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The ultimate assisted annotation tool for images running on Jupyter

Jupyter Notebook 12.51% Shell 0.32% Python 67.34% TypeScript 17.82% JavaScript 1.10% Cython 0.85% CSS 0.06%

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jupyter_segmentation's Issues

Tool won't build

This tool looked interesting, and I figured I would give it a try but it won't seem to build.

WSL Ubuntu 20.04.5 LTS
npm v8.19.3
Node.js v16.19.1
Python 3.9.13 in a clean environment

pip install -e . results in:

Building wheels for collected packages: ipyfan
  Building wheel for ipyfan (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [84 lines of output]
      /home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
        warnings.warn(
      /home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/config/setupcfg.py:508: SetuptoolsDeprecationWarning: The license_file parameter is deprecated, use license_files instead.
        warnings.warn(msg, warning_class)
      running bdist_wheel
      running jsdeps
      > npm run build:all

      > ipyfan@0.2.0 build:all
      > npm run build:labextension && npm run build:nbextension


      > ipyfan@0.2.0 build:labextension
      > npm run clean:labextension && mkdirp ipyfan/labextension && cd ipyfan/labextension && npm pack ../..


      > ipyfan@0.2.0 clean:labextension
      > rimraf ipyfan/labextension


      > ipyfan@0.2.0 prepack
      > npm run build:lib


      > ipyfan@0.2.0 build:lib
      > tsc

      src/widget.ts(52,5): error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
        Types of property 'deserialize' are incompatible.
          Type '(obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>' is not assignable to type '(value?: any, manager?: ManagerBase<any> | undefined) => any'.
            Types of parameters 'manager' and 'manager' are incompatible.
              Type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any> | undefined' is not assignable to type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any> | undefined'.
                Type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any>' is not assignable to type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any>'.
                  Types of property 'display_model' are incompatible.
                    Type '(msg: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").IMessage<import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").MessageType>, model: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_mo...' is not assignable to type '(msg: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyterlab/services/lib/kernel/messages").IMessage<import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").MessageType>, model: import("/mnt/d/Desktop/g...'.
                      Types of parameters 'model' and 'model' are incompatible.
                        Type 'DOMWidgetModel' is missing the following properties from type 'DOMWidgetModel': rememberLastUpdateFor, _expectedEchoMsgIds, _attrsToUpdate
      src/widget.ts(53,5): error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
      src/widget.ts(54,5): error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
      src/widget.ts(55,5): error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
      src/widget.ts(56,5): error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
      npm ERR! code 1
      npm ERR! path /mnt/d/Desktop/git_pulls/jupyter_segmentation
      npm ERR! command failed
      npm ERR! command sh -c -- npm run build:lib

      npm ERR! A complete log of this run can be found in:
      npm ERR!     /home/irrev/.npm/_logs/2023-02-27T13_09_29_414Z-debug-0.log
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setup.py", line 113, in <module>
          setup(**setup_args)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup
          return distutils.core.setup(**attrs)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
          self.run_command(cmd)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setupbase.py", line 502, in run
          [self.run_command(cmd) for cmd in cmds]
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setupbase.py", line 502, in <listcomp>
          [self.run_command(cmd) for cmd in cmds]
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
          self.distribution.run_command(command)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command
          super().run_command(command)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
          cmd_obj.run()
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setupbase.py", line 280, in run
          c.run()
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setupbase.py", line 400, in run
          run(npm_cmd + ["run", build_cmd], cwd=node_package)
        File "/mnt/d/Desktop/git_pulls/jupyter_segmentation/setupbase.py", line 230, in run
          return subprocess.check_call(cmd, **kwargs)
        File "/home/irrev/miniconda3/envs/stradivarius/lib/python3.9/subprocess.py", line 373, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['/usr/bin/npm', 'run', 'build:all']' returned non-zero exit status 1.
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for ipyfan
  Running setup.py clean for ipyfan

A very similar error occurs when I run:
npm build:all

> ipyfan@0.2.0 build:all
> npm run build:labextension && npm run build:nbextension


> ipyfan@0.2.0 build:labextension
> npm run clean:labextension && mkdirp ipyfan/labextension && cd ipyfan/labextension && npm pack ../..


