in-silico-cancer-cell 0.2.4__tar.gz → 0.2.5__tar.gz

{in_silico_cancer_cell-0.2.4 → in_silico_cancer_cell-0.2.5}/Cargo.lock

@@ -350,7 +350,7 @@ checksum = "77ce24cb58228fbb8aa041425bb1050850ac19177686ea6e0f41a70416f56fdb"
 
 [[package]]
 name = "frontend"
-version = "0.2.4"
+version = "0.2.5"
 dependencies = [
  "console_error_panic_hook",
  "futures",
@@ -486,7 +486,7 @@ checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
 [[package]]
 name = "in_silico_cancer_cell"
-version = "0.2.4"
+version = "0.2.5"
 dependencies = [
  "argmin",
  "argmin-math",

{in_silico_cancer_cell-0.2.4 → in_silico_cancer_cell-0.2.5}/Cargo.toml

@@ -1,7 +1,8 @@
 [package]
 name = "in_silico_cancer_cell"
-version = "0.2.4"
+version = "0.2.5"
 edition = "2024"
+include = ["/src", "/python/in_silico_cancer_cell"]
 readme = "README.md"
 
 [lib]

{in_silico_cancer_cell-0.2.4 → in_silico_cancer_cell-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: in_silico_cancer_cell
-Version: 0.2.4
+Version: 0.2.5
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy

{in_silico_cancer_cell-0.2.4 → in_silico_cancer_cell-0.2.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "in_silico_cancer_cell"
-version = "0.2.4"
+version = "0.2.5"
 description = "Simulation of an electrophysiological A549 cancer cell model using individual ion channels across the membrane"
 authors = [{ name = "MrP01", email = "peter@waldert.at" }]
 requires-python = ">=3.11"
@@ -33,11 +33,3 @@ features = ["pyo3/extension-module"]
 
 [tool.ruff]
 line-length = 120
-
-[tool.nitpick]
-style = [
-  "github://MrP01/lint-me-now/nitpick-base-style.toml",
-  "github://MrP01/lint-me-now/nitpick-rust-style.toml",
-  "github://MrP01/lint-me-now/nitpick-python-style.toml",
-]
-cache = "never"

{in_silico_cancer_cell-0.2.4 → in_silico_cancer_cell-0.2.5}/src/main.rs

@@ -111,7 +111,7 @@ pub fn compare_delta_tolerance(measurements: PatchClampData) {
 #[command(
   about = "In-Silico Cancer Cell Model Simulator",
   author = "Peter Waldert <peter@waldert.at>",
-  version = "0.2.4"
+  version = "0.2.5"
 )]
 struct Cli {
   /// Turn debugging information on

in_silico_cancer_cell-0.2.4/.editorconfig

@@ -1,13 +0,0 @@
-root = True
-
-[*]
-charset = utf-8
-end_of_line = lf
-tab_width = 2
-indent_size = 2
-indent_style = space
-insert_final_newline = True
-max_line_length = 120
-
-[*.py]
-indent_size = 4

in_silico_cancer_cell-0.2.4/.github/workflows/main.yml

@@ -1,50 +0,0 @@
-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: oven-sh/setup-bun@v2
-      - run: bun install --frozen-lockfile # also include the "dev" dependencies (e.g. wasm-pack)
-      - run: bun 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
-          echo "[]" > frontend/pkg/delta-tolerance.json
-      - run: bun run build
-      # deploy to Netlify
-      - 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-0.2.4/.github/workflows/maturin.yml

