v1.1 change setup.py and update ensembl-vep

Makefile

 PYTHON ?= python
 PYTEST ?= pytest
 CTAGS ?= ctags
-PIP ?= pip
 
 # .PHONY defines parts of the makefile that are not dependant on any specific file
 # This is most often used to store functions
-.PHONY = help test tags clean
+.PHONY = clean develop install tags test
 
-# Defines the default target that `make` will to try to make, or in the case of a phony target, execute the specified commands
-# This target is executed whenever we just type `make`
-.DEFAULT_GOAL = help
+develop:
+	@echo "---------------Install varannot in develop mode-----------------"
+	$(PYTHON) -m pip install -e .
 
-# The @ makes sure that the command itself isn't echoed in the terminal
-help:
-	@echo "---------------HELP-----------------"
-	@echo "make setup to setup the project"
-	@echo "make test to run the tests"
-	@echo "make clean to remove build/dev files"
-	@echo "make install to install"
-	@echo "------------------------------------"
+install:
+	@echo "---------------Install varannot-----------------"
+	$(PYTHON) setup.py install
+
+tags:
+	$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R .
 
 test:
-	$(PIP) install --upgrade pytest pytest-cov
+	@echo "---------------Run varannot tests-----------------"
+	$(PYTHON) -m pip install pytest pytest-cov
 	$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . . 
 
 codecov:
 	bash <(curl -s https://codecov.io/bash) -t c8bcf054-f0cb-4bf1-8866-1b862905ef89
 
-build:
-	@echo "---------------Build variant_annotator-----------------"
-	$(PYTHON) -m pip install --user --upgrade setuptools wheel
-	$(PYTHON) setup.py sdist bdist_wheel
-
-install:
-	@echo "---------------Install variant_annotator-----------------"
-	git submodule update --init
-	$(PIP) install --upgrade pip setuptools wheel
-	$(PIP) install -r reqs/requirements.txt
-	$(PIP) install .
-
 update:
 	@echo "---------------Update vcf2maf-----------------"
 	cd tools/vcf2maf
@@ -56,3 +42,6 @@ clean:
 	rm -rf build
 	rm -rf dist
 	rm -rf *.egg-info
+	rm -rf ./*.pyc
+	rm -rf ./*.tgz
+

examples/run_example_tcga_GA.py

@@ -27,7 +27,7 @@ import sys
 if "." not in sys.path:
     sys.path.append(".")
 
-from variant_annotator import run_annotator, Vcf2mafConfig, VepConfig
+from varannot import run_annotator, Vcf2mafConfig, VepConfig
 
 #### # SCRIPT PARAMETERS 
 #### #####################################################################################################

examples/run_example_tcga_HS.py

@@ -27,7 +27,7 @@ import sys
 if "." not in sys.path:
     sys.path.append(".")
 
-from variant_annotator import run_annotator, Vcf2mafConfig, VepConfig
+from varannot import run_annotator, Vcf2mafConfig, VepConfig
 
 #### # SCRIPT PARAMETERS 
 #### #####################################################################################################

pyproject.toml

+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

reqs/requirements.txt

-numpy>=1.14.0
-pandas>=0.23.0

reqs/requirements.yml

-channels:
-  - defaults
-dependencies:
-  - numpy
-  - pandas
-  - pytest
-  - pytest-cov
-  - ipython

setup.cfg

+[metadata]
+name = varannot
+description = "Variant annotation with VEP and vcf2maf"
+license = BSD 2-Clause License
+version = 1.1
+classifiers =
+    Topic :: Scientific/Engineering :: Bio-Informatics
+    Development Status :: 4 - Beta
+    License :: OSI Approved :: BSD License
+    Programming Language :: Python :: 3
+
+[options]
+packages = 
+    varannot
+install_requires = 
+    numpy >= 1.14.0
+    pandas >= 0.23.0

setup.py

-import os
-from setuptools import setup, Command
-
-class CleanCommand(Command):
-    user_options = []
-    def initialize_options(self):
-        self.cwd = None
-    def finalize_options(self):
-        self.cwd = os.getcwd()
-    def run(self):
-        assert os.getcwd() == self.cwd, 'Must be in package root: %s' % self.cwd
-        os.system ('rm -rf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info')
-
-setup(
-    name = "variant_annotator",
-    version = "1.0.0",
-    author = "Yoann Pradat",
-    author_email = "yoann.pradat@centralesupelec.fr",
-    install_requires = [
-        "numpy",
-        "pandas",
-    ],
-    cmdclass={
-        'clean': CleanCommand
-    }
-)
-
+import setuptools
+setuptools.setup()

variant_annotator/__init__.py → varannot/__init__.py

 """
-The :mod:`variant_annotator` module defines functions for annotating variants using a combination of manual, vep and
+The :mod:`varannot` module defines functions for annotating variants using a combination of manual, vep and
 vcf2maf annotations.
 """