From 63f6c3924edf305154059a985dae527ea9b4e9ee Mon Sep 17 00:00:00 2001 From: Francesco Terenzi Date: Wed, 3 Apr 2024 14:05:55 +0100 Subject: [PATCH] v4.3.1 --- CHANGELOG.md | 3 ++ Cargo.lock | 2 +- Cargo.toml | 2 +- docs/hsc/all.html | 2 +- docs/hsc/constant.MAX_SUBCLONES.html | 2 +- docs/hsc/constant.TIME_AT_BIRTH.html | 2 +- docs/hsc/fn.write2file.html | 2 +- docs/hsc/genotype/index.html | 2 +- .../hsc/genotype/struct.MutationalBurden.html | 2 +- .../struct.NeutralMutationPoisson.html | 2 +- docs/hsc/genotype/struct.Sfs.html | 2 +- docs/hsc/genotype/type.Variant.html | 2 +- docs/hsc/index.html | 2 +- docs/hsc/process/enum.SavingCells.html | 2 +- docs/hsc/process/enum.Stats2Save.html | 2 +- docs/hsc/process/index.html | 2 +- .../struct.CellDivisionProbabilities.html | 2 +- docs/hsc/process/struct.Exponential.html | 2 +- docs/hsc/process/struct.Moran.html | 2 +- docs/hsc/process/struct.ProcessOptions.html | 2 +- docs/hsc/process/struct.SavingOptions.html | 2 +- docs/hsc/process/struct.Snapshot.html | 2 +- docs/hsc/proliferation/enum.Division.html | 4 +- .../proliferation/enum.NeutralMutations.html | 4 +- docs/hsc/proliferation/index.html | 2 +- .../proliferation/struct.Proliferation.html | 6 +-- .../fn.assign_background_mutations.html | 2 +- .../fn.assign_divisional_mutations.html | 2 +- docs/hsc/stemcell/index.html | 2 +- docs/hsc/stemcell/struct.StemCell.html | 9 ++--- docs/hsc/subclone/enum.Fitness.html | 2 +- .../fn.from_mean_std_to_shape_scale.html | 2 +- docs/hsc/subclone/fn.next_clone.html | 2 +- docs/hsc/subclone/fn.proliferating_cell.html | 2 +- .../subclone/fn.save_variant_fraction.html | 2 +- docs/hsc/subclone/index.html | 2 +- docs/hsc/subclone/struct.Distributions.html | 2 +- docs/hsc/subclone/struct.SubClone.html | 2 +- docs/hsc/subclone/struct.SubClones.html | 2 +- docs/hsc/subclone/struct.Variants.html | 2 +- docs/hsc/subclone/type.CloneId.html | 2 +- docs/search-index.js | 2 +- docs/src/hsc/process.rs.html | 40 ++++++++++++++----- docs/src/hsc/proliferation.rs.html | 14 +++++-- docs/src/hsc/stemcell.rs.html | 34 ++++++++++++---- docs/src/hsc/subclone.rs.html | 6 +-- docs/trait.impl/core/clone/trait.Clone.js | 2 +- docs/trait.impl/core/default/trait.Default.js | 2 +- docs/trait.impl/core/fmt/trait.Debug.js | 2 +- docs/trait.impl/sosa/trait.AdvanceStep.js | 2 +- src/process.rs | 2 +- src/proliferation.rs | 8 +++- src/stemcell.rs | 25 ++++++++---- src/subclone.rs | 6 +-- 54 files changed, 151 insertions(+), 92 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c8478290e..2535c0d66 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,9 @@ # Changelog The semantic versioning is kind of random. +## 4.3.1 +- relax the assumption on the interdivision time: an intervidision time can be 0 + ## 4.3.0 - decouple the arrival of fit mutants from the division by implementing an interdivision time diff --git a/Cargo.lock b/Cargo.lock index b64d80993..c02124360 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -311,7 +311,7 @@ checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" [[package]] name = "hsc" -version = "4.3.0" +version = "4.3.1" dependencies = [ "anyhow", "chrono", diff --git a/Cargo.toml b/Cargo.toml index 82a072a74..d881d52f8 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,6 +1,6 @@ [package] name = "hsc" -version = "4.3.0" +version = "4.3.1" edition = "2021" [dependencies] diff --git a/docs/hsc/all.html b/docs/hsc/all.html index a554e35b4..9668e936d 100644 --- a/docs/hsc/all.html +++ b/docs/hsc/all.html @@ -1 +1 @@ -List of all items in this crate

