Proposed V16 README and index page updates

.github/workflows/Test.yml

@@ -16,9 +16,68 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
 
+permissions:
+  actions: write
+  contents: read
+
 jobs:
+  prewarm-cache:
+    name: "Prewarm Cache"
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1"
+          - "lts"
+          - "pre"
+    runs-on: ubuntu-latest
+    outputs:
+      deps-hash: ${{ steps.deps-hash.outputs.hash }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: "Compute dependency hash"
+        id: deps-hash
+        run: echo "hash=${{ hashFiles('Project.toml') }}" >> "$GITHUB_OUTPUT"
+
+      - name: "Setup Julia ${{ matrix.version }}"
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: "${{ matrix.version }}"
+          arch: "${{ runner.arch }}"
+
+      - name: "Restore Julia cache"
+        id: cache-restore
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.julia/artifacts
+            ~/.julia/packages
+            ~/.julia/registries
+            ~/.julia/compiled
+            ~/.julia/scratchspaces
+            ~/.julia/logs
+          key: "tests-cache-v2;os=${{ runner.os }};julia=${{ matrix.version }};deps=${{ steps.deps-hash.outputs.hash }}"
+
+      - name: "Build package"
+        uses: julia-actions/julia-buildpkg@v1
+
+      - name: "Save Julia cache"
+        if: steps.cache-restore.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.julia/artifacts
+            ~/.julia/packages
+            ~/.julia/registries
+            ~/.julia/compiled
+            ~/.julia/scratchspaces
+            ~/.julia/logs
+          key: "tests-cache-v2;os=${{ runner.os }};julia=${{ matrix.version }};deps=${{ steps.deps-hash.outputs.hash }}"
+
   tests:
     name: "Tests"
+    needs: prewarm-cache
     strategy:
       fail-fast: false
       matrix:
@@ -38,3 +97,45 @@ jobs:
       group: "${{ matrix.group }}"
       coverage: false
     secrets: "inherit"
+
+      - name: "Setup Julia ${{ matrix.version }}"
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: "${{ matrix.version }}"
+          arch: "${{ runner.arch }}"
+
+      - name: "Restore Julia cache"
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.julia/artifacts
+            ~/.julia/packages
+            ~/.julia/registries
+            ~/.julia/compiled
+            ~/.julia/scratchspaces
+            ~/.julia/logs
+          key: "tests-cache-v2;os=${{ runner.os }};julia=${{ matrix.version }};deps=${{ needs.prewarm-cache.outputs.deps-hash }}"
+
+      - name: "Build package"
+        uses: julia-actions/julia-buildpkg@v1
+
+      - name: "Run tests on ubuntu-latest with Julia v${{ matrix.version }} - ${{ matrix.group }}"
+        uses: julia-actions/julia-runtest@v1
+        with:
+          project: "@."
+          depwarn: "yes"
+          coverage: "true"
+        env:
+          GROUP: "${{ matrix.group }}"
+
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: "src,ext"
+
+      - name: "Report Coverage with Codecov"
+        uses: codecov/codecov-action@v5
+        if: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }}
+        with:
+          files: lcov.info
+          token: "${{ secrets.CODECOV_TOKEN }}"
+          fail_ci_if_error: true

.github/workflows/TestExtensions.yml

@@ -36,6 +36,8 @@ jobs:
       - name: "Cache Julia packages"
         uses: julia-actions/cache@v2
         with:
+          include-matrix: "false"
+          cache-name: "extensions-cache;julia=${{ matrix.version }}"
           token: "${{ secrets.GITHUB_TOKEN }}"
 
       - name: "Build main package"

docs/src/api/core_api.md

@@ -88,8 +88,8 @@ of all options currently available.
 - [`compounds`](@ref chemistry_functionality_compounds): Allows the designation of compound species.
 - [`observables`](@ref dsl_advanced_options_observables): Allows the designation of compound observables.
 - [`default_noise_scaling`](@ref simulation_intro_SDEs_noise_saling): Enables the setting of a default noise scaling expression.
-- [`differentials`](@ref constraint_equations_coupling_constraints): Allows the designation of differentials.
-- [`equations`](@ref constraint_equations_coupling_constraints): Allows the creation of algebraic and/or differential equations.
+- [`differentials`](@ref coupled_models_dsl): Allows the designation of differentials.
+- [`equations`](@ref coupled_models_dsl): Allows the creation of algebraic and/or differential equations.
 - [`continuous_events`](@ref events): Allows the creation of continuous events.
 - [`discrete_events`](@ref events): Allows the creation of discrete events.
 - `brownians`: Allows the creation of brownian processes that can be used to add noise to non-species variables.
@@ -103,7 +103,7 @@ A [`ReactionSystem`](@ref) is an instance of a
 `ModelingToolkitBase.AbstractSystem`, and has a number of fields that
 can be accessed using the Catalyst API and the [ModelingToolkitBase.jl Abstract
 System
-Interface](https://docs.sciml.ai/ModelingToolkit/stable/basics/AbstractSystem/).
+Interface](https://docs.sciml.ai/ModelingToolkit/stable/API/System/).
 Below we overview these components.
 
 There are three basic sets of convenience accessors that will return information
@@ -185,7 +185,7 @@ isautonomous
 
 ## Coupled reaction/equation system properties
 The following system property accessor functions are primarily relevant to reaction system [coupled
-to differential and/or algebraic equations](@ref constraint_equations).
+to differential and/or algebraic equations](@ref coupled_models).
 ```@docs
 ModelingToolkitBase.has_alg_equations
 ModelingToolkitBase.alg_equations
@@ -220,6 +220,7 @@ substoichmat
 prodstoichmat
 netstoichmat
 reactionrates
+PhysicalScale
 ```
 
 ## [Reaction metadata](@id api_rx_metadata)
@@ -268,13 +269,12 @@ network's ODE (as generated by the reaction rate equation) or SDE (as generated
 by the chemical Langevin equation) form:
 ```julia
 latexify(rn; form=:ode)
+latexify(rn; form = :ode, math_delimiters = true) # hide
 ```
 ```julia
 latexify(rn; form=:sde)
+latexify(rn; form = :sde, math_delimiters = true) # hide
 ```
-(As of writing this, an upstream bug causes the SDE form to be erroneously
-displayed as the ODE form)
-
 Finally, another optional argument (`expand_functions=true`) automatically expands functions defined by Catalyst (such as `mm`). To disable this, set `expand_functions=false`.
 
 Reaction networks can be plotted using the `GraphMakie` extension, which is loaded whenever all of `Catalyst`, `GraphMakie`, and `NetworkLayout` are loaded (note that a Makie backend, like `CairoMakie`, must be loaded as well). The two functions for plotting networks are `plot_network` and `plot_complexes`, which are two distinct representations. 
@@ -297,8 +297,13 @@ hillr
 hillar
 ```
 
-## Transformations
+## Transformations and `ReactionSystem` Conversions
 ```@docs
+ode_model
+ss_ode_model
+sde_model
+jump_model
+hybrid_model
 ModelingToolkitBase.mtkcompile
 set_default_noise_scaling
 ```