badges

.github/workflows/docs.yml

@@ -1,26 +1,29 @@
-
-# ref: https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#GitHub-Actions-1
 name: Documentation
 
 on:
-  pull_request:
   push:
     branches:
-      - master
+      - master # update to match your development branch (master, main, dev, trunk, ...)
     tags: '*'
-  release:
-    types: [published, created]
+  pull_request:
 
 jobs:
   build:
+    permissions:
+      contents: write
+      pull-requests: read
+      statuses: write
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.10'
       - uses: julia-actions/cache@v1
       - name: Install dependencies
-        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --color=yes --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

README.md

@@ -2,7 +2,7 @@
 
 | Build status | Documentation |
 |:---:|:---:|
-| ![CI status](https://github.com/stelmo/DifferentiableMetabolism.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl/branch/master/graph/badge.svg?token=A2ui7exGIH)](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl) | [![stable documentation](https://img.shields.io/badge/docs-stable-blue)](https://stelmo.github.io/DifferentiableMetabolism.jl/stable) |
+| ![CI status](https://github.com/stelmo/DifferentiableMetabolism.jl/workflows/CI/badge.svg) [![codecov](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl/branch/master/graph/badge.svg?token=A2ui7exGIH)](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl) | [![Documentation](https://img.shields.io/badge/documentation-8e44ad?style=for-the-badge)](https://stelmo.github.io/DifferentiableMetabolism.jl/dev) |
 
 This package extends [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl)
 with the ability to differentiate an optimal solution of a constraint-based

docs/make.jl

@@ -17,16 +17,6 @@ limitations under the License.
 =#
 
 using Documenter, Literate, DifferentiableMetabolism
-import ConstraintTrees
-import Symbolics
-import COBREXA
-
-import ConstraintTrees.LinearValue
-import ConstraintTrees.QuadraticValue
-import ConstraintTrees.ConstraintTree
-import Symbolics.Num
-import COBREXA.optimization_model
-import ConstraintTrees.Constraint
 
 examples =
     sort(filter(x -> endswith(x, ".jl"), readdir(joinpath(@__DIR__, "src"), join = true)))