Feature/issue 1399 switch to pyrefly by rosspeili · Pull Request #1433 · quantumlib/OpenFermion

rosspeili · 2026-07-25T12:26:18Z

This switches mypy to pyrefly, matching the Cirq 8182 direction.

Migrated the old [tool.mypy] settings with pyrefly init, then tightened the config so we check src/, skip notebooks/docs, and ignore heavy third-party imports the way CI effectively was doing with mypy. The first pass flagged a lot of Cirq/sympy noise and missing optional deps, but local mypy was noisy too without the full CI env, so aimed at the same practical bar as CI rather than matching a bare local mypy run.

After, some annotation issues were left (Optional defaults, bool returns, Expr typing), which are fixed in a few source files, and a couple of Cirq/sympy-only error kinds stay disabled in config for now so the migration stays green without a large Cirq typing follow-up.

Wiring: added check/typecheck, kept check/mypy as a deprecated wrapper, updated check/all, CI, deps/env files, pre-commit, and CONTRIBUTING.

Test plan

pyrefly check → 0 errors locally
Black clean on touched Python files
CI green on this PR

Fixes #1399

google-cla · 2026-07-25T12:26:29Z

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gemini-code-assist

Code Review

This pull request migrates the project's type-checking tool from mypy to Pyrefly, updating configuration files, dependencies, CI workflows, and documentation accordingly. It also resolves several type annotation issues across the codebase. Feedback on the changes highlights that the use of the | union operator in src/openfermion/chem/pubchem.py requires from __future__ import annotations to prevent runtime errors on Python versions older than 3.10. Additionally, it is recommended to use a trap in the new check/typecheck script to guarantee that terminal colors are reset even if the execution is interrupted.

gemini-code-assist · 2026-07-25T12:28:09Z

 #   limitations under the License.


-def geometry_from_pubchem(name: str, structure: str = None):
+def geometry_from_pubchem(name: str, structure: str | None = None):


The use of the PEP 604 union operator | (e.g., str | None) in type annotations is only supported at runtime in Python 3.10 or newer. If this codebase supports Python 3.9 or older, this will raise a TypeError at import time unless from __future__ import annotations is imported at the top of the file. To prevent runtime errors on older Python versions, please add from __future__ import annotations at the beginning of the file.

# limitations under the License. from __future__ import annotations def geometry_from_pubchem(name: str, structure: str | None = None):

OpenFermion requires Python 3.10+, so str | None is fine here, will leave for now as-is, unless otherwise advised @mhucka

Replace mypy with Pyrefly via check/typecheck, migrate config, fix a few annotations, and update CI, deps, and docs. Keep check/mypy as a deprecated wrapper.

Use EXIT trap so Ctrl+C does not leave the shell stuck in red after pyrefly.

This PR is only the Pyrefly migration; the workflow is not included here.

python-checks installs pylint.env.txt which includes pyscf; Pyrefly then rejects scf.HF-style annotations as not-a-type. replace-imports-with-any keeps typecheck stable whether or not pyscf is installed.

rosspeili · 2026-07-25T12:54:37Z

Treating pyscf as Any via replace-imports-with-any, hoping CI typecheck no longer fails on scf.HF-style annotations when pyscf is installed via pylint.env.txt.

arettig

Thanks for doing this! I was able to run pyrefly and it seemed quicker than mypy!

I went ahead and did a partial review. It is worth waiting for @mhucka to take a look at this too though, as he's the expert here.

Some comments and questions below. Mostly I am worried we will have lowered coverage due to the 3 globally disabled settings.

arettig · 2026-07-29T22:16:42Z

-          echo '::add-matcher::.github/problem-matchers/mypy.json'
-          check/mypy
+          echo '::add-matcher::.github/problem-matchers/typecheck.json'
+          check/typecheck --output-format github


I suspect we don't need the matcher here since pyrefly has a --output-format github flag. If so, you could delete the typecheck.json.

arettig · 2026-07-29T22:26:24Z

-echo -e -n "\033[0m"
-
-exit ${result}
+exec check/typecheck "$@"


@mhucka Do we want to fully remove mypy support immediately? We could alternatively leave it in for now and just print the deprecation warning if anyone runs it. This would make it easy to run both and ensure that pyrefly isn't lowering our coverage for now.

arettig · 2026-07-29T23:59:13Z

    --hash=sha256:fbccdc05410c9ee21bbf16a35f4c1d16123dcdeb8a1d38f33654fa21d0234f79 \
    --hash=sha256:fea24543955a6a729c45a73fe90e08c743f0b3334bbf3201e6c4bc1b0c7fa464
    # via requests
-cirq-core==1.5.0 ; python_full_version < '3.11' \


It looks like support for python 3.10 was removed, you probably need to rerun the ./dev_tools/requirements/create-env-files.sh script with the older python version to fix.

arettig · 2026-07-30T01:17:42Z

+unsupported-operation = false
+invalid-inheritance = false
+bad-override = false


I'm assuming these are turned off as pyrefly is more strict than mypy and we get a bunch of errors? Disabling them seems like it will result in less coverage than mypy.

arettig · 2026-07-30T01:46:35Z

+    "cirq",
+    "cirq.*",
    "h5py",
+    "jax",
+    "jax.*",
    "numpy.*",
+    "pandas",
+    "pandas.*",
    "pubchempy",
    "pybtas",
+    "pyscf",
    "pyscf.*",
    "pytest.*",
    "scipy.*",
+    "sympy",
+    "sympy.*",
    "tensorflow_docs",
+    "tensorflow_docs.*",


Why are all of these modules added? A lot of these are mandatory dependencies so I assume they are never missing.

arettig · 2026-07-30T15:13:19Z

-pandas-stubs
-types-requests
-types-setuptools
-types-networkx


I get a warning about missing networkx types. You probably need to add types-networkx back in to typecheck.txt.

gemini-code-assist Bot reviewed Jul 25, 2026

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Switch type checking from mypy to Pyrefly (quantumlib#1399)

788ba63

Replace mypy with Pyrefly via check/typecheck, migrate config, fix a few annotations, and update CI, deps, and docs. Keep check/mypy as a deprecated wrapper.

rosspeili force-pushed the feature/issue-1399-switch-to-pyrefly branch from b641ff4 to 788ba63 Compare July 25, 2026 12:31

rosspeili added 3 commits July 25, 2026 15:34

Reset terminal color in check/typecheck on interrupt

6d4ef5a

Use EXIT trap so Ctrl+C does not leave the shell stuck in red after pyrefly.

Drop regenerate-env-files docs leftover from unrelated work

2a2ce76

This PR is only the Pyrefly migration; the workflow is not included here.

Treat pyscf imports as Any for Pyrefly CI

688bdd0

python-checks installs pylint.env.txt which includes pyscf; Pyrefly then rejects scf.HF-style annotations as not-a-type. replace-imports-with-any keeps typecheck stable whether or not pyscf is installed.

This was referenced Jul 25, 2026

Switch to Pyrefly for type checking instead of mypy #1399

Open

Switch type checking from mypy to Pyrefly (#8182) quantumlib/Cirq#8227

Open

arettig self-assigned this Jul 29, 2026

arettig requested changes Jul 30, 2026

View reviewed changes

arettig removed their assignment Jul 30, 2026

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Feature/issue 1399 switch to pyrefly - #1433

Feature/issue 1399 switch to pyrefly#1433
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rosspeili commented Jul 25, 2026 •

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