Add GitHub workflows

.github/workflows/CI.yml

@@ -0,0 +1,60 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+    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:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+          - '1.11'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v5
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using Fides
+            DocMeta.setdocmeta!(Fides, :DocTestSetup, :(using Fides); recursive=true)
+            doctest(Fides)'

.github/workflows/CompatHelper.yml

@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - 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: '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
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/FormatCheck.yml

@@ -0,0 +1,48 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'release-'
+    tags: '*'
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always, but for the master branch and tags.
+  # Cancel intermediate builds: always, but for the master branch and tags.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/master' && github.refs != 'refs/tags/*'}}
+
+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@v4
+      - 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`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/TagBot.yml

@@ -0,0 +1,33 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+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 }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

Project.toml

@@ -15,11 +15,11 @@ Aqua = "0.8"
 ComponentArrays = "0.15"
 CondaPkg = "0.2"
 ForwardDiff = "0.10"
-Printf = "1.11.0"
+Printf = "1"
 PythonCall = "0.9"
 SafeTestsets = "0.1"
 SimpleUnPack = "1"
-StyledStrings = "1.11.0"
+StyledStrings = "1"
 Test = "1"
 julia = "1.10"
 

README.md

@@ -1,10 +1,10 @@
 # Fides.jl
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://sebapersson.github.io/Fides.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://sebapersson.github.io/Fides.jl/dev/)
-[![Build Status](https://github.com/sebapersson/Fides.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/sebapersson/Fides.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://fides-dev.github.io/Fides.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://fides-dev.github.io/Fides.jl/dev/)
+[![Build Status](https://github.com/fides-dev/Fides.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/fides-dev/Fides.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
-[![codecov](https://codecov.io/gh/sebapersson/Fides.jl/graph/badge.svg?token=J7PXRF30JG)](https://codecov.io/gh/sebapersson/Fides.jl)
+[![codecov](https://codecov.io/gh/fides-dev/Fides.jl/graph/badge.svg?token=J7PXRF30JG)](https://codecov.io/gh/fides-dev/Fides.jl)
 [![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
 
 Fides.jl is a Julia wrapper of the Python package [Fides.py](https://github.com/fides-dev/fides), which implements an Interior Trust Region Reflective for bounds constrained optimization problems based on [1, 2]. Fides targets problems on the form:

docs/make.jl

@@ -5,11 +5,11 @@ DocMeta.setdocmeta!(Fides, :DocTestSetup, :(using Fides); recursive = true)
 
 format = Documenter.HTML(;prettyurls = get(ENV, "CI", "false") == "true",
                          assets = String["assets/custom_theme.css"],
-                         repolink = "https://github.com/sebapersson/Fides.jl",
+                         repolink = "https://github.com/fides-dev/Fides.jl",
                          edit_link = "main")
 
 makedocs(; modules = [Fides],
-         repo = "https://github.com/sebapersson/Fides.jl/blob/{commit}{path}#{line}",
+         repo = "https://github.com/fides-dev/Fides.jl/blob/{commit}{path}#{line}",
          checkdocs = :exports,
          warnonly = false,
          format = format,
@@ -20,5 +20,5 @@ makedocs(; modules = [Fides],
              "API" => "API.md",
          ],)
 
-deploydocs(; repo = "github.com/sebapersson/Fides.jl.git",
+deploydocs(; repo = "github.com/fides-dev/Fides.jl.git",
            devbranch = "main",)

docs/src/index.md

@@ -17,7 +17,7 @@ Where `f` is a continues at least twice-differentaible function, and `lb` and `u
 - Good performance for parameter estimating Ordinary Differential Equation models [3].
 
 !!! note "Star us on GitHub!"
-    If you find the package useful in your work please consider giving us a star on [GitHub](https://github.com/sebapersson/Fides.jl). This will help us secure funding in the future to continue maintaining the package.
+    If you find the package useful in your work please consider giving us a star on [GitHub](https://github.com/fides-dev/Fides.jl). This will help us secure funding in the future to continue maintaining the package.
 
 ## Installation
 
@@ -41,7 +41,7 @@ If you have any problems using Fides, here are some helpful tips:
 
 - Check the Fides Python [documentation](https://fides-optimizer.readthedocs.io/en/latest/about.html).
 - Post your questions in the `#sciml-sysbio` or `#math-optimization` channel on the [Julia Slack](https://julialang.org/slack/).
-- If you have encountered unexpected behavior or a bug, please open an issue on [GitHub](https://github.com/sebapersson/Fides.jl).
+- If you have encountered unexpected behavior or a bug, please open an issue on [GitHub](https://github.com/fides-dev/Fides.jl).
 
 ## Citation
 

test/show.jl

@@ -8,5 +8,6 @@ sol = solve(prob, Fides.BFGS())
 
 @testset "show" begin
     @test @sprintf("%s", prob) == "FidesProblem with 2 parameters to estimate"
-    @test @sprintf("%s", sol)[1:140] == "FidesSolution\n---------------- Summary ---------------\nmin(f)                = 3.30e-14\nParameters estimated  = 2\nOptimiser iterations  = 46"
+    @test @sprintf("%s", sol)[1:140] ==
+          "FidesSolution\n---------------- Summary ---------------\nmin(f)                = 3.30e-14\nParameters estimated  = 2\nOptimiser iterations  = 46"
 end