update ensembl-vep to release 102 and Makefile

.coveragerc

 [run]
-omit = */__init__.py, *tests*
+omit = */__init__.py, *tests*, setup.py

.gitignore

@@ -22,6 +22,7 @@ __pycache__/
 *.coverage
 *.egg-info/
 *htmlcov/
+*.coveragerc
 
 # Open cached files 
 *.m~

Makefile

 PYTHON ?= python
 PYTEST ?= pytest
 CTAGS ?= ctags
+PIP ?= pip
 
-ifeq (,$(CONDA_PREFIX))
-    CONDA_ACTIVATED=True
-else
-    CONDA_ACTIVATED=False
-endif
+# .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
 
-#environment:
-#ifeq (True, $(CONDA_ACTIVATED))
-#    @echo ">>> Found $(CONDA_PREFIX)  environment activated. Install the requirements in this environment."
-#    conda env update --file reqs/requirements.yml
-#else
-#    pip install -r requirements.txt
-#endif
+# 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
 
-clean:
-	$(PYTHON) setup.py clean
-
-# installation instructions are not clear to me:
-#   setup.py install -> the package cannot be imported from outside the repository even though he is 
-#   visible in the conda list as <develop> in the same way as when 
-#   setup.py develop -> everything is ok
-#install: clean-ctags
-#	$(PYTHON) setup.py install
-
-install: ctags
-	$(PYTHON) setup.py develop
+# 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 "------------------------------------"
 
-develop: ctags
-	$(PYTHON) setup.py develop
 test:
-	$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov variant_annotator variant_annotator
+	$(PIP) install --upgrade pytest pytest-cov
+	$(PYTEST) --cov-config=.coveragerc --cov-report term-missing --cov . . 
+
+build:
+	@echo "---------------Build variant_annotator-----------------"
+	$(PYTHON) -m pip install --user --upgrade setuptools wheel
+	$(PYTHON) setup.py sdist bdist_wheel
+
+install:
+	@echo "---------------Install variant_annotator-----------------"
+	$(PIP) install --upgrade pip setuptools wheel
+	$(PIP) install -r reqs/requirements.txt
+	$(PIP) install .
+
+update:
+	@echo "---------------Update vcf2maf-----------------"
+	cd tools/vcf2maf
+	git pull
+	cd ../..
+	@echo "---------------Update ensembl-vep-----------------"
+	cd tools/ensembl-vep
+	git pull
+	cd ../..
+tags:
+	$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R .
 
-ctags:
-	$(CTAGS) --python-kinds=-i --exclude=*/tests/* -R variant_annotator
-
-clean-ctags:
+clean:
 	rm -f tags
+	rm -rf build
+	rm -rf dist
+	rm -rf *.egg-info

ensembl-vep @ ef2b5865

-Subproject commit bf8fce94cfe1889c92771695bb57931b43b72484
+Subproject commit ef2b5865f0c4c5fb8f8be31dafcb478c151e9214