Update Makefile

Makefile

@@ -1,3 +1,6 @@
+Here is the updated Makefile with `$PIP` and `$PYTHON` variables used in the appropriate sections, including for `black`, `pyment`, and `pylint`:
+
+```makefile
 # .ONESHELL tells make to run each recipe line in a single shell
 .ONESHELL:
 
@@ -22,49 +25,55 @@ activate:
 	. .venv/bin/activate
 
 install: requirements.txt # prerequisite
-	# install commands
-	# in local use
-	# $(PIP) install --no-cache-dir --upgrade pip &&\
-	# $(PIP) install --no-cache-dir -r requirements.txt
-	pip --no-cache-dir install --upgrade pip &&\
-		pip --no-cache-dir install -r requirements.txt
+	# install commands using pip from the virtual environment
+	$(PIP) install --no-cache-dir --upgrade pip &&\
+	$(PIP) install --no-cache-dir -r requirements.txt
 
 format: install
-	#format code
-	black *.py utils/*.py testing/*.py
+	# format code using black
+	$(PYTHON) -m black *.py utils/*.py testing/*.py
+
 clean: 
 	# clean directory of cache files, virtual environment, and data
 	rm -rf __pycache__ &&\
 	rm -rf utils/__pycache__ &&\
 	rm -rf testing/__pycache__ &&\
 	rm -rf .pytest_cache &&\
 	rm -rf .venv &&\
-	rm updated_data/sequences.fasta 
+	rm updated_data/sequences.fasta &&\
 	rm updated_data/sequence_metrics.csv
+
 docstring: activate install
-	# format docstring
-	pyment -w -o numpydoc *.py
+	# format docstring using pyment
+	$(PYTHON) -m pyment -w -o numpydoc *.py
+
 lint: activate install format
-	#flake8 or #pylint
-	pylint --disable=R,C --errors-only *.py utils/*.py testing/*.py
+	# lint code using pylint
+	$(PYTHON) -m pylint --disable=R,C --errors-only *.py utils/*.py testing/*.py
+
 test: activate install format lint
-	#test
-	python -m pytest testing/*.py
+	# run tests using pytest
+	$(PYTHON) -m pytest testing/*.py
+
 run_script:
 	# run script: load fasta, create sequence_metrics
-	# calculate cosine similiarity averages
-	python multifastaloader.py
-	python load_multifasta_metrics.py
-	python tokenize_compare_sequences.py
+	# calculate cosine similarity averages
+	$(PYTHON) multifastaloader.py
+	$(PYTHON) load_multifasta_metrics.py
+	$(PYTHON) tokenize_compare_sequences.py
+
 docker_build: Dockerfile requirements.txt 
 	# build the container: More important for the CI/CD
 	sudo docker build -t phylo-exp .
+
 docker_run_test: Dockerfile
-	# linting Dockerfile
+	# lint Dockerfile
 	sudo docker run --rm -i hadolint/hadolint < Dockerfile
+
 docker_run: docker_build 
 	# run the container
 	sudo docker run -it -p 8888:8888 --rm phylo-exp:latest
+
 deploy:
 	# add step to deploy to cloud provider if any
 	echo "todo"
@@ -74,3 +83,6 @@ deploy:
 
 # what all steps to run
 all: install docstring format lint test docker_build docker_run
+```
+
+This ensures that `black`, `pyment`, and `pylint` use the appropriate Python and pip from the virtual environment.