ENH: allow for flexible order (#76)

* allow for flexible order

* clarify readme

* typo

README.rst

@@ -53,18 +53,18 @@ The general syntax is
 
 .. code-block:: bash
 
-    nbqa <command> <notebook or directory> <flags>
+    nbqa -c <command> <args>
 
-For example, you could run:
+, where :code:`command` is any Python code quality tool. For example, you could run:
 
 .. code-block:: bash
 
-    $ nbqa flake8 my_notebook.ipynb
-    $ nbqa black my_notebook.ipynb --check
-    $ nbqa mypy my_notebook.ipynb --ignore-missing-imports
-    $ nbqa pytest my_notebook.ipynb --doctest-modules
+    $ nbqa -c flake8 my_notebook.ipynb
+    $ nbqa -c black my_notebook.ipynb --check
+    $ nbqa -c mypy my_notebook.ipynb --ignore-missing-imports
+    $ nbqa -c pytest my_notebook.ipynb --doctest-modules
 
-You can also pass an entire directory instead of a single file, e.g. :code:`nbqa flake8 my_notebooks`.
+You can also pass an entire directory instead of a single file, e.g. :code:`nbqa -c flake8 my_notebooks`.
 
 Examples
 --------
@@ -73,7 +73,7 @@ Format your notebooks using :code:`black`:
 
 .. code-block:: bash
 
-    $ nbqa black .
+    $ nbqa -c black .
     reformatted tweet-sentiment-roberta-pytorch.ipynb
     All done! ✨ 🍰 ✨
     1 files reformatted.
@@ -82,14 +82,14 @@ Check static type annotations:
 
 .. code-block:: bash
 
-    $ nbqa mypy tweet-sentiment-roberta-pytorch.ipynb --ignore-missing-imports
+    $ nbqa -c mypy tweet-sentiment-roberta-pytorch.ipynb --ignore-missing-imports
     tweet-sentiment-roberta-pytorch.ipynb:cell_10:5: error: Argument "batch_size" to "get_test_loader" has incompatible type "str"; expected "int"
 
 Check any examples in your docstrings are correct:
 
 .. code-block:: bash
 
-    $ nbqa pytest tweet-sentiment-roberta-pytorch.ipynb --doctest-modules
+    $ nbqa -c pytest tweet-sentiment-roberta-pytorch.ipynb --doctest-modules
     ============================= test session starts ==============================
     platform linux -- Python 3.8.2, pytest-5.4.3, py-1.9.0, pluggy-0.13.1
     rootdir: /home/marco/tweet-sentiment-extraction

nbqa/__main__.py

@@ -24,7 +24,7 @@ def _parse_args(raw_args):
         description="Adapter to run any code-quality tool on a Jupyter notebook.",
         usage="nbqa <command> <notebook or directory> <flags>",
     )
-    parser.add_argument("command", help="Command to run, e.g. `flake8`.")
+    parser.add_argument("-c", "--command", help="Command to run, e.g. `flake8`.")
     parser.add_argument(
         "root_dir", default=".", nargs="?", help="File or directory to run command on."
     )

tests/data/test_isort_works.py

@@ -13,7 +13,7 @@ def test_isort_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["isort", "tests/data/notebook_for_testing.ipynb"])
+        main(["--command=isort", "tests/data/notebook_for_testing.ipynb"])
 
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()

tests/test_black.py

@@ -13,7 +13,7 @@ def test_black_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["black", "tests/data/notebook_for_testing.ipynb"])
+        main(["--command=black", "tests/data/notebook_for_testing.ipynb"])
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()
 

tests/test_doctest.py

@@ -17,7 +17,7 @@ def test_pytest_doctest_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["pytest", "--doctest-modules"])
+        main(["--command=pytest", "--doctest-modules"])
 
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()

tests/test_flake8_works.py

@@ -13,7 +13,7 @@ def test_flake8_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["flake8"])
+        main(["--command=flake8"])
 
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()

tests/test_isort_works.py

@@ -13,7 +13,7 @@ def test_isort_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["isort", "tests/data/notebook_for_testing.ipynb"])
+        main(["--command=isort", "tests/data/notebook_for_testing.ipynb"])
 
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()
@@ -38,7 +38,7 @@ def test_isort_initial_md(tmp_notebook_starting_with_md, capsys):
     with open(tmp_notebook_starting_with_md, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["isort", "tests/data/notebook_starting_with_md.ipynb"])
+        main(["--command=isort", "tests/data/notebook_starting_with_md.ipynb"])
 
     with open(tmp_notebook_starting_with_md, "r") as handle:
         after = handle.readlines()

tests/test_missing_command.py

@@ -10,4 +10,4 @@ def test_missing_command():
         "Please make sure you have it installed before running nbQA on it."
     )
     with pytest.raises(ValueError, match=msg):
-        main([command, "--some-flag"])
+        main([f"--command={command}", "--some-flag"])

tests/test_mypy_works.py

@@ -14,7 +14,7 @@ def test_mypy_works(tmp_notebook_for_testing, capsys):
     with open(tmp_notebook_for_testing, "r") as handle:
         before = handle.readlines()
     with pytest.raises(SystemExit):
-        main(["mypy", "--ignore-missing-imports"])
+        main(["--command=mypy", "--ignore-missing-imports"])
 
     with open(tmp_notebook_for_testing, "r") as handle:
         after = handle.readlines()

tests/test_return_code.py

@@ -3,14 +3,28 @@
 
 def test_flake8_return_code():
     output = subprocess.run(
-        ["python", "-m", "nbqa", "flake8", "tests/data/notebook_for_testing.ipynb"]
+        [
+            "python",
+            "-m",
+            "nbqa",
+            "--command",
+            "flake8",
+            "tests/data/notebook_for_testing.ipynb",
+        ]
     )
     result = output.returncode
     expected = 1
     assert result == expected
 
     output = subprocess.run(
-        ["python", "-m", "nbqa", "flake8", "tests/data/clean_notebook.ipynb"]
+        [
+            "python",
+            "-m",
+            "nbqa",
+            "--command",
+            "flake8",
+            "tests/data/clean_notebook.ipynb",
+        ]
     )
     result = output.returncode
     expected = 0
@@ -33,13 +47,21 @@ def test_black_return_code():
     assert result == expected
 
     output = subprocess.run(
-        ["python", "-m", "nbqa", "black", "tests/data/clean_notebook.ipynb", "--check"]
+        [
+            "python",
+            "-m",
+            "nbqa",
+            "-c",
+            "black",
+            "--check",
+            "tests/data/clean_notebook.ipynb",
+        ]
     )
     result = output.returncode
     expected = 0
     assert result == expected
 
-    output = subprocess.run(["python", "-m", "nbqa", "black", "--check"])
+    output = subprocess.run(["python", "-m", "nbqa", "--command", "black", "--check"])
     result = output.returncode
     expected = 1
     assert result == expected
@@ -49,6 +71,7 @@ def test_black_return_code():
             "python",
             "-m",
             "nbqa",
+            "--command",
             "black",
             "tests/data/clean_notebook.ipynb",
             "--check",