> ipyfan@0.2.0 clean:labextension
> rimraf ipyfan/labextension


> ipyfan@0.2.0 prepack
> npm run build:lib


> ipyfan@0.2.0 build:lib
> tsc

src/widget.ts:52:5 - error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.
  Types of property 'deserialize' are incompatible.
    Type '(obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>' is not assignable to type '(value?: any, manager?: ManagerBase<any> | undefined) => any'.
      Types of parameters 'manager' and 'manager' are incompatible.
        Type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any> | undefined' is not assignable to type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any> | undefined'.
          Type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any>' is not assignable to type 'import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyter-widgets/base/lib/manager-base").ManagerBase<any>'.
            Types of property 'display_model' are incompatible.
              Type '(msg: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").IMessage<import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").MessageType>, model: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_mo...' is not assignable to type '(msg: import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/jupyter-dataserializers/node_modules/@jupyterlab/services/lib/kernel/messages").IMessage<import("/mnt/d/Desktop/git_pulls/jupyter_segmentation/node_modules/@jupyterlab/services/lib/kernel/messages").MessageType>, model: import("/mnt/d/Desktop/g...'.
                Types of parameters 'model' and 'model' are incompatible.
                  Type 'DOMWidgetModel' is missing the following properties from type 'DOMWidgetModel': rememberLastUpdateFor, _expectedEchoMsgIds, _attrsToUpdate

52     annI: data_union_serialization,
       ~~~~

  node_modules/@jupyter-widgets/base/lib/widget.d.ts:17:5
    17     [key: string]: {
           ~~~~~~~~~~~~~~~~
    18         deserialize?: (value?: any, manager?: managerBase.ManagerBase<any>) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    19         serialize?: (value?: any, widget?: WidgetModel) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    20     };
       ~~~~~~
    The expected type comes from this index signature.

src/widget.ts:53:5 - error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.

53     annL: data_union_serialization,
       ~~~~

  node_modules/@jupyter-widgets/base/lib/widget.d.ts:17:5
    17     [key: string]: {
           ~~~~~~~~~~~~~~~~
    18         deserialize?: (value?: any, manager?: managerBase.ManagerBase<any>) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    19         serialize?: (value?: any, widget?: WidgetModel) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    20     };
       ~~~~~~
    The expected type comes from this index signature.

src/widget.ts:54:5 - error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.

54     imgL: data_union_serialization,
       ~~~~

  node_modules/@jupyter-widgets/base/lib/widget.d.ts:17:5
    17     [key: string]: {
           ~~~~~~~~~~~~~~~~
    18         deserialize?: (value?: any, manager?: managerBase.ManagerBase<any>) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    19         serialize?: (value?: any, widget?: WidgetModel) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    20     };
       ~~~~~~
    The expected type comes from this index signature.

src/widget.ts:55:5 - error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.

55     propL: data_union_serialization,
       ~~~~~

  node_modules/@jupyter-widgets/base/lib/widget.d.ts:17:5
    17     [key: string]: {
           ~~~~~~~~~~~~~~~~
    18         deserialize?: (value?: any, manager?: managerBase.ManagerBase<any>) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    19         serialize?: (value?: any, widget?: WidgetModel) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    20     };
       ~~~~~~
    The expected type comes from this index signature.

src/widget.ts:56:5 - error TS2322: Type '{ deserialize: (obj: string | IReceivedSerializedArray | null, manager?: ManagerBase<any> | undefined) => Promise<ndarray<number> | DataWidget | null>; serialize: (obj: DataWidget | ... 1 more ... | null, widget?: WidgetModel | undefined) => string | ... 1 more ... | null; }' is not assignable to type '{ deserialize?: ((value?: any, manager?: ManagerBase<any> | undefined) => any) | undefined; serialize?: ((value?: any, widget?: WidgetModel | undefined) => any) | undefined; }'.

56     prevPropL: data_union_serialization,
       ~~~~~~~~~

  node_modules/@jupyter-widgets/base/lib/widget.d.ts:17:5
    17     [key: string]: {
           ~~~~~~~~~~~~~~~~
    18         deserialize?: (value?: any, manager?: managerBase.ManagerBase<any>) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    19         serialize?: (value?: any, widget?: WidgetModel) => any;
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    20     };
       ~~~~~~
    The expected type comes from this index signature.


Found 5 errors.

npm ERR! code 1
npm ERR! path /mnt/d/Desktop/git_pulls/jupyter_segmentation
npm ERR! command failed
npm ERR! command sh -c -- npm run build:lib

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/irrev/.npm/_logs/2023-02-27T13_05_31_637Z-debug-0.log

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