GitHub has just apologized for not being transparent enough about its internal investigation into claims of sexism and harassment by former employee Julie Ann Horvath.

GitHub CEO Chris Wanstrath offered new details about what happened before, after, and during the investigation — although the full story is still withheld, he says, due to confidentiality promises to employees. "We failed to admit and own up to our mistakes, and for that I'm sorry," he wrote. "GitHub has a reputation for being transparent and taking responsibility for our actions, but last week we did neither. There's no excuse. We can do a lot better."

Last week, the company announced that an inquiry by a third-party investigator had produced no evidence of a hostile work environment or anything illegal, but enough "mistakes and errors of judgment" that co-founder Tom Preston-Werner resigned. The company declined to elaborate on what Preston-Werner was guilty of, and left it ambiguous as to whether he was asked to leave.

There was backlash against both sides

In response, Horvath started naming names and publishing emails between herself and other GitHub employees related to the incidents. She also said "there was no investigation." There was backlash against both sides, with vitriol directed against Horvath and GitHub criticized for its response.

Wanstrath now reveals that the investigation was done by Rhoma Young, a consultant with 30 years of experience who has sided as often with employees as she has for companies, he wrote.

Rhoma identified the employees she wanted to talk to based on an initial list we provided, the evidence she gathered, employees who asked to speak with her, people Julie asked her to speak with, and anyone else she determined was relevant, including Julie herself. Ultimately she conducted over 50 interviews during a four week period. Along with the interviews, Rhoma gathered and reviewed evidence consisting of emails, texts, transcripts, and code from the dozens of current and former GitHubbers she spoke with. She then took everything she learned and summarized her findings for GitHub's Board of Directors.

Wanstrath also reveals that Preston-Werner was in fact pushed out after the investigation found that he "acted inappropriately, including confrontational conduct, disregard of workplace complaints, insensitivity to the impact of his spouse's presence in the workplace, and failure to enforce an agreement that his spouse should not work in the office."

There were also complaints about his wife asking GitHub employees to help with her startup and "inappropriate handling of employee concerns regarding those solicitations."

Young found that Horvath's other allegations, about being harassed by an engineer and working in a hostile environment for women, were unfounded. "Women at GitHub reported feeling supported, mentored, and protected at work, and felt they are treated equitably and are provided opportunities," Wanstrath wrote.

The second, more frank version of the story makes a more compelling case for GitHub, where female employees who spoke to The Verge reported that they had never felt gender-based discrimination.

Horvath is still unconvinced.

Horvath now works for software development shop &yet. GitHub has hired Kelli Dragovich, who previously worked at Barnes and Noble's Nook division and Yahoo, as vice president of human resources, and promises more positive changes will be announced in May.