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Fast, parallel, extensible and adaptable genetic algorithms framework written in Rust

License: Mozilla Public License 2.0

Rust 100.00%

genetic-algorithm rust

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ccaballe dirvine jdeeny garro95 alapini n0uk acidnik aneksteind kn666 nightly-target chenyukang ielizaga cruelu nessex standardgalactic rubenrubiom cgubbin playfloor amarrerod iq-scm

oxigen's Issues

Trouble building 3.0

I noticed that travis tends to build 3.0 just fine, so I wonder if I'm missing something here, perhaps the wrong rust version.

When building 3.0 I get the following compilation error:

error[E0046]: not all trait items implemented, missing: `GenotypeHash`, `hash`
  --> onemax-oxigen/src/main.rs:19:1
   |
19 | impl Genotype<bool> for OneMax {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing `GenotypeHash`, `hash` in implementation
   |
   = help: implement the missing item: `type GenotypeHash = Type;`
   = help: implement the missing item: `fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { unimplemented!() }`

error[E0046]: not all trait items implemented, missing: `GenotypeHash`, `hash`
  --> knapsack-oxigen/src/main.rs:52:1
   |
52 | impl<'a> Genotype<bool> for Knapsack<'a> {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing `GenotypeHash`, `hash` in implementation
   |
   = help: implement the missing item: `type GenotypeHash = Type;`
   = help: implement the missing item: `fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { unimplemented!() }`

error: aborting due to previous error

For more information about this error, try `rustc --explain E0046`.
error: could not compile `onemax-oxigen`.
warning: build failed, waiting for other jobs to finish...
error: aborting due to previous error

For more information about this error, try `rustc --explain E0046`.
error: could not compile `knapsack-oxigen`.
warning: build failed, waiting for other jobs to finish...
error: build failed

I was under the impression that there was a default hash implementation for these items, so I'm unsure what could be causing the problem. Any idea?

Thanks

error[E0046]: not all trait items implemented, missing: GenotypeHash, hash
--> onemax-oxigen/src/main.rs:19:1
|
19 | impl Genotype for OneMax {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing GenotypeHash, hash in implementation
|
= help: implement the missing item: type GenotypeHash = Type;
= help: implement the missing item: fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { todo!() }

error[E0046]: not all trait items implemented, missing: GenotypeHash, hash
--> knapsack-oxigen/src/main.rs:52:1
|
52 | impl<'a> Genotype for Knapsack<'a> {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing GenotypeHash, hash in implementation
|
= help: implement the missing item: type GenotypeHash = Type;
= help: implement the missing item: fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { todo!() }

For more information about this error, try rustc --explain E0046.
error: could not compile onemax-oxigen due to previous error
warning: build failed, waiting for other jobs to finish...
warning: panic message is not a string literal
--> fd-oxigen/src/main.rs:220:25
|
220 | _ => panic!(format!("Incorrect index passed to n_values: {}", index)),
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
= note: #[warn(non_fmt_panics)] on by default
= note: this usage of panic!() is deprecated; it will be a hard error in Rust 2021
= note: for more information, see https://doc.rust-lang.org/nightly/edition-guide/rust-2021/panic-macro-consistency.html
= note: the panic!() macro supports formatting, so there's no need for the format!() macro here
help: remove the format!(..) macro call
|
220 - _ => panic!(format!("Incorrect index passed to n_values: {}", index)),
220 + _ => panic!("Incorrect index passed to n_values: {}", index),
|

warning: fd-oxigen (bin "fd-oxigen") generated 1 warning
error: build failed

Thanks,

Jianshu

build error for nightly compiler

rustc 1.52.0-nightly (83b30a639 2021-02-20)

Build with error message:

error[E0046]: not all trait items implemented, missing: `GenotypeHash`, `hash`
  --> onemax-oxigen/src/main.rs:19:1
   |
19 | impl Genotype<bool> for OneMax {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing `GenotypeHash`, `hash` in implementation
   |
   = help: implement the missing item: `type GenotypeHash = Type;`
   = help: implement the missing item: `fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { todo!() }`

error[E0046]: not all trait items implemented, missing: `GenotypeHash`, `hash`
  --> knapsack-oxigen/src/main.rs:52:1
   |
52 | impl<'a> Genotype<bool> for Knapsack<'a> {
   | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ missing `GenotypeHash`, `hash` in implementation
   |
   = help: implement the missing item: `type GenotypeHash = Type;`
   = help: implement the missing item: `fn hash(&self) -> <Self as oxigen::Genotype<T>>::GenotypeHash { todo!() }`

error: aborting due to previous error

For more information about this error, try `rustc --explain E0046`.
error: could not compile `onemax-oxigen`

To learn more, run the command again with --verbose.
warning: build failed, waiting for other jobs to finish...
error: aborting due to previous error

For more information about this error, try `rustc --explain E0046`.
error: build failed

Support for a reference environment

Is your feature request related to a problem? Please describe.
I am attempting to optimize for a graph-related problem and would like to create a genotype whose fitness function is calculated based on some reference graph, which ideally would be part of some read-only environment.

