From 8f6e646d6d209213b07b0911be9f0432a53e9fff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Eva=20=C5=A0mij=C3=A1kov=C3=A1?= <smijakova.eva@gmail.com>
Date: Thu, 28 Nov 2024 10:43:13 +0100
Subject: [PATCH] Initial states for phenotype control (#36)

* Initial states for phenotype control

* fmt

* Remove `clap`.

---------

Co-authored-by: Samuel Pastva <sam.pastva@gmail.com>
---
 Cargo.toml                          |  4 ++--
 pyproject.toml                      |  2 +-
 src/bindings/pbn_control/control.rs | 15 ++++++++++++++-
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 6f494af..93a499a 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "biodivine-aeon-py"
-version = "1.2.0"
+version = "1.2.1"
 edition = "2021"
 
 [lib]
@@ -21,7 +21,7 @@ pyo3 = { version = "0.22.5", features = ["abi3-py37", "extension-module", "num-b
 biodivine-lib-param-bn = { version="0.5.13", features=["solver-z3"] }
 biodivine-lib-bdd = "0.5.22"
 #biodivine-pbn-control = "0.3.1"
-biodivine-pbn-control = { git = "https://github.com/sybila/biodivine-pbn-control", rev = "99f9da756c370daf5428b3d61ef76c24e7d8de5f" }
+biodivine-pbn-control = { git = "https://github.com/sybila/biodivine-pbn-control", rev = "1fcef228bd6accd89cb3a287d82c80c9c8f9b6a4" }
 biodivine-hctl-model-checker = "0.3.0"
 rand = "0.8.5"
 macros = { path = "macros" }
diff --git a/pyproject.toml b/pyproject.toml
index 8830ccf..dd59bc2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "maturin"
 [project]
 name = "biodivine_aeon"
 description = "Python bindings for the tool AEON."
-version = "1.2.0"
+version = "1.2.1"
 requires-python = ">=3.9"
 classifiers = [
     "Programming Language :: Rust",
diff --git a/src/bindings/pbn_control/control.rs b/src/bindings/pbn_control/control.rs
index 94f2c67..03d8348 100644
--- a/src/bindings/pbn_control/control.rs
+++ b/src/bindings/pbn_control/control.rs
@@ -139,7 +139,7 @@ impl Control {
     /// so far are still returned.
     ///
     #[staticmethod]
-    #[pyo3(signature = (graph, phenotype, oscillation_type = None, size_limit = None, stop_when_found = false))]
+    #[pyo3(signature = (graph, phenotype, oscillation_type = None, size_limit = None, stop_when_found = false, initial_states = None))]
     pub fn phenotype_permanent(
         py: Python,
         graph: Py<AsynchronousPerturbationGraph>,
@@ -147,6 +147,7 @@ impl Control {
         oscillation_type: Option<String>,
         size_limit: Option<usize>,
         stop_when_found: bool,
+        initial_states: Option<&VertexSet>,
     ) -> PyResult<ColoredPerturbationSet> {
         let verbose = should_log(global_log_level(py)?);
 
@@ -156,6 +157,17 @@ impl Control {
             PhenotypeOscillationType::Forbidden
         };
 
+        // If initial states is not set, we consider all networks states as potential initial states
+        let initial_states_native = match initial_states {
+            Some(x) => x.as_native().clone(),
+            None => graph
+                .get()
+                .as_native()
+                .mk_unit_colored_vertices()
+                .vertices()
+                .clone(),
+        };
+
         // If size limit is not set, we consider the largest possible size.
         let size_limit =
             size_limit.unwrap_or_else(|| graph.get().as_native().perturbable_variables().len());
@@ -164,6 +176,7 @@ impl Control {
             phenotype.as_native().clone(),
             size_limit,
             p_type,
+            initial_states_native,
             stop_when_found,
             verbose,
         );