touchup with PkgSkeleton

.github/workflows/CI.yml

@@ -0,0 +1,68 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.0' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+          - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.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
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: |
+          julia --project=docs -e '
+            using Documenter: doctest
+            using MYPACKAGE
+            doctest(MYPACKAGE)' # change MYPACKAGE to the name of your package
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/CompatHelper.yml

@@ -3,6 +3,7 @@ name: CompatHelper
 on:
   schedule:
     - cron: '00 00 * * *'
+  workflow_dispatch:
 
 jobs:
   CompatHelper:
@@ -13,9 +14,6 @@ jobs:
         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()

.github/workflows/TagBot.yml

@@ -1,11 +1,15 @@
 name: TagBot
 on:
-  schedule:
-    - cron: 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 }}

.gitignore

@@ -2,6 +2,8 @@
 *.jl.*.cov
 *.jl.mem
 /notes.org
+/Manifest.toml
+/deps/deps.jl
 /docs/build
-/docs/site
-# /docs/Manifest.toml
+/docs/Manifest.toml
+/test/coverage/Manifest.toml

.travis.yml

@@ -1,8 +1,9 @@
 ## Documentation: http://docs.travis-ci.com/user/languages/julia/
 language: julia
+dist: focal
 os:
   - linux
-  # - osx
+  - osx
 julia:
   - 1.0
   - 1.5
@@ -12,21 +13,18 @@ notifications:
 git:
   depth: 99999999
 
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-#matrix:
-#  allow_failures:
-#  - julia: nightly
-
 jobs:
-  include:
-    - stage: Documentation
-      julia: 1.5
-      os: linux
-      script:
-        - julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.develop(PackageSpec(path=pwd()))'
-        - julia --project=docs --color=yes docs/make.jl
-      after_success: skip
+  ## uncomment following lines to deploy documentation
+  # include:
+  #   - stage: "Documentation"
+  #     julia: 1.3
+  #     os: linux
+  #     script:
+  #       - julia --project=docs -e 'using Pkg; Pkg.instantiate(); Pkg.develop(PackageSpec(path=pwd()))'
+  #       - julia --project=docs --color=yes docs/make.jl
+  #     after_success: skip
+  allow_failures:
+    - julia: nightly
 after_success:
   - julia --project=test/coverage -e 'using Pkg; Pkg.instantiate()'
   - julia --project=test/coverage test/coverage/coverage.jl

LICENSE.md

@@ -1,22 +1,22 @@
 The DynamicHMC.jl package is licensed under the MIT "Expat" License:
 
-> Copyright (c) 2017: Tamas K. Papp.
-> 
+> Copyright (c) 2020: Tamas K. Papp.
+>
 > 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.
-> 
+>

README.md

@@ -4,9 +4,10 @@ Implementation of robust dynamic Hamiltonian Monte Carlo methods in Julia.
 
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Build Status](https://travis-ci.org/tpapp/DynamicHMC.jl.svg?branch=master)](https://travis-ci.org/tpapp/DynamicHMC.jl)
+[![build](https://github.com/tpapp/DynamicHMC.jl/workflows/CI/badge.svg)](https://github.com/tpapp/DynamicHMC.jl/actions?query=workflow%3ACI)
 [![codecov.io](http://codecov.io/github/tpapp/DynamicHMC.jl/coverage.svg?branch=master)](http://codecov.io/github/tpapp/DynamicHMC.jl?branch=master)
 [![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://tpapp.github.io/DynamicHMC.jl/stable)
-[![Documentation](https://img.shields.io/badge/docs-master-blue.svg)](https://tpapp.github.io/DynamicHMC.jl/latest)
+[![Documentation](https://img.shields.io/badge/docs-master-blue.svg)](https://tpapp.github.io/DynamicHMC.jl/dev)
 [![DOI](https://zenodo.org/badge/93741413.svg)](https://zenodo.org/badge/latestdoi/93741413)
 
 ## Overview

appveyor.yml

@@ -1,9 +1,17 @@
 environment:
   matrix:
-  - JULIAVERSION: "julialang/bin/winnt/x86/0.5/julia-0.5-latest-win32.exe"
-  - JULIAVERSION: "julialang/bin/winnt/x64/0.5/julia-0.5-latest-win64.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x86/julia-latest-win32.exe"
-  - JULIAVERSION: "julianightlies/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 1
+  - julia_version: nightly
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+# matrix:
+#   allow_failures:
+#   - julia_version: nightly
 
 branches:
   only:
@@ -17,18 +25,18 @@ notifications:
     on_build_status_changed: false
 
 install:
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $("http://s3.amazonaws.com/"+$env:JULIAVERSION),
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"DynamicHMC\"); Pkg.build(\"DynamicHMC\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"DynamicHMC\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"

docs/Project.toml

@@ -7,4 +7,4 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff"
 
 [compat]
-Documenter = "~0.24"
+Documenter = "~0.26"