Merge pull request #89 from SciML/dw/subpackages

Split DiffEqProblemLibrary into subpackages

.github/workflows/CI.yml

@@ -1,39 +1,50 @@
 name: CI
+
 on:
   pull_request:
     branches:
       - master
   push:
     branches:
       - master
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        group:
-          - Core
+        pkg:
+          - DiffEqProblemLibrary
+          - DAEProblemLibrary
+          - DDEProblemLibrary
+          - JumpProblemLibrary
+          - ODEProblemLibrary
+          - SDEProblemLibrary
         version:
           - '1'
           - '1.6'
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-      - 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-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
+        with:
+          project: "${{ matrix.pkg == 'DiffEqProblemLibrary' && '.' || format('lib/{0}', matrix.pkg) }}"
       - uses: julia-actions/julia-runtest@v1
+        with:
+          project: "${{ matrix.pkg == 'DiffEqProblemLibrary' && '.' || format('lib/{0}', matrix.pkg) }}"
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
         with:
-          file: lcov.info
+          directories: "${{ matrix.pkg == 'DiffEqProblemLibrary' && 'src' || format('lib/{0}/src', matrix.pkg) }}"
+      - uses: codecov/codecov-action@v3
+        with:
+          files: lcov.info

.github/workflows/CompatHelper.yml

@@ -1,26 +1,51 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '00 * * * *'
-  issues:
-    types: [opened, reopened]
-
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+  CompatHelper:
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          subdirs = [""]
+          for f in readdir("lib"; join=true)
+              if isdir(f)
+                  push!(subdirs, f)
+              end
+          end
+          @info "CompatHelper directories" subdirs
+          CompatHelper.main(; subdirs)
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/FormatCheck.yml

@@ -8,6 +8,12 @@ on:
     tags: '*'
   pull_request:
 
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   build:
     runs-on: ubuntu-latest

.gitignore

@@ -1,4 +1,4 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
-/Manifest.toml
+Manifest.toml

Project.toml

@@ -1,28 +1,19 @@
 name = "DiffEqProblemLibrary"
 uuid = "a077e3f3-b75c-5d7f-a0c6-6bc4c8ec64a9"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>"]
-version = "4.17.0"
+version = "5.0.0"
 
 [deps]
-Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
-DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-DiffEqOperators = "9fdde737-9c7f-55bf-ade8-46b3f136cc48"
-Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+DAEProblemLibrary = "dfb8ca35-80a1-48ba-a605-84916a45b4f8"
+DDEProblemLibrary = "f42792ee-6ffc-4e2a-ae83-8ee2f22de800"
+JumpProblemLibrary = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e"
+ODEProblemLibrary = "fdc4e326-1af4-4b90-96e7-779fcce2daa5"
+SDEProblemLibrary = "c72e72a9-a271-4b2b-8966-303ed956772e"
 
 [compat]
-Catalyst = "11, 12"
-DiffEqBase = "6"
-DiffEqOperators = "4"
-Latexify = "0.15"
-ModelingToolkit = "7,8"
+DAEProblemLibrary = "0.1"
+DDEProblemLibrary = "0.1"
+JumpProblemLibrary = "0.1"
+ODEProblemLibrary = "0.1"
+SDEProblemLibrary = "0.1"
 julia = "1.6"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]

lib/DAEProblemLibrary/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2022 SciML
+Copyright (c) 2016 Chris Rackauckas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lib/DAEProblemLibrary/Project.toml

@@ -0,0 +1,11 @@
+name = "DAEProblemLibrary"
+uuid = "dfb8ca35-80a1-48ba-a605-84916a45b4f8"
+version = "0.1.0"
+
+[deps]
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[compat]
+DiffEqBase = "6"
+julia = "1.6"

src/dae_premade_problems.jl → lib/DAEProblemLibrary/src/DAEProblemLibrary.jl

@@ -1,3 +1,5 @@
+module DAEProblemLibrary
+
 using DiffEqBase, Markdown
 
 #DAE Example Problems
@@ -31,3 +33,5 @@ Hairer Norsett Wanner Solving Ordinary Differential Equations I - Nonstiff Probl
 Usually solved on ``[0,1e11]``
 """
 prob_dae_resrob = DAEProblem(f, du0, u0, (0.0, 100000.0))
+
+end # module

lib/DAEProblemLibrary/test/runtests.jl

@@ -0,0 +1,2 @@
+# The test is simply that all of the examples build!
+using DAEProblemLibrary

lib/DDEProblemLibrary/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2022 SciML
+Copyright (c) 2016 Chris Rackauckas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lib/DDEProblemLibrary/Project.toml