@@ -1,163 +0,0 @@
-# This file is autogenerated by maturin v1.10.2
-# To update, run
-#
-#    maturin generate-ci github
-#
-name: Build Maturin (Python Package)
-
-on:
-  push:
-    branches:
-      - main
-      - master
-    tags:
-      - "*"
-  pull_request:
-  workflow_dispatch:
-
-permissions:
-  contents: read
-
-jobs:
-  linux:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: ubuntu-latest
-            target: x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-          manylinux: auto
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-linux-${{ matrix.platform.target }}
-          path: dist
-
-  musllinux:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: ubuntu-latest
-            target: x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-          manylinux: musllinux_1_2
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-musllinux-${{ matrix.platform.target }}
-          path: dist
-
-  windows:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: windows-latest
-            target: x64
-          - runner: windows-latest
-            target: x86
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-          architecture: ${{ matrix.platform.target }}
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-windows-${{ matrix.platform.target }}
-          path: dist
-
-  macos:
-    runs-on: ${{ matrix.platform.runner }}
-    strategy:
-      matrix:
-        platform:
-          - runner: macos-14
-            target: aarch64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.x
-      - name: Build wheels
-        uses: PyO3/maturin-action@v1
-        with:
-          target: ${{ matrix.platform.target }}
-          args: --release --out dist --find-interpreter
-          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
-      - name: Upload wheels
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-macos-${{ matrix.platform.target }}
-          path: dist
-
-  sdist:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Build sdist
-        uses: PyO3/maturin-action@v1
-        with:
-          command: sdist
-          args: --out dist
-      - name: Upload sdist as a GitHub artifact
-        uses: actions/upload-artifact@v4
-        with:
-          name: wheels-sdist
-          path: dist
-
-  release:
-    name: Release
-    runs-on: ubuntu-latest
-    if: ${{ startsWith(github.ref, 'refs/tags/') || github.event_name == 'workflow_dispatch' }}
-    needs: [linux, musllinux, windows, macos, sdist]
-    permissions:
-      # Use to sign the release artifacts
-      id-token: write
-      # Used to upload release artifacts
-      contents: write
-      # Used to generate artifact attestation
-      attestations: write
-    steps:
-      - uses: actions/download-artifact@v4
-      - name: Generate artifact attestation
-        uses: actions/attest-build-provenance@v2
-        with:
-          subject-path: "wheels-*/*"
-      - name: Publish to PyPI
-        if: ${{ startsWith(github.ref, 'refs/tags/') }}
-        uses: PyO3/maturin-action@v1
-        env:
-          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
-        with:
-          command: upload
-          args: --non-interactive --skip-existing wheels-*/*

in_silico_cancer_cell-0.2.4/.gitignore

@@ -1,22 +0,0 @@
-.idea/
-.vscode/
-.venv
-.cache/
-__pycache__/
-
-.astro/
-node_modules/
-npm-debug.log*
-pnpm-debug.log*
-
-.env
-.env.production
-.DS_Store
-
-report/dgruyter.sty
-*.protected.*
-
-stuff/
-dist/
-/target
-*.so

in_silico_cancer_cell-0.2.4/.gitmodules

@@ -1,3 +0,0 @@
-[submodule "paper"]
-	path = paper
-	url = https://git@git.overleaf.com/6887c395dbab934264cd6ecf

in_silico_cancer_cell-0.2.4/.pre-commit-config.yaml

@@ -1,55 +0,0 @@
-repos:
-  - repo: local
-    hooks:
-      - id: prettier
-        name: prettier
-        entry: prettier --write --ignore-unknown
-        language: system
-        types:
-          - text
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-      - id: end-of-file-fixer
-      - id: trailing-whitespace
-  - repo: https://github.com/doublify/pre-commit-rust
-    rev: v1.0
-    hooks:
-      - id: fmt
-      - id: cargo-check
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
-    hooks:
-      - id: ruff
-        args:
-          - --fix
-      - id: ruff-format
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-      - id: python-check-blanket-noqa
-      - id: python-no-eval
-      - id: python-no-log-warn
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.16.0
-    hooks:
-      - id: pyupgrade
-  - repo: local
-    hooks:
-      - id: pyright
-        name: pyright
-        entry: pyright
-        language: system
-        types:
-          - python
-        pass_filenames: false
-  - repo: https://github.com/myint/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        args:
-          - --in-place
-          - --remove-all-unused-imports
-          - --remove-unused-variables
-          - --remove-duplicate-keys
-          - --ignore-init-module-imports

in_silico_cancer_cell-0.2.4/.rustfmt.toml

@@ -1,3 +0,0 @@
-tab_spaces = 2
-max_width = 120
-group_imports = "StdExternalCrate"

in_silico_cancer_cell-0.2.4/.vscode/extensions.json

@@ -1,4 +0,0 @@
-{
-  "recommendations": ["astro-build.astro-vscode"],
-  "unwantedRecommendations": []
-}

in_silico_cancer_cell-0.2.4/.vscode/launch.json

@@ -1,20 +0,0 @@
-{
-  "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",
-      "request": "launch",
-      "type": "node-terminal"
-    }
-  ]
-}

in_silico_cancer_cell-0.2.4/astro.config.mjs

@@ -1,20 +0,0 @@
-import { defineConfig } from "astro/config";
-import wasm from "vite-plugin-wasm";
-
-// https://astro.build/config
-export default defineConfig({
-  srcDir: "frontend",
-  vite: {
-    optimizeDeps: {
-      entries: ["layouts", "pages", "components"],
-    },
-    css: {
-      preprocessorOptions: {
-        scss: {
-          api: "modern-compiler",
-        },
-      },
-    },
-    plugins: [wasm()],
-  },
-});