Merge pull request #27 from BioJulia/ci-update

Fix package CI/update actions, and update [compat]

Author: jangevaare

.github/workflows/CompatHelper.yml

@@ -1,16 +1,32 @@
 name: CompatHelper
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - cron: 0 0 * * *
   workflow_dispatch:
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - 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.COMPATHELPER_PRIV }}  # optional
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/TagBot.yml

@@ -1,12 +1,25 @@
 name: TagBot
 on:
-  schedule:
-    - cron: 0 0 * * *
+  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 }}
+          changelog: |
+            ## {{ package }} {{ version }}
+            
+            {% if custom %}
+            {{ custom }}
+            {% endif %}
+            
+            {% if previous_release %}
+            [Diff since {{ previous_release }}]({{ compare_url }})
+            {% endif %}

.github/workflows/ci-stable.yml

@@ -0,0 +1,38 @@
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.0', '1']
+        julia-arch: [x64]
+        os: [ubuntu-latest, macOS-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-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
+        with:
+          depwarn: no
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v2
+        with:
+          file: lcov.info

.github/workflows/docs.yml

@@ -1,32 +1,25 @@
 name: Documentation
 
 on:
-    push:
-        branches:
-            - 'master'
-            - 'release-'
-        tags: '*'
-    pull_request:
+  push:
+    branches:
+      - master
+      - 'release-'
+    tags: '*'
+  pull_request:
 
 jobs:
-    build:
-        runs-on: ${{ matrix.os }}
-        strategy:
-            matrix:
-                julia-version: [1.3.0]
-                julia-arch: [x86]
-                os: [ubuntu-latest]
-        steps:
-            - uses: actions/[email protected]
-            - uses: julia-actions/setup-julia@latest
-              with:
-                  version: ${{ matrix.julia-version }}
-            - name: Install dependencies
-              run: |
-                julia -e 'using Pkg.Registry; Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))'
-                julia -e 'using Pkg.Registry; Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))'
-                julia --project=docs -e 'using Pkg; Pkg.add(PackageSpec(path="./")); Pkg.instantiate(); Pkg.update()'
-            - name: Build and deploy
-              env:
-                  DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-              run: julia --project=docs --color=yes docs/make.jl
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.6'
+      - 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 }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.travis.yml

@@ -9,9 +9,9 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
-BioSymbols = "3, 4"
-StaticArrays = "0.12"
-julia = "0.7, ^1"
+BioSymbols = "3, 4, 5"
+StaticArrays = "0.12, 1"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

Project.toml

@@ -10,7 +10,7 @@
 
 **Development status:**
 
-[![Build Status](https://travis-ci.org/BioJulia/SubstitutionModels.jl.svg?branch=master)](https://travis-ci.org/BioJulia/SubstitutionModels.jl)
+[![CI-stable](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/ci-stable.yml/badge.svg)](https://github.com/BioJulia/SubstitutionModels.jl/actions/workflows/ci-stable.yml)
 [![codecov.io](http://codecov.io/github/BioJulia/SubstitutionModels.jl/coverage.svg?branch=master)](http://codecov.io/github/BioJulia/SubstitutionModels.jl?branch=master)
 [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://BioJulia.github.io/SubstitutionModels.jl/latest)