This Sept. 2, opening day for the Chicago Public Schools, is a day to celebrate recent academic growth — but also to look honestly at the huge challenges ahead.

In the week leading up to opening day, CPS and the mayor’s office made sure to spread the good news: Attendance, ACT scores, freshman pass rates and graduation rates are all on the rise. While the current administration can claim some credit, these gains also are an outgrowth of policies put in place years ago, reforms continued under the current mayor. The big applause, of course, goes to students and their teachers.

CPS graduation numbers a system of musical chairs

CPS’ graduation rate reached an all-time high , 69 percent, up from 65 percent just one year ago, the school system says. Most significantly, the graduation rate has steadily been increasing since 2008, when it was just 54 percent.

This is a direct result of a tight CPS focus, beginning in 2007, on helping freshmen successfully transition to high school . Ground-breaking research by the University of Chicago’s Consortium on Chicago School Research identified this critical link — revealing that passing ninth grade is more predictive of high school graduation than race, ethnicity, poverty or test scores.

As a result of this targeted intervention, ninth-grade pass rates , or “on-track” to graduate rates , have skyrocketed, from 57 percent in 2007 to 84 percent in 2014.

In the 2000s, CPS also set its sites on an average ACT score of 20 out of 36. CPS this year reached a record high of 18. That’s still far too low, but marks the highest point in a five-year upward trend.

Despite these advances, no one should underestimate the massive problems facing CPS and the threats they represent to continued progress.

Here are just a few:

Budget woes: As we said this summer, 2015 will be yet another year for CPS to limp along budget-wise, strait-jacketed by rising pension and personnel costs and constrained by limited revenue. Neighborhood schools, CPS’ lifeblood, took it on the chin for a second year in a row, losing $67 million in funding. “Welcoming” schools that absorbed students from closed schools also took a hit, losing about 5 percent of their budgets on average, a Sun-Times analysis found.

CPS’ leaders point to explosive pension costs as the cause of the budget woes, and call on Springfield to cut teacher pension benefits. They’re right, mostly. Pension reform will not solve all of CPS’ money problems, but it’s essential for the long-term financial health of the school system and the pension fund itself.

Charter woes: This year, the CPS charter budget increased by $62 million as charter enrollment increased — about as much as neighborhood schools lost. The mayor and CPS continue to be highly invested in charter growth, making it time to call the question: Is this the right priority, especially when there isn’t enough money to support the schools CPS already has? New student test data analyzed by the Sun-Times casts doubt on the efficacy of charters. Students at neighborhood schools showed significantly more academic growth in reading in 2014 than did students in charter schools, the Sun-Times found.

We have urged CPS to slow charter expansion after years of unprecedented growth. Twenty-six new charters opened in 2012 and 2013, and another five open this fall (meanwhile, CPS in 2013 voted to close 50 under-enrolled schools). CPS has showed more restraint in the last year, and the call for new charter proposals is delayed this year, a sign, hopefully, that CPS may be planning for even greater restraint in 2014 and 2015.

Social woes: No editorial on CPS’ struggles is complete without a nod to the social and emotional challenge students bring to school and the woefully inadequate supply of mental-health professionals to help address them. A recent op-ed in the Sun-Times by a CPS counselor described the heartbreaking choices she makes each day in the face of crushing student needs and extremely limited resources to address them. CPS has invested in school -wide social-emotional training for staff, which is a good start, but the effort is incomplete without more mental-health professionals to help students confront the vexing social problems that prevent them from learning.