Merge branch 'release/v1.1.0'

.travis.yml

@@ -4,14 +4,14 @@ env:
   - [email protected]:mordred-descriptor/documentation.git
   - secure: 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
   matrix:
-  - PYTHON_VERSION=3.6 COVERAGE=true DOCUMENTATION=true
+  - PYTHON_VERSION=3.6 COVERAGE=true DOCUMENTATION=true LINT=true
   - PYTHON_VERSION=3.5 COVERAGE=true
   - PYTHON_VERSION=2.7 COVERAGE=true
 os:
 - linux
 - osx
 sudo: false
-before_install: "./scripts/travis/before_install.sh"
-install: "./scripts/install.sh"
-script: "./scripts/test_script.sh"
-after_success: "./scripts/after_success.sh"
+before_install: "./extra/ci/before_install.sh"
+install: "./extra/ci/install.sh"
+script: "./extra/ci/test_script.sh"
+after_success: "./extra/ci/after_success.sh"

README.rst

@@ -24,6 +24,18 @@ molecular descriptor calculator.
 .. image:: https://img.shields.io/badge/doi-10.1186%2Fs13321--018--0258--y-blue.svg
    :target: https://doi.org/10.1186/s13321-018-0258-y
 
+number of descriptors
+---------------------
+.. code:: python
+
+    >>> from mordred import Calculator, descriptors
+    >>> n_all = len(Calculator(descriptors, ignore_3D=False).descriptors)
+    >>> n_2D = len(Calculator(descriptors, ignore_3D=True).descriptors)
+    >>> print("2D:    {:5}\n3D:    {:5}\n------------\ntotal: {:5}".format(n_2D, n_all - n_2D, n_all))
+    2D:     1613
+    3D:      212
+    ------------
+    total:  1825
 
 Installation
 ------------
@@ -161,7 +173,10 @@ as library
     >>> calc = Calculator(descriptors, ignore_3D=True)
 
     >>> len(calc.descriptors)
-    1615
+    1613
+
+    >>> len(Calculator(descriptors, ignore_3D=True, version="1.0.0"))
+    1612
 
     # calculate single molecule
     >>> mol = Chem.MolFromSmiles('c1ccccc1')
@@ -191,4 +206,5 @@ Documentation
 -  `master <http://mordred-descriptor.github.io/documentation/master>`__
 -  `develop <http://mordred-descriptor.github.io/documentation/develop>`__
 
+-  `v1.1.0 <http://mordred-descriptor.github.io/documentation/v1.1.0>`__
 -  `v1.0.0 <http://mordred-descriptor.github.io/documentation/v1.0.0>`__

appveyor.yml

@@ -17,6 +17,6 @@ environment:
     - PYTHON_VERSION: 2.7
       MINICONDA: C:\Miniconda
 
-install: '%CYG_ROOT%/bin/bash ./scripts/install.sh'
-test_script: '%CYG_ROOT%/bin/bash ./scripts/test_script.sh'
-on_success: '%CYG_ROOT%/bin/bash ./scripts/after_success.sh'
+install: '%CYG_ROOT%/bin/bash ./extra/ci/install.sh'
+test_script: '%CYG_ROOT%/bin/bash ./extra/ci/test_script.sh'
+on_success: '%CYG_ROOT%/bin/bash ./extra/ci/after_success.sh'

examples/article/Code4.py

@@ -1,5 +1,7 @@
+from distutils.version import StrictVersion
+
 from mordred.RingCount import RingCount
 
 # Start Code 4
-presets = list(RingCount.preset())
+presets = list(RingCount.preset(version=StrictVersion("1.0.0")))
 print(len(presets))

scripts/after_success.sh → extra/ci/after_success.sh

@@ -1,7 +1,12 @@
 #!/bin/bash
 
 set -e
-source ./scripts/add_path.sh
+
+if [[ ! -f ~/.ssh/id_rsa ]]; then
+    exit 0
+fi
+
+source ./extra/ci/conda.sh
 
