Merge pull request #34 from MagneticResonanceImaging/jf-url

Fix URLs after repo move
MagneticResonanceImaging · Apr 11, 2024 · 86a0acb · 86a0acb
2 parents 53f073d + 11394a4
commit 86a0acb
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,8 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -2,19 +2,47 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - cron: 0 0 * * 0 # weekly
   workflow_dispatch:
-
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - 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@latest
         with:
-          version: 1
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+          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 }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+
+# based on:
+# https://github.com/JuliaRegistries/CompatHelper.jl
diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -16,7 +16,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'

diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -14,3 +14,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/clean.yml b/.github/workflows/clean.yml
@@ -0,0 +1,28 @@
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#gh-pages-Branch
+
+name: DocPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "documenter@juliadocs.github.io"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}
diff --git a/.github/workflows/runtests.yml b/.github/workflows/runtests.yml
@@ -3,43 +3,38 @@ name: Unit Tests
 on:
   create:
     tags:
-  pull_request:
+  push:
     branches:
       - main
     paths-ignore:
       - '**.md'
       - 'docs/**'
-  push:
-    branches:
-      - main
+  pull_request:
     paths-ignore:
       - '**.md'
       - 'docs/**'
-  schedule:
-    - cron: '0 1 * * 1' # Every Monday at 1am
+  workflow_dispatch:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - '1' # Leave this line unchanged; '1' will automatically expand to the latest stable 1.x release of Julia.
-          - 'nightly'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
+        version: ['1', 'nightly']
+        os: [ubuntu-latest, windows-latest, macOS-latest]
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+
+#     - name: "Set up Julia"
+      - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+
+      - name: Cache artifacts
+        uses: actions/cache@v3
         env:
           cache-name: cache-artifacts
         with:
@@ -49,9 +44,14 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+
+#     - name: "Unit Test"
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
+
+#     - name: "Cover"
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
+        if: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
         with:
           file: lcov.info
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # BlochSim.jl
 
-https://github.com/StevenWhitaker/BlochSim.jl
+https://github.com/MagneticResonanceImaging/BlochSim.jl
 
 [![docs-stable][docs-stable-img]][docs-stable-url]
 [![docs-dev][docs-dev-img]][docs-dev-url]
@@ -24,9 +24,11 @@ The main functionality is provided by the functions
 `freeprecess`, `excite`, and `spoil`
 (and their mutating variants `freeprecess!`, `excite!`, and `spoil!`).
 These functions can be used to simulate a wide variety of MRI sequences.
-In addition, this package provides implementations for
-a multi-echo spin echo (MESE) scan (`MESEBlochSim`)
-and a spoiled gradient-recalled echo (SPGR) scan (`SPGRBlochSim`).
+In addition, this package provides implementations
+for specific scan sequences:
+
+- multi-echo spin echo (MESE) scan (`MESEBlochSim`)
+- spoiled gradient-recalled echo (SPGR) scan (`SPGRBlochSim`).
 
 ## Examples
 See the examples given in the documentation strings for how to use the provided
@@ -128,6 +130,8 @@ julia> signal(spinmc)
 
 * [MRIgeneralizedBloch.jl](https://github.com/JakobAsslaender/MRIgeneralizedBloch.jl)
   focuses on [magnetization transfer](https://doi.org/10.1002/mrm.29071)
+* [KomaMRI.jl](https://github.com/JuliaHealth/KomaMRI.jl)
+  has Pulseq compatability
 
 
 ## Acknowledgement
@@ -137,16 +141,24 @@ All tests for this package of the form `testX0x` (like `testA5b` or `testF3d`)
 are based on the corresponding section in the tutorial (see
 [test/matlab.jl](test/matlab.jl)).
 
+
+## Status
+
+On 2024-04-08 this repo moved here from
+https://github.com/StevenWhitaker/BlochSim.jl.
+Submit issues for outdated URLs.
+
+
 <!-- URLs -->
-[action-img]: https://github.com/StevenWhitaker/BlochSim.jl/actions/workflows/runtests.yml/badge.svg
-[action-url]: https://github.com/StevenWhitaker/BlochSim.jl/actions
+[action-img]: https://github.com/MagneticResonanceImaging/BlochSim.jl/actions/workflows/runtests.yml/badge.svg
+[action-url]: https://github.com/MagneticResonanceImaging/BlochSim.jl/actions
 [pkgeval-img]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/B/BlochSim.svg
 [pkgeval-url]: https://juliaci.github.io/NanosoldierReports/pkgeval_badges/B/BlochSim.html
-[codecov-img]: https://codecov.io/gh/StevenWhitaker/BlochSim.jl/branch/main/graph/badge.svg?token=tduieBgema
-[codecov-url]: https://codecov.io/gh/StevenWhitaker/BlochSim.jl
+[codecov-img]: https://codecov.io/gh/MagneticResonanceImaging/BlochSim.jl/branch/main/graph/badge.svg?token=tduieBgema
+[codecov-url]: https://codecov.io/gh/MagneticResonanceImaging/BlochSim.jl
 [docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
-[docs-stable-url]: https://StevenWhitaker.github.io/BlochSim.jl/stable
+[docs-stable-url]: https://MagneticResonanceImaging.github.io/BlochSim.jl/stable
 [docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
-[docs-dev-url]: https://StevenWhitaker.github.io/BlochSim.jl/dev
+[docs-dev-url]: https://MagneticResonanceImaging.github.io/BlochSim.jl/dev
 [license-img]: http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat
 [license-url]: LICENSE
diff --git a/docs/make.jl b/docs/make.jl
@@ -82,7 +82,7 @@ Documenter.makedocs(;
     authors = "Amaya Murgia, Steven Whitaker, Jeff Fessler and contributors",
     sitename = "$repo.jl",
     format,
-    strict = true, # fail on "warnings"
+#   strict = true, # fail on "warnings" - deprecated
     pages = [
         "Home" => "index.md",
         "Methods" => "methods.md",