Replace pylint with ruff for repository linting, modernize packaging, and update CI for Python 3.10+ (#23)

Author: Copilot

.github/workflows/doc.yml

@@ -9,8 +9,10 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
       - name: Install dependencies
         run: |
           pip install sphinx sphinx_rtd_theme myst_parser

.github/workflows/release.yml

@@ -10,15 +10,22 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
 
     - name: Install dependencies
-      run: pip3 install --upgrade setuptools wheel twine
+      run: pip3 install --upgrade build twine
+
+    - name: Build package
+      run: python -m build
 
-    - name: Build and publish
+    - name: Publish to PyPI
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
-        python3 setup.py sdist bdist_wheel
         twine upload --repository pypi dist/*

.github/workflows/status.yml

@@ -9,10 +9,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
 
-    - name: Update pylint
-      run: pip3 install -U pylint
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
 
-    - name: Check pylint
-      run: pylint -rn --rcfile pylintrc nbtools
+    - name: Install ruff
+      run: pip3 install -U ruff
+
+    - name: Check ruff
+      run: ruff check nbtools

.github/workflows/test-install.yml

@@ -16,15 +16,15 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, '3.10', 3.11]
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -47,13 +47,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9, '3.10', 3.11]
+        python-version: ['3.10', '3.11', '3.12']
 
     runs-on: ${{ matrix.os }}
 
     steps:
     - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -65,3 +65,42 @@ jobs:
 
     - name: Run 'import nbtools'
       run: python -c 'import nbtools'
+
+
+# -----------------------------------------
+#    Install with uv
+# -----------------------------------------
+  install_with_uv:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+
+    - name: Install with uv
+      run: uv sync
+
+    - name: Test import with uv
+      run: uv run python -c 'import nbtools; print("nbtools version:", nbtools.__version__)'
+
+    - name: Test console scripts with uv
+      run: uv run nbstat --help
+
+    - name: Test optional dependencies with uv
+      run: |
+        uv sync --extra dev --extra nbrun
+        uv run python -c 'import ruff; print("ruff available")'

nbtools/__init__.py

@@ -1,7 +1,11 @@
 """ Init file. """
-#pylint: disable=wildcard-import
+from importlib.metadata import PackageNotFoundError, version
+
 from .core import *
 from .exec_notebook import exec_notebook, run_notebook
 from .pylint_notebook import pylint_notebook
 
-__version__ = '0.9.14'
+try:
+    __version__ = version("py-nbtools")
+except PackageNotFoundError:
+    __version__ = "0.0.0"  # e.g., running from a source tree

nbtools/core.py

@@ -1,5 +1,4 @@
 """ Core utility functions to work with Jupyter Notebooks. """
-#pylint: disable=import-outside-toplevel
 import os
 import sys
 import re
@@ -34,7 +33,6 @@ def get_notebook_path():
 
     If run outside Jupyter notebook, returns None.
     """
-    #pylint: disable=missing-timeout
     if not in_notebook():
         return None
 
@@ -74,7 +72,7 @@ def get_notebook_name():
 
 def notebook_to_script(path_script, path_notebook=None, ignore_markdown=True, return_info=False):
     """ Convert a notebook to a script. """
-    import nbformat #pylint: disable=import-outside-toplevel
+    import nbformat
     path_notebook = path_notebook or get_notebook_path()
     if path_notebook is None:
         raise ValueError('Provide path to Jupyter Notebook or run `notebook_to_script` inside of it!')
@@ -267,7 +265,6 @@ def set_gpus(n=1, min_free_memory=0.9, max_processes=2, verbose=False, raise_err
     devices : list
         Indices of selected and reserved GPUs.
     """
-    #pylint: disable=consider-iterating-dictionary
     if 'CUDA_VISIBLE_DEVICES' in os.environ.keys():
         str_devices = os.environ["CUDA_VISIBLE_DEVICES"]
         warnings.warn(f'`CUDA_VISIBLE_DEVICES` is already set to "{str_devices}"!')

nbtools/exec_notebook.py

@@ -1,5 +1,4 @@
 """ Functions for running Jupyter Notebooks programmatically."""
-#pylint: disable=import-outside-toplevel
 import os
 import time
 import json
@@ -10,7 +9,7 @@
 import psutil
 
 
-TMP_DIR = '/tmp/nbtools_exec_notebook'
+TMP_DIR = '/tmp/nbtools_exec_notebook'  # noqa: S108
 os.makedirs(TMP_DIR, exist_ok=True)
 
 
@@ -19,7 +18,6 @@ def run_in_process(func):
     """ Decorator to run the ``func`` in a separate process for terminating all related processes properly. """
     @wraps(func)
     def _wrapper(*args, **kwargs):
-        # pylint: disable=broad-exception-caught, broad-exception-raised
         _output_queue = Queue()
         kwargs = {**kwargs, '_output_queue': _output_queue}
 