It seems that, internally in oxigen/lib.rs, fitness is calculated for individuals generated with generate (see here), which can only take in a ProblemSize instance passed via genotype_size().

So, either it appears that any fitness method I define cannot refer to the graph I wish to optimize against because that is decided at runtime or I must smuggle the graph in as part of the ProblemSize passed into the genotype_size() method. Is this the correct interpretation?

In effect, ProblemSize is acting as the environment type and field. For example, it appears this is the case in the knap-sack example where the items are constructed (see here) and passed in as part of the problem size.

Describe the solution you'd like
Rename

ProblemSize
genotype_size(mut self, new_size: Ind::ProblemSize), and
GeneticExecution.genotype_size

Environment
set_environment(mut self, env: Ind::Environment), and
GeneticExecution.environment, respectively

Describe alternatives you've considered
No alternatives considered.

Additional context
No additional context.

Use traits instead of structs

The Genotype iter and into_iter methods should return a Type that implements the Iterator and IntoIterator traits and not the specific implementation of these traits for slices.
This would improve usability of the framework

Wrong comment for the fitness function in Knapsack example

Seems like a comment for the N Queen example instead.

oxigen/knapsack-oxigen/src/main.rs

Lines 79 to 81 in c39aee2

 // This function returns the mximum punctuaction possible (n-1, since in the 

 // worst case n-1 queens must be moved to get a solution) minus the number of 

 // queens that collide with others

Extra example(s)

Would it be possible to provide more examples?

I'd like to see how a more simple problem is tackled with oxigen, so to see how the mechanism works. Could this example (https://deap.readthedocs.io/en/master/examples/ga_onemax.html) be translated to oxigen?

I really would like to help, but my Rust-knowledge is not good enough...

Thanks in advance!

Introduce a GeneticExecutionBuilder

I like the way a new GeneticExecution object is built.
According to the Rust Guidelines, although, there should be another object, called ...Builder, that provides such an API.
The builder methods could take &mut Builder and return the reference, thus being more flexible, while only the final method, that build the actual object, would take the ownership.
On the final type, methods that have the name of a field should be getters for that field instead.

Individuals from shorter iterators

Why at a certain point the optimizer starts to generate individuals with a minor number of elements?
Is it intended behavior?
How can this effect be counteracted?
Thanks!

feature request: polymorphic fitness types

Is your feature request related to a problem? Please describe.

My use case involves very large numbers whose precision I'd like to maintain. Casting my BigInt type to an f64 causes a loss of information.

Describe the solution you'd like

Polymorphic fitness types, e.g. changing

fn fitness(&self) -> f64

to something like

fn fitness(&self) -> S where
S: std::ops::Add {
...
}

Describe alternatives you've considered
Casting my big int type to f64 (which is my current fix)

I'd be willing to help with this myself if it's of interest

Spelling mistake

The word 'cuadratic' doesn't exist in english. You probably meant 'quadratic'.

https://en.wikipedia.org/wiki/Quadratic_function

`Uniform::new called with `low >= high`

Describe the bug
Oxigen fails to create the next generation of individuals.

To Reproduce
I'm not sure how to reproduce it with a simple use case, but I can reproduce it systematically with a small variation to the orbit_design_ga project. Specifically, if my genome is only one gene long, this problem shows up. Two or more genes, and it doesn't happen.

I understand/expect that the information I provide is not enough to fix. Hence, can you explain to me in which cases the following line from crossover.rs would fail:

let cross_point = SmallRng::from_entropy().sample(Uniform::from(1..ind_size));

I'm guessing that ind_size is zero, but I don't know what would cause it to be zero.

