WIP: batched synchronous zip writing

[bluegenes]

No description provided.

[bluegenes]

Benchmarking:

software/version	command	acc details	time	max RAM
v0.1.0	gbsketch	9 fungal	6min	156 MB
sync-zip branch	gbsketch	9 fungal	2min	190 MB

9 fungal accessions total

/usr/bin/time -v sourmash scripts gbsketch update.20240503-fungi.head10.csv -o test10.zip --failed test10.failed.csv -r 1 --param-str dna,k=31,scaled=1000 --genomes-only

this branch:

Loaded 9 rows in total
Writing manifest
...gbsketch is done! Sigs in 'test10.zip'. Fastas in '.'.
        Command being timed: "sourmash scripts gbsketch update.20240503-fungi.head10.csv -o test10.zip --failed test10.failed.csv -r 1 --param-str dna,k=31,scaled=1000 --genomes-only"
        User time (seconds): 5.74
        System time (seconds): 0.94
        Percent of CPU this job got: 5%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 1:57.22
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 189108
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 68
        Minor (reclaiming a frame) page faults: 79681
        Voluntary context switches: 26612
        Involuntary context switches: 587
        Swaps: 0
        File system inputs: 10224
        File system outputs: 2088
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

main:

Command being timed: "sourmash scripts gbsketch update.20240503-fungi.head10.csv -o test10.zip --failed test10.failed.csv -r 1 --param-str dna,k=31,scaled=1000 --genomes-only"
        User time (seconds): 5.98
        System time (seconds): 1.05
        Percent of CPU this job got: 1%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 5:59.30
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 156624
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 112
        Minor (reclaiming a frame) page faults: 66385
        Voluntary context switches: 30159
        Involuntary context switches: 2821
        Swaps: 0
        File system inputs: 19776
        File system outputs: 2160
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

[bluegenes]

Closing in favor of #8