test?

BiocPy · Oct 18, 2024 · cb86ad9 · cb86ad9
1 parent 7e4eae7
commit cb86ad9
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Showing 4 changed files with 17 additions and 9 deletions.
diff --git a/lib/src/rdswrapper.cpp b/lib/src/rdswrapper.cpp
@@ -1,7 +1,9 @@
+// rds_bindings.cpp
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 #include <pybind11/numpy.h>
 #include "rds2cpp/rds2cpp.hpp"
+#include <memory>
 
 namespace py = pybind11;
 
@@ -85,6 +87,9 @@ class RdsObject {
     }
 
     std::vector<std::string> get_attribute_names() const {
+        if (!ptr) {
+            throw std::runtime_error("Null pointer in get_attribute_names");
+        }
         switch (ptr->type()) {
             case rds2cpp::SEXPType::INT:
                 return static_cast<const rds2cpp::IntegerVector*>(ptr.get())->attributes.names;
@@ -191,7 +196,7 @@ class RdsParser {
 public:
     RdsParser(const std::string& filename) {
         try {
-            parsed = std::make_unique<rds2cpp::Parsed>(rds2cpp::parse_rds(filename));        
+            parsed = std::make_unique<rds2cpp::Parsed>(rds2cpp::parse_rds(filename));
         } catch (const std::exception& e) {
             throw std::runtime_error("Failed to parse RDS file: " + std::string(e.what()));
         }
@@ -211,6 +216,7 @@ PYBIND11_MODULE(rds_parser, m) {
     py::register_exception<std::runtime_error>(m, "RdsParserError");
 
     py::class_<RdsObject>(m, "RdsObject")
+        // .def(py::init<const RdsObject&>())
         .def("get_type", &RdsObject::get_type)
         .def("get_size", &RdsObject::get_size)
         .def("get_numeric_data", &RdsObject::get_numeric_data)

diff --git a/src/rds2py/PyRdsReader.py b/src/rds2py/PyRdsReader.py
@@ -81,7 +81,7 @@ def _handle_special_cases(self, result: Dict) -> Dict:
                     result["data"] = range(-data[1])
         return result
 
-def get_dimensions(self) -> Tuple[int, int]:
+    def get_dimensions(self) -> Tuple[int, int]:
         """Get dimensions of the RDS object"""
         try:
             return self.obj.get_dimensions()

diff --git a/tests/test_atomic-attr.py b/tests/test_atomic-attr.py
@@ -9,9 +9,11 @@
 
 def test_read_atomic_attrs():
     parsed_obj = PyRdsReader("tests/data/atomic_attr.rds")
+    print(parsed_obj)
     data = parsed_obj.read()
+    print(data)
 
     assert data is not None
     assert len(data["data"]) > 0
     assert len(data["attributes"]) >0
-    assert len(data["attributes"]["names"]["data"]) >0
+    assert len(data["attributes"]["names"]["data"]) != 0
diff --git a/tests/test_list.py b/tests/test_list.py
@@ -8,40 +8,40 @@
 
 
 def test_read_atomic_lists():
-    parsed_obj = PyRdsObject("tests/data/lists.rds")
+    parsed_obj = PyRdsReader("tests/data/lists.rds")
     array = parsed_obj.read()
 
     assert array is not None
     assert len(array) > 0
 
 
 def test_read_atomic_lists_nested():
-    parsed_obj = PyRdsObject("tests/data/lists_nested.rds")
+    parsed_obj = PyRdsReader("tests/data/lists_nested.rds")
     array = parsed_obj.read()
 
     assert array is not None
     assert len(array) > 0
 
 
 def test_read_atomic_lists_nested_deep():
-    parsed_obj = PyRdsObject("tests/data/lists_nested_deep.rds")
+    parsed_obj = PyRdsReader("tests/data/lists_nested_deep.rds")
     array = parsed_obj.read()
 
     assert array is not None
     assert len(array) > 0
 
 
 def test_read_atomic_lists_df():
-    parsed_obj = PyRdsObject("tests/data/lists_df.rds")
+    parsed_obj = PyRdsReader("tests/data/lists_df.rds")
     array = parsed_obj.read()
 
     assert array is not None
     assert len(array) > 0
 
 
 def test_read_atomic_lists_nested_deep_rownames():
-    parsed_obj = PyRdsObject("tests/data/lists_df_rownames.rds")
+    parsed_obj = PyRdsReader("tests/data/lists_df_rownames.rds")
     array = parsed_obj.read()
-    
+
     assert array is not None
     assert len(array) > 0