Checked compatibility with different of python interpreters (removed …

…variable type annotation so that support for versions < 3.6 is guaranteed).

.gitignore

@@ -14,3 +14,4 @@ docs/_build/
 **/.ipynb_checkpoints/
 **/dask-worker-space/
 scripts/cli_test_data/
+.python-version

README.rst

@@ -46,7 +46,7 @@ Installation
 The lastest stable release of the **package** itself can be installed via :code:`pip install pyscenic`.
 
 .. caution::
-    pySCENIC needs a python 3.x interpreter.
+    pySCENIC needs a python 3.5 or greater interpreter.
 
 You can also install the bleeding edge (i.e. less stable) version of the package directly from the source:
 

docs/index.rst

@@ -47,7 +47,7 @@ Installation
 The lastest stable release of the **package** itself can be installed via :code:`pip install pyscenic`.
 
 .. caution::
-    pySCENIC needs a python 3.x interpreter.
+    pySCENIC needs a python 3.5 or greater interpreter.
 
 You can also install the bleeding edge (i.e. less stable) version of the package directly from the source:
 

runtox.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+
+# Installation for MacOS X
+# 1. brew update
+# 2. brew install pyenv
+# Check latest versions of python interpreters on
+# 3. pyenv install 3.5.5 && pyenv install 3.6.4
+# In same directory as setup.py:
+# 4. pyenv local 3.5.5 3.6.4
+
+eval "$(pyenv init -)"
+tox

setup.py

@@ -64,12 +64,11 @@ def read_requirements(fname):
         'Operating System :: POSIX',
         'Programming Language :: Python',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: Implementation :: CPython',
     ],
-    python_requires=">3.3",
+    python_requires=">=3.5",
     keywords='single-cell transcriptomics gene-regulatory-network transcription-factors',
     author="Bram Van de Sande",
     url='https://github.com/aertslab/pySCENIC',

src/pyscenic/genesig.py

@@ -122,9 +122,9 @@ def columns():
                              nomenclature=nomenclature,
                              gene2weights=list(columns()))
 
-    name: str = attr.ib()
-    nomenclature: str = attr.ib()
-    gene2weights: Mapping[str, float] = attr.ib(converter=convert)
+    name = attr.ib()  # str
+    nomenclature = attr.ib()  # str
+    gene2weights = attr.ib(converter=convert)  # Mapping[str, float]
 
     @name.validator
     def name_validator(self, attribute, value):
@@ -308,9 +308,9 @@ def from_yaml(cls, loader, node):
                          context=frozenset(data['context']),
                          transcription_factor=data['transcription_factor'])
 
-    transcription_factor: str = attr.ib()
-    context: FrozenSet[str] = attr.ib(default=frozenset())
-    score: float = attr.ib(default=0.0)
+    transcription_factor = attr.ib()  # str
+    context = attr.ib(default=frozenset())  # FrozenSet[str]
+    score = attr.ib(default=0.0)  # float
 
     @transcription_factor.validator
     def non_empty(self, attribute, value):

tox.ini

@@ -4,7 +4,7 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py36,py35,py34,py33
+envlist = py36,py35
 
 [testenv]
 commands = pytest