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course-ds-base's Issues

Task 3.5 - Step 5: Automate pipelines with DVC

Branch: step-5-automate-ml-pipeline

Tasks:

  • install DVC (in a virtual environment)
  • automate ML pipeline with DVC
  • setup dependencies and outputs
  • setup parameters

Requirements:

  • for each stage, explicitly define dependencies (code and data)

Task 5.2 - Plots and graphics with DVC

Branch: step-7-metrics-and-experiments

Tasks:

  • save 'reports/classes.csv` file
  • get confusion matrix plot withdvc plots show reports/classes.csv --template confusion --template confusion
  • dvc plots show
  • dvc plots diff

Task 4.1 - How data versioning works?

Branch: step-6-data-and-model-version-control

Tasks:

  • create a file.txt
  • add file.txt to version control with DVC
  • create a datadir and add it to version control with DVC

Task 4.3 - Tracking changes and switching between versions

Branch: step-6-data-and-model-version-control
(continue from #11)

Tasks:

  • add remote storage
  • store file.txt to remote storage
  • delete file.txt in workspace
  • restore file.txt from DVC cache with dvc checkout file.txt
  • clean cache with dvc gc
  • try to restore file.txt from DVC cache with dvc checkout file.txt (failure is expected)
  • restore file.txt from DVC Remote Storage dvc pull (success is expected)
  • update 'file.txt' (version 2) and push it to remote storage
  • switch btw Git branches and 'file.txt' versions

Task 6.1 - Experimenting Workflow

Branch: step-9-experimenting-workflow

Tasks:
Experiment 1

  • run a new experiment with updated parameter:
    dvc exp run -S train.cv=2
  • show metrics with CLI:
    dvc exp show
  • apply to the current branch / commit & push to remote /
    dvc exp apply <exp>
    git add . & git commit -m "Experiment 1: train.cv=2"

Experiment 2

  • run a new experiment
    dvc exp run -S train.estimator_name=svm
  • create a branch / commit / push to remote / check updates in Studio
    dvc exp branch <exp> experiment-2
    git add . & git commit -m "Experiment 2: SVM"
    git push origin experiment-2
  • merge to step-9-experimenting / check updates in Studio

Task 2.2 - Set up the project repository structure

Branch: step-1-organize-ml-project
Tasks:

  • checkout to the branch: step-1-organize-ml-project
  • create the project structure
  • commit & push to remote

Check yourself:

  • branch: step-1-organize-ml-project_SOLUTION

Task 3.6 - Reproduce end-to-end ML pipelines

Branch: step-5-automate-ml-pipeline

Tasks:

  • make sure that you've completed the Task 3.5
  • run dvc repro (assume we do this for 1st time)
  • run dvc repro (no changes, DVC skips all stages)
  • run dvc repro -f (force running ML pipeline)
  • run dvc repro train (run only train stage from dvc.yaml)
  • update train stage configs and run dvc repro
  • update src/stage/train.py code and run dvc repro
  • remove reports/metrics.json and run dvc repro

Task 3.4 - Step 4: Build ML experiment pipeline

Branch: step-4-build-ml-pipeline

Tasks:

  • create src/stages directory

  • create .py modules for each pipeline stage:

    • data_load.py
    • data_split.py
    • featurize.py
    • train.py
    • evaluate.py
  • run each stage

Requirements:

  • use params.yaml to manage stages configuration

Requirements could not deploy on Python3.10

@Team,
Trying to deploy requirements on Python3.10 version. Please let us know, is this specific specific python version have to deploy and test myself this code.

(dvc-venv) PS C:\Jan5-2021\DVC\course-ds-base> pip install -r .\requirements.txt
Collecting dvc==2.8.3
Downloading dvc-2.8.3-py3-none-any.whl (399 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 399.3/399.3 kB 2.3 MB/s eta 0:00:00
Collecting joblib==1.0.1
Downloading joblib-1.0.1-py3-none-any.whl (303 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 303.1/303.1 kB 6.2 MB/s eta 0:00:00
Collecting jupyter==1.0.0
Using cached jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting jupyter_contrib_nbextensions==0.5.1
Downloading jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl (20.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.9/20.9 MB 1.3 MB/s eta 0:00:00
Collecting matplotlib==3.4.3
Downloading matplotlib-3.4.3.tar.gz (37.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.9/37.9 MB 1.3 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Collecting numpy==1.21.2
Downloading numpy-1.21.2.zip (10.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 1.6 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting pandas==1.3.2
Downloading pandas-1.3.2.tar.gz (4.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 4.6 MB/s eta 0:00:00
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [297 lines of output]
Ignoring numpy: markers 'python_version == "3.7" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_machine != "aarch64
"' don't match your environment
Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_machine != "aarch64
"' don't match your environment
Ignoring numpy: markers 'python_version == "3.7" and platform_machine == "aarch64"' don't match your environment
Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "aarch64"' don't match your environment
Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment
Ignoring numpy: markers 'python_version == "3.9" and platform_machine == "arm64" and platform_system == "Darwin"' don't match your environment
Collecting setuptools>=51.0.0
Using cached setuptools-65.5.0-py3-none-any.whl (1.2 MB)
Collecting wheel
Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
Collecting Cython<3,>=0.29.21
Using cached Cython-0.29.32-py2.py3-none-any.whl (986 kB)
Collecting numpy==1.19.3
Downloading numpy-1.19.3.zip (7.3 MB)
---------------------------------------- 7.3/7.3 MB 485.5 kB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

