v0.2.5 (#59)

* modernized setup.py * include insertion codes in amino3to1 * pep8 fixes * update conda command * update travis config * update travis installer scripts * disable systemwide packages * old conda style syntax to disable system conda * use more recent conda installer * fix conda install * conda init * conda init
BioPandas · Jul 9, 2019 · 3f78c91 · 3f78c91
1 parent 615a7cf
commit 3f78c91
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diff --git a/.travis.yml b/.travis.yml
@@ -1,12 +1,12 @@
 language: python
 virtualenv:
-  system_site_packages: true
+  system_site_packages: false
 env:
   matrix:
     - PYTHON_VERSION="2.7" LATEST="true"
-    - PYTHON_VERSION="3.5" LATEST="true"
-    - PYTHON_VERSION="3.6" NUMPY_VERSION="1.11.2" SCIPY_VERSION="0.18.1" PANDAS_VERSION="0.19.1"
-    - PYTHON_VERSION="3.6" COVERAGE="true" LATEST="true"
+    - PYTHON_VERSION="3.7" LATEST="true"
+    - PYTHON_VERSION="3.7" COVERAGE="false" NUMPY_VERSION="1.16.2" SCIPY_VERSION="1.2.1" PANDAS_VERSION="0.24.2"
+    - PYTHON_VERSION="3.7" COVERAGE="true" LATEST="true"
 install: source ./ci/.travis_install.sh
 script: bash ./ci/.travis_test.sh
 after_success:

diff --git a/LICENSE → LICENSE.txt b/LICENSE → LICENSE.txt
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'
+__version__ = '0.2.5'
 __author__ = "Sebastian Raschka <mail@sebastianraschka.com>"
diff --git a/biopandas/pdb/pandas_pdb.py b/biopandas/pdb/pandas_pdb.py
@@ -406,7 +406,10 @@ def amino3to1(self, record='ATOM',
         cmp = 'placeholder'
         indices = []
 
-        for num, ind in zip(tmp['residue_number'], np.arange(tmp.shape[0])):
+        residue_number_insertion = (tmp['residue_number'].astype(str)
+                                    + tmp['insertion'])
+
+        for num, ind in zip(residue_number_insertion, np.arange(tmp.shape[0])):
             if num != cmp:
                 indices.append(ind)
             cmp = num
@@ -526,7 +529,7 @@ def to_pdb(self, path, records=None, gz=False, append_newline=True):
                  " Please consider updating your pandas"
                  " installation to a more recent version.",
                  DeprecationWarning)
-            df.sort(columns='line_idx', inplace=True)
+            dfs.sort(columns='line_idx', inplace=True)
 
         elif pd_version < LooseVersion('0.23.0'):
             df = pd.concat(dfs)

diff --git a/biopandas/pdb/tests/data/2d7t.pdb b/biopandas/pdb/tests/data/2d7t.pdb
diff --git a/biopandas/pdb/tests/test_amino3to1.py b/biopandas/pdb/tests/test_amino3to1.py
@@ -106,3 +106,12 @@ def test_multichain():
     assert expect_res_a == got_res_a
     assert expect_res_b == got_res_b
 
+
+def test_pdb_with_insertion_codes():
+
+    PDB_2D7T_PATH = os.path.join(os.path.dirname(__file__),
+                                 'data', '2d7t.pdb')
+
+    ppdb = PandasPdb().read_pdb(PDB_2D7T_PATH)
+    sequence = ppdb.amino3to1()
+    assert "".join(sequence[50:60]['residue_name'].values) == 'INPKSGDTNY'
diff --git a/ci/.travis_install.sh b/ci/.travis_install.sh
@@ -19,11 +19,15 @@ deactivate
 
 # Use the miniconda installer for faster download / install of conda
 # itself
-wget http://repo.continuum.io/miniconda/Miniconda-3.9.1-Linux-x86_64.sh \
-    -O miniconda.sh
-chmod +x miniconda.sh && ./miniconda.sh -b
-export PATH=/home/travis/miniconda/bin:$PATH
-conda update --yes conda
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+
+bash miniconda.sh -b -p $HOME/miniconda
+export PATH="$HOME/miniconda/bin:$PATH"
+hash -r
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+conda update -q pip
+conda info -a
 
 # Configure the conda environment and put it in the path using the
 # provided versions
@@ -36,6 +40,7 @@ else
 	    pandas=$PANDAS_VERSION 
 fi
 
+conda init bash
 source activate testenv
 
 if [[ "$COVERAGE" == "true" ]]; then

diff --git a/docs/sources/CHANGELOG.md b/docs/sources/CHANGELOG.md
@@ -3,12 +3,33 @@
 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).
 
