create package

.github/workflows/CI.yml

@@ -0,0 +1,42 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        group:
+          - Core
+        version:
+          - '1'
+          - '1.6'
+    steps:
+      - uses: actions/checkout@v2
+      - 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/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: ${{ matrix.group }}
+          JULIA_NUM_THREADS: 11
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/CompatHelper.yml

@@ -0,0 +1,26 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 * * * *'
+  issues:
+    types: [opened, reopened]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main(;subdirs=["", "docs"])'

.github/workflows/Documentation.yml

@@ -0,0 +1,29 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ --code-coverage=user docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/Downstream.yml

@@ -0,0 +1,55 @@
+name: IntegrationTest
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  test:
+    name: ${{ matrix.package.repo }}/${{ matrix.package.group }}/${{ matrix.julia-version }}
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.package.group }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: [1,1.6]
+        os: [ubuntu-latest]
+        package:
+          - {user: SciML, repo: ModelingToolkit.jl, group: All}
+          - {user: SciML, repo: OrdinaryDiffEq.jl, group: Interface}
+          - {user: SciML, repo: OrdinaryDiffEq.jl, group: Regression}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - uses: julia-actions/julia-buildpkg@latest
+      - name: Clone Downstream
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          try
+            # force it to use this PR's version of the package
+            Pkg.develop(PackageSpec(path="."))  # resolver may fail with main deps
+            Pkg.update()
+            Pkg.test(coverage=true)  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine
+            # It means we marked this as a breaking change, so we don't need to worry about
+            # Mistakenly introducing a breaking change, as we have intentionally made one
+            @info "Not compatible with this release. No problem." exception=err
+            exit(0)  # Exit immediately, as a success
+          end
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/Invalidations.yml

@@ -0,0 +1,40 @@
+name: Invalidations
+
+on:
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: always.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  evaluate:
+    # Only run on PRs to the default branch.
+    # In the PR trigger above branches can be specified only explicitly whereas this check should work for master, main, or any other default branch
+    if: github.base_ref == github.event.repository.default_branch
+    runs-on: ubuntu-latest
+    steps:
+    - uses: julia-actions/setup-julia@v1
+      with:
+        version: '1'
+    - uses: actions/checkout@v3
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_pr
+
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.event.repository.default_branch }}
+    - uses: julia-actions/julia-buildpkg@v1
+    - uses: julia-actions/julia-invalidations@v1
+      id: invs_default
+
+    - name: Report invalidation counts
+      run: |
+        echo "Invalidations on default branch: ${{ steps.invs_default.outputs.total }} (${{ steps.invs_default.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+        echo "This branch: ${{ steps.invs_pr.outputs.total }} (${{ steps.invs_pr.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
+    - name: Check if the PR does increase number of invalidations
+      if: steps.invs_pr.outputs.total > steps.invs_default.outputs.total
+      run: exit 1

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -1,24 +1,11 @@
-# Files generated by invoking Julia with --code-coverage
-*.jl.cov
 *.jl.*.cov
-
-# Files generated by invoking Julia with --track-allocation
+*.jl.cov
 *.jl.mem
-
-# System-specific files and directories generated by the BinaryProvider and BinDeps packages
-# They contain absolute paths specific to the host computer, and so should not be committed
-deps/deps.jl
-deps/build.log
-deps/downloads/
-deps/usr/
-deps/src/
-
-# Build artifacts for creating documentation generated by the Documenter package
-docs/build/
-docs/site/
-
-# File generated by Pkg, the package manager, based on a corresponding Project.toml
-# It records a fixed state of all packages used by the project. As such, it should not be
-# committed for packages, but should be committed for applications that require a static
-# environment.
+/docs/build/
+/docs/src/modules
 Manifest.toml
+*.swp
+
+# vscode stuff
+.vscode
+.vscode/*

LICENSE.md

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2022 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.

Project.toml

@@ -0,0 +1,19 @@
+name = "EasyModelAnalysis"
+uuid = "ef4b24a4-a090-4686-a932-e7e56a5a83bd"
+authors = ["SciML"]
+version = "0.0.1"
+
+[deps]
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
+
+[compat]
+julia = "1.6"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -1 +1,6 @@
-# EasyModelAnalysis
+# EasyModelAnalysis.jl
+
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](http://docs.sciml.ai/stable)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](http://docs.sciml.ai/dev)
+[![Documentation and Deployment](https://badge.buildkite.com/b4720f5f3a8d2d1ac8bbaebf5e0e38aaae28b6c8fb436ba05e.svg)](https://buildkite.com/julialang/scimldocs?branch=main)
+

docs/Project.toml

@@ -0,0 +1,6 @@
+[deps]
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+EasyModelAnalysis = "ef4b24a4-a090-4686-a932-e7e56a5a83bd"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

docs/make.jl

@@ -0,0 +1,37 @@
+using Documenter
+
+# Make sure that plots don't throw a bunch of warnings / errors!
+ENV["GKSwstype"] = "100"
+using Plots
+
+mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]),
+                           :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
+                                        "packages" => [
+                                            "base",
+                                            "ams",
+                                            "autoload",
+                                            "mathtools",
+                                            "require",
+                                        ])))
+
+makedocs(sitename = "Overview of Julia's SciML",
+         authors = "Chris Rackauckas",
+         modules = Module[],
+         clean = true, doctest = false,
+         strict = [
+             :doctest,
+             :linkcheck,
+             :parse_error,
+             :example_block,
+             # Other available options are
+             # :autodocs_block, :cross_references, :docs_block, :eval_block, :example_block, :footnote, :meta_block, :missing_docs, :setup_block
+         ],
+         format = Documenter.HTML(analytics = "UA-90474609-3",
+                                  assets = ["assets/favicon.ico"],
+                                  canonical = "https://docs.sciml.ai/stable/",
+                                  mathengine = mathengine),
+         pages = [
+            "EasyModelAnalysis.jl: Quick and Easy Queries to Simulation Results" => "index.md",
+            ])
+
+deploydocs(repo = "github.com/SciML/EasyModelAnalysis.jl")