Update .pre-commit-config.yaml (#1274)

* Update .pre-commit-config.yaml

* Fix precommit

Signed-off-by: Sachidanand Alle <[email protected]>

---------

Signed-off-by: Sachidanand Alle <[email protected]>

Author: SachidanandAlle

.pre-commit-config.yaml

@@ -17,34 +17,43 @@ repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
+  - id: check-merge-conflict
   - id: trailing-whitespace
+  - id: check-yaml
+  - id: check-executables-have-shebangs
+  - id: check-toml
+  - id: check-case-conflict
   - id: check-added-large-files
     args: ['--maxkb=1024']
-  - id: check-case-conflict
-  - id: check-merge-conflict
+  - id: detect-private-key
+  - id: forbid-new-submodules
+  - id: pretty-format-json
+    args: ['--autofix', '--no-sort-keys', '--indent=4']
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.4
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python)
     args: ["--line-length=120", "--profile=black"]
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.4
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python) (check)
     args: ["--line-length=120", "--profile=black", "--check"]
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
     args: ["--line-length=120"]
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.1.0
   hooks:
   - id: black
     name: black (check)

CITATION.cff

@@ -26,4 +26,4 @@ license: "Apache-2.0"
 repository-code: "https://github.com/Project-MONAI/MONAILabel"
 cff-version: "1.1.0"
 message: "If you use this software, please cite it using these metadata."
-...
+...

docs/_static/custom.css

@@ -14,4 +14,4 @@ limitations under the License.
 @import url('https://fonts.googleapis.com/css?family=Lekton:700|Roboto&display=swap');
 body{font-family:'Roboto',sans-serif;}.wy-menu-vertical p.caption{color:#7cccc7;}
 *{font-variant-ligatures: none;}.autoclasstoc td {padding:0.2rem;line-height:normal;}
-dl.field-list>dt{word-break: normal}
+dl.field-list>dt{word-break: normal}

docs/images/modules.svg

@@ -158,7 +158,6 @@ def generate_apidocs(*args):
 
 
 class GenerateTagLinks(SphinxTransform):
-
     linkref_prefix = "LINKREF_"
     git_tag = "MONAILABEL_GIT_TAG"
     linkref_lut = {"LINKREF_GITHUB_MONAILABEL": f"https://github.com/Project-MONAI/MONAILabel/tree/{{{git_tag}}}"}
@@ -174,9 +173,7 @@ def basetext(obj):
         return isinstance(obj, Text) and obj.startswith(GenerateTagLinks.linkref_prefix)
 
     def apply(self):
-
         for node in self.document.traverse(GenerateTagLinks.baseref):
-
             # find the entry for the link reference we want to substitute
             link_key = None
             for k in self.linkref_lut.keys():

docs/images/monai-server-application-callflow.svg

@@ -353,5 +353,3 @@ If you have `DSA <https://digitalslidearchive.github.io/digital_slide_archive/>`
   monailabel start_server --app apps/pathology --studies http://0.0.0.0:8080/api/v1
 
 Refer `DSA Plugin <https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/dsa>`_ for running a sample pathology use-case in MONAILabel using DSA.
-
-

docs/source/conf.py

@@ -495,12 +495,12 @@ def save_result(files, tmpdir):
     def encode_multipart_formdata(fields, files):
         limit = "----------lImIt_of_THE_fIle_eW_$"
         lines = []
-        for (key, value) in fields.items():
+        for key, value in fields.items():
             lines.append("--" + limit)
             lines.append('Content-Disposition: form-data; name="%s"' % key)
             lines.append("")
             lines.append(value)
-        for (key, filename) in files.items():
+        for key, filename in files.items():
             if isinstance(filename, tuple):
                 filename, data = filename
             else:

docs/source/installation.rst

@@ -46,7 +46,6 @@ def __init__(
         click_probability_key: str = "probability",
         max_interactions: int = 1,
     ) -> None:
-
         self.deepgrow_probability = deepgrow_probability
         self.transforms = Compose(transforms) if not isinstance(transforms, Compose) else transforms
         self.train = train

monailabel/client/client.py

@@ -1,48 +1,48 @@
 {
-  "admin": {
-    "username": "admin",
-    "full_name": "Admin",
-    "email": "[email protected]",
-    "hashed_password": "$2b$12$CexVjWGTX//w8kt.f3CbGuznFtnlHCVte1EUScwzDCRKMRmltGBDa",
-    "disabled": false,
-    "scopes": [
-      "admin",
-      "reviewer",
-      "annotator",
-      "user"
-    ]
-  },
-  "reviewer": {
-    "username": "reviewer",
-    "full_name": "Reviewer",
-    "email": "[email protected]",
-    "hashed_password": "$2b$12$KJzEvm8iQFOwiLLecBjxg./g/9XLt1VMIDBrEFqJnqEOonxaWZ1y2",
-    "disabled": false,
-    "scopes": [
-      "reviewer",
-      "annotator",
-      "user"
-    ]
-  },
-  "annotator": {
-    "username": "annotator",
-    "full_name": "Annotator",
-    "email": "[email protected]",
-    "hashed_password": "$2b$12$6RPP.jL.8GZmP7DtJhWRLO.Exvh6LGUleXq.KLyBv9/leoV8KY8Pm",
-    "disabled": false,
-    "scopes": [
-      "annotator",
-      "user"
-    ]
-  },
-  "user": {
-    "username": "user",
-    "full_name": "User",
-    "email": "[email protected]",
-    "hashed_password": "$2b$12$Py6rSaJyhJIYfgnEOmCzLuQ9Kz7FtMdzjRCimtPUmPspbIPbRH6Dq",
-    "disabled": false,
-    "scopes": [
-      "user"
-    ]
-  }
-}
+    "admin": {
+        "username": "admin",
+        "full_name": "Admin",
+        "email": "[email protected]",
+        "hashed_password": "$2b$12$CexVjWGTX//w8kt.f3CbGuznFtnlHCVte1EUScwzDCRKMRmltGBDa",
+        "disabled": false,
+        "scopes": [
+            "admin",
+            "reviewer",
+            "annotator",
+            "user"
+        ]
+    },
+    "reviewer": {
+        "username": "reviewer",
+        "full_name": "Reviewer",
+        "email": "[email protected]",
+        "hashed_password": "$2b$12$KJzEvm8iQFOwiLLecBjxg./g/9XLt1VMIDBrEFqJnqEOonxaWZ1y2",
+        "disabled": false,
+        "scopes": [
+            "reviewer",
+            "annotator",
+            "user"
+        ]
+    },
+    "annotator": {
+        "username": "annotator",
+        "full_name": "Annotator",
+        "email": "[email protected]",
+        "hashed_password": "$2b$12$6RPP.jL.8GZmP7DtJhWRLO.Exvh6LGUleXq.KLyBv9/leoV8KY8Pm",
+        "disabled": false,
+        "scopes": [
+            "annotator",
+            "user"
+        ]
+    },
+    "user": {
+        "username": "user",
+        "full_name": "User",
+        "email": "[email protected]",
+        "hashed_password": "$2b$12$Py6rSaJyhJIYfgnEOmCzLuQ9Kz7FtMdzjRCimtPUmPspbIPbRH6Dq",
+        "disabled": false,
+        "scopes": [
+            "user"
+        ]
+    }
+}