Merge pull request #259 from techno-sam/feat/kb_extract

Add kb extract command
Co-author: @techno-sam

Author: lauraluebbert

.gitignore

@@ -109,3 +109,9 @@ venv.bak/
 .DS_Store
 .vscode/
 .Rhistory
+
+# PyCharm
+/.idea/
+
+# Temp files
+/scratch/

Makefile

@@ -2,7 +2,8 @@
 
 test:
 	rm -f .coverage
-	nosetests --verbose --with-coverage --cover-package kb_python tests/* tests/dry/*
+	pytest --verbose --cov=kb_python tests/* tests/dry/* && coverage report && coverage xml
+#	nosetests --verbose --with-coverage --cover-package kb_python tests/* tests/dry/*
 
 check:
 	flake8 kb_python && echo OK

dev-requirements.txt

@@ -1,7 +1,8 @@
 bumpversion==0.6.0
 coverage==5.1
 flake8==3.8.2
-nose==1.3.7
+pytest==8.2.2
+pytest-cov==5.0.0
 pre-commit==2.4.0
 sphinx>=3.3.1
 sphinx-autoapi>=1.5.1

docs/index.rst

@@ -18,7 +18,7 @@ necessary packages by running::
   pip install -r requirements.txt
   pip install -r dev-requirements.txt
 
-Code qualty and unit tests are strictly enforced for every pull request via
+Code quality and unit tests are strictly enforced for every pull request via
 Github actions.
 
 Code Quality
@@ -33,7 +33,7 @@ at the root of the repository.
 
 Unit-testing
 """"""""""""
-``kb-python`` uses ``nose`` to run unit tests. There is a convenient Makefile
+``kb-python`` uses ``pytest`` to run unit tests. There is a convenient Makefile
 rule in place to run all tests.::
 
   make test

kb_python/config.py

@@ -58,7 +58,7 @@ def get_compiled_kallisto_path(alias: str = COMPILED_DIR) -> Optional[str]:
     """Finds platform-dependent kallisto binary compiled with `compile`.
 
     Args:
-        Alias: Alias of compiled binary.
+        alias: Alias of compiled binary.
 
     Returns:
         Path to the binary, `None` if not found
@@ -74,7 +74,7 @@ def get_compiled_bustools_path(alias: str = COMPILED_DIR) -> Optional[str]:
     """Finds platform-dependent bustools binary compiled with `compile`.
 
     Args:
-        Alias: Alias of compiled binary.
+        alias: Alias of compiled binary.
 
     Returns:
         Path to the binary, `None` if not found