Merge pull request #60 from mwouts/v0.6.3

V0.6.3
Fixes #57 
Fixes #46

HISTORY.rst

@@ -6,6 +6,19 @@ Release History
 dev
 +++
 
+0.6.3 (2018-09-07)
++++++++++++++++++++
+
+**Improvements**
+
+- Lighter cell markers for Python and Julia scripts (#57). Corresponding file
+format version at 1.2. Scripts in previous version 1.1 can still be opened.
+- New screenshots for the README.
+
+**BugFixes**
+
+- Command line conversion tool `jupytext` fixed on Python 2.7 (#46)
+
 0.6.2 (2018-09-05)
 +++++++++++++++++++
 

README.md

@@ -146,7 +146,7 @@ Implement these [specifications](https://rmarkdown.rstudio.com/articles_report_f
 We wanted to represent Jupyter notebooks with the least explicit markers possible. The rationale for that is to allow **arbitrary** python files to open as Jupyter notebooks, even files which were never prepared to become a notebook. Precisely:
 - Jupyter metadata go to an escaped YAML header
 - Markdown cells are commented with `# `, and separated with a blank line
-- Code cells are exported verbatim (except for Jupyter magics, which are escaped), and separated with blank lines. Code cells are reconstructed from consistent python paragraphs (no function, class or multiline comment will be broken). A start-of-cell delimiter `# + {}` is used for cells that have explicit metadata (inside the curly bracket, in JSON format), and for cells that include blank lines (outside of functions, classes, etc). The end of cell delimiter is `# -`, and is omitted when followed by another explicit start of cell marker.
+- Code cells are exported verbatim (except for Jupyter magics, which are escaped), and separated with blank lines. Code cells are reconstructed from consistent python paragraphs (no function, class or multiline comment will be broken). A start-of-cell delimiter `# + {}` is used for cells that have explicit metadata (inside the curly bracket, in JSON format), and `# +` is used for cells that include blank lines (outside of functions, classes, etc). The end of cell delimiter is `# -`, and is omitted when followed by another explicit start of cell marker.
 
 ## Will my notebook really run in an IDE?
 

binder/requirements.txt

@@ -1,4 +1,4 @@
-jupytext>=0.6.2
+jupytext>=0.6.3
 plotly
 matplotlib
 pandas

demo/Paired Jupyter notebook and python script.py

@@ -14,7 +14,7 @@
 #     nbconvert_exporter: python
 #     pygments_lexer: ipython3
 #     version: 3.6.5
-#   jupytext_format_version: '1.1'
+#   jupytext_format_version: '1.2'
 #   jupytext_formats: ipynb,py
 # ---
 
@@ -36,7 +36,7 @@
 
 # %matplotlib inline
 
-# + {}
+# +
 import matplotlib.pyplot as plt
 import numpy as np
 

demo/World population.py

@@ -1,6 +1,6 @@
 # ---
 # jupyter:
-#   jupytext_format_version: '1.1'
+#   jupytext_format_version: '1.2'
 #   jupytext_formats: ipynb,py,md
 #   kernelspec:
 #     display_name: Python 3
@@ -26,7 +26,7 @@
 # [World Bank](http://www.worldbank.org/)
 # using the [wbdata](https://github.com/OliverSherouse/wbdata) python package
 
-# + {}
+# +
 import pandas as pd
 import wbdata as wb
 
@@ -90,7 +90,7 @@
 # [on their way](https://github.com/plotly/plotly.js/pull/2960) at Plotly. For
 # now we just do a stacked bar plot.
 
-# + {}
+# +
 import plotly.offline as offline
 import plotly.graph_objs as go
 

jupytext/cell_reader.py

@@ -12,6 +12,7 @@
 _END_CODE_MD = re.compile(r"^```\s*$")
 _CODE_OPTION_R = re.compile(r"^#\+(.*)\s*$")
 _CODE_OPTION_PY = re.compile(r"^(#|# )\+(\s*){(.*)}\s*$")
+_SIMPLE_START_CODE_PY = re.compile(r"^(#|# )\+(\s*)$")
 _BLANK_LINE = re.compile(r"^\s*$")
 _PY_COMMENT = re.compile(r"^\s*#")
 _PY_INDENTED = re.compile(r"^\s")
@@ -123,10 +124,14 @@ def metadata_and_language_from_option_line(self, line):
             self.language, self.metadata = \
                 rmd_options_to_metadata('r ' + _CODE_OPTION_R.findall(line)[0])
 
