Merge remote-tracking branch 'myrepo/update_to_catalyst13' into update_to_catalyst13

Author: isaacsas

.github/workflows/ci.yml

@@ -1,41 +1,40 @@
-name: CI
-on:
-  - push
-  - pull_request
-jobs:
-  test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1.5'
-          - '1.6'
-          - '1.7'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
-        with:
-          file: lcov.info
+name: CI
+on:
+  - push
+  - pull_request
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

test/birthdeath2D.jl

@@ -22,14 +22,14 @@ prs = exp.(2 .* rand(2))
 ps = [ prs[1], prs[1] / exp(4 * rand()),
        prs[2], prs[2] / exp(4 * rand()) ]
 
-Nmax = 130
+Nmax = 100
 u0 = zeros(Nmax+1, Nmax+1)
 u0[1] = 1.0
 
 tt = [ 0.25, 1.0, 10.0 ]
 
 prob = convert(ODEProblem, sys, u0, 10.0, ps)
-sol = solve(prob, Vern7(), abstol=1e-9, reltol=1e-6, saveat=tt)
+sol = solve(prob, Vern7(), abstol=1e-6, saveat=tt)
 
 @test marg(sol.u[1], dims=2) ≈ pdf.(Poisson(ps[1] / ps[2] * (1 - exp(-ps[2] * tt[1]))), 0:Nmax) atol=1e-4
 @test marg(sol.u[1], dims=1) ≈ pdf.(Poisson(ps[3] / ps[4] * (1 - exp(-ps[4] * tt[1]))), 0:Nmax) atol=1e-4
@@ -44,7 +44,7 @@ A = convert(SparseMatrixCSC, sys, (Nmax+1, Nmax+1), ps, 0)
 f = (du,u,t) -> mul!(du, A, u)
 
 probA = ODEProblem(f, u0, 10.0)
-solA = solve(prob, Vern7(), abstol=1e-9, reltol=1e-6, saveat=tt)
+solA = solve(prob, Vern7(), abstol=1e-6, saveat=tt)
 
 @test sol.u[1] ≈ solA.u[1] atol=1e-4
 @test sol.u[2] ≈ solA.u[2] atol=1e-4

test/feedbackloop.jl

@@ -47,12 +47,12 @@ u0 = zeros(2, Nmax)
 u0[1] = 1.0
 
 prob = convert(ODEProblem, sys, u0, maximum(tt), ps)
-sol = solve(prob, Vern7(), abstol=1e-9, reltol=1e-6, saveat=tt)
+sol = solve(prob, Vern7(), abstol=1e-6, saveat=tt)
 
 f = (du,u,t) -> mul!(du, A, u)
 
 probA = ODEProblem(f, u0, 10.0)
-solA = solve(prob, Vern7(), abstol=1e-9, reltol=1e-6, saveat=tt)
+solA = solve(prob, Vern7(), abstol=1e-6, saveat=tt)
 
 @test sol.u[1] ≈ solA.u[1] atol=1e-4
 @test sol.u[2] ≈ solA.u[2] atol=1e-4