Thanks for your help

Stack trace

     Running `target/debug/orbit_design_ga`
Fitness: 2000
Fitness: 2001
Fitness: 2001
Fitness: 2001
Fitness: 2000
Fitness: 2001
Fitness: 2000
Fitness: 2001
Fitness: 0
Fitness: 0
Fitness: 0
Fitness: 2000
Fitness: 2001
Fitness: 2000
Fitness: 2001
Fitness: 2001
thread 'main' panicked at 'Uniform::new called with `low >= high`', /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rand-0.7.3/src/distributions/uniform.rs:477:1
stack backtrace:
   0: std::panicking::begin_panic
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/std/src/panicking.rs:519:12
   1: <rand::distributions::uniform::UniformInt<usize> as rand::distributions::uniform::UniformSampler>::new
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rand-0.7.3/src/distributions/uniform.rs:379:17
   2: rand::distributions::uniform::Uniform<X>::new
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rand-0.7.3/src/distributions/uniform.rs:172:17
   3: <rand::distributions::uniform::Uniform<X> as core::convert::From<core::ops::range::Range<X>>>::from
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rand-0.7.3/src/distributions/uniform.rs:272:9
   4: <oxigen::crossover::CrossoverFunctions as oxigen::crossover::Crossover<T,G>>::cross
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/oxigen-2.2.0/src/crossover.rs:31:67
   5: oxigen::GeneticExecution<T,Ind>::cross::{{closure}}
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/oxigen-2.2.0/src/lib.rs:639:40
   6: core::ops::function::impls::<impl core::ops::function::Fn<A> for &F>::call
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/ops/function.rs:237:13
   7: <rayon::iter::map_with::MapWithFolder<C,U,F> as rayon::iter::plumbing::Folder<T>>::consume_iter::with::{{closure}}
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/map_with.rs:317:22
   8: core::iter::adapters::map::map_fold::{{closure}}
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/iter/adapters/map.rs:80:28
   9: core::iter::traits::iterator::Iterator::fold
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/iter/traits/iterator.rs:2023:21
  10: <core::iter::adapters::map::Map<I,F> as core::iter::traits::iterator::Iterator>::fold
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/iter/adapters/map.rs:120:9
  11: core::iter::traits::iterator::Iterator::for_each
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/iter/traits/iterator.rs:678:9
  12: <rayon::iter::noop::NoopConsumer as rayon::iter::plumbing::Folder<T>>::consume_iter
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/noop.rs:34:9
  13: <rayon::iter::map_with::MapWithFolder<C,U,F> as rayon::iter::plumbing::Folder<T>>::consume_iter
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/map_with.rs:322:25
  14: rayon::iter::plumbing::Producer::fold_with
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/plumbing/mod.rs:110:9
  15: rayon::iter::plumbing::bridge_producer_consumer::helper
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/plumbing/mod.rs:438:13
  16: rayon::iter::plumbing::bridge_producer_consumer
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/plumbing/mod.rs:397:12
  17: <rayon::iter::plumbing::bridge::Callback<C> as rayon::iter::plumbing::ProducerCallback<I>>::callback
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/plumbing/mod.rs:373:13
  18: <rayon::range::Iter<usize> as rayon::iter::IndexedParallelIterator>::with_producer
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/range.rs:112:17
  19: rayon::iter::plumbing::bridge
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/plumbing/mod.rs:357:12
  20: <rayon::range::Iter<usize> as rayon::iter::ParallelIterator>::drive_unindexed
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/range.rs:88:17
  21: <rayon::iter::map_with::MapWith<I,T,F> as rayon::iter::ParallelIterator>::drive_unindexed
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/map_with.rs:53:9
  22: rayon::iter::from_par_iter::<impl rayon::iter::FromParallelIterator<()> for ()>::from_par_iter
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/from_par_iter.rs:226:9
  23: rayon::iter::ParallelIterator::collect
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/mod.rs:1973:9
  24: rayon::iter::ParallelIterator::for_each_with
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/rayon-1.5.0/src/iter/mod.rs:400:9
  25: oxigen::GeneticExecution<T,Ind>::cross
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/oxigen-2.2.0/src/lib.rs:626:9
  26: oxigen::GeneticExecution<T,Ind>::run_loop
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/oxigen-2.2.0/src/lib.rs:345:36
  27: oxigen::GeneticExecution<T,Ind>::run
             at /home/chris/.cargo/registry/src/github.com-1ecc6299db9ec823/oxigen-2.2.0/src/lib.rs:311:49
  28: orbit_design_ga::main
             at ./src/main.rs:32:9
  29: core::ops::function::FnOnce::call_once
             at /home/chris/.rustup/toolchains/stable-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/library/core/src/ops/function.rs:227:5
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.

	// This function returns the mximum punctuaction possible (n-1, since in the
	// worst case n-1 queens must be moved to get a solution) minus the number of
	// queens that collide with others

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