 [[ -n "$COVERAGE" ]] && coveralls
 

scripts/travis/before_install.sh → extra/ci/before_install.sh

@@ -2,7 +2,12 @@
 
 set -e
 
-openssl aes-256-cbc -K $encrypted_9f3357583363_key -iv $encrypted_9f3357583363_iv -in ./scripts/id_rsa.enc -out ~/.ssh/id_rsa -d
+if [[ "$TRAVIS_PULL_REQUEST" != "false" ]]; then
+    echo this is PR
+    exit 0
+fi
+
+openssl aes-256-cbc -K $encrypted_9f3357583363_key -iv $encrypted_9f3357583363_iv -in ./extra/id_rsa.enc -out ~/.ssh/id_rsa -d
 chmod 600 ~/.ssh/id_rsa
 
 echo "StrictHostKeyChecking no" >> ~/.ssh/config

scripts/install.sh → extra/ci/install.sh

@@ -2,6 +2,10 @@
 
 set -e
 
+REQUIREMENTS=./extra/requirements
+CONDA_REQ_FILE=requirements-conda.txt
+PIP_REQ_FILE=requirements-pip.txt
+
 # install conda
 
 if [[ "$TRAVIS_OS_NAME" == osx ]]; then
@@ -17,7 +21,7 @@ if [[ -n "$TRAVIS_OS_NAME" ]]; then
     bash miniconda.sh -b -p $HOME/miniconda
 fi
 
-source ./scripts/add_path.sh
+source ./extra/ci/conda.sh
 
 # setup conda
 
@@ -28,19 +32,20 @@ conda config --add channels rdkit --add channels mordred-descriptor
 
 # install requirements
 
-CONDA_REQ_FILE=requirements-conda.txt
-PIP_REQ_FILE=requirements-pip.txt
+cat $REQUIREMENTS/requirements-conda.txt $REQUIREMENTS/requirements.txt > $CONDA_REQ_FILE
 
-cat ./scripts/requirements-conda.txt ./scripts/requirements.txt > $CONDA_REQ_FILE
+if [[ "$PYTHON_VERSION" < 3.4 ]]; then
+    echo enum34 >> $CONDA_REQ_FILE
+fi
 
 [[ "$PYTHON_VERSION" < 3.4 ]] && echo enum34 >> $CONDA_REQ_FILE
 
-[[ -n "$COVERAGE" ]] && echo coveralls >> $PIP_REQ_FILE
+if [[ -n "$LINT" ]]; then
+    cat $REQUIREMENTS/requirements-flake8.txt >> $PIP_REQ_FILE
+fi
 
 if [[ -n "$DOCUMENTATION" ]]; then
-    echo sphinx >> $CONDA_REQ_FILE
-    echo sphinx_rtd_theme >> $CONDA_REQ_FILE
-    echo sphinxcontrib-bibtex >> $PIP_REQ_FILE
+    cat $REQUIREMENTS/requirements-documentation.txt >> $PIP_REQ_FILE
 fi
 
 conda install python=$PYTHON_VERSION --file $CONDA_REQ_FILE

scripts/test_script.sh → extra/ci/test_script.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 set -e
-source ./scripts/add_path.sh
+source ./extra/ci/conda.sh
 
 if [[ -n "$COVERAGE" ]]; then
     python -m mordred.tests -q --with-coverage
@@ -16,3 +16,8 @@ for example in `find examples -name '*.py'`; do
     echo "test $example" >&2
     PYTHONPATH=. python $example > /dev/null
 done
+
+if [[ -n "$LINT" ]]; then
+    python setup.py flake8
+    python setup.py isort
+fi

extra/requirements/requirements-documentation.txt

@@ -0,0 +1,3 @@
+sphinx
+sphinx_rtd_theme
+sphinxcontrib-bibtex

mordred/ABCIndex.py

@@ -10,14 +10,14 @@
 from ._base import Descriptor
 from ._graph_matrix import DistanceMatrix
 
-__all__ = ("ABCIndex", "ABCGGIndex",)
+__all__ = ("ABCIndex", "ABCGGIndex")
 
 
 class ABCIndexBase(Descriptor):
     __slots__ = ()
 
     @classmethod
-    def preset(cls):
+    def preset(cls, version):
         yield cls()
 
     explicit_hydrogens = False
@@ -39,6 +39,7 @@ class ABCIndex(ABCIndexBase):
 
     """
 
+    since = "1.0.0"
     __slots__ = ()
 
     def description(self):
@@ -68,6 +69,7 @@ class ABCGGIndex(ABCIndexBase):
 
     """  # noqa: E501
 
+    since = "1.0.0"
     __slots__ = ()
 
     def description(self):

mordred/AcidBase.py

@@ -12,14 +12,14 @@
 
 from ._base import Descriptor
 
-__all__ = ("AcidicGroupCount", "BasicGroupCount",)
+__all__ = ("AcidicGroupCount", "BasicGroupCount")
 
 
 class SmartsCountBase(Descriptor):
-    __slots__ = "_mol",
+    __slots__ = ("_mol",)
 
     @classmethod
-    def preset(cls):
+    def preset(cls, version):
         yield cls()
 
     def _create_smarts(self):
@@ -43,12 +43,13 @@ def calculate(self):
 
     rtype = int
 
-    _extra_docs = "SMARTS",
+    _extra_docs = ("SMARTS",)
 
 
 class AcidicGroupCount(SmartsCountBase):
     r"""acidic group count descriptor."""
 
