I139 ir

[richfitz]

A complete rewrite of the odin engine, designed to increase future maintainability but have few user-visible effects. In brief, this does add

• Ability to transpile to R (removing the need for a C compiler, though creating code that is necessarily much slower than the compiled verison). Pass target = "r" to use this.
• A new intermediate representation for odin models that can be used to determine features of a model
• Better caching (#64)
• Delays on discrete time models are much more efficient and work properly with stochastic equations (#72, #98)

This does introduce a few user-visible breaking changes:

• use of array indices outside of an array subset (e.g., x[] <- i) produces output that is off-by-one compared with the previous version (see #136)
• The "safe" mode has been removed, at least for now. This failed to compile for complex models and was not well used. A better static check mechanism will be introduced (#148)
• Arguments to odin() have been modified slightly
• odin_package() no longer supports multi-file mode (I don't think this was ever used).
• Argument order in generated functions, as well as variable/output order, is likely to change but this should not generally be relied upon.
• The methods for a model object have been extensively rationalised. I don't think that anything has been removed that anyone is using in their code.
• The parameters passed as a list user are validated and providing additional parameters is an error

[codecov]

Codecov Report

Merging #156 into master will increase coverage by 0.69%.
The diff coverage is 100%.

@@           Coverage Diff            @@
##           master   #156      +/-   ##
========================================
+ Coverage    99.3%   100%   +0.69%     
========================================
  Files          22     37      +15     
  Lines        3592   4388     +796     
========================================
+ Hits         3567   4388     +821     
+ Misses         25      0      -25

Impacted Files	Coverage Δ
R/common.R	100% <100%> (ø)	⬆️
R/generate_r_support.R	100% <100%> (ø)
R/generate_c_equation.R	100% <100%> (ø)
R/generate_r_utils.R	100% <100%> (ø)
R/support.R	100% <100%> (ø)
R/ir_parse_config.R	100% <100%> (ø)
R/generate_c_class.R	100% <100%> (ø)
R/ir_parse_error.R	100% <100%> (ø)
R/ir_validate.R	100% <100%> (ø)
R/dependencies.R	100% <100%> (ø)	⬆️
... and 58 more

---

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[codecov]

Codecov Report

Merging #156 into master will increase coverage by 0.69%.
The diff coverage is 100%.

@@           Coverage Diff            @@
##           master   #156      +/-   ##
========================================
+ Coverage    99.3%   100%   +0.69%     
========================================
  Files          22     38      +16     
  Lines        3591   4455     +864     
========================================
+ Hits         3566   4455     +889     
+ Misses         25      0      -25

Impacted Files	Coverage Δ
R/support.R	100% <100%> (ø)
R/ir_parse_config.R	100% <100%> (ø)
R/generate_c_class.R	100% <100%> (ø)
R/ir_parse_error.R	100% <100%> (ø)
R/dependencies.R	100% <100%> (ø)	⬆️
R/generate_r_equation.R	100% <100%> (ø)
R/ring_cache.R	100% <100%> (ø)
R/generate_r_sexp.R	100% <100%> (ø)
R/odin_validate.R	100% <100%> (ø)
R/ir_parse.R	100% <100%> (ø)
... and 60 more

---

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[richfitz]

Fixes #139 #136 #132 #130 #129 #127 #123 #122 #121 #120 #117 #115 #112 #106 #99 #98 #84 #75 #72 #64 #57 #52 #12 #4

[codecov-io]

Codecov Report

Merging #156 into master will increase coverage by 0.69%.
The diff coverage is 100%.

@@           Coverage Diff            @@
##           master   #156      +/-   ##
========================================
+ Coverage    99.3%   100%   +0.69%     
========================================
  Files          22     38      +16     
  Lines        3591   4458     +867     
========================================
+ Hits         3566   4458     +892     
+ Misses         25      0      -25

Impacted Files	Coverage Δ
R/support.R	100% <100%> (ø)
R/ir_parse_config.R	100% <100%> (ø)
R/generate_c_class.R	100% <100%> (ø)
R/ir_parse_error.R	100% <100%> (ø)
R/dependencies.R	100% <100%> (ø)	⬆️
R/generate_r_equation.R	100% <100%> (ø)
R/ring_cache.R	100% <100%> (ø)
R/generate_r_sexp.R	100% <100%> (ø)
R/odin_validate.R	100% <100%> (ø)
R/ir_parse.R	100% <100%> (ø)
... and 60 more

---

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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[codecov-io]

Codecov Report

Merging #156 into master will increase coverage by 0.69%.
The diff coverage is 100%.

@@           Coverage Diff            @@
##           master   #156      +/-   ##
========================================
+ Coverage    99.3%   100%   +0.69%     
========================================
  Files          22     38      +16     
  Lines        3591   4474     +883     
========================================
+ Hits         3566   4474     +908     
+ Misses         25      0      -25

Impacted Files	Coverage Δ
R/support.R	100% <100%> (ø)
R/ir_parse_config.R	100% <100%> (ø)
R/generate_c_class.R	100% <100%> (ø)
R/ir_parse_error.R	100% <100%> (ø)
R/dependencies.R	100% <100%> (ø)	⬆️
R/generate_r_equation.R	100% <100%> (ø)
R/ring_cache.R	100% <100%> (ø)
R/generate_r_sexp.R	100% <100%> (ø)
R/odin_validate.R	100% <100%> (ø)
R/ir_parse.R	100% <100%> (ø)
... and 60 more

---

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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