    Preparing metadata (pyproject.toml) did not run successfully.
    exit code: 1
 
    [259 lines of output]
    setup.py:67: RuntimeWarning: NumPy 1.19.3 may not yet support Python 3.10.
      warnings.warn(
    Running from numpy source directory.
    setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
      run_build = parse_setuppy_commands()
    Processing numpy/random\_bounded_integers.pxd.in
    Processing numpy/random\bit_generator.pyx
    Processing numpy/random\mtrand.pyx
    Processing numpy/random\_bounded_integers.pyx.in
    Processing numpy/random\_common.pyx
    Processing numpy/random\_generator.pyx
    Processing numpy/random\_mt19937.pyx
    Processing numpy/random\_pcg64.pyx
    Processing numpy/random\_philox.pyx
    Processing numpy/random\_sfc64.pyx
    Cythonizing sources
    blas_opt_info:
    blas_mkl_info:
    No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
    customize MSVCCompiler
      libraries mkl_rt not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    blis_info:
      libraries blis not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    openblas_info:
      libraries openblas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
    get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'      
    customize GnuFCompiler
    Could not locate executable g77
    Could not locate executable f77
    customize IntelVisualFCompiler
    Could not locate executable ifort
    Could not locate executable ifl
    customize AbsoftFCompiler
    Could not locate executable f90
    customize CompaqVisualFCompiler
    Could not locate executable DF
    customize IntelItaniumVisualFCompiler
    Could not locate executable efl
    customize Gnu95FCompiler
    Could not locate executable gfortran
    Could not locate executable f95
    customize G95FCompiler
    Could not locate executable g95
    customize IntelEM64VisualFCompiler
    customize IntelEM64TFCompiler
    Could not locate executable efort
    Could not locate executable efc
    customize PGroupFlangCompiler
    Could not locate executable flang
    don't know how to compile Fortran code on platform 'nt'
      NOT AVAILABLE
 
    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries tatlas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    atlas_3_10_blas_info:
      libraries satlas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    atlas_blas_info:
      libraries f77blas,cblas,atlas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    accelerate_info:
      NOT AVAILABLE
 
    C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\system_info.py:1914: UserWarning

:
Optimized (vendor) Blas libraries are not found.
Falls back to netlib Blas library which has worse performance.
A better performance should be easily gained by switching
Blas library.
if self._calc_info(blas):
blas_info:
libraries blas not found in ['C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib', 'C:\']
NOT AVAILABLE

    C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\system_info.py:1914: UserWarning

:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
if self._calc_info(blas):
blas_src_info:
NOT AVAILABLE

    C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\system_info.py:1914: UserWarning

:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
if self._calc_info(blas):
NOT AVAILABLE

    non-existing path in 'numpy\\distutils': 'site.cfg'
    lapack_opt_info:
    lapack_mkl_info:
      libraries mkl_rt not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    openblas_lapack_info:
      libraries openblas not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    openblas_clapack_info:
      libraries openblas,lapack not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    flame_info:
      libraries flame not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
      libraries lapack_atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries tatlas,tatlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries lapack_atlas not found in C:\
      libraries tatlas,tatlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE
 
    atlas_3_10_info:
      libraries lapack_atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries satlas,satlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries lapack_atlas not found in C:\
      libraries satlas,satlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE
 
    atlas_threads_info:
    Setting PTATLAS=ATLAS
      libraries lapack_atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries ptf77blas,ptcblas,atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries lapack_atlas not found in C:\
      libraries ptf77blas,ptcblas,atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE
 
    atlas_info:
      libraries lapack_atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries f77blas,cblas,atlas not found in C:\Jan5-2021\DVC\course-ds-base\dvc-venv\lib
      libraries lapack_atlas not found in C:\
      libraries f77blas,cblas,atlas not found in C:\
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE
 
    lapack_info:
      libraries lapack not found in ['C:\\Jan5-2021\\DVC\\course-ds-base\\dvc-venv\\lib', 'C:\\']
      NOT AVAILABLE
 