+### 0.2.5 (07-09-2019)
+
+##### Downloads
+
+- [Source code (zip)](https://github.com/rasbt/biopandas/archive/v0.2.5.zip)
+- [Source code (tar.gz)](https://github.com/rasbt/biopandas/archive/v0.2.5.tar.gz)
+
+##### New Features
+
+- -
+
+##### Changes
+
+- -
+
+##### Bug Fixes
+
+- The `PandasPdb.amino3to1` method now also considers insertion codes when converting the amino acid codes; before, inserted amino acides were skipped. 
+
+
+
 ### 0.2.4 (02-05-2019)
 
 ##### Downloads
 
-- [Source code (zip)]
-- [Source code (tar.gz)]
+- [Source code (zip)](https://github.com/rasbt/biopandas/archive/v0.2.4.zip)
+- [Source code (tar.gz)](https://github.com/rasbt/biopandas/archive/v0.2.4.tar.gz)
 
 ##### New Features
 

diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,2 @@
+numpy>=1.16.2
+pandas>=0.24.2
diff --git a/setup.py b/setup.py
@@ -1,65 +1,43 @@
-from pkgutil import walk_packages
-from fnmatch import fnmatch as wc_match
-from itertools import chain
+from os.path import realpath, dirname, join
+from setuptools import setup, find_packages
+import biopandas
 
+VERSION = biopandas.__version__
+PROJECT_ROOT = dirname(realpath(__file__))
 
-try:
-    from setuptools import setup
-except ImportError:
-    from distutils.core import setup
+REQUIREMENTS_FILE = join(PROJECT_ROOT, 'requirements.txt')
 
+with open(REQUIREMENTS_FILE) as f:
+    install_reqs = f.read().splitlines()
 
-def find_packages(where, exclude=None):
-    if not exclude:
-        exclude = ()
-    if isinstance(where, str):
-        where = (where, )
-
-    ret_list = []
-    for name in chain.from_iterable(map(lambda w: (
-      n for _, n, ispkg in w if ispkg), (walk_packages(p) for p in where))):
-        if not any(wc_match(name, p) for p in exclude):
-            ret_list.append(name)
-
-    return tuple(ret_list)
-
-
-def calculate_version():
-    initpy = open('biopandas/__init__.py').read().split('\n')
-    version = list(filter(lambda x: '__version__'
-                          in x, initpy))[0].split('\'')[1]
-    return version
-
-
-package_version = calculate_version()
+install_reqs.append('setuptools')
 
 setup(name='biopandas',
-      version=package_version,
-      description='Molecular Structures in Pandas DataFrames',
+      version=VERSION,
+      description='Machine Learning Library Extensions',
       author='Sebastian Raschka',
       author_email='mail@sebastianraschka.com',
       url='https://github.com/rasbt/biopandas',
-      license='new BSD',
-      zip_safe=True,
-      packages=find_packages('.'),
+      packages=find_packages(),
+      package_data={'': ['LICENSE.txt',
+                         'README.md',
+                         'requirements.txt']
+                    },
+      include_package_data=True,
+      install_requires=install_reqs,
+      license='BSD 3-Clause',
       platforms='any',
-      install_requires=['numpy', 'pandas'],
-      keywords=['bioinformatics', 'molecular structures',
-                'protein databank', 'computational biology',
-                'protein structures'],
       classifiers=[
              'License :: OSI Approved :: BSD License',
              'Development Status :: 5 - Production/Stable',
              'Operating System :: Microsoft :: Windows',
              'Operating System :: POSIX',
              'Operating System :: Unix',
              'Operating System :: MacOS',
-             'Programming Language :: Python :: 2',
-             'Programming Language :: Python :: 2.7',
              'Programming Language :: Python :: 3',
-             'Programming Language :: Python :: 3.3',
-             'Programming Language :: Python :: 3.4',
              'Programming Language :: Python :: 3.5',
+             'Programming Language :: Python :: 3.6',
+             'Programming Language :: Python :: 3.7',
              'Topic :: Scientific/Engineering',
       ],
       long_description="""