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feat: replace mypy with ty for static type analysis #8868

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ba56a6d
Move test_image_filter.py
garciadias Feb 5, 2025
5216b7a
Merge remote-tracking branch 'origin/dev' into dev
garciadias Feb 12, 2025
eacd783
Merge remote-tracking branch 'origin/dev' into dev
garciadias Feb 14, 2025
c64825f
Merge remote-tracking branch 'upstream/dev' into dev
garciadias Feb 19, 2025
66b6c17
Merge remote-tracking branch 'origin/dev' into dev
garciadias Feb 27, 2025
19cab57
Merge remote-tracking branch 'upstream/dev' into dev
garciadias Apr 11, 2025
4b8086b
feat: replace mypy with ty for static type analysis
garciadias May 22, 2026
763b7ff
fix: restore mypy config and tune ty to match zero-error baseline
garciadias May 22, 2026
ae31bb2
chore: pin ty dev dependency to ty>=0.0.38
garciadias May 22, 2026
42ec9b2
fix: restore --mypy flag alongside --ty in runtests.sh
garciadias May 22, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/pythonapp.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
opt: ["codeformat", "pytype", "mypy"]
opt: ["codeformat", "pytype", "ty"]
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.9
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2 changes: 1 addition & 1 deletion .github/workflows/weekly-preview.yml
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Expand Up @@ -9,7 +9,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
opt: ["codeformat", "pytype", "mypy"]
opt: ["codeformat", "pytype", "ty"]
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.9
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -116,6 +116,7 @@ examples/scd_lvsegs.npz
temp/
.idea/
.dmypy.json
.ty_cache/

*~

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2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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Expand Up @@ -38,7 +38,7 @@ Please note that, as per PyTorch, MONAI uses American English spelling. This mea

### Preparing pull requests
To ensure the code quality, MONAI relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort), [ruff](https://github.com/astral-sh/ruff)),
static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.
static type analysis tools ([ty](https://docs.astral.sh/ty/), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration tests.

This section highlights all the necessary preparation steps required before sending a pull request.
To collaborate efficiently, please read through this section and follow them.
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51 changes: 51 additions & 0 deletions pyproject.toml
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Expand Up @@ -52,6 +52,57 @@ extend-ignore = [
"NPY002", # numpy-legacy-random
]

[tool.ty]
[tool.ty.environment]
python-version = "3.9"

[tool.ty.src]
exclude = [
"**/venv/**",
"**/.venv/**",
"versioneer.py",
"monai/_version.py",
]

[tool.ty.rules]
# Only rules explicitly listed here; all unlisted rules are ignored.
# This provides a stable baseline matching mypy's output (zero diagnostics on monai/).
# Rules can be re-enabled incrementally as the codebase is improved.
Comment on lines +68 to +70
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@coderabbitai coderabbitai Bot May 22, 2026

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⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

🧩 Analysis chain

🌐 Web query:

What is the default behavior of ty type checker for unlisted rules in tool.ty.rules configuration?

💡 Result:

Default behavior: if you configure [tool.ty.rules] without setting a particular rule, ty does not automatically invent a severity for it; instead, each rule uses ty’s built-in default level (per-rule default). The only “fallback” supported by the global config is setting all (e.g. all = "error") to apply the same severity to every rule that doesn’t have an explicit entry in tool.ty.rules. [1][2] What this means for “unlisted rules”: - Unlisted rule name in [tool.ty.rules] ⇒ it keeps its per-rule default level (not ignore/warn/error from the config), unless you set all in the same config. [1][2] - Unrecognized rule names in the config are treated separately from rule severity defaults (ty has a rule ignore-comment-unknown-rule that warns when a # ty: ignore[...] references an unknown rule). [3] Evidence examples from docs: - tool.ty.rules keys are either a specific rule name or all to set a default severity for all rules. [1][2] - Rule levels are error, warn, ignore, and all = "error" is documented as equivalent to ty check --error all. [2]

Citations:

🏁 Script executed:

#!/bin/bash
# Verify ty configuration syntax and default behavior
ty --help 2>&1 | head -20

Repository: Project-MONAI/MONAI

Length of output: 104

🏁 Script executed:

