Refactor ODE analyses through ODESemantics in catlog, catlog-wasm, and frontend

.github/workflows/build.yml

@@ -105,10 +105,9 @@ jobs:
 
       - name: Install Rust toolchain from file
         if: github.event_name == 'release' || steps.cache-frontend-build.outputs.cache-hit != 'true'
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
-          # Don't override flags in cargo config files.
-          rustflags: ""
+          build-warnings: ""
 
       - name: Build for Staging
         if: (github.event_name == 'push' || github.event_name == 'pull_request') && steps.cache-frontend-build.outputs.cache-hit != 'true'
@@ -357,10 +356,9 @@ jobs:
 
       - name: Install Rust toolchain from file
         if: steps.cache-gaios-build.outputs.cache-hit != 'true'
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
-          # Don't override flags in cargo config files.
-          rustflags: ""
+          build-warnings: ""
 
       - name: Build gaios plugin
         if: steps.cache-gaios-build.outputs.cache-hit != 'true'

.github/workflows/ci.yml

@@ -23,11 +23,10 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install Rust toolchain
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
           toolchain: ${{ matrix.toolchain }}
-          # Don't override flags in cargo config files.
-          rustflags: ""
+          build-warnings: ""
 
       - name: Tests
         run: |
@@ -42,10 +41,11 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install Rust toolchain from file
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
           toolchain: nightly
           components: rustfmt
+          build-warnings: ""
 
       - name: Check formatting
         run: |
@@ -59,15 +59,9 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install Rust toolchain from file
-        uses: actions-rust-lang/setup-rust-toolchain@v1
-        with:
-          # Don't override flags in cargo config files. Warnings are denied
-          # through `CARGO_BUILD_WARNINGS` instead of `RUSTFLAGS`.
-          rustflags: ""
+        uses: actions-rust-lang/setup-rust-toolchain@v2
 
       - name: Check clippy warnings
-        env:
-          CARGO_BUILD_WARNINGS: deny
         run: |
           cargo clippy --all-targets --all-features --keep-going
 
@@ -112,10 +106,9 @@ jobs:
           pnpm install
 
       - name: Install Rust toolchain from file
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
-          # Don't override flags in cargo config files.
-          rustflags: ""
+          build-warnings: ""
 
       - name: Format/linting/import sorting
         run: |
@@ -124,7 +117,7 @@ jobs:
 
       - name: Typescript documents package tests
         run: |
-          pnpm --filter catcolab-documents exec vitest run test/creating-and-editing.test.ts test/definitions.test.ts test/binder.test-d.ts test/llm-conversation.test.ts
+          pnpm --filter catcolab-documents test
 
       - name: Typescript logic package tests
         run: |
@@ -158,10 +151,9 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install Rust toolchain from file
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
-          # Don't override flags in cargo config files.
-          rustflags: ""
+          build-warnings: ""
 
       - name: Setup pnpm
         uses: pnpm/action-setup@v6
@@ -190,9 +182,9 @@ jobs:
         uses: actions/checkout@v7
 
       - name: Install Rust toolchain from file
-        uses: actions-rust-lang/setup-rust-toolchain@v1
+        uses: actions-rust-lang/setup-rust-toolchain@v2
         with:
-          rustflags: ""
+          build-warnings: ""
 
       - name: Start PostgreSQL
         run: |

.github/workflows/deploy.yml

@@ -253,7 +253,7 @@ jobs:
 
     - name: Deploy to catcolab-next
       run: |
-       nix run github:serokell/deploy-rs -- --skip-checks .#catcolab-next
+       nix run .#deploy-rs -- --skip-checks .#catcolab-next
 
     - name: Verify deployment
       run: |

flake.nix

@@ -75,6 +75,22 @@
       pkgsLinux = nixpkgsFor linuxSystem;
       rustToolchainLinux = rustToolchainFor linuxSystem;
 
