Fix tests

.github/workflows/test.yml

@@ -29,10 +29,7 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
-        conda create -y --prefix ./env -c bioconda hmmer prodigal
-        conda activate ./env
-        pip install . pytest pytest-mock
+        make env
     - name: Test with pytest
       run: |
-        conda activate ./env
         make test

Makefile

@@ -1,10 +1,13 @@
+ENV_NAME := deepbgc-dev
+SHELL := /bin/bash
+CONDA_ACTIVATE = eval "$$(conda shell.bash hook)" && conda activate $(ENV_NAME)
 .PHONY: install release dist test
 
-install:
-	python setup.py install
-	pip install pytest pytest-mock hmmlearn twine
+env:
+	conda create -n $(ENV_NAME) -c bioconda hmmer prodigal
+	$(CONDA_ACTIVATE); pip install . pytest pytest-mock hmmlearn
 
-conda-env:
+bioconda-install:
 ifndef VERSION
 	$(error "Usage: make conda-env VERSION=0.1.9")
 endif
@@ -31,10 +34,7 @@ dist:
 	python setup.py sdist bdist_wheel	
 
 test:
-	pytest test
-
-pip-install:
-	pip install --upgrade deepbgc
+	$(CONDA_ACTIVATE); pytest test
 
 local-test:
 	mkdir -p work