Test and document how to use isort on a notebook

.github/workflows/continuous-integration-conda.yml

@@ -60,6 +60,8 @@ jobs:
           conda install mock --freeze-installed
           # install black if available (Python 3.6 and above), and autopep8 for testing the pipe mode
           conda install black --freeze-installed
+          # install isort from source
+          pip install git+https://github.com/timothycrosley/isort.git
           conda install autopep8 --freeze-installed
           # install sphinx_gallery and matplotlib if available
           conda install sphinx-gallery --freeze-installed

CHANGELOG.md

@@ -4,6 +4,7 @@
 **Added**
 - Activated GitHub code scanning alerts
 - New option `hide_notebook_metadata` to encapsulate the notebook metadata in an HTML comment (#527)
+- Tested `isort` on notebooks (#553)
 
 **Changed**
 - Install Jupytext from source on MyBinder to avoid cache issues (#567)
@@ -13,6 +14,7 @@
 **Fixed**
 - Configured coverage targets in `codecov.yml`
 - Only scripts can have an encoding comment, not Markdown or R Markdown files (#576)
+- Support spaces in `--pipe` commands (#562)
 
 
 1.5.2 (2020-07-21)

docs/using-cli.md

@@ -43,6 +43,12 @@ You may also find useful to `--pipe` the text representation of a notebook into
 jupytext --sync --pipe black notebook.ipynb    # read most recent version of notebook, reformat with black, save
 ```
 
+To reorder the imports in your notebook, use
+```bash
+jupytext --pipe 'isort - --treat-comment-as-code "# %%" --float-to-top' notebook.ipynb
+```
+(remove the `--float-to-top` argument if you prefer to run `isort` per cell).
+
 For programs that don't accept pipes, use `{}` as a placeholder for the name of a temporary file that will contain the text representation of the notebook. For instance, run `pytest` on your notebook with:
 ```bash
 jupytext --check 'pytest {}' notebook.ipynb    # export the notebook in format py:percent in a temp file, run pytest

environment.yml

@@ -17,6 +17,7 @@ dependencies:
   - pylint
   - flake8
   - black
+  - isort
   - autopep8
   - sphinx-gallery
   - nodejs<13

jupytext/cli.py

@@ -4,6 +4,7 @@
 import re
 import sys
 import glob
+import shlex
 import subprocess
 import argparse
 import json
@@ -774,8 +775,7 @@ def read_one_file(path, fmt):
 
 def exec_command(command, input=None, capture=False):
     """Execute the desired command, and pipe the given input into it"""
-    if not isinstance(command, list):
-        command = command.split(" ")
+    assert isinstance(command, list)
     sys.stdout.write("[jupytext] Executing {}\n".format(" ".join(command)))
     process = subprocess.Popen(
         command,
@@ -816,7 +816,7 @@ def pipe_notebook(notebook, command, fmt="py:percent", update=True, prefix=None)
     fmt = check_auto_ext(fmt, notebook.metadata, "--pipe-fmt")
     text = writes(notebook, fmt)
 
-    command = command.split(" ")
+    command = shlex.split(command)
     if "{}" in command:
         if prefix is not None:
             prefix = prefix + (" " if " " in prefix else "_")

tests/test_isort.py

@@ -0,0 +1,43 @@
+from jupytext import reads, writes
+from jupytext.cli import pipe_notebook
+from jupytext.compare import compare
+
+from .utils import requires_isort
+
+
+@requires_isort
+def test_pipe_into_isort():
+    text_org = """# %%
+import numpy as np
+np.array([1,2,3])
+
+# %%
+import pandas as pd
+pd.Series([1,2,3])
+
+# %%
+# This is a comment on the second import
+import pandas as pd
+pd.Series([4,5,6])
+"""
+
+    text_target = """# %%
+import numpy as np
+# This is a comment on the second import
+import pandas as pd
+
+np.array([1,2,3])
+
+# %%
+pd.Series([1,2,3])
+
+# %%
+pd.Series([4,5,6])
+"""
+
+    nb_org = reads(text_org, fmt="py:percent")
+    nb_pipe = pipe_notebook(
+        nb_org, 'isort - --treat-comment-as-code "# %%" --float-to-top'
+    )
+    text_actual = writes(nb_pipe, "py:percent")
+    compare(text_actual, text_target)

tests/test_using_cli.py

@@ -1,5 +1,4 @@
 import os
-import re
 import shlex
 import pytest
 import jupytext
@@ -36,12 +35,23 @@ def test_jupytext_commands_in_the_documentation_work(tmpdir):
         for cmd in cell.source.splitlines():
             if not cmd.startswith("jupytext"):
                 continue
+
+            # Do not test commands that involve reading a notebook from stdin
             if "read ipynb from stdin" in cmd:
                 continue
+
+            # We can't run pytest inside pytest
             if "pytest {}" in cmd:
                 continue
+
+            # We need to remove the comments that may follow the jupytext command
+            if "#" in cmd:
+                left, comment = cmd.rsplit("#", 1)
+                if '"' not in comment:
+                    cmd = left
+
             print("Testing: {}".format(cmd))
-            args = shlex.split(re.sub(r"#.*", "", cmd))[1:]
+            args = shlex.split(cmd)[1:]
             assert not jupytext_cli(args), cmd
             cmd_tested += 1
 

tests/utils.py

@@ -27,6 +27,7 @@ def tool_version(tool):
     not tool_version("jupytext"), reason="jupytext is not installed"
 )
 requires_black = pytest.mark.skipif(not tool_version("black"), reason="black not found")
+requires_isort = pytest.mark.skipif(not tool_version("isort"), reason="isort not found")
 requires_flake8 = pytest.mark.skipif(
     not tool_version("flake8"), reason="flake8 not found"
 )