-        if self.ext in ['.py', '.jl'] and _CODE_OPTION_PY.match(line):
-            self.language = 'python' if self.ext == '.py' else 'julia'
-            self.metadata = json_options_to_metadata(
-                _CODE_OPTION_PY.match(line).group(3))
+        if self.ext in ['.py', '.jl']:
+            if _CODE_OPTION_PY.match(line):
+                self.language = 'python' if self.ext == '.py' else 'julia'
+                self.metadata = json_options_to_metadata(
+                    _CODE_OPTION_PY.match(line).group(3))
+            if _SIMPLE_START_CODE_PY.match(line):
+                self.language = 'python' if self.ext == '.py' else 'julia'
+                self.metadata = {}
 
         if self.metadata and 'language' in self.metadata:
             self.language = self.metadata['language']
@@ -225,6 +230,11 @@ def find_cell_end_code(self, lines, cell_end_re,
                     return i - 1, i, False
                 return i, i, False
 
+            if i > 0 and cell_start_re == _CODE_OPTION_PY and \
+                    _BLANK_LINE.match(lines[i - 1]) and \
+                    _SIMPLE_START_CODE_PY.match(line):
+                return i - 1, i, False
+
             if cell_end_re:
                 if cell_end_re.match(line):
                     return i, i + 1, True

jupytext/file_format_version.py

@@ -12,8 +12,10 @@
     # Version 1.0 on 2018-08-31 - jupytext v0.6.0 : Initial version
 
     # Python and Julia scripts
-    '.py': '1.1',
-    '.jl': '1.1',
+    '.py': '1.2',
+    '.jl': '1.2',
+    # Version 1.2 on 2018-09-05 - jupytext v0.6.3 : Metadata bracket can be
+    # omitted when empty, if previous line is empty #57
     # Version 1.1 on 2018-08-25 - jupytext v0.6.0 : Cells separated with one
     # blank line #38
     # Version 1.0 on 2018-08-22 - jupytext v0.5.2 : Initial version
@@ -23,6 +25,9 @@
     # Version 1.0 on 2018-08-22 - jupytext v0.5.2 : Initial version
 }
 
+MIN_FILE_FORMAT_VERSION = {'.Rmd': '1.0', '.md': '1.0', '.py': '1.1',
+                           '.jl': '1.1', '.R': '1.0'}
+
 FILE_FORMAT_VERSION_ORG = FILE_FORMAT_VERSION
 
 
@@ -31,6 +36,11 @@ def file_format_version(ext):
     return FILE_FORMAT_VERSION.get(ext)
 
 
+def min_file_format_version(ext):
+    """Return minimum file format version for given ext"""
+    return MIN_FILE_FORMAT_VERSION.get(ext)
+
+
 def check_file_version(notebook, source_path, outputs_path):
     """Raise if file version in source file would override outputs"""
     _, ext = os.path.splitext(source_path)
@@ -47,7 +57,11 @@ def check_file_version(notebook, source_path, outputs_path):
     if version == current:
         return
 
-    # Not merging? OK
+    # Version larger than minimum readable version
+    if version <= current and version >= min_file_format_version(ext):
+        return
+
+        # Not merging? OK
     if source_path == outputs_path:
         return
 

jupytext/jupytext.py

@@ -125,6 +125,10 @@ def writes(self, nb, **kwargs):
         for i, cell in enumerate(cells):
             text = texts[i]
 
+            # Simplify cell marker when previous line is blank
+            if text[0] == '# + {}' and (not lines or not lines[-1]):
+                text[0] = '# +'
+
             # remove end of cell marker when redundant
             # with next explicit marker
             if self.ext in ['.py', '.jl'] and cell.is_code() \

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='jupytext',
-    version='0.6.2',
+    version='0.6.3',
     author='Marc Wouts',
     author_email='marc.wouts@gmail.com',
     description='Jupyter notebooks as Markdown documents, '

tests/python_notebook_sample.py

@@ -31,7 +31,7 @@ def f(x):
 # metadata and an end-of-cell marker. Metadata information in json format,
 # escaped with '#+' or '# +'
 
-# + {}
+# +
 def g(x):
     return x + 2
 

tests/test_cli.py

@@ -10,6 +10,7 @@
 from .utils import list_all_notebooks, list_py_notebooks
 
 file_format_version.FILE_FORMAT_VERSION = {}
+file_format_version.MIN_FILE_FORMAT_VERSION = {}
 
