refactoring

nbclean/__init__.py

@@ -3,4 +3,4 @@
 __version__ = "0.3.2"
 
 from .clean import NotebookCleaner
-from .run import run_notebook_directory, run_notebook
+from .run import run_notebooks, run_notebook

nbclean/clean.py

@@ -4,7 +4,7 @@
 from nbgrader.preprocessors import ClearSolutions
 from glob import glob
 from .preprocessors import RemoveCells, ClearCells, ConvertCells
-from .utils import _check_nb_file
+from .utils import _check_nb_file, _find_notebooks
 
 
 class NotebookCleaner(object):
@@ -167,3 +167,13 @@ def save(self, path_save):
             os.makedirs(dir_save)
         nbf.write(self.ntbk, path_save)
 
+
+def clear_notebooks(path, kind, skip=".ipynb_checkpoints", **kwargs):
+    notebooks = _find_notebooks(path, skip)
+    if len(notebooks) == 0:
+        print("Note: no notebooks were found to be cleared.")
+    for path in notebooks:
+        print(f"Clearing {kind} in {path}")
+        cleaner = NotebookCleaner(str(path))
+        cleaner.clear(kind, **kwargs)
+        cleaner.save(str(path))

nbclean/cli.py

@@ -1,9 +1,8 @@
 import click
 import nbformat as nbf
 from glob import glob
-from nbclient import execute
-from .clean import NotebookCleaner
-from .run import run_notebook
+from .clean import clear_notebooks
+from .run import run_notebooks
 
 @click.group()
 def main():
@@ -17,44 +16,8 @@ def main():
 def clear(path, kind, skip, **kwargs):
     clear_notebooks(path, kind, skip=skip, **kwargs)
 
-def _find_notebooks(path, skip):
-    from pathlib import Path
-    path = Path(path)
-    if not path.exists():
-        raise ValueError(f"You gave a path that doesn't exist: {path}")
-    elif path.is_dir():
-        notebooks = list(path.rglob("*.ipynb"))
-        notebooks = [ii for ii in notebooks if skip not in str(ii)]
-    elif path.suffix == ".ipynb":
-        notebooks = [str(path)]
-    else:
-        raise ValueError(f"You gave a path that isn't a folder or a notebook file: {path}")
-    return notebooks
-
-def clear_notebooks(path, kind, skip=".ipynb_checkpoints", **kwargs):
-    notebooks = _find_notebooks(path, skip)
-    if len(notebooks) == 0:
-        print("Note: no notebooks were found to be cleared.")
-    for path in notebooks:
-        print(f"Clearing {kind} in {path}")
-        cleaner = NotebookCleaner(str(path))
-        cleaner.clear(kind, **kwargs)
-        cleaner.save(str(path))
-
-
 @main.command()
 @click.argument("path")
 @click.option("--skip", default=".ipynb_checkpoints", help="What element of the notebooks you wish to clear")
 def run(path, skip, **kwargs):
     run_notebooks(path, skip, **kwargs)
-
-def run_notebooks(path, skip, **kwargs):
-    notebooks = _find_notebooks(path, skip)
-    if len(notebooks) == 0:
-        print("Note: no notebooks were found to be executed.")
-
-    for path in notebooks:
-        print(f"Running {path}")
-        ntbk = nbf.read(str(path), nbf.NO_CONVERT)
-        ntbk = execute(ntbk, cwd=str(path.parent))
-        nbf.write(ntbk, str(path))

nbclean/run.py

@@ -2,65 +2,22 @@
 import os
 import os.path as op
 from nbgrader.preprocessors import LimitOutput, Execute
-from .utils import _check_nb_file
+from .utils import _check_nb_file, _find_notebooks
 from glob import glob
+from pathlib import Path
 from tqdm import tqdm
+from nbclient import execute
 
 
-def run_notebook_directory(path, path_save=None, max_output_lines=1000,
-                           overwrite=False):
-    """Run all the notebooks in a directory and save them somewhere else.
+def run_notebooks(path, skip, **kwargs):
+    notebooks = _find_notebooks(path, skip)
+    if len(notebooks) == 0:
+        print("Note: no notebooks were found to be executed.")
 
-    Parameters
-    ----------
-    path : str
-        A path to a directory that contains jupyter notebooks.
-        All notebooks in this folder ending in `.ipynb` will be run,
-        and the outputs will be placed in `path_save`. This may
-        optionally contain a wildcard matching ``<something>.ipynb`` in which
-        case only notebooks that match will be run.
-    path_save : str | None
-        A path to a directory to save the notebooks. If this doesn't exist,
-        it will be created. If `None`, notebooks will not be saved.
-    max_output_lines : int | None
-        The maximum number of lines allowed in notebook outputs.
-    overwrite : bool
-        Whether to overwrite the output directory if it exists.
-
-    Returns
-    -------
-    notebooks : list
-        A list of the `NotebookNode` instances, one for each notebook.
-    """
-    if not op.exists(path):
-        raise ValueError("You've specified an input path that doesn't exist")
-    to_glob = op.join(path, '*.ipynb') if '.ipynb' not in path else path
-    notebooks = glob(to_glob)
-
-    # Execute notebooks
-    outputs = []
-    for notebook in tqdm(notebooks):
-        outputs.append(run_notebook(notebook,
-                                    max_output_lines=max_output_lines))
-
-    # Now save them
-    if path_save is not None:
-        print('Saving {} notebooks to: {}'.format(len(notebooks), path_save))
-        if not op.exists(path_save):
-            os.makedirs(path_save)
-        elif overwrite is True:
-            print('Overwriting output directory')
-            for ifile in glob(path_save + '*-exe.ipynb'):
-                os.remove(ifile)
-        else:
-            raise ValueError('path_save exists and overwrite is not True')
-
-        for filename, notebook in zip(notebooks, outputs):
-            this_name = op.basename(filename)
-            left, right = this_name.split('.')
-            left += '-exe'
-            this_name = '.'.join([left, right])
-            nbf.write(notebook, op.join(path_save, this_name))
+    for path in notebooks:
+        print(f"Running {path}")
+        ntbk = run_notebook(path)
+        nbf.write(ntbk, str(path))
 
