Initial repo setup.

.github/workflows/build.yml

@@ -0,0 +1,77 @@
+name: build
+# This should ensure that the workflow won't run on `dev-*` branches, but will
+# otherwise execute on any other branch and any pull request (including dev
+# branches).
+on:
+  push:
+    branches-ignore:
+      - 'dev-*'
+  pull_request:
+    branches:
+      - '*'
+
+env:
+  # A fixed version used for testing, so that the builds don't
+  # spontaneously break after a few years.
+  # Make sure to update this from time to time.
+  RUST_VERSION: "1.77.0"
+jobs:
+  # Check formatting
+  fmt:
+    name: Rustfmt
+    runs-on: ubuntu-latest
+    env:
+      RUSTFLAGS: "-D warnings"
+    steps:
+      - name: Checkout.
+        uses: actions/checkout@v3
+      - name: Install Rust toolchain.
+        run: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain ${{ env.RUST_VERSION }}
+      - name: Rust format check.
+        run: cargo fmt --all -- --check
+
+  # Run basic code validity check
+  check:
+    needs: fmt
+    name: Check
+    runs-on: ubuntu-latest
+    env:
+      RUSTFLAGS: "-D warnings"
+    steps:
+      - name: Checkout.
+        uses: actions/checkout@v3
+      - name: Install Rust toolchain.
+        run: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain ${{ env.RUST_VERSION }}
+      - name: Rust code validity check.
+        run: cargo check
+
+  # Run all tests
+  test:
+    needs: check
+    name: Test Suite
+    runs-on: ubuntu-latest
+    env:
+      RUSTFLAGS: "-D warnings"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Checkout.
+        uses: actions/checkout@v3
+      - name: Install Rust toolchain.
+        run: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain ${{ env.RUST_VERSION }}
+      - name: Run tests.
+        run: cargo test --all-features
+
+  # Check code style
+  clippy:
+    needs: check
+    name: Clippy
+    runs-on: ubuntu-latest
+    env:
+      RUSTFLAGS: "-D warnings"
+    steps:
+      - name: Checkout.
+        uses: actions/checkout@v3
+      - name: Install Rust toolchain.
+        run: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain ${{ env.RUST_VERSION }}
+      - name: Run clippy.
+        run: cargo clippy

.gitignore

@@ -12,3 +12,5 @@ Cargo.lock
 
 # MSVC Windows builds of rustc generate these, which store debugging information
 *.pdb
+
+.idea/

Cargo.toml

@@ -0,0 +1,21 @@
+[package]
+name = "biodivine-lib-bma-data"
+version = "0.0.1"
+authors = ["Ondřej Huvar <[email protected]>", "Samuel Pastva <[email protected]>"]
+edition = "2021"
+description = "Library for working with models in BMA format."
+homepage = "https://github.com/sybila/biodivine-lib-bma-data"
+repository = "https://github.com/sybila/biodivine-lib-bma-data"
+readme = "README.md"
+keywords = ["boolean-network", "BMA", "systems-biology"]
+categories = ["science", "simulation"]
+license = "MIT"
+
+[lib]
+name = "biodivine_lib_bma_data"
+path = "src/lib.rs"
+
+[dependencies]
+biodivine-lib-param-bn = ">=0.5.11, <1.0.0"
+clap = { version = "4.1.4", features = ["derive"] }
+rand = "0.8.5"

