in-silico-cancer-cell 0.2.0__tar.gz → 0.2.4__tar.gz

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

@@ -0,0 +1,50 @@
+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-0.2.0 → in_silico_cancer_cell-0.2.4}/.github/workflows/maturin.yml

@@ -1,4 +1,4 @@
-# This file is autogenerated by maturin v1.5.1
+# This file is autogenerated by maturin v1.10.2
 # To update, run
 #
 #    maturin generate-ci github
@@ -26,25 +26,17 @@ jobs:
         platform:
           - runner: ubuntu-latest
             target: x86_64
-          # - runner: ubuntu-latest
-          #   target: aarch64
-          # - runner: ubuntu-latest
-          #   target: armv7
-          # - runner: ubuntu-latest
-          #   target: s390x
-          # - runner: ubuntu-latest
-          #   target: ppc64le
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: "true"
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
           manylinux: auto
       - name: Upload wheels
         uses: actions/upload-artifact@v4
@@ -52,27 +44,52 @@ jobs:
           name: wheels-linux-${{ 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: x64
           - runner: windows-latest
             target: x86
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          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: "true"
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
@@ -84,21 +101,19 @@ jobs:
     strategy:
       matrix:
         platform:
-          - runner: macos-latest
-            target: x86_64
-          # - runner: macos-14
-          #   target: aarch64
+          - runner: macos-14
+            target: aarch64
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
-          sccache: "true"
+          sccache: ${{ !startsWith(github.ref, 'refs/tags/') }}
       - name: Upload wheels
         uses: actions/upload-artifact@v4
         with:
@@ -114,7 +129,7 @@ jobs:
         with:
           command: sdist
           args: --out dist
-      - name: Upload sdist
+      - name: Upload sdist as a GitHub artifact
         uses: actions/upload-artifact@v4
         with:
           name: wheels-sdist
@@ -123,11 +138,23 @@ jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
-    if: startsWith(github.ref, 'refs/tags/')
-    needs: [linux, windows, macos, sdist]
+    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 }}

{in_silico_cancer_cell-0.2.0 → in_silico_cancer_cell-0.2.4}/.gitignore

@@ -7,8 +7,6 @@ __pycache__/
 .astro/
 node_modules/
 npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
 pnpm-debug.log*
 
 .env

in_silico_cancer_cell-0.2.4/.gitmodules

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

{in_silico_cancer_cell-0.2.0 → in_silico_cancer_cell-0.2.4}/.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: fmt
       - id: cargo-check
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+    rev: v0.5.0
     hooks:
       - id: ruff
         args:
@@ -31,7 +31,7 @@ repos:
       - id: python-no-eval
       - id: python-no-log-warn
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.16.0
     hooks:
       - id: pyupgrade
   - repo: local

{in_silico_cancer_cell-0.2.0 → in_silico_cancer_cell-0.2.4}/.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",