feat: replace mypy and pytype with pyrefly for static type analysis

.github/workflows/pythonapp.yml

@@ -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

.github/workflows/weekly-preview.yml

@@ -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

.gitignore

@@ -116,6 +116,7 @@ examples/scd_lvsegs.npz
 temp/
 .idea/
 .dmypy.json
+.ty_cache/
 
 *~
 

CONTRIBUTING.md

@@ -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.

pyproject.toml

@@ -52,6 +52,28 @@ 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]
+unresolved-import = "ignore"
+unused-ignore-comment = "ignore"
+unused-type-ignore-comment = "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"]

requirements-dev.txt

@@ -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
 ninja
 torchio
 torchvision

runtests.sh

@@ -50,7 +50,7 @@ doRuffFix=false
 doClangFormat=false
 doCopyRight=false
 doPytypeFormat=false
-doMypyFormat=false
+doTyFormat=false
 doCleanup=false
 doDistTests=false
 doPrecommit=false
@@ -61,7 +61,7 @@ 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] [--ty]"
     echo "            [--unittests] [--disttests] [--coverage] [--quick] [--min] [--net] [--build] [--list_tests]"
     echo "            [--dryrun] [--copyright] [--clean] [--help] [--version] [--path] [--formatfix]"
     echo ""
@@ -89,7 +89,7 @@ function print_usage {
     echo "Python type check options:"
     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"
@@ -314,8 +314,8 @@ do
         --pytype)
             doPytypeFormat=true
         ;;
-        --mypy)
-            doMypyFormat=true
+        --ty)
+            doTyFormat=true
         ;;
         -j|--jobs)
             NUM_PARALLEL=$2
@@ -654,26 +654,26 @@ then
 fi
 
 
-if [ $doMypyFormat = true ]
+if [ $doTyFormat = true ]
 then
     set +e  # disable exit on failure so that diagnostics can be given on failure
-    echo "${separator}${blue}mypy${noColor}"
+    echo "${separator}${blue}ty${noColor}"
 
     # ensure that the necessary packages for code format testing are installed
-    if ! is_pip_installed mypy
+    if ! is_pip_installed ty
     then
         install_deps
     fi
-    ${cmdPrefix}"${PY_EXE}" -m mypy --version
-    ${cmdPrefix}"${PY_EXE}" -m mypy "$homedir"
+    ${cmdPrefix}"${PY_EXE}" -m ty --version
+    ${cmdPrefix}"${PY_EXE}" -m ty check "$homedir"
 
-    mypy_status=$?
-    if [ ${mypy_status} -ne 0 ]
+    ty_status=$?
+    if [ ${ty_status} -ne 0 ]
     then
-        : # mypy output already follows format
-        exit ${mypy_status}
+        : # ty output already follows format
+        exit ${ty_status}
     else
-        : # mypy output already follows format
+        : # ty output already follows format
     fi
     set -e # enable exit on failure
 fi

setup.cfg

@@ -225,56 +225,6 @@ versionfile_build = monai/_version.py
 tag_prefix =
 parentdir_prefix =
 
-[mypy]
-# Suppresses error messages about imports that cannot be resolved.
-ignore_missing_imports = True
-# Changes the treatment of arguments with a default value of None by not implicitly making their type Optional.
-no_implicit_optional = True
-# Warns about casting an expression to its inferred type.
-warn_redundant_casts = True
-# No error on unneeded # type: ignore comments.
-warn_unused_ignores = False
-# Shows a warning when returning a value with type Any from a function declared with a non-Any return type.
-warn_return_any = True
-# Prohibit equality checks, identity checks, and container checks between non-overlapping types.
-strict_equality = True
-# Shows column numbers in error messages.
-show_column_numbers = True
-# Shows error codes in error messages.
-show_error_codes = True
-# Use visually nicer output in error messages: use soft word wrap, show source code snippets, and show error location markers.
-pretty = False
-# Warns about per-module sections in the config file that do not match any files processed when invoking mypy.
-warn_unused_configs = True
-# Make arguments prepended via Concatenate be truly positional-only.
-extra_checks = True
-# Allows variables to be redefined with an arbitrary type,
-# as long as the redefinition is in the same block and nesting level as the original definition.
-# allow_redefinition = True
-
-exclude = venv/
-
-[mypy-versioneer]
-# Ignores all non-fatal errors.
-ignore_errors = True
-
-[mypy-monai._version]
-# Ignores all non-fatal errors.
-ignore_errors = True
-
-[mypy-monai.eggs]
-# Ignores all non-fatal errors.
-ignore_errors = True
-
-[mypy-monai.*]
-# Also check the body of functions with no types in their type signature.
-check_untyped_defs = True
-# Warns about usage of untyped decorators.
-disallow_untyped_decorators = True
-
-[mypy-monai.visualize.*,monai.utils.*,monai.optimizers.*,monai.losses.*,monai.inferers.*,monai.config.*,monai._extensions.*,monai.fl.*,monai.engines.*,monai.handlers.*,monai.auto3dseg.*,monai.bundle.*,monai.metrics.*,monai.apps.*]
-disallow_incomplete_defs = True
-
 [coverage:run]
 concurrency = multiprocessing
 source = .