Merge branch 'main' into docs-masked-array

Author: mkcor

.coderabbit.yaml

@@ -0,0 +1,52 @@
+reviews:
+  profile: "chill" # "assertive" — more nitpicky
+  review_status: false
+  review_details: false
+  high_level_summary: false
+  request_changes_workflow: false
+  estimate_code_review_effort: true
+  labeling_instructions:
+    - label: ":scroll: type: API"
+      instructions: >-
+        For backward-incompatible changes to the API and deprecations. Mutually exclusive.
+    - label: ":baby: type: New feature"
+      instructions: >-
+        For new features that previously did not exist. Mutually exclusive.
+    - label: ":wrench: type: Maintenance"
+      instructions: >-
+        For internal code changes and cleanups. Mutually exclusive.
+    - label: ":adhesive_bandage: type: Bug fix"
+      instructions: >-
+        For bug fixes. Mutually exclusive.
+    - label: ":page_facing_up: type: Documentation"
+      instructions: >-
+        For changes dedicated to documentation (i.e., not as part of a new feature). Mutually exclusive.
+    - label: ":robot: type: Infrastructure"
+      instructions: >-
+        Fixes to CI and other infrastructure. Mutually exclusive.
+    - label: ":fast_forward: type: Enhancement"
+      instructions: >-
+        Improvements made to an existing feature. Mutually exclusive.
+    - label: ":chart_with_upwards_trend: type: Performance"
+      instructions: >-
+        For changes intended to improve performance. Mutually exclusive.
+  auto_apply_labels: true
+  in_progress_fortune: false
+  poem: false
+  enable_prompt_for_ai_agents: false
+  auto_review:
+    base_branches:
+      - main
+  pre_merge_checks:
+    title:
+      requirements: >-
+        Title should be concise and descriptive, ideally under 80 characters, and not end on `.`
+
+chat:
+  auto_reply: false
+
+knowledge_base:
+  code_guidelines:
+    filePatterns:
+      - CONTRIBUTING.rst
+      - doc/source/development/core_developer.md

.github/workflows/typing.yml

@@ -37,31 +37,44 @@ jobs:
           cache: "pip"
           cache-dependency-path: "requirements/*.txt"
 
-      - name: Install build dependencies
-        env:
-          PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
-        run: |
-          source .github/scripts/setup-build-env.sh
-
-      - name: Build and install from source
-        run: |
-          pip install -v --no-build-isolation .
-
       - name: Install docstub
         run: |
-          pip install docstub==0.3.0.post0
+          pip install docstub~=0.7.0rc0
           docstub --version
 
-      - name: Create stubs with docstub
+      - name: Create skimage-stubs with docstub
+        shell: bash
+        run: |
+          echo -e "## docstub output\n\`\`\`" >> $GITHUB_STEP_SUMMARY
+          (set -o pipefail && \
+           docstub run --verbose --group-errors --allow-errors=622 \
+                       --workers -1 --out-dir ${MYPYPATH}/skimage src/skimage/ \
+           2>&1 | tee -a $GITHUB_STEP_SUMMARY)
+           echo -e "\`\`\`" >> $GITHUB_STEP_SUMMARY
+
+      - name: Create skimage2-stubs with docstub
         shell: bash
         run: |
           echo -e "## docstub output\n\`\`\`" >> $GITHUB_STEP_SUMMARY
           (set -o pipefail && \
-           docstub run --verbose --group-errors --allow-errors=626 \
-                       --out-dir ${MYPYPATH}/skimage src/skimage/ \
+           docstub run --verbose --group-errors \
+                       --out-dir ${MYPYPATH}/skimage2 src/skimage2/ \
            2>&1 | tee -a $GITHUB_STEP_SUMMARY)
            echo -e "\`\`\`" >> $GITHUB_STEP_SUMMARY
 
