in-silico-cancer-cell 0.1.0__tar.gz → 0.2.3__tar.gz

in_silico_cancer_cell-0.2.3/.github/workflows/main.yml

@@ -0,0 +1,48 @@
+name: Build Main, Frontend and Deploy
+on:
+  push:
+env:
+  CARGO_TERM_COLOR: always
+jobs:
+  build:
+    strategy:
+      matrix:
+        include:
+          - target: x86_64-unknown-linux-gnu
+            os: ubuntu-latest
+          - target: x86_64-pc-windows-msvc
+            os: windows-latest
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - run: rustup toolchain install nightly --profile minimal
+      - uses: Swatinem/rust-cache@v2
+
+      # builds main.rs
+      - name: Build project
+        run: cargo build --release --target=${{ matrix.target }}
+
+      # builds frontend with wasm-pack
+      - uses: bahmutov/npm-install@v1
+      - run: yarn run wasm-pack build frontend --release
+      - run: |
+          cargo run --release --target=${{ matrix.target }} -- --protocol activation --phase g0 save-patch-clamp-data
+          cargo run --release --target=${{ matrix.target }} -- --protocol deactivation --phase g0 save-patch-clamp-data
+          cargo run --release --target=${{ matrix.target }} -- --protocol ramp --phase g0 save-patch-clamp-data
+          cargo run --release --target=${{ matrix.target }} -- --protocol activation --phase g1 save-patch-clamp-data
+          cargo run --release --target=${{ matrix.target }} -- --protocol deactivation --phase g1 save-patch-clamp-data
+          cargo run --release --target=${{ matrix.target }} -- --protocol ramp --phase g1 save-patch-clamp-data
+      - run: yarn run build
+      # deploy
+      - uses: jsmrcaga/action-netlify-deploy@master
+        # if: startsWith(github.ref, 'refs/tags/') && runner.os == 'Linux'
+        if: runner.os == 'Linux'
+        with:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+          NETLIFY_DEPLOY_MESSAGE: "Production deploy v${{ github.ref }}"
+          NETLIFY_DEPLOY_TO_PROD: true
+          install_command: "echo Skipping..."
+          build_command: "echo Skipping..."
+          build_directory: dist/

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.3}/.vscode/launch.json

@@ -1,6 +1,15 @@
 {
   "version": "0.2.0",
   "configurations": [
+    {
+      "type": "lldb",
+      "request": "launch",
+      "name": "Cargo launch",
+      "cargo": {
+        "args": ["build"]
+      },
+      "args": ["single"]
+    },
     {
       "command": "./node_modules/.bin/astro dev",
       "name": "Development server",

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.3}/Cargo.lock

@@ -302,7 +302,7 @@ dependencies = [
 
 [[package]]
 name = "frontend"
-version = "0.1.0"
+version = "0.2.3"
 dependencies = [
  "console_error_panic_hook",
  "futures",
@@ -443,15 +443,17 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "in_silico_cancer_cell"
-version = "0.1.0"
+version = "0.2.3"
 dependencies = [
  "argmin",
  "argmin-math",
  "clap",
+ "getrandom",
  "log",
  "matfile",
  "nalgebra",
  "pyo3",
+ "rand",
  "regex",
  "serde",
  "serde_json",
@@ -750,9 +752,9 @@ checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.84"
+version = "1.0.85"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ec96c6a92621310b51366f1e28d05ef11489516e93be030060e5fc12024a49d6"
+checksum = "22244ce15aa966053a896d1accb3a6e68469b97c7f33f284b99f0d576879fc23"
 dependencies = [
  "unicode-ident",
 ]

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.3}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "in_silico_cancer_cell"
-version = "0.1.0"
+version = "0.2.3"
 edition = "2021"
 
 [lib]
@@ -36,6 +36,8 @@ argmin-math = { version = "0.4.0", features = ["nalgebra_latest"], optional = tr
 serde = { version = "1.0.203", features = ["derive"], optional = true }
 serde_json = { version = "1.0.117", optional = true }
 clap = { version = "4.5.4", features = ["derive"], optional = true }
+rand = "0.8.5"
+getrandom = { version = "0.2.15", features = ["js"] }
 
 [profile.release]
 # This makes the compiled code faster and smaller, but it makes compiling slower,

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.3}/PKG-INFO

@@ -1,14 +1,19 @@
 Metadata-Version: 2.3
 Name: in_silico_cancer_cell
-Version: 0.1.0
+Version: 0.2.3
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
+Summary: Simulation of an electrophysiological A549 cancer cell model using individual ion channels across the membrane
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: homepage, https://in-silico-cancer-cell.waldert.at/
+Project-URL: repository, https://github.com/MrP01/InSilicoCancerCell
 
 # Electrophysiological Cancer Cell Model
 
+![PyPI - Version](https://img.shields.io/pypi/v/in-silico-cancer-cell)
+
 Attempt to model an A549 cancer cell's ion channels using an HMM (Hidden Markov Model) and simulation of voltage + current development accross the membrane of the cell.
 
 This software comes in three flavours:
@@ -24,3 +29,7 @@ This software comes in three flavours:
 
 This computational model is based on [Langthaler et al., 2021](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009091): **A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma**.
 
+## The Simulation Dashboard
+
+![Screenshot of the User Interface](./figures/screenshot.png)
+

{in_silico_cancer_cell-0.1.0 → in_silico_cancer_cell-0.2.3}/README.md

@@ -1,5 +1,7 @@
 # Electrophysiological Cancer Cell Model
 
+![PyPI - Version](https://img.shields.io/pypi/v/in-silico-cancer-cell)
+
 Attempt to model an A549 cancer cell's ion channels using an HMM (Hidden Markov Model) and simulation of voltage + current development accross the membrane of the cell.
 
 This software comes in three flavours:
@@ -14,3 +16,7 @@ This software comes in three flavours:
 (Image source: [here](https://doi.org/10.1371/journal.pcbi.1009091.g002)).
 
 This computational model is based on [Langthaler et al., 2021](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009091): **A549 in-silico 1.0: A first computational model to simulate cell cycle dependent ion current modulation in the human lung adenocarcinoma**.
+
+## The Simulation Dashboard
+
+![Screenshot of the User Interface](./figures/screenshot.png)