#!/bin/bash
# Inspect tool.ty.rules config around the referenced lines
sed -n '1,120p' pyproject.toml | nl -ba | sed -n '1,120p'
rg -n "^\[tool\.ty\.rules\]" -n pyproject.toml || true
rg -n "tool\.ty\.rules|^\s*all\s*=" pyproject.toml || true
# Print the full rules block (up to the next [section])
awk '
  BEGIN{inblock=0}
  /^\[tool\.ty\.rules\]/{inblock=1; print; next}
  inblock && /^\[/{inblock=0}
  inblock{print}
' pyproject.toml | nl -ba

Repository: Project-MONAI/MONAI

Length of output: 237

🏁 Script executed:

#!/bin/bash
set -euo pipefail
# Show the relevant ty config area with line numbers via `cat -n` (nl isn't available)
sed -n '55,115p' pyproject.toml | cat -n
# Extract just the tool.ty.rules block
awk '
  /^\[tool\.ty\.rules\]/{inblock=1}
  inblock{print}
  inblock && /^\[/{ if($0 !~ /^\[tool\.ty\.rules\]/){exit} }
' pyproject.toml | cat -n
# List rule keys under tool.ty.rules (excluding the header line)
awk '
  $0 ~ /^\[tool\.ty\.rules\]/{inblock=1; next}
  inblock{
    if($0 ~ /^\[/{exit}
    if($0 ~ /^[[:space:]]*`#/` || $0 ~ /^[[:space:]]*$/) next
    if($0 ~ /=/) print
  }
' pyproject.toml | rg -n "^[0-9]+:.*=" || true

Repository: Project-MONAI/MONAI

Length of output: 3829

🌐 Web query:

ty configuration [tool.ty.rules] unlisted rules ignored all fallback per-rule default wording

💡 Result:

In ty, per-rule configuration works by merging configured rule severities from global rules ([tool.ty.rules] / [rules]) and then applying overrides; later overrides take precedence, and override rules “will be merged with the global rules” ([1], [2]). There’s no statement in the official configuration docs that “unlisted rules are ignored” or that fallback “per-rule default wording” is skipped when [tool.ty.rules] contains an incomplete set; instead, the documented model is that you can specify only the rules you care about, and the rest follow their normal configured defaults unless you disable them globally (for example via all = “ignore”) or enable/disable via CLI flags like --warn/--error/--ignore [1]. Your quoted behavior is more likely to be explained by how ty treats “type: ignore” codes vs “ty: ignore” codes, which can appear as “unlisted rules ignored” in practice. ty’s configuration includes respect-type-ignore-comments (default true): when false, ty treats type: ignore as a normal comment and “can’t be used to suppress ty errors” (you must use ty: ignore instead) [1]. Separately, ty has a rule ignore-comment-unknown-rule that warns when you use ty: ignore[code] or type: ignore[ty:code] with a code that isn’t a known lint rule, i.e., unrecognized codes in ignore comments won’t suppress anything and are likely a mistake [3]. So, based on the current official docs: (1) [tool.ty.rules] doesn’t imply that unlisted rules are ignored; it only sets severities for the rules you name, while other rules use their normal defaults unless you change them globally; and (2) apparent “ignoring fallback/default wording” is commonly due to suppression behavior (especially around type: ignore vs ty: ignore, and unknown ignore codes) rather than a bug in configuration merging [1][3].

Citations:

Fix misleading tool.ty.rules comment about “unlisted rules are ignored” in pyproject.toml
The comment at lines 68-70 is inaccurate: [tool.ty.rules] only sets severities for the named rules, while rules not listed there follow their normal defaults; all = "ignore" exists only under [tool.ty.overrides.rules] (for versioneer.py / monai/_version.py), not for the whole project.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@pyproject.toml` around lines 68 - 70, Update the misleading comment about
tool.ty.rules in pyproject.toml: change the wording to state that
[tool.ty.rules] only sets severities for the listed rules and that unlisted
rules keep their normal defaults, and note that the "all = \"ignore\"" behavior
applies only under [tool.ty.overrides.rules] (used for versioneer.py /
monai/_version.py), so replace the current inaccurate lines with a concise
comment reflecting these facts and referencing [tool.ty.rules] and
[tool.ty.overrides.rules].