@@ -39,7 +37,7 @@ def _wrapper(*args, **kwargs):
 
             output = _output_queue.get()
             process.join()
-        except (KeyboardInterrupt, Exception) as e:
+        except (KeyboardInterrupt, Exception) as e:  # noqa: BLE001
             output = {'failed': True, 'traceback': e}
 
             # Terminate all relevant processes when something went wrong, e.g. Keyboard Interrupt
@@ -245,7 +243,6 @@ def exec_notebook(path, inputs=None, outputs=None, inputs_pos=1, replace_inputs_
             - ``'notebook'`` : :class:`nbformat.notebooknode.NotebookNode`, optional
                 Executed notebook object. Note that this output is provided only if ``return_notebook`` is ``True``.
     """
-    # pylint: disable=bare-except, lost-exception, return-in-finally
     import nbformat
     from jupyter_client.manager import KernelManager
     from nbconvert.preprocessors import ExecutePreprocessor
@@ -321,7 +318,7 @@ def exec_notebook(path, inputs=None, outputs=None, inputs_pos=1, replace_inputs_
     exec_failed = False
     try:
         executor.preprocess(notebook, {'metadata': {'path': working_dir}}, km=kernel_manager)
-    except:
+    except:  # noqa: E722
         exec_failed = True
 
         # Save notebook outputs in the shelve db
@@ -359,7 +356,7 @@ def exec_notebook(path, inputs=None, outputs=None, inputs_pos=1, replace_inputs_
             # Re-raise exception if needed
             if raise_exception:
                 _output_queue.put(exec_res)
-                return None
+                return None  # noqa: RET501
         else:
             exec_res = {'failed': failed, 'failed cell number': None, 'traceback': ''}
 
@@ -397,7 +394,7 @@ def exec_notebook(path, inputs=None, outputs=None, inputs_pos=1, replace_inputs_
             exec_res['notebook'] = notebook
 
         _output_queue.put(exec_res) # return for parent process
-    return None
+    return None  # noqa: RET501
 
 # Functions for database operations cells masking
 def _display_inputs_reading(notebook, pos):

nbtools/nbstat/__init__.py

@@ -1,5 +1,4 @@
 """ NBstat module: monitoring running Python processes and Notebooks. """
-#pylint: disable=wildcard-import
 from .resource import Resource
 from .resource_entry import ResourceEntry
 from .resource_table import ResourceTable

nbtools/nbstat/cli.py

@@ -1,7 +1,6 @@
 """ Command line interface of `nbstat`.
 Also provides `nbwatch`, `devicestat` and `devicewatch` functions.
 """
-#pylint: disable=redefined-outer-name, too-many-nested-blocks
 import sys
 import traceback
 from inspect import cleandoc
@@ -21,9 +20,9 @@ def main(name, interval=None):
     """ Run command `name`. If `interval` is given, continuously output it to a terminal in fullscreen mode. """
     # Attach SIGPIPE handler to properly handle broken pipe
     try: # sigpipe not available under windows. just ignore in this case
-        import signal # pylint: disable=import-outside-toplevel
+        import signal  # noqa: E402
         signal.signal(signal.SIGPIPE, signal.SIG_DFL)
-    except Exception: # pylint: disable=broad-except
+    except Exception:  # noqa: BLE001, S110
         pass
 
     # Make parameters for requested view
@@ -54,15 +53,14 @@ def output_once(inspector, name, formatter, view_args):
     try:
         view = inspector.get_view(name=name, formatter=formatter, **view_args)
         print(view)
-    except Exception as e: # pylint: disable=broad-except
+    except Exception as e:
         _ = e
         print('Error on getting system information!' + str(e))
         raise e
 
 def output_looped(inspector, name, formatter, view_args,
                   other_name, other_formatter, other_view_args, interval=0.5):
     """ Output visualization to a stdout once each `interval` seconds in a fullscreen mode. """
-    #pylint: disable=too-many-statements
     terminal = Terminal()
 
     initial_view_args = dict(view_args)
@@ -194,7 +192,7 @@ def output_looped(inspector, name, formatter, view_args,
                         else:
                             print(f'\nUnrecognized key={inkey}, code={inkey.code}.')
 
-                except Exception as e: # pylint: disable=broad-except
+                except Exception as e:  # noqa: BLE001
                     sys.stderr.write(traceback.format_exc())
                     sys.stderr.write('Error on getting system information!')
                     sys.stderr.write(str(e))

nbtools/nbstat/resource_entry.py

@@ -39,7 +39,6 @@ def to_format_data(self, resource, terminal, **kwargs):
         kwargs : dict
             Other parameters for string creation like memory format, width, etc.
         """
-        #pylint: disable=too-many-statements
         resource = Resource.parse_alias(resource)
         default_string = '-'
         style, string = None, None