+      # Not needed yet, since we don't run mypy.stubtest or similar
+      # which would require importing scikit-image.
+      #
+      #      - name: Install build dependencies
+      #        env:
+      #          PIP_FLAGS: ${{ matrix.PIP_FLAGS }}
+      #        run: |
+      #          source .github/scripts/setup-build-env.sh
+      #
+      #      - name: Build and install from source
+      #        run: |
+      #          pip install -v --no-build-isolation .
+
       - uses: actions/upload-artifact@v4
         with:
           name: skimage-stubs

TODO.txt

@@ -15,8 +15,6 @@ Version 0.28
 
 Version 0.27
 ------------
-* Remove deprecated `skimage.io.imshow`,
-  `skimage.io.imshow_collection`, `skimage.io.show`. Remove related plugins.
 * Complete deprecation of plugin infrastructure by doing the following:
   - Replace calls to `call_plugin` with functions from the imageio plugin
   - Remove `skimage/io/_plugins`

environment.yml

@@ -24,7 +24,7 @@ dependencies:
   # developer
   - pre-commit
   - ipython
-  - docstub==0.3.0.post0
+  - docstub==0.7.0rc0
   # asv
   - asv
   # docs

pyproject.toml

@@ -59,7 +59,7 @@ data = ['pooch>=1.6.0']
 developer = [
     'pre-commit',
     'ipython',
-    'docstub==0.3.0.post0',
+    'docstub==0.7.0rc0',
     'scikit-image[asv]',
 ]
 asv = [
@@ -196,14 +196,15 @@ xfail_strict = true
 testpaths = ["tests"]
 filterwarnings = [
     "error",
+    "ignore:Importing from the `skimage2` namespace is experimental:UserWarning",
     "ignore:.*use `imageio` or other I/O packages directly.*:FutureWarning",
     # warn by pyamg in ruge_stuben_solver
     "ignore:Implicit conversion of A to CSR:scipy.sparse.SparseEfficiencyWarning",
     # Pyodide warning coming via threadpoolctl, remove when
     # https://github.com/joblib/threadpoolctl/pull/201 is released
     "ignore:.*JsProxy\\.as_object_map.*:RuntimeWarning",
     # Warning caused by matplotlib 3.7.0 because it uses deprecated API of pyparsing 3.3.1
-    "ignore:.*(parseString|resetCache).*:DeprecationWarning:matplotlib",
+    "ignore:.*(parseString|resetCache|enablePackrat).*:DeprecationWarning:matplotlib",
 ]
 norecursedirs = ["io/_plugins"]
 
@@ -214,9 +215,24 @@ ignored_user_logins = [
 ]
 
 
+[tool.docstub]
+ignore_files = [
+    # deprecated, to be removed before v0.27
+    "io/_plugins",
+    "io/manage_plugins.py",
+]
+
 [tool.docstub.type_prefixes]
+warnings = "warnings"
 matplotlib = "matplotlib"
 scipy = "scipy"
+dask = "dask"
+
+[tool.docstub.type_nicknames]
+dtype-like = "np.typing.DTypeLike"
+
+[tool.docstub.types]
+Path = "pathlib.Path"
 
 [tool.cibuildwheel]
 test-command = "pytest --doctest-plus --pyargs skimage ./tests"

requirements/developer.txt

@@ -2,5 +2,5 @@
 # Do not edit this file; modify pyproject.toml instead.
 pre-commit
 ipython
-docstub==0.3.0.post0
+docstub==0.7.0rc0
 asv; sys_platform != "emscripten"

src/skimage/_shared/_warnings.py

@@ -77,7 +77,7 @@ def expected_warnings(matching):
 
     Parameters
     ----------
-    matching : None or a list of strings or compiled regexes
+    matching : list of str or re.Pattern or None
         Regexes for the desired warning to catch
         If matching is None, this behaves as a no-op.
 

src/skimage/_shared/tester.py

@@ -29,7 +29,7 @@ class PytestTester:
 
     Parameters
     ----------
-    module_name : module name
+    module_name : str
         The name of the module to test.
 