 
 def run_notebook(ntbk, max_output_lines=1000):
@@ -73,12 +30,12 @@ def run_notebook(ntbk, max_output_lines=1000):
     max_output_lines : int | None
         The maximum number of lines allowed in notebook outputs.
     """
+    if isinstance(ntbk, (str, type(Path))):
+        ntbk = Path(ntbk)
+        wd = str(ntbk.parent)
+        ntbk = str(ntbk)
+    else:
+        wd = str(Path())
     ntbk = _check_nb_file(ntbk)
-
-    preprocessors = [Execute()]
-    if max_output_lines is not None:
-        preprocessors.append(LimitOutput(max_lines=max_output_lines,
-                                         max_traceback=max_output_lines))
-    for prep in preprocessors:
-        ntbk, _ = prep.preprocess(ntbk, {})
+    ntbk = execute(ntbk, cwd=wd)
     return ntbk

nbclean/tests/test_ntbk.ipynb

@@ -14,31 +14,7 @@
    "cell_type": "code",
    "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[-0.1291054   0.12687936 -0.43424441 -0.42527338 -1.06042428  0.873431\n",
-      " -1.41487395  0.16180383 -0.36963902 -1.47040749  0.5380093   1.64442094\n",
-      "  0.01550058 -0.36913987  1.3185561   1.47267394 -0.24117057 -0.1868983\n",
-      " -2.39743438  1.97167598 -0.17841205 -0.52284158 -0.18303555 -0.00747752\n",
-      "  0.26361847  0.91230463 -1.17812049 -0.11316573  0.37338041  0.55512641\n",
-      " -0.72108943  1.6370304  -0.95906868 -0.32059531 -1.5615334  -1.07300787\n",
-      "  0.68033934  0.67717045  1.02077096 -0.15936002 -0.71579344 -1.18348182\n",
-      " -1.40105323 -0.09305708 -0.79004453 -0.83884275 -1.03279955 -1.50604434\n",
-      " -0.84528241  1.83662664  0.93372929  0.7034139  -0.43927167  0.06370446\n",
-      "  1.28176304 -0.3374127  -0.573012   -0.89501561  1.26972311  0.03706608\n",
-      "  0.38862378  0.64093822  0.64688551  0.9963434   0.53692001  0.33476171\n",
-      "  0.13735019 -1.04149315  0.63202144 -1.1908394   0.54666563  1.74715812\n",
-      " -1.10135633 -0.51360652  1.26403823 -1.24094441  1.50736803  0.10323768\n",
-      " -0.92334085 -1.66044892 -0.02672489 -0.06145144  0.96691626 -0.01344665\n",
-      " -1.26492364  1.33620823 -0.11632291 -2.2070902  -0.15912759  2.1311936\n",
-      " -0.56929863 -0.63117047  0.32744059  0.68677507 -0.28456693  0.48483996\n",
-      " -1.05184195 -0.80990045 -2.42788281  1.58669496]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "data = np.random.randn(2, 100)\n",
     "print(data[0])"
@@ -48,30 +24,7 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<matplotlib.collections.PathCollection at 0x7fe25a9ddb38>"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    },
-    {
-     "data": {
-      "image/png": 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\n",
-      "text/plain": [
-       "<Figure size 432x288 with 1 Axes>"
-      ]
-     },
-     "metadata": {
-      "needs_background": "light"
-     },
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "plt.scatter(*data)"
    ]

nbclean/utils.py

@@ -1,12 +1,30 @@
 import nbformat as nbf
 from nbformat.notebooknode import NotebookNode
 from copy import deepcopy
+from pathlib import Path
 
 
 def _check_nb_file(ntbk):
+    if isinstance(ntbk, Path):
+        ntbk = str(ntbk)
     if isinstance(ntbk, str):
         ntbk = nbf.read(ntbk, nbf.NO_CONVERT)
     elif not isinstance(ntbk, NotebookNode):
-        raise TypeError('`ntbk` must be type string or `NotebookNode`')
+        raise TypeError(f'`ntbk` must be type string or `NotebookNode`, found: {type(ntbk)}')
     ntbk = deepcopy(ntbk)
     return ntbk
+
+
+def _find_notebooks(path, skip):
+    from pathlib import Path
+    path = Path(path)
+    if not path.exists():
+        raise ValueError(f"You gave a path that doesn't exist: {path}")
+    elif path.is_dir():
+        notebooks = list(path.rglob("*.ipynb"))
+        notebooks = [ii for ii in notebooks if skip not in str(ii)]
+    elif path.suffix == ".ipynb":
+        notebooks = [str(path)]
+    else:
+        raise ValueError(f"You gave a path that isn't a folder or a notebook file: {path}")
+    return notebooks