update ADTypes in EpiAware

[SamuelBrand1]

This proposed fix to #302 is to update to ADTypes to 1.3 for EpiAware and pin the document environment to the same version as EpiAware

Closes #302

[github-actions]

Benchmark result

Judge result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

• Time of benchmarks:
  • Target: 26 Jun 2024 - 09:37
  • Baseline: 26 Jun 2024 - 09:38
• Package commits:
  • Target: 3474c0
  • Baseline: 816622
• Julia commits:
  • Target: 48d4fd
  • Baseline: 48d4fd
• Julia command flags:
  • Target: None
  • Baseline: None
• Environment variables:
  • Target: None
  • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID	time ratio	memory ratio

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

• ["EpiAwareUtils"]

Julia versioninfo

Target

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2617 MHz       2400 s          0 s        264 s       2885 s          0 s
       #2  2445 MHz       2584 s          0 s        255 s       2693 s          0 s
       #3  3243 MHz       2392 s          0 s        265 s       2882 s          0 s
       #4  3271 MHz       2602 s          0 s        248 s       2697 s          0 s
  Memory: 15.606491088867188 GB (14044.921875 MB free)
  Uptime: 557.7 sec
  Load Avg:  2.8  2.82  1.36
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

Baseline

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       2433 s          0 s        270 s       2986 s          0 s
       #2  3146 MHz       2655 s          0 s        257 s       2760 s          0 s
       #3  3244 MHz       2395 s          0 s        269 s       3017 s          0 s
       #4  3238 MHz       2631 s          0 s        250 s       2806 s          0 s
  Memory: 15.606491088867188 GB (14023.78515625 MB free)
  Uptime: 571.75 sec
  Load Avg:  2.4  2.73  1.36
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

---

Target result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

• Time of benchmark: 26 Jun 2024 - 9:37
• Package commit: 3474c0
• Julia commit: 48d4fd
• Julia command flags: None
• Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	GC time	memory	allocations
["EpiAwareUtils", "censored_pmf"]	1.102 μs (5%)		352 bytes (1%)	4

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

• ["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2617 MHz       2400 s          0 s        264 s       2885 s          0 s
       #2  2445 MHz       2584 s          0 s        255 s       2693 s          0 s
       #3  3243 MHz       2392 s          0 s        265 s       2882 s          0 s
       #4  3271 MHz       2602 s          0 s        248 s       2697 s          0 s
  Memory: 15.606491088867188 GB (14044.921875 MB free)
  Uptime: 557.7 sec
  Load Avg:  2.8  2.82  1.36
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

---

Baseline result

Benchmark Report for /home/runner/work/Rt-without-renewal/Rt-without-renewal

Job Properties

• Time of benchmark: 26 Jun 2024 - 9:38
• Package commit: 816622
• Julia commit: 48d4fd
• Julia command flags: None
• Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID	time	GC time	memory	allocations
["EpiAwareUtils", "censored_pmf"]	1.100 μs (5%)		352 bytes (1%)	4

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

• ["EpiAwareUtils"]

Julia versioninfo

Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.4 LTS
  uname: Linux 6.5.0-1022-azure #23~22.04.1-Ubuntu SMP Thu May  9 17:59:24 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       2433 s          0 s        270 s       2986 s          0 s
       #2  3146 MHz       2655 s          0 s        257 s       2760 s          0 s
       #3  3244 MHz       2395 s          0 s        269 s       3017 s          0 s
       #4  3238 MHz       2631 s          0 s        250 s       2806 s          0 s
  Memory: 15.606491088867188 GB (14023.78515625 MB free)
  Uptime: 571.75 sec
  Load Avg:  2.4  2.73  1.36
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

---

Runtime information

Runtime Info
BLAS #threads	2
BLAS.vendor()	lbt
Sys.CPU_THREADS	4

lscpu output:

Architecture:                       x86_64
CPU op-mode(s):                     32-bit, 64-bit
Address sizes:                      48 bits physical, 48 bits virtual
Byte Order:                         Little Endian
CPU(s):                             4
On-line CPU(s) list:                0-3
Vendor ID:                          AuthenticAMD
Model name:                         AMD EPYC 7763 64-Core Processor
CPU family:                         25
Model:                              1
Thread(s) per core:                 2
Core(s) per socket:                 2
Socket(s):                          1
Stepping:                           1
BogoMIPS:                           4890.86
Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                     AMD-V
Hypervisor vendor:                  Microsoft
Virtualization type:                full
L1d cache:                          64 KiB (2 instances)
L1i cache:                          64 KiB (2 instances)
L2 cache:                           1 MiB (2 instances)
L3 cache:                           32 MiB (1 instance)
NUMA node(s):                       1
NUMA node0 CPU(s):                  0-3
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit:        Not affected
Vulnerability L1tf:                 Not affected
Vulnerability Mds:                  Not affected
Vulnerability Meltdown:             Not affected
Vulnerability Mmio stale data:      Not affected
Vulnerability Retbleed:             Not affected
Vulnerability Spec rstack overflow: Vulnerable: Safe RET, no microcode
Vulnerability Spec store bypass:    Vulnerable
Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:           Mitigation; Retpolines; STIBP disabled; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds:                Not affected
Vulnerability Tsx async abort:      Not affected

Cpu Property	Value
Brand	AMD EPYC 7763 64-Core Processor
Vendor	:AMD
Architecture	:Unknown
Model	Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores	16 physical cores, 16 logical cores (on executing CPU)
	No Hyperthreading hardware capability detected
Clock Frequencies	Not supported by CPU
Data Cache	Level 1:3 : (32, 512, 32768) kbytes
	64 byte cache line size
Address Size	48 bits virtual, 48 bits physical
SIMD	256 bit = 32 byte max. SIMD vector size
Time Stamp Counter	TSC is accessible via rdtsc
	TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring	Performance Monitoring Counters (PMC) are not supported
Hypervisor	Yes, Microsoft

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Please upload report for BASE (main@8166227). Learn more about missing BASE report.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #303   +/-   ##
=======================================
  Coverage        ?   92.85%           
=======================================
  Files           ?       47           
  Lines           ?      490           
  Branches        ?        0           
=======================================
  Hits            ?      455           
  Misses          ?       35           
  Partials        ?        0           

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