     """
@@ -68,7 +68,7 @@ def __call__(
         durations : int, optional
             If < 0, do nothing, If 0, report time of all tests, if > 0,
             report the time of the slowest `timer` tests. Default is -1.
-        tests : test or list of tests
+        tests : Sequence of str
             Tests to be executed with pytest '--pyargs'
 
         Returns

src/skimage/_shared/testing.py

@@ -282,7 +282,7 @@ def assert_stacklevel(warnings, *, offset=-1):
 
     Parameters
     ----------
-    warnings : collections.abc.Iterable[warning.WarningMessage]
+    warnings : Iterable[warnings.WarningMessage]
         Warnings that were captured by `pytest.warns`.
     offset : int, optional
         Offset from the line this function is called to the line were the

src/skimage/_shared/utils.py

@@ -205,11 +205,23 @@ def __repr__(cls):
 
 
 class DEPRECATED(metaclass=PatchClassRepr):
-    """Signal value to help with deprecating parameters that use None.
+    """Signal that a deprecated parameter has not been set.
 
-    This is a proxy object, used to signal that a parameter has not been set.
     This is useful if ``None`` is already used for a different purpose or just
     to highlight a deprecated parameter in the signature.
+
+    This is a sentinel and not meant to be initialized.
+    """
+
+
+class DEPRECATED_GOT_VALUE(metaclass=PatchClassRepr):
+    """Signal that a value was passed to a deprecated parameter.
+
+    Used by :class:`deprecate_parameter` to replace values that were passed to
+    deprecated parameters. This allows further handling of the deprecated case
+    inside the decorated function.
+
+    This is a sentinel and not meant to be initialized.
     """
 
 
@@ -228,9 +240,13 @@ class deprecate_parameter:
     template : str, optional
         If given, this message template is used instead of the default one.
     new_name : str, optional
-        If given, the default message will recommend the new parameter name and an
-        error will be raised if the user uses both old and new names for the
-        same parameter.
+        The name of a new parameter replacing the deprecated one. If given:
+        - The default message will recommend the new parameter name.
+        - Values passed to `deprecated_name` are replaced with
+          :class:`DEPRECATED_GOT_VALUE`, and the replaced value is passed to
+          `new_name` instead.
+        - An error will be raised if the user uses both `deprecated_name` and
+          `new_name`.
     modify_docstring : bool, optional
         If the wrapped function has a docstring, add the deprecated parameters
         to the "Other Parameters" section.
@@ -267,6 +283,7 @@ class deprecate_parameter:
     """
 
     DEPRECATED = DEPRECATED  # Make signal value accessible for convenience
+    DEPRECATED_GOT_VALUE = DEPRECATED_GOT_VALUE
 
     remove_parameter_template = (
         "Parameter `{deprecated_name}` is deprecated since version "
@@ -341,21 +358,20 @@ def fixed_func(*args, **kwargs):
             deprecated_value = DEPRECATED
             new_value = DEPRECATED
 
-            # Extract value of deprecated parameter
+            # Extract value of deprecated parameter and overwrite with
+            # DEPRECATED_GOT_VALUE if replacement exists
             if len(args) > deprecated_idx:
                 deprecated_value = args[deprecated_idx]
-                # Overwrite old with DEPRECATED if replacement exists
                 if self.new_name is not None:
                     args = (
                         args[:deprecated_idx]
-                        + (DEPRECATED,)
+                        + (DEPRECATED_GOT_VALUE,)
                         + args[deprecated_idx + 1 :]
                     )
             if self.deprecated_name in kwargs.keys():
                 deprecated_value = kwargs[self.deprecated_name]
-                # Overwrite old with DEPRECATED if replacement exists
                 if self.new_name is not None:
-                    kwargs[self.deprecated_name] = DEPRECATED
+                    kwargs[self.deprecated_name] = DEPRECATED_GOT_VALUE
 
             # Extract value of new parameter (if present)
             if new_idx is not False and len(args) > new_idx: