v0.2.4 (#56)

BioPandas · Feb 6, 2019 · 615a7cf · 615a7cf
1 parent 985dbaf
commit 615a7cf
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Showing 18 changed files with 543 additions and 284 deletions.
diff --git a/biopandas/__init__.py b/biopandas/__init__.py
@@ -24,5 +24,5 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.2.4.dev0'
+__version__ = '0.2.4'
 __author__ = "Sebastian Raschka <mail@sebastianraschka.com>"
diff --git a/biopandas/pdb/pandas_pdb.py b/biopandas/pdb/pandas_pdb.py
@@ -20,6 +20,10 @@
 from .engines import pdb_df_columns
 from .engines import amino3to1dict
 import warnings
+from distutils.version import LooseVersion
+
+
+pd_version = LooseVersion(pd.__version__)
 
 
 class PandasPdb(object):
@@ -516,16 +520,22 @@ def to_pdb(self, path, records=None, gz=False, append_newline=True):
                 else:
                     dfs[r]['OUT'] = dfs[r]['OUT'] + dfs[r][c]
 
-        df = pd.concat(dfs)
-        if pd.__version__ < '0.17.0':
+        if pd_version < LooseVersion('0.17.0'):
             warn("You are using an old pandas version (< 0.17)"
                  " that relies on the old sorting syntax."
                  " Please consider updating your pandas"
                  " installation to a more recent version.",
                  DeprecationWarning)
             df.sort(columns='line_idx', inplace=True)
+
+        elif pd_version < LooseVersion('0.23.0'):
+            df = pd.concat(dfs)
+
         else:
-            df.sort_values(by='line_idx', inplace=True)
+            df = pd.concat(dfs, sort=False)
+
+        df.sort_values(by='line_idx', inplace=True)
+
         with openf(path, w_mode) as f:
 
             s = df['OUT'].tolist()

diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -11,13 +11,15 @@ docs_dir: sources
 
 site_favicon: favicon.ico
 
-theme_dir: cinder
+theme:
+  name: null
+  custom_dir: "./cinder"
 
 markdown_extensions:
-  - extra
   - tables
   - fenced_code
-  - mathjax
+  - mdx_math:
+      enable_dollar_delimiter: True #for use of inline $..$
 extra_javascript:
   - https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML
   - mathjaxhelper.js

diff --git a/docs/sources/CHANGELOG.md b/docs/sources/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-### 0.2.4 (TBD)
+### 0.2.4 (02-05-2019)
 
 ##### Downloads
 
@@ -16,7 +16,7 @@ The CHANGELOG for the current development version is available at
 
 ##### Changes
 
-- -
+- Minor adjustments to support to address deprecation warnings in pandas >= 23.0
 
 ##### Bug Fixes
 

diff --git a/docs/sources/api_subpackages/biopandas.mol2.md b/docs/sources/api_subpackages/biopandas.mol2.md
@@ -1,4 +1,4 @@
-biopandas version: 0.2.3dev0
+biopandas version: 0.2.4
 ## PandasMol2
 
 *PandasMol2()*

diff --git a/docs/sources/api_subpackages/biopandas.pdb.md b/docs/sources/api_subpackages/biopandas.pdb.md
@@ -1,4 +1,4 @@
-biopandas version: 0.2.3dev0
+biopandas version: 0.2.4
 ## PandasPdb
 
 *PandasPdb()*

diff --git a/docs/sources/api_subpackages/biopandas.testutils.md b/docs/sources/api_subpackages/biopandas.testutils.md
@@ -1,4 +1,4 @@
-biopandas version: 0.2.3dev0
+biopandas version: 0.2.4
 ## assert_raises
 
 *assert_raises(exception_type, message, func, *args, **kwargs)*

diff --git a/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb b/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb