envs/dev.env.txt
# matplotlib
Expand Down Expand Up @@ -154,23 +154,23 @@ sympy==1.14.0
# -c envs/dev.env.txt
# -r deps/runtime.txt
# cirq-core
tomli==2.4.0
tomli==2.4.1
# via
# -c envs/dev.env.txt
# mypy
tqdm==4.67.3
# via
# -c envs/dev.env.txt
# cirq-core
types-networkx==3.6.1.20260303
types-networkx==3.6.1.20260321
# via
# -c envs/dev.env.txt
# -r deps/mypy.txt
types-pytz==2026.1.1.20260304
# via
# -c envs/dev.env.txt
# pandas-stubs
types-requests==2.32.4.20260107
types-requests==2.32.4.20260324
# via
# -c envs/dev.env.txt
# -r deps/mypy.txt
Expand Down
4 changes: 2 additions & 2 deletions dev_tools/requirements/envs/pip-tools.env.txt
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Expand Up @@ -4,7 +4,7 @@
#
# pip-compile --constraint=envs/dev.env.txt --output-file=envs/pip-tools.env.txt deps/pip-tools.txt
#
build==1.4.0
build==1.4.2
# via
# -c envs/dev.env.txt
# pip-tools
Expand All @@ -26,7 +26,7 @@ pyproject-hooks==1.2.0
# -c envs/dev.env.txt
# build
# pip-tools
tomli==2.4.0
tomli==2.4.1
# via
# -c envs/dev.env.txt
# build
Expand Down
19 changes: 12 additions & 7 deletions dev_tools/requirements/envs/pylint.env.txt
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Expand Up @@ -4,15 +4,15 @@
#
# pip-compile --constraint=envs/dev.env.txt --output-file=envs/pylint.env.txt deps/pylint.txt deps/runtime.txt
#
ase==3.27.0
ase==3.28.0
# via
# -c envs/dev.env.txt
# -r deps/resource_estimates_runtime.txt
astroid==3.3.11
# via
# -c envs/dev.env.txt
# pylint
attrs==25.4.0
attrs==26.1.0
# via
# -c envs/dev.env.txt
# cirq-core
Expand All @@ -27,7 +27,7 @@ certifi==2026.2.25
# via
# -c envs/dev.env.txt
# requests
charset-normalizer==3.4.5
charset-normalizer==3.4.6
# via
# -c envs/dev.env.txt
# requests
Expand All @@ -40,7 +40,7 @@ contourpy==1.3.2
# -c envs/dev.env.txt
# -r deps/runtime.txt
# matplotlib
coverage[toml]==7.13.4
coverage[toml]==7.13.5
# via
# -c envs/dev.env.txt
# pytest-cov
Expand Down Expand Up @@ -72,7 +72,7 @@ fastjsonschema==2.21.2
# via
# -c envs/dev.env.txt
# nbformat
fonttools==4.62.0
fonttools==4.62.1
# via
# -c envs/dev.env.txt
# matplotlib
Expand Down Expand Up @@ -214,12 +214,17 @@ pytest==9.0.2
# -r deps/pytest.txt
# pytest-asyncio
# pytest-cov
# pytest-retry
# pytest-xdist
pytest-asyncio==1.3.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
pytest-cov==7.0.0
pytest-cov==7.1.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
pytest-retry==1.7.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
Expand Down Expand Up @@ -272,7 +277,7 @@ sympy==1.14.0
# -c envs/dev.env.txt
# -r deps/runtime.txt
# cirq-core
tomli==2.4.0
tomli==2.4.1
# via
# -c envs/dev.env.txt
# coverage
Expand Down
19 changes: 12 additions & 7 deletions dev_tools/requirements/envs/pytest-extra.env.txt
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Expand Up @@ -4,11 +4,11 @@
#
# pip-compile --constraint=envs/dev.env.txt --output-file=envs/pytest-extra.env.txt deps/pytest.txt deps/resource_estimates_runtime.txt deps/runtime.txt
#
ase==3.27.0
ase==3.28.0
# via
# -c envs/dev.env.txt
# -r deps/resource_estimates_runtime.txt
attrs==25.4.0
attrs==26.1.0
# via
# -c envs/dev.env.txt
# cirq-core
Expand All @@ -23,7 +23,7 @@ certifi==2026.2.25
# via
# -c envs/dev.env.txt
# requests
charset-normalizer==3.4.5
charset-normalizer==3.4.6
# via
# -c envs/dev.env.txt
# requests
Expand All @@ -36,7 +36,7 @@ contourpy==1.3.2
# -c envs/dev.env.txt
# -r deps/runtime.txt
# matplotlib
coverage[toml]==7.13.4
coverage[toml]==7.13.5
# via
# -c envs/dev.env.txt
# pytest-cov
Expand Down Expand Up @@ -64,7 +64,7 @@ fastjsonschema==2.21.2
# via
# -c envs/dev.env.txt
# nbformat
fonttools==4.62.0
fonttools==4.62.1
# via
# -c envs/dev.env.txt
# matplotlib
Expand Down Expand Up @@ -193,12 +193,17 @@ pytest==9.0.2
# -r deps/pytest.txt
# pytest-asyncio
# pytest-cov
# pytest-retry
# pytest-xdist
pytest-asyncio==1.3.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
pytest-cov==7.0.0
pytest-cov==7.1.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
pytest-retry==1.7.0
# via
# -c envs/dev.env.txt
# -r deps/pytest.txt
Expand Down Expand Up @@ -251,7 +256,7 @@ sympy==1.14.0
# -c envs/dev.env.txt
# -r deps/runtime.txt
# cirq-core
tomli==2.4.0
tomli==2.4.1
# via
# -c envs/dev.env.txt
# coverage
Expand Down
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