diff --git a/.gitignore b/.gitignore index 9de3ddd..059aa07 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,4 @@ docs/_build/ **/.ipynb_checkpoints/ **/dask-worker-space/ scripts/cli_test_data/ +.python-version diff --git a/README.rst b/README.rst index 04e659e..d19e4d2 100644 --- a/README.rst +++ b/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: diff --git a/docs/index.rst b/docs/index.rst index ed3485c..8fb21b6 100644 --- a/docs/index.rst +++ b/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: diff --git a/runtox.sh b/runtox.sh new file mode 100644 index 0000000..282d528 --- /dev/null +++ b/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 diff --git a/setup.py b/setup.py index c5a0426..e267df3 100644 --- a/setup.py +++ b/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', diff --git a/src/pyscenic/genesig.py b/src/pyscenic/genesig.py index d527ef5..8531366 100644 --- a/src/pyscenic/genesig.py +++ b/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): diff --git a/tox.ini b/tox.ini index 78328b4..7defa8d 100644 --- a/tox.ini +++ b/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