Fix matplotlib 3.9.0 has no attribute 'get_cmap` (Project-MONAI#7780)

Fixes Project-MONAI#7776 

### Description

A few sentences describing the changes proposed in this pull request.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: YunLiu <[email protected]>

docs/source/conf.py

@@ -139,7 +139,7 @@ def generate_apidocs(*args):
     "github_user": "Project-MONAI",
     "github_repo": "MONAI",
     "github_version": "dev",
-    "doc_path": "docs/",
+    "doc_path": "docs/source",
     "conf_py_path": "/docs/",
     "VERSION": version,
 }
@@ -167,17 +167,10 @@ def setup(app):
 
 
 # -- Linkcode configuration --------------------------------------------------
-DEFAULT_REF = "dev"
-if os.environ.get("GITHUB_REF_TYPE", "branch") == "tag":
-    # When building a tag, link to the tag itself
-    git_ref = os.environ.get("GITHUB_REF", DEFAULT_REF)
-else:
-    git_ref = os.environ.get("GITHUB_SHA", DEFAULT_REF)
-
 DEFAULT_REPOSITORY = "Project-MONAI/MONAI"
 repository = os.environ.get("GITHUB_REPOSITORY", DEFAULT_REPOSITORY)
 
-base_code_url = f"https://github.com/{repository}/blob/{git_ref}"
+base_code_url = f"https://github.com/{repository}/blob/{version}"
 MODULE_ROOT_FOLDER = "monai"
 
 
@@ -208,7 +201,7 @@ def linkcode_resolve(domain, info):
     except TypeError:
         # e.g. object is a typing.Union
         return None
-    file = os.path.relpath(file, os.path.abspath(".."))
+    file = os.path.relpath(file, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
     if not file.startswith(MODULE_ROOT_FOLDER):
         # e.g. object is a typing.NewType
         return None

monai/visualize/utils.py

@@ -24,11 +24,9 @@
 from monai.utils.type_conversion import convert_data_type, convert_to_dst_type
 
 if TYPE_CHECKING:
-    from matplotlib import cm
     from matplotlib import pyplot as plt
 else:
     plt, _ = optional_import("matplotlib", name="pyplot")
-    cm, _ = optional_import("matplotlib", name="cm")
 
 __all__ = ["matshow3d", "blend_images"]
 
@@ -210,7 +208,7 @@ def blend_images(
         image = repeat(image, 3, axis=0)
 
     def get_label_rgb(cmap: str, label: NdarrayOrTensor) -> NdarrayOrTensor:
-        _cmap = cm.get_cmap(cmap)
+        _cmap = plt.colormaps.get_cmap(cmap)
         label_np, *_ = convert_data_type(label, np.ndarray)
         label_rgb_np = _cmap(label_np[0])
         label_rgb_np = np.moveaxis(label_rgb_np, -1, 0)[:3]

requirements-dev.txt

@@ -36,7 +36,7 @@ einops
 transformers>=4.36.0
 mlflow>=2.12.2
 clearml>=1.10.0rc0
-matplotlib!=3.5.0
+matplotlib>=3.6.3
 tensorboardX
 types-PyYAML
 pyyaml

setup.cfg

@@ -68,7 +68,7 @@ all =
     transformers<4.22; python_version <= '3.10'
     mlflow>=2.12.2
     clearml>=1.10.0rc0
-    matplotlib
+    matplotlib>=3.6.3
     tensorboardX
     pyyaml
     fire
@@ -127,7 +127,7 @@ transformers =
 mlflow =
     mlflow>=2.12.2
 matplotlib =
-    matplotlib
+    matplotlib>=3.6.3
 clearml =
     clearml
 tensorboardX =

tests/test_matshow3d.py

@@ -114,6 +114,7 @@ def test_3d_rgb(self):
             every_n=2,
             frame_dim=-1,
             channel_dim=0,
+            fill_value=0,
             show=False,
         )