    C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\system_info.py:1748: UserWarning

:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
return getattr(self, 'calc_info{}'.format(name))()
lapack_src_info:
NOT AVAILABLE

    C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\system_info.py:1748: UserWarning

:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
return getattr(self, 'calc_info{}'.format(name))()
NOT AVAILABLE

    numpy_linalg_lapack_lite:
      FOUND:
        language = c
        define_macros = [('HAVE_BLAS_ILP64', None), ('BLAS_SYMBOL_SUFFIX', '64_')]
 
    C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools\_distutils\dist.py:275: UserWarning: Unknown dis

tribution option: 'define_macros'
warnings.warn(msg)
running dist_info
running build_src
build_src
building py_modules sources
creating build
creating build\src.win-amd64-3.10
creating build\src.win-amd64-3.10\numpy
creating build\src.win-amd64-3.10\numpy\distutils
building library "npymath" sources
Traceback (most recent call last):
File "C:\Jan5-2021\DVC\course-ds-base\dvc-venv\Lib\site-packages\pip_vendor\pep517\in_process_in_process.py", line 351, in
main()
File "C:\Jan5-2021\DVC\course-ds-base\dvc-venv\Lib\site-packages\pip_vendor\pep517\in_process_in_process.py", line 333, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "C:\Jan5-2021\DVC\course-ds-base\dvc-venv\Lib\site-packages\pip_vendor\pep517\in_process_in_process.py", line 152, in prepare_metadata_
for_build_wheel
return hook(metadata_directory, config_settings)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools\build_meta.py", line 157, in prepare_met
adata_for_build_wheel
self.run_setup()
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools\build_meta.py", line 248, in run_setup
super(BuildMetaLegacyBackend,
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools\build_meta.py", line 142, in run_setup
exec(compile(code, file, 'exec'), locals())
File "setup.py", line 508, in
setup_package()
File "setup.py", line 500, in setup_package
setup(**metadata)
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\core.py", line 169, in s
etup
return old_setup(**new_attr)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_init
.py", line 165, in setup
return distutils.core.setup(**attrs)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\core.py", line 148, in setup
dist.run_commands()
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\dist.py", line 967, in run_co
mmands
self.run_command(cmd)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\dist.py", line 986, in run_co
mmand
cmd_obj.run()
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools\command\dist_info.py", line 31, in run
egg_info.run()
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\egg_info.py", li
ne 24, in run
self.run_command("build_src")
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\cmd.py", line 313, in run_com
mand
self.distribution.run_command(command)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\dist.py", line 986, in run_co
mmand
cmd_obj.run()
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\build_src.py", l
ine 144, in run
self.build_sources()
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\build_src.py", l
ine 155, in build_sources
self.build_library_sources(libname_info)
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\build_src.py", l
ine 288, in build_library_sources
sources = self.generate_sources(sources, (lib_name, build_info))
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\build_src.py", l
ine 378, in generate_sources
source = func(extension, build_dir)
File "numpy\core\setup.py", line 658, in get_mathlib_info
st = config_cmd.try_link('int main(void) { return 0;}')
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\command\config.py", line 243,
in try_link
self._link(body, headers, include_dirs,
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\config.py", line
162, in _link
return self._wrap_method(old_config._link, lang,
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\config.py", line
96, in _wrap_method
ret = mth(
((self,)+args))
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\command\config.py", line 137,
in _link
(src, obj) = self._compile(body, headers, include_dirs, lang)
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\config.py", line
105, in _compile
src, obj = self._wrap_method(old_config._compile, lang,
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\command\config.py", line
96, in _wrap_method
ret = mth(*((self,)+args))
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils\command\config.py", line 132,
in _compile
self.compiler.compile([src], include_dirs=include_dirs)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils_msvccompiler.py", line 401,
in compile
self.spawn(args)
File "C:\Users\seerapu\AppData\Local\Temp\pip-build-env-r0sar12d\overlay\Lib\site-packages\setuptools_distutils_msvccompiler.py", line 505,
in spawn
return super().spawn(cmd, env=env)
File "C:\Users\seerapu\AppData\Local\Temp\pip-install-jsn8okah\numpy_c87dffe387db45458072f04c8df762c4\numpy\distutils\ccompiler.py", line 90,
in
m = lambda self, *args, **kw: func(self, *args, **kw)
TypeError: CCompiler_spawn() got an unexpected keyword argument 'env'
[end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: metadata-generation-failed
 
  Encountered error while generating package metadata.
 
  See above for output.
 
  note: This is an issue with the package mentioned above, not pip.
  hint: See above for details.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Task 4.4 - Data Access

Branch: step-6-data-and-model-version-control

Tasks:

  • show example of dvc list and dvc get commands

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