models/json/RestingNeuron.json

@@ -0,0 +1 @@
+{"Model":{"Name":"Resting Neuron","Variables":[{"Id":6,"RangeFrom":0,"RangeTo":1,"Formula":"0"},{"Id":24,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":25,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":26,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":27,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":1,"RangeFrom":0,"RangeTo":1,"Formula":"max(var(3),var(1))-var(5)"},{"Id":3,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":4,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":5,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":28,"RangeFrom":0,"RangeTo":1,"Formula":"max(var(29),var(28))-var(31)"},{"Id":29,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":30,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":31,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":32,"RangeFrom":0,"RangeTo":1,"Formula":"max(var(33),var(32))-var(35)"},{"Id":33,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":34,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":35,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":36,"RangeFrom":0,"RangeTo":1,"Formula":"max(var(37),var(36))-var(39)"},{"Id":37,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":38,"RangeFrom":0,"RangeTo":1,"Formula":""},{"Id":39,"RangeFrom":0,"RangeTo":1,"Formula":""}],"Relationships":[{"Id":4,"FromVariable":4,"ToVariable":5,"Type":"Activator"},{"Id":21,"FromVariable":30,"ToVariable":31,"Type":"Activator"},{"Id":21,"FromVariable":34,"ToVariable":35,"Type":"Activator"},{"Id":21,"FromVariable":38,"ToVariable":39,"Type":"Activator"},{"Id":2,"FromVariable":3,"ToVariable":1,"Type":"Activator"},{"Id":3,"FromVariable":1,"ToVariable":4,"Type":"Activator"},{"Id":5,"FromVariable":5,"ToVariable":1,"Type":"Inhibitor"},{"Id":10,"FromVariable":1,"ToVariable":24,"Type":"Activator"},{"Id":18,"FromVariable":1,"ToVariable":1,"Type":"Activator"},{"Id":1,"FromVariable":6,"ToVariable":3,"Type":"Activator"},{"Id":19,"FromVariable":29,"ToVariable":28,"Type":"Activator"},{"Id":20,"FromVariable":28,"ToVariable":30,"Type":"Activator"},{"Id":22,"FromVariable":31,"ToVariable":28,"Type":"Inhibitor"},{"Id":23,"FromVariable":28,"ToVariable":28,"Type":"Activator"},{"Id":25,"FromVariable":28,"ToVariable":25,"Type":"Activator"},{"Id":24,"FromVariable":24,"ToVariable":29,"Type":"Activator"},{"Id":19,"FromVariable":33,"ToVariable":32,"Type":"Activator"},{"Id":20,"FromVariable":32,"ToVariable":34,"Type":"Activator"},{"Id":22,"FromVariable":35,"ToVariable":32,"Type":"Inhibitor"},{"Id":23,"FromVariable":32,"ToVariable":32,"Type":"Activator"},{"Id":27,"FromVariable":32,"ToVariable":26,"Type":"Activator"},{"Id":26,"FromVariable":25,"ToVariable":33,"Type":"Activator"},{"Id":19,"FromVariable":37,"ToVariable":36,"Type":"Activator"},{"Id":20,"FromVariable":36,"ToVariable":38,"Type":"Activator"},{"Id":22,"FromVariable":39,"ToVariable":36,"Type":"Inhibitor"},{"Id":23,"FromVariable":36,"ToVariable":36,"Type":"Activator"},{"Id":29,"FromVariable":36,"ToVariable":27,"Type":"Activator"},{"Id":28,"FromVariable":26,"ToVariable":37,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":6,"Name":"Potential","Type":"Constant","ContainerId":0,"PositionX":454.16666666666663,"PositionY":222.14285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":24,"Name":"P2","Type":"Constant","ContainerId":0,"PositionX":704.1666666666666,"PositionY":222.14285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":25,"Name":"P3","Type":"Constant","ContainerId":0,"PositionX":954.1666666666666,"PositionY":222.14285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":26,"Name":"P4","Type":"Constant","ContainerId":0,"PositionX":1204.1666666666667,"PositionY":222.14285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":27,"Name":"Output","Type":"Constant","ContainerId":0,"PositionX":1454.1666666666667,"PositionY":222.14285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":1,"Name":"Pore","Type":"MembraneReceptor","ContainerId":1,"PositionX":378.7883124043404,"PositionY":293.0092058578739,"CellX":null,"CellY":null,"Angle":0},{"Id":3,"Name":"VS","Type":"MembraneReceptor","ContainerId":1,"PositionX":451.29012214872057,"PositionY":328.0311128390987,"CellX":null,"CellY":null,"Angle":45},{"Id":4,"Name":"CTD_connect","Type":"Default","ContainerId":1,"PositionX":399.06666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":5,"Name":"CTD","Type":"Default","ContainerId":1,"PositionX":351.56666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":28,"Name":"Pore","Type":"MembraneReceptor","ContainerId":2,"PositionX":628.7883124043486,"PositionY":293.00920585707354,"CellX":null,"CellY":null,"Angle":0},{"Id":29,"Name":"VS","Type":"MembraneReceptor","ContainerId":2,"PositionX":701.29012214872,"PositionY":328.03111283909914,"CellX":null,"CellY":null,"Angle":45},{"Id":30,"Name":"CTD_connect","Type":"Default","ContainerId":2,"PositionX":649.0666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":31,"Name":"CTD","Type":"Default","ContainerId":2,"PositionX":601.5666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":32,"Name":"Pore","Type":"MembraneReceptor","ContainerId":3,"PositionX":878.7883124042828,"PositionY":293.00920586354914,"CellX":null,"CellY":null,"Angle":0},{"Id":33,"Name":"VS","Type":"MembraneReceptor","ContainerId":3,"PositionX":951.2901221487209,"PositionY":328.03111283909834,"CellX":null,"CellY":null,"Angle":45},{"Id":34,"Name":"CTD_connect","Type":"Default","ContainerId":3,"PositionX":899.0666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":35,"Name":"CTD","Type":"Default","ContainerId":3,"PositionX":851.5666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":36,"Name":"Pore","Type":"MembraneReceptor","ContainerId":4,"PositionX":1128.788312404283,"PositionY":293.0092058635637,"CellX":null,"CellY":null,"Angle":0},{"Id":37,"Name":"VS","Type":"MembraneReceptor","ContainerId":4,"PositionX":1201.29012214872,"PositionY":328.03111283909925,"CellX":null,"CellY":null,"Angle":45},{"Id":38,"Name":"CTD_connect","Type":"Default","ContainerId":4,"PositionX":1149.0666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":39,"Name":"CTD","Type":"Default","ContainerId":4,"PositionX":1101.5666666666666,"PositionY":381.2285714285714,"CellX":null,"CellY":null,"Angle":0}],"Containers":[{"Id":1,"Name":"","Size":1,"PositionX":1,"PositionY":1},{"Id":2,"Name":"","Size":1,"PositionX":2,"PositionY":1},{"Id":3,"Name":"","Size":1,"PositionX":3,"PositionY":1},{"Id":4,"Name":"","Size":1,"PositionX":4,"PositionY":1}]}}

models/json/SimpleBifurcation.json

@@ -0,0 +1,44 @@
+{
+  "Model": {
+    "Name": "model 1",
+    "Variables": [
+      {
+        "Id": 3,
+        "RangeFrom": 0,
+        "RangeTo": 1,
+        "Formula": ""
+      }
+    ],
+    "Relationships": [
+      {
+        "Id": 12,
+        "FromVariable": 3,
+        "ToVariable": 3,
+        "Type": "Activator"
+      }
+    ]
+  },
+  "Layout": {
+    "Variables": [
+      {
+        "Id": 3,
+        "Name": "A",
+        "Type": "Default",
+        "ContainerId": 1,
+        "PositionX": 632.5,
+        "PositionY": -493.33333333333337,
+        "CellX": 0,
+        "CellY": 0,
+        "Angle": 0
+      }
+    ],
+    "Containers": [
+      {
+        "Id": 1,
+        "Size": 1,
+        "PositionX": 2,
+        "PositionY": -2
+      }
+    ]
+  }
+}