Merge pull request #78 from rasbt/v0.2.8

Version 0.2.8

Author: rasbt

biopandas/__init__.py

@@ -24,5 +24,5 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.3.0'
+__version__ = '0.2.8'
 __author__ = "Sebastian Raschka <[email protected]>"

docs/CHANGELOG.md

@@ -4,12 +4,12 @@ The CHANGELOG for the current development version is available at
 [https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md).
 
 
-### 0.3.0 (TBA)
+### 0.2.8 (03-30-2021)
 
 ##### Downloads
 
-- [Source code (zip)](https://github.com/rasbt/biopandas/archive/v0.3.0.zip)
-- [Source code (tar.gz)](https://github.com/rasbt/biopandas/archive/v0.3.0.tar.gz)
+- [Source code (zip)](https://github.com/rasbt/biopandas/archive/v0.2.8.zip)
+- [Source code (tar.gz)](https://github.com/rasbt/biopandas/archive/v0.2.8.tar.gz)
 
 ##### New Features
 

docs/ipynb2markdown.py

@@ -0,0 +1,100 @@
+# IPython Notebook to Markdown conversion script
+#
+# Sebastian Raschka 2014-2021
+#
+# Author: Sebastian Raschka <sebastianraschka.com>
+#
+# License: BSD 3 clause
+
+import subprocess
+import glob
+import shutil
+import os
+import markdown
+from markdown.treeprocessors import Treeprocessor
+from markdown.extensions import Extension
+from nbconvert.exporters import MarkdownExporter
+
+
+class ImgExtractor(Treeprocessor):
+    def run(self, doc):
+        self.markdown.images = []
+        for image in doc.findall('.//img'):
+            self.markdown.images.append(image.get('src'))
+
+
+class ImgExtExtension(Extension):
+    def extendMarkdown(self, md, md_globals):
+        img_ext = ImgExtractor(md)
+        md.treeprocessors.add('imgext', img_ext, '>inline')
+
+
+def ipynb_to_md(ipynb_path):
+    orig_path = os.getcwd()
+    os.chdir(os.path.dirname(ipynb_path))
+    file_name = os.path.basename(ipynb_path)
+    subprocess.call(['python', '-m', 'nbconvert',
+                     '--to', 'markdown', file_name])
+
+    new_s = []
+    md_name = file_name.replace('.ipynb', '.md')
+    with open(md_name, 'r') as f:
+        for line in f:
+            if line.startswith('#'):
+                new_s.append(line)
+                break
+        for line in f:
+            if line.startswith(('## API', '# API')):
+                new_s.append(line)
+                new_s.append('\n')
+                break
+            new_s.append(line)
+        for line in f:
+            if line.lstrip().startswith('#'):
+                break
+        for line in f:
+            new_s.append(line[4:])
+
+    with open(md_name, 'w') as f:
+        f.write(''.join(new_s))
+    os.chdir(orig_path)
+
+
+# md = markdown.Markdown(extensions=[ImgExtExtension()])
+# html = md.convert(data)
+# print(md.images)
+
+
+if __name__ == "__main__":
+
+    import argparse
+    parser = argparse.ArgumentParser(
+            description='Convert docstring into a markdown API documentation.',
+            formatter_class=argparse.RawTextHelpFormatter)
+
+    parser.add_argument('-i', '--ipynb',
+                        help='Path to the IPython file')
+
+    parser.add_argument('-a', '--all',
+                        help='Path to parse all ipynb recursively')
+
+    parser.add_argument('-v', '--version',
+                        action='version',
+                        version='v. 0.1')
+
+    args = parser.parse_args()
+
+    if args.all and args.ipynb:
+        raise AttributeError('Conflicting flags --ipynb and --all; choose one')
+
+    if args.ipynb:
+        ipynb_to_md(ipynb_path=args.ipynb)
+    else:
+        tree = os.walk(args.all)
+        for d in tree:
+            filenames = glob.glob(os.path.join(d[0], '*'))
+            for f in filenames:
+                if f.endswith('.ipynb'):
+                    print(f)
+
+                    ipynb_to_md(ipynb_path=f)

docs/sources/api_subpackages/biopandas.mol2.md

@@ -1,4 +1,5 @@
-biopandas version: 0.3.0
+biopandas version: 0.2.8
+
 ## PandasMol2
 
 *PandasMol2()*

docs/sources/api_subpackages/biopandas.pdb.md

@@ -1,4 +1,5 @@
-biopandas version: 0.3.0
+biopandas version: 0.2.8
+
 ## PandasPdb
 
 *PandasPdb()*

docs/sources/api_subpackages/biopandas.testutils.md

@@ -1,4 +1,5 @@
-biopandas version: 0.3.0
+biopandas version: 0.2.8
+
 ## assert_raises
 
 *assert_raises(exception_type, message, func, *args, **kwargs)*

docs/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb

@@ -52,7 +52,7 @@ print('\nRaw MOL2 file contents:\n\n%s\n...' % pmol.mol2_text[:500])
     ...
 
 
-The most interesting and useful attribute, however, is the [`PandasMol2.df`](../api_subpackages/biopandas.mol2#pandasmol2df) DataFrame, which contains the ATOM section of the MOL2 structure. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:
+The most interesting and useful attribute, however, is the [`PandasMol2.df`](../api/biopandas.mol2#pandasmol2df) DataFrame, which contains the ATOM section of the MOL2 structure. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:
 
 
 ```python
@@ -689,7 +689,9 @@ plt.show()
 ```
 
 
+    
 ![png](Working_with_MOL2_Structures_in_DataFrames_files/Working_with_MOL2_Structures_in_DataFrames_34_0.png)
+    
 
 
 If this is too fine-grained for our needs, we could summarize the different atom types by atomic elements:
@@ -705,7 +707,9 @@ plt.show()
 ```
 
 
+    
 ![png](Working_with_MOL2_Structures_in_DataFrames_files/Working_with_MOL2_Structures_in_DataFrames_36_0.png)
+    
 
 
 One of the coolest features in pandas is the groupby method. Below is an example plotting the average charge of the different atom types with the standard deviation as error bars:
@@ -719,7 +723,9 @@ plt.show()
 ```
 
 
+    
 ![png](Working_with_MOL2_Structures_in_DataFrames_files/Working_with_MOL2_Structures_in_DataFrames_38_0.png)
+    
 
 
 ## Computing the Root Mean Square Deviation
@@ -1180,21 +1186,6 @@ from biopandas.mol2 import split_multimol2
 ```
 
 
-    ---------------------------------------------------------------------------
-
-    ModuleNotFoundError                       Traceback (most recent call last)
-
-    <ipython-input-23-1a655249f2ec> in <module>()
-          1 import pandas as pd
-    ----> 2 from mputil import lazy_imap
-          3 from biopandas.mol2 import PandasMol2
-          4 from biopandas.mol2 import split_multimol2
-
-
-    ModuleNotFoundError: No module named 'mputil'
-
-
-
 ```python
 # Selection strings to capture
 # all molecules that contain at least one sp2 hybridized