CompatHelper: bump compat for Parameters to 0.13, (keep existing compat)

.github/pull_request_template.md

@@ -0,0 +1,16 @@
+*We set up this PR template to confirm that you have considered all the necessary aspects of your contribution so that we are on the right track. Please fill out the template below to the best of your ability. If you have any questions, please feel free to get in touch.*
+
+## Proposed Changes
+*Give a brief overview of your contribution here in a few sentences. For bug fixes, please detail the bug and include a test case. For a new feature, please clearly describe the design, its rationale, the possible alternatives considered. Note that each PR should address only one issue*
+
+## Related Work
+*Resolve any issues (bug fix or feature request), note any related PRs, or mention interactions with the work of others, if any.*
+
+## Checklist
+*Put an x by all that apply. You can fill this out after submitting the PR.*
+
+- [ ] I am submitting my contribution to the development branch.
+- [ ] My contribution is commented and uses the code style of the project (see .JuliaFormatter.toml).
+- [ ] I have added a unit test to verify my contribution, if necessary.
+- [ ] I have updated appropriate documentation (README, documentation, tutorials, etc.), if applicable.
+- [ ] I have added an entry in NEWS.md, if necessary.

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.12'
 #          - 'nightly'
         os:
           - ubuntu-latest
@@ -32,14 +32,13 @@ jobs:
         arch:
           - x64
     steps:
-      - run: |
-          pip3 install meshio scipy --user
+      - run: pip3 install scipy --user
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -56,6 +55,8 @@ jobs:
       - uses: julia-actions/julia-runtest@latest
         continue-on-error: ${{ matrix.version == 'nightly' }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
-          file: lcov.info
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/compat.yml

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

.github/workflows/documentation.yml

@@ -0,0 +1,38 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - ge # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    # These permissions are needed to:
+    # - Deploy the documentation: https://documenter.juliadocs.org/stable/man/hosting/#Permissions
+    # - Delete old caches: https://github.com/julia-actions/cache#usage
+    permissions:
+      actions: write
+      contents: write
+      pull-requests: read
+      statuses: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v2
+      - name: Install dependencies
+        shell: julia --color=yes --project=docs {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+      - name: Build and deploy
+        run: julia --color=yes --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+

.github/workflows/format.yml

@@ -2,6 +2,7 @@ name: FormatPR
 on:
   schedule:
     - cron: '0 0 * * *'
+permissions: write-all
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -28,4 +29,4 @@ jobs:
       - name: Check outputs
         run: |
           echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
-          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

.github/workflows/tag.yml

@@ -1,12 +1,12 @@
-name: TagBot
-on:
-  schedule:
-    - cron: 0 0 * * *
-jobs:
-  TagBot:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+name: TagBot
+on:
+  schedule:
+    - cron: 0 0 * * *
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -1,4 +1,18 @@
-Manifest.toml
-result/
-tuto/
-.CondaPkg/
+Manifest.toml
+result/
+tuto/
+.CondaPkg/
+p
+check.png
+.vscode
+.DS_Store
+result20*
+boundary_vs
+*.vtp
+*.csv
+*.nsys-rep
+result_*
+*.pvtp
+animation
+*.json
+*.jld2

LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2024 CFDML
-
-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.
+MIT License
+
+Copyright (c) 2024 CFDML
+
+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.

Project.toml

@@ -1,30 +1,74 @@
 name = "KitAMR"
 uuid = "c7589248-7317-493e-9871-fc2fc0963dfd"
-authors = ["CFDML and contributors"]
 version = "0.1.0"
+authors = ["CFDML and contributors"]
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-JLD = "4138dd39-2aa7-5051-a626-17a0bb65d9c8"
+ExportAll = "ad2082ca-a69e-11e9-38fa-e96309a31fe4"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
-MKL_jll = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-MPICH_jll = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-P4est = "7d669430-f675-4ae7-b43e-fab78ec5a902"
+MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
+MeshIO = "7269a6da-0436-5bbc-96c2-40638cbb6118"
+NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
+P4est_jll = "6b5a15aa-cf52-5330-8376-5e5d90283449"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
+PreferenceTools = "ba661fbb-e901-4445-b070-854aec6bfbc5"
+Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-Tar = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
+UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
+
+[compat]
+AbstractTrees = "0.4"
+BenchmarkTools = "1.5.0"
+CEnum = "0.4, 0.5"
+CSV = "0.10.15"
+DataFrames = "1.7.0"
+Dates = "1.11.0"
+DocStringExtensions = "0.9"
+FileIO = "1.17.1"
+GeometryBasics = "0.5.10"
+JLD2 = "0.6.2"
+LinearAlgebra = "<0.0.1, 1"
+MPI = "0.20.24"
+MPIPreferences = "0.1.3"
+MeshIO = "0.5.3"
+NearestNeighbors = "0.4.26"
+P4est_jll = "=2.8.1"
+Parameters = "0.12, 0.13"
+PrecompileTools = "^1"
+Preferences = "1.2"
+RecipesBase = "^1"
+Reexport = "^1"
+SparseArrays = "1.10"
+SpecialFunctions = "^2"
+StaticArrays = "1.9"
+Statistics = "1.11.1"
+StructArrays = "0.7.2"
+Suppressor = "0.2.8"
+UUIDs = "1.6"
+julia = "^1"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]