Fix memory bug

.gitignore

@@ -8,3 +8,6 @@ docs/source/meds_reader.py
 docs/source/README_copy.md
 src/meds_reader/meds_reader_convert
 *.swp
+docs/source/html/
+docs/source/latex/
+docs/source/_build/

README.md

@@ -1,6 +1,6 @@
 ## meds_reader: A Pythonic interface for MEDS datasets
 
-[![pypy](https://img.shields.io/pypi/v/meds_reader.svg)](https://pypi.org/project/meds_reader/) [![docs](https://readthedocs.org/projects/meds_reader/badge/?version=latest)](https://meds-reader.readthedocs.io/en/latest/) [![Build wheels](https://github.com/EthanSteinberg/meds_reader/actions/workflows/python-build.yml/badge.svg?branch=main)](https://github.com/EthanSteinberg/meds_reader/actions/workflows/python-build.yml?query=branch%3Amain) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![pypy](https://img.shields.io/pypi/v/meds_reader.svg)](https://pypi.org/project/meds_reader/) [![docs](https://readthedocs.org/projects/meds_reader/badge/?version=latest)](https://meds-reader.readthedocs.io/en/latest/) [![Build wheels](https://github.com/som-shahlab/meds_reader/actions/workflows/python-build.yml/badge.svg?branch=main)](https://github.com/som-shahlab/meds_reader/actions/workflows/python-build.yml?query=branch%3Amain) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
 meds_reader is a fast and easy-to-use library for reading and processing subject data stored in [MEDS (Medical Event Data Standard)](https://github.com/Medical-Event-Data-Standard/) format using a Python-native API.
 

native/meds_reader.cc

@@ -597,14 +597,14 @@ inline PyObject* Subject::get_property(size_t index, Event* event_ptr) {
     if (properties_initialized.test(index) == 0) {
         num_allocated += subject_database->get_property_data(
             index, subject_offset, subject_length,
-            saved_properties + capacity * index,
+            saved_properties + subject_length * index,
             saved_properties +
-                capacity * subject_database->get_num_properties() +
+                subject_length * subject_database->get_num_properties() +
                 num_allocated);
         properties_initialized.set(index);
     }
 
-    PyObject* res = saved_properties[capacity * index + event_index];
+    PyObject* res = saved_properties[subject_length * index + event_index];
 
     if (res == nullptr) {
         Py_RETURN_NONE;
@@ -688,25 +688,25 @@ void Subject::dealloc() {
     Py_DECREF(subject_id);
     Py_DECREF(static_cast<PyObject*>(&events_obj));
 
+    decref();
+}
+
+void Subject::delete_self() {
     for (size_t p_index = 0; p_index < subject_database->get_num_properties();
          p_index++) {
         if (!properties_initialized.test(p_index)) {
             continue;
         }
-        memset(saved_properties + p_index * capacity, 0,
+        memset(saved_properties + p_index * subject_length, 0,
                subject_length * sizeof(PyObject*));
     }
 
     PyObject** to_remove =
-        saved_properties + subject_database->get_num_properties() * capacity;
+        saved_properties + subject_database->get_num_properties() * subject_length;
     for (size_t i = 0; i < num_allocated; i++) {
         Py_DECREF(to_remove[i]);
     }
 
-    decref();
-}
-
-void Subject::delete_self() {
     in_use = false;
     subject_database->decref();
 }

pyproject.toml

@@ -19,10 +19,10 @@ dependencies = [
 [tool.setuptools_scm]
 
 [project.urls]
-Homepage = "https://github.com/EthanSteinberg/meds_reader"
+Homepage = "https://github.com/som-shahlab/meds_reader"
 Documentation = "https://meds-reader.readthedocs.io/en/latest/"
-Repository = "https://github.com/EthanSteinberg/meds_reader"
-Tracker = "https://github.com/EthanSteinberg/meds_reader/issues"
+Repository = "https://github.com/som-shahlab/meds_reader"
+Tracker = "https://github.com/som-shahlab/meds_reader/issues"
 
 [project.scripts]
 meds_reader_convert = "meds_reader:meds_reader_convert"