The microfilmed records at the State Archives in Sacramento do not contain a single statewide canvass for the election of 1879. The figures are drawn from the individual county returns, except for San Francisco, which is not included on the microfilm. The City and County of San Francisco took over a month to count its votes in 1879; the figures were ultimately reported in the 10/6/1879 Daily Alta California and that is the source for San Francisco's vote. Once San Francisco completed its count, the statewide canvass commenced and the totals were reported in various newspapers throughout the state; for instance, the 10/20/1879 Sacramento Daily Record-Union. All of the county figures add up to the reported totals except for those of Smith; Smith's stated total is 41,045 but the county figures add up to 41,065.
Candidates' party affiliations sourced from 9/3/1879 Daily Morning Times (of San Jose). https://www.cdnc.ucr.edu/?a=d&d=DMT18790903.2.29.3&e=-------en--20--1--txt-txIN--------
Source for Popular Vote data: California State Archives, "Secretary of State," Abstract Statement of the Vote of California, polled at the General Election, held September 3d, A.D. 1879 (Sacramento, 1879)