 
 @pytest.mark.parametrize('nb_file',
@@ -172,4 +173,7 @@ def test_combine_lower_version_raises(tmpdir):
     with pytest.raises(SystemExit):
         with mock.patch('jupytext.file_format_version.FILE_FORMAT_VERSION',
                         {'.py': '1.0'}):
-            jupytext(args=[tmp_nbpy, '--to', 'ipynb', '--update'])
+            with mock.patch(
+                    'jupytext.file_format_version.MIN_FILE_FORMAT_VERSION',
+                            {'.py': '1.0'}):
+                jupytext(args=[tmp_nbpy, '--to', 'ipynb', '--update'])

tests/test_contentsmanager.py

@@ -7,6 +7,7 @@
 from .utils import list_all_notebooks, list_py_notebooks
 
 jupytext.file_format_version.FILE_FORMAT_VERSION = {}
+jupytext.file_format_version.MIN_FILE_FORMAT_VERSION = {}
 
 
 @pytest.mark.skipif(isinstance(TextFileContentsManager, str),

tests/test_load_multiple.py

@@ -60,4 +60,7 @@ def test_combine_lower_version_raises(tmpdir):
     with pytest.raises(HTTPError):
         with mock.patch('jupytext.file_format_version.FILE_FORMAT_VERSION',
                         {'.py': '1.0'}):
-            cm.get(tmp_ipynb)
+            with mock.patch(
+                    'jupytext.file_format_version.MIN_FILE_FORMAT_VERSION',
+                            {'.py': '1.0'}):
+                cm.get(tmp_ipynb)

tests/test_read_simple_python.py

@@ -116,7 +116,7 @@ def test_read_cell_two_blank_lines(pynb="""# ---
 # title: cell with two consecutive blank lines
 # ---
 
-# + {}
+# +
 a = 1
 
 
@@ -137,7 +137,7 @@ def test_read_cell_two_blank_lines(pynb="""# ---
 
 def test_read_cell_explicit_start(pynb='''
 import pandas as pd
-# + {}
+# +
 def data():
     return pd.DataFrame({'A': [0, 1]})
 
@@ -151,21 +151,21 @@ def data():
 
 def test_read_complex_cells(pynb='''import pandas as pd
 
-# + {}
+# +
 def data():
     return pd.DataFrame({'A': [0, 1]})
 
 
 data()
 
-# + {}
+# +
 def data2():
     return pd.DataFrame({'B': [0, 1]})
 
 
 data2()
 
-# + {}
+# +
 # Finally we have a cell with only comments
 # This cell should remain a code cell and not get converted
 # to markdown
@@ -203,7 +203,7 @@ def data2():
 def test_read_prev_function(
         pynb="""def test_read_cell_explicit_start_end(pynb='''
 import pandas as pd
-# + {}
+# +
 def data():
     return pd.DataFrame({'A': [0, 1]})
 
@@ -228,7 +228,7 @@ def test_read_cell_with_one_blank_line_end(pynb="""import pandas
     compare(pynb, pynb2)
 
 
-def test_read_code_cell_fully_commented(pynb="""# + {}
+def test_read_code_cell_fully_commented(pynb="""# +
 # This is a code cell that
 # only contains comments
 """):
@@ -250,7 +250,7 @@ def test_file_with_two_blank_line_end(pynb="""import pandas
     compare(pynb, pynb2)
 
 
-def test_one_blank_lines_after_endofcell(pynb="""# + {}
+def test_one_blank_lines_after_endofcell(pynb="""# +
 # This is a code cell with explicit end of cell
 1 + 1
 
@@ -275,13 +275,13 @@ def test_one_blank_lines_after_endofcell(pynb="""# + {}
     compare(pynb, pynb2)
 
 
-def test_two_cells_with_explicit_start(pynb="""# + {}
+def test_two_cells_with_explicit_start(pynb="""# +
 # Cell one
 1 + 1
 
 1 + 1
 
-# + {}
+# +
 # Cell two
 2 + 2
 
@@ -303,7 +303,7 @@ def test_two_cells_with_explicit_start(pynb="""# + {}
     compare(pynb, pynb2)
 
 
-def test_escape_start_pattern(pynb="""# The code start pattern '# + {}' can
+def test_escape_start_pattern(pynb="""# The code start pattern '# +' can
 # appear in code and markdown cells.
 
 # In markdown cells it is escaped like here:
@@ -454,7 +454,7 @@ def test_read_write_script(pynb="""#!/usr/bin/env python
     compare(pynb, pynb2)
 
 
-def test_notebook_blank_lines(script="""# + {}
+def test_notebook_blank_lines(script="""# +
 # This is a comment
 # followed by two variables
 a = 3
@@ -466,7 +466,7 @@ def test_notebook_blank_lines(script="""# + {}
 c = 5
 
 
-# + {}
+# +
 # Now we have two functions
 def f(x):
     return x + x