List of all items

Structs

Enums

Functions

Type Aliases

Constants

\ No newline at end of file +List of all items in this crate

List of all items

Structs

Enums

Functions

Type Aliases

Constants

\ No newline at end of file diff --git a/docs/hsc/constant.MAX_SUBCLONES.html b/docs/hsc/constant.MAX_SUBCLONES.html index 9c9b15ba9..fd7a1b61c 100644 --- a/docs/hsc/constant.MAX_SUBCLONES.html +++ b/docs/hsc/constant.MAX_SUBCLONES.html @@ -1,4 +1,4 @@ -MAX_SUBCLONES in hsc - Rust

Constant hsc::MAX_SUBCLONES

source · 
pub const MAX_SUBCLONES: usize = 1200;
Expand description

Maximal number of fit clones that can arise during the simulation.

+MAX_SUBCLONES in hsc - Rust

Constant hsc::MAX_SUBCLONES

source · 
pub const MAX_SUBCLONES: usize = 1200;
Expand description

Maximal number of fit clones that can arise during the simulation.

If the parameters of the simulation provided by the user (e.g. fit mutation rate) are too extreme, the program will exit with error. To avoid this, increase here the number of clones.

diff --git a/docs/hsc/constant.TIME_AT_BIRTH.html b/docs/hsc/constant.TIME_AT_BIRTH.html index d71b858d7..e04c47569 100644 --- a/docs/hsc/constant.TIME_AT_BIRTH.html +++ b/docs/hsc/constant.TIME_AT_BIRTH.html @@ -1,3 +1,3 @@ -TIME_AT_BIRTH in hsc - Rust

Constant hsc::TIME_AT_BIRTH

source · 
pub const TIME_AT_BIRTH: f32 = _; // 0.75f32
Expand description

The time at birth measured in years used for background mutations in the +TIME_AT_BIRTH in hsc - Rust

Constant hsc::TIME_AT_BIRTH

source · 
pub const TIME_AT_BIRTH: f32 = _; // 0.75f32
Expand description

The time at birth measured in years used for background mutations in the exponential growing phase.

\ No newline at end of file diff --git a/docs/hsc/fn.write2file.html b/docs/hsc/fn.write2file.html index 2de0d101d..9a6c10952 100644 --- a/docs/hsc/fn.write2file.html +++ b/docs/hsc/fn.write2file.html @@ -1,4 +1,4 @@ -write2file in hsc - Rust

Function hsc::write2file

source · 
pub fn write2file<T: Display>(
+write2file in hsc - Rust
Function hsc::write2file
source · 
pub fn write2file<T: Display>(
     data: &[T],
     path: &Path,
     header: Option<&str>,
diff --git a/docs/hsc/genotype/index.html b/docs/hsc/genotype/index.html
index f0a11cc0d..7570bc9a8 100644
--- a/docs/hsc/genotype/index.html
+++ b/docs/hsc/genotype/index.html
@@ -1,4 +1,4 @@
-hsc::genotype - Rust
Module hsc::genotype
source · 
Expand description
The neutral mutations representing the genotype of the stem cells.

+hsc::genotype - Rust
Module hsc::genotype
source · 
Expand description
The neutral mutations representing the genotype of the stem cells.