+    since = "1.0.0"
     __slots__ = ()
 
     def description(self):
@@ -67,6 +68,7 @@ def description(self):
 class BasicGroupCount(SmartsCountBase):
     r"""basic group count descriptor."""
 
+    since = "1.0.0"
     __slots__ = ()
 
     def description(self):

mordred/AdjacencyMatrix.py

@@ -1,32 +1,41 @@
+from distutils.version import StrictVersion
+
 from ._base import Descriptor
 from ._graph_matrix import AdjacencyMatrix as A
-from ._matrix_attributes import methods, get_method
+from ._matrix_attributes import SM1, methods, get_method
 
 __all__ = ("AdjacencyMatrix",)
 
 
+_version_remove_SM1_A = StrictVersion("1.1.0")
+
+
 class AdjacencyMatrix(Descriptor):
     r"""adjacency matrix descriptor.
 
     :type type: :py:class:`str`
     :param type: :ref:`matrix_aggregating_methods`
     """
 
+    since = "1.0.0"
     __slots__ = ("_type",)
     explicit_hydrogens = False
 
     def description(self):
         return "{} of adjacency matrix".format(self._type.__name__)
 
     @classmethod
-    def preset(cls):
-        return map(cls, methods)
+    def preset(cls, version):
+        if version >= _version_remove_SM1_A:
+            return (cls(m) for m in methods if m != SM1)
+        else:
+            return map(cls, methods)
 
     def __str__(self):
         return "{}_A".format(self._type.__name__)
 
     def parameters(self):
-        return self._type,
+        return (self._type,)
 
     def __init__(self, type="SpMax"):
         self._type = get_method(type)

mordred/Aromatic.py

@@ -9,7 +9,7 @@ class AromaticBase(Descriptor):
     __slots__ = ()
 
     @classmethod
-    def preset(cls):
+    def preset(cls, version):
         yield cls()
 
     def __str__(self):
@@ -24,6 +24,7 @@ def parameters(self):
 class AromaticAtomsCount(AromaticBase):
     r"""aromatic atoms count descriptor."""
 
+    since = "1.0.0"
     __slots__ = ()
     _name = "nAromAtom"
 
@@ -41,6 +42,7 @@ def calculate(self):
 class AromaticBondsCount(AromaticBase):
     r"""aromatic bonds count descriptor."""
 
+    since = "1.0.0"
     __slots__ = ()
     _name = "nAromBond"
 

mordred/AtomCount.py

@@ -1,3 +1,5 @@
+from distutils.version import StrictVersion
+
 from rdkit.Chem import rdMolDescriptors
 
 from ._base import Descriptor
@@ -11,12 +13,15 @@
     "Atom": "all",
     "Bridgehead": "bridgehead",
     "HeavyAtom": "heavy",
-    "Spiro": "spiro",
     "Hetero": "hetero",
+    "Spiro": "spiro",
     "X": "halogen",
 }
 
 
+_version_add_Nhetero = StrictVersion("1.1.0")
+
+
 class AtomCount(Descriptor):
     r"""atom count descriptor.
 
@@ -32,17 +37,26 @@ class AtomCount(Descriptor):
         * element symbol
     """
 
+    since = "1.0.0"
     __slots__ = ("_type",)
 
     def description(self):
         return "number of {} atoms".format(_desc_conv.get(self._type, self._type))
 
     @classmethod
-    def preset(cls):
-        return map(cls, [
-            "Atom", "HeavyAtom", "Spiro", "Bridgehead", "Hetero",
-            "H", "B", "C", "N", "O", "S", "P", "F", "Cl", "Br", "I", "X",
-        ])
+    def preset(cls, version):
+        if version >= _version_add_Nhetero:
+            t = [
+                "Atom", "HeavyAtom", "Spiro", "Bridgehead", "Hetero",
+                "H", "B", "C", "N", "O", "S", "P", "F", "Cl", "Br", "I", "X",
+            ]
+        else:
+            t = [
+                "Atom", "HeavyAtom", "Spiro", "Bridgehead",
+                "H", "B", "C", "N", "O", "S", "P", "F", "Cl", "Br", "I", "X",
+            ]
+
+        return map(cls, t)
 
     @property
     def explicit_hydrogens(self):
@@ -53,7 +67,7 @@ def __str__(self):
         return "n" + self._type
 
     def parameters(self):
-        return self._type,
+        return (self._type,)
 
     def __init__(self, type="Atom"):
         self._type = type