@@ -0,0 +1,10 @@
+name = "DDEProblemLibrary"
+uuid = "f42792ee-6ffc-4e2a-ae83-8ee2f22de800"
+version = "0.1.0"
+
+[deps]
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+
+[compat]
+DiffEqBase = "6"
+julia = "1.6"

lib/DDEProblemLibrary/src/DDEProblemLibrary.jl

@@ -0,0 +1,46 @@
+module DDEProblemLibrary
+
+using DiffEqBase
+# DDE Example Problems
+
+# examples with constant delays
+export
+# DDEs with 1 constant delay
+      prob_dde_1delay_ip, prob_dde_1delay_oop, prob_dde_1delay_scalar,
+      prob_dde_1delay_long_ip, prob_dde_1delay_long_oop, prob_dde_1delay_long_scalar,
+# DDEs with 2 constant delays
+      prob_dde_2delays_ip, prob_dde_2delays_oop, prob_dde_2delays_scalar,
+      prob_dde_2delays_long_ip, prob_dde_2delays_long_oop, prob_dde_2delays_long_scalar
+
+# DDETST problems
+export
+# DDEs with time dependent delays
+      prob_dde_DDETST_A1, prob_dde_DDETST_A2,
+# DDEs with vanishing time dependent delays
+      prob_dde_DDETST_B1, prob_dde_DDETST_B2,
+# DDEs with state dependent delays
+      prob_dde_DDETST_C1, prob_dde_DDETST_C2, prob_dde_DDETST_C3, prob_dde_DDETST_C4,
+# DDEs with vanishing state dependent delays
+      prob_dde_DDETST_D1, prob_dde_DDETST_D2,
+# neutral DDEs with time dependent delays
+      prob_dde_DDETST_E1, prob_dde_DDETST_E2,
+# neutral DDEs with vanishing time dependent delays
+      prob_dde_DDETST_F1, prob_dde_DDETST_F2, prob_dde_DDETST_F3, prob_dde_DDETST_F4,
+      prob_dde_DDETST_F5,
+# neutral DDEs with state dependent delays
+      prob_dde_DDETST_G1, prob_dde_DDETST_G2,
+# neutral DDEs with vanishing state dependent delays
+      prob_dde_DDETST_H1, prob_dde_DDETST_H2, prob_dde_DDETST_H3, prob_dde_DDETST_H4
+
+# RADAR5 problems
+export prob_dde_RADAR5_oregonator, prob_dde_RADAR5_robertson, prob_dde_RADAR5_waltman
+
+# QS exaple
+export prob_dde_qs
+
+include("constant_delays.jl")
+include("ddetst.jl")
+include("qs.jl")
+include("radar5.jl")
+
+end # module

lib/DDEProblemLibrary/test/runtests.jl

@@ -0,0 +1,2 @@
+# The test is simply that all of the examples build!
+using DDEProblemLibrary

lib/JumpProblemLibrary/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2022 SciML
+Copyright (c) 2016 Chris Rackauckas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lib/JumpProblemLibrary/Project.toml

@@ -0,0 +1,12 @@
+name = "JumpProblemLibrary"
+uuid = "faf0f6d7-8cee-47cb-b27c-1eb80cef534e"
+version = "0.1.0"
+
+[deps]
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+
+[compat]
+Catalyst = "11, 12"
+DiffEqBase = "6"
+julia = "1.6"

src/jump_premade_problems.jl → lib/JumpProblemLibrary/src/JumpProblemLibrary.jl

@@ -1,3 +1,5 @@
+module JumpProblemLibrary
+
 using DiffEqBase, Catalyst
 # Jump Example Problems
 export prob_jump_dnarepressor, prob_jump_constproduct, prob_jump_nonlinrxs,
@@ -260,3 +262,5 @@ tf = 10.0
 """
 prob_jump_diffnetwork = JumpProblemNetwork(getDiffNetwork, params, tf, getDiffu0, nothing,
                                            nothing)
+
+end # module

lib/JumpProblemLibrary/test/runtests.jl

@@ -0,0 +1,2 @@
+# The test is simply that all of the examples build!
+using JumpProblemLibrary