 
Structs
  • MutationalBurden
    Single-cell mutational burden is a mapping of cells sharing a number of
 mutations.
  • NeutralMutationPoisson
    The Poisson probability distribution modeling the appearance of neutral
 mutations, which are assumed to follow a
diff --git a/docs/hsc/genotype/struct.MutationalBurden.html b/docs/hsc/genotype/struct.MutationalBurden.html
index b233ad224..d206e8f08 100644
--- a/docs/hsc/genotype/struct.MutationalBurden.html
+++ b/docs/hsc/genotype/struct.MutationalBurden.html
@@ -1,4 +1,4 @@
-MutationalBurden in hsc::genotype - Rust
    Struct hsc::genotype::MutationalBurden
    source · 
    pub struct MutationalBurden(pub FxHashMap<u16, u64>);
    Expand description
    Single-cell mutational burden is a mapping of cells sharing a number of
+MutationalBurden in hsc::genotype - Rust
    Struct hsc::genotype::MutationalBurden
    source · 
    pub struct MutationalBurden(pub FxHashMap<u16, u64>);
    Expand description
    Single-cell mutational burden is a mapping of cells sharing a number of
 mutations.
    
 
    To plot it, plot on the x-axis the keys (number of mutations) and on the
 y-axis the values (the number of cells with those mutations).
    
diff --git a/docs/hsc/genotype/struct.NeutralMutationPoisson.html b/docs/hsc/genotype/struct.NeutralMutationPoisson.html
index b5643ecc6..deb7ebb96 100644
--- a/docs/hsc/genotype/struct.NeutralMutationPoisson.html
+++ b/docs/hsc/genotype/struct.NeutralMutationPoisson.html
@@ -1,4 +1,4 @@
-NeutralMutationPoisson in hsc::genotype - Rust
    Struct hsc::genotype::NeutralMutationPoisson
    source · 
    pub struct NeutralMutationPoisson {
+NeutralMutationPoisson in hsc::genotype - Rust
    Struct hsc::genotype::NeutralMutationPoisson
    source · 
    pub struct NeutralMutationPoisson {
     pub lambda_background: f32,
     pub lambda_division: f32,
     /* private fields */
diff --git a/docs/hsc/genotype/struct.Sfs.html b/docs/hsc/genotype/struct.Sfs.html
index ee2f01bc6..a1e4c965c 100644
--- a/docs/hsc/genotype/struct.Sfs.html
+++ b/docs/hsc/genotype/struct.Sfs.html
@@ -1,4 +1,4 @@
-Sfs in hsc::genotype - Rust
    Struct hsc::genotype::Sfs
    source · 
    pub struct Sfs(pub FxHashMap<u64, u64>);
    Expand description
    Site frequency spectrum
+Sfs in hsc::genotype - Rust
    Struct hsc::genotype::Sfs
    source · 
    pub struct Sfs(pub FxHashMap<u64, u64>);
    Expand description
    Site frequency spectrum
 implemented as mapping with keys being j cells (x-axis) and values being
 the number of variants with j cells (y-axis).
    
 
    Tuple Fields§
    §0: FxHashMap<u64, u64>
    Implementations§
    source§
    impl Sfs
    source
    pub fn from_cells(cells: &[&StemCell], verbosity: u8) -> Result<Self>
    Compute the SFS from the stem cell population.
    
diff --git a/docs/hsc/genotype/type.Variant.html b/docs/hsc/genotype/type.Variant.html
index b0b8f8f85..f826b97a6 100644
--- a/docs/hsc/genotype/type.Variant.html
+++ b/docs/hsc/genotype/type.Variant.html
@@ -1 +1 @@
-Variant in hsc::genotype - Rust
    Type Alias hsc::genotype::Variant
    source · 
    pub type Variant = Uuid;
    Aliased Type§
    struct Variant(/* private fields */);
    
\ No newline at end of file
+Variant in hsc::genotype - Rust
    Type Alias hsc::genotype::Variant
    source · 
    pub type Variant = Uuid;
    Aliased Type§
    struct Variant(/* private fields */);
    
\ No newline at end of file
diff --git a/docs/hsc/index.html b/docs/hsc/index.html
index ccbb9cfa1..132ef4064 100644
--- a/docs/hsc/index.html
+++ b/docs/hsc/index.html
@@ -1,4 +1,4 @@
-hsc - Rust