Refactor. Rename. Extract. Move. Remove.

Rename Helper to Helpers.
Extract fields of Student.report object into Student object.
Rename Student.report.graded_curriculum to Student.curriculum.
Remove gpa calculation logic. Gpa is already int the transcript.
Remove Course.numberGrade() and Course.effectsGpa().
Rename Course.letter_grade Course.grade.
Rename Grader.gradeCurriculum() to Grader.grade().
Rename Grader.fillReport() to Grader.analyze().
Move Grader.place_course() into its caller Grader.grade().