Changed makefile and checkpoints.txt marked with incomplete

Makefile

 CLEAN=mvn clean package
 TEST=java -cp "chocopy-ref.jar:target/assignment.jar" chocopy.ChocoPy --pass=..s --run --dir src/test/data/pa3/sample/ --test
 FILE=op_cmp_int
+CHECKPOINTS=src/test/data/pa3/sample/literal_bool.py src/test/data/pa3/sample/literal_int.py src/test/data/pa3/sample/literal_str.py src/test/data/pa3/sample/id_global.py src/test/data/pa3/sample/id_local.py src/test/data/pa3/sample/var_assign.py src/test/data/pa3/sample/call.py src/test/data/pa3/sample/call_with_args.py src/test/data/pa3/sample/nested.py src/test/data/pa3/sample/nested2.py src/test/data/pa3/sample/op_add.py src/test/data/pa3/sample/op_cmp_bool.py src/test/data/pa3/sample/op_cmp_int.py src/test/data/pa3/sample/op_div_mod.py	 src/test/data/pa3/sample/op_logical.py src/test/data/pa3/sample/op_mul.py src/test/data/pa3/sample/op_negate.py src/test/data/pa3/sample/op_sub.py src/test/data/pa3/sample/stmt_if.py src/test/data/pa3/sample/stmt_while.py src/test/data/pa3/sample/stmt_return_early.py src/test/data/pa3/benchmarks/exp.py src/test/data/pa3/benchmarks/prime.py
+
 clean:
 	$(CLEAN)
 test:

checkpoint_tests.txt

@@ -5,19 +5,18 @@ src/test/data/pa3/sample/id_global.py
 src/test/data/pa3/sample/id_local.py
 src/test/data/pa3/sample/var_assign.py
 src/test/data/pa3/sample/call.py
-src/test/data/pa3/sample/call_with_args.py
-src/test/data/pa3/sample/nested.py
-src/test/data/pa3/sample/nested2.py
+src/test/data/pa3/sample/call_with_args.py # NOT DONE
+src/test/data/pa3/sample/nested.py # NOT DONE
+src/test/data/pa3/sample/nested2.py # NOT DONE
 src/test/data/pa3/sample/op_add.py
 src/test/data/pa3/sample/op_cmp_bool.py
 src/test/data/pa3/sample/op_cmp_int.py
 src/test/data/pa3/sample/op_div_mod.py	
-src/test/data/pa3/sample/op_logical.py
+src/test/data/pa3/sample/op_logical.py # NOT DONE
 src/test/data/pa3/sample/op_mul.py
 src/test/data/pa3/sample/op_negate.py
 src/test/data/pa3/sample/op_sub.py
 src/test/data/pa3/sample/stmt_if.py
 src/test/data/pa3/sample/stmt_while.py
 src/test/data/pa3/sample/stmt_return_early.py
-src/test/data/pa3/benchmarks/exp.py
-src/test/data/pa3/benchmarks/prime.py
+