+      # deploy-rs lib whose activate-rs uses the nixpkgs-built (binary cached) deploy-rs,
+      # rather than building the flake's own copy from crates.io.
+      deployLib =
+        (import nixpkgs {
+          system = linuxSystem;
+          overlays = [
+            deploy-rs.overlays.default
+            (final: prev: {
+              deploy-rs = {
+                inherit (pkgsLinux) deploy-rs;
+                lib = prev.deploy-rs.lib;
+              };
+            })
+          ];
+        }).deploy-rs.lib;
+
       # Per-system crane library + prebuilt cargo dependency layer. The
       # frontend package is exposed for every system in `devShellSystems` so
       # macOS developers can `nix build .#frontend` against the same wasm/api
@@ -211,23 +227,23 @@
         };
 
       # NOTE: this is not currently used, but was painful to build and might be useful in the future.
-      # Wraps the typical `deploy-rs.lib.${linuxSystem}.activate.nixos` activation function
+      # Wraps the typical `deployLib.activate.nixos` activation function
       # with a custom script that can run additional health checks. The script runs on the remote host
       # and if it fails the whole deployment will fail.
       # use:
       # `deploy.nodes.${host}.profiles.system.path = healthcheckWrapper self.nixosConfigurations.host;`
       healthcheckWrapper =
         nixosConfiguration:
         let
-          defaultNixos = deploy-rs.lib.${linuxSystem}.activate.nixos nixosConfiguration;
+          defaultNixos = deployLib.activate.nixos nixosConfiguration;
 
           healthcheckWrapperScript = pkgsLinux.writeShellScriptBin "healthcheck-wrapper-script" ''
             PROFILE=${defaultNixos}
             # insert healthchecks
             ${defaultNixos}/deploy-rs-activate
           '';
         in
-        deploy-rs.lib.${linuxSystem}.activate.custom healthcheckWrapperScript
+        deployLib.activate.custom healthcheckWrapperScript
           "./bin/healthcheck-wrapper-script";
     in
     {
@@ -277,6 +293,8 @@
             };
 
           linuxOnlyPackages = {
+            deploy-rs = pkgsLinux.deploy-rs;
+
             backend = pkgsLinux.callPackage ./packages/backend/default.nix {
               inherit craneLib cargoArtifacts;
               pkgs = pkgsLinux;
@@ -386,15 +404,15 @@
           profiles.system = {
             sshUser = "catcolab";
             user = "root";
-            path = deploy-rs.lib.${linuxSystem}.activate.nixos self.nixosConfigurations.catcolab;
+            path = deployLib.activate.nixos self.nixosConfigurations.catcolab;
           };
         };
         catcolab-next = {
           hostname = "backend-next.catcolab.org";
           profiles.system = {
             sshUser = "catcolab";
             user = "root";
-            path = deploy-rs.lib.${linuxSystem}.activate.nixos self.nixosConfigurations.catcolab-next;
+            path = deployLib.activate.nixos self.nixosConfigurations.catcolab-next;
           };
         };
         catcolab-vm = {
@@ -406,7 +424,7 @@
               "2221"
             ];
             sshUser = "catcolab";
-            path = deploy-rs.lib.${linuxSystem}.activate.nixos self.nixosConfigurations.catcolab-vm;
+            path = deployLib.activate.nixos self.nixosConfigurations.catcolab-vm;
             user = "root";
           };
         };

package.json

@@ -17,7 +17,8 @@
     "scripts": {
         "test": "echo \"Error: no test specified\" && exit 1",
         "build:deps": "pnpm --filter ./packages/frontend run build:deps",
-        "dev": "pnpm --filter ./packages/frontend run dev"
+        "dev": "pnpm --filter ./packages/frontend run dev",
+        "check": "cargo +nightly fmt && cargo clippy && pnpm --filter ./packages/frontend run check"
     },
     "engines": {
         "node": "^24.4.0"