unresolved-import = "ignore"
unused-ignore-comment = "ignore"
unused-type-ignore-comment = "ignore"
unresolved-attribute = "ignore"
unresolved-reference = "ignore"
invalid-method-override = "ignore"
invalid-argument-type = "ignore"
invalid-assignment = "ignore"
invalid-return-type = "ignore"
invalid-type-form = "ignore"
invalid-declaration = "ignore"
invalid-yield = "ignore"
call-non-callable = "ignore"
call-top-callable = "ignore"
index-out-of-bounds = "ignore"
missing-argument = "ignore"
no-matching-overload = "ignore"
not-iterable = "ignore"
not-subscriptable = "ignore"
parameter-already-assigned = "ignore"
unsupported-operator = "ignore"
deprecated = "ignore"
division-by-zero = "ignore"
invalid-enum-member-annotation = "ignore"
possibly-missing-attribute = "ignore"
possibly-missing-submodule = "ignore"
possibly-unresolved-reference = "ignore"
unknown-argument = "ignore"
too-many-positional-arguments = "ignore"

[[tool.ty.overrides]]
include = ["versioneer.py", "monai/_version.py"]
[tool.ty.overrides.rules]
all = "ignore"

[tool.pytype]
# Space-separated list of files or directories to exclude.
exclude = ["versioneer.py", "_version.py"]
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2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -22,7 +22,7 @@ isort>=5.1, <6.0
ruff
pytype>=2020.6.1; platform_system != "Windows"
types-setuptools
mypy>=1.5.0, <1.12.0
ty>=0.0.38
ninja
torchio
torchvision
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32 changes: 31 additions & 1 deletion runtests.sh
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Expand Up @@ -51,6 +51,7 @@ doClangFormat=false
doCopyRight=false
doPytypeFormat=false
doMypyFormat=false
doTyFormat=false
doCleanup=false
doDistTests=false
doPrecommit=false
Expand All @@ -61,7 +62,7 @@ PY_EXE=${MONAI_PY_EXE:-$(which python)}

function print_usage {
echo "runtests.sh [--codeformat] [--autofix] [--black] [--isort] [--flake8] [--pylint] [--ruff]"
echo " [--clangformat] [--precommit] [--pytype] [-j number] [--mypy]"
echo " [--clangformat] [--precommit] [--pytype] [-j number] [--mypy] [--ty]"
echo " [--unittests] [--disttests] [--coverage] [--quick] [--min] [--net] [--build] [--list_tests]"
echo " [--dryrun] [--copyright] [--clean] [--help] [--version] [--path] [--formatfix]"
echo ""
Expand Down Expand Up @@ -90,6 +91,7 @@ function print_usage {
echo " --pytype : perform \"pytype\" static type checks"
echo " -j, --jobs : number of parallel jobs to run \"pytype\" (default $NUM_PARALLEL)"
echo " --mypy : perform \"mypy\" static type checks"
echo " --ty : perform \"ty\" static type checks"
echo ""
echo "MONAI unit testing options:"
echo " -u, --unittests : perform unit testing"
Expand Down Expand Up @@ -317,6 +319,9 @@ do
--mypy)
doMypyFormat=true
;;
--ty)
doTyFormat=true
;;
-j|--jobs)
NUM_PARALLEL=$2
shift
Expand Down Expand Up @@ -679,6 +684,31 @@ then
fi


if [ $doTyFormat = true ]
then
set +e # disable exit on failure so that diagnostics can be given on failure
echo "${separator}${blue}ty${noColor}"

# ensure that the necessary packages for code format testing are installed
if ! is_pip_installed ty
then
install_deps
fi
${cmdPrefix}"${PY_EXE}" -m ty --version
${cmdPrefix}"${PY_EXE}" -m ty check "$homedir"

ty_status=$?
if [ ${ty_status} -ne 0 ]
then
: # ty output already follows format
exit ${ty_status}
else
: # ty output already follows format
fi
set -e # enable exit on failure
fi


# testing command to run
cmd="${PY_EXE}"

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