chore: apply BestieTemplate :local version

.JuliaFormatter.toml

@@ -1,2 +1,4 @@
-# See https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options
+indent = 4
+margin = 92
+normalize_line_endings = "unix"
 style = "yas"

.cirrus.yml

@@ -0,0 +1,13 @@
+freebsd_instance:
+  image_family: freebsd-13-3
+task:
+  name: FreeBSD
+  env:
+    matrix:
+      - JULIA_VERSION: 1
+  install_script:
+    - sh -c "$(fetch https://raw.githubusercontent.com/ararslan/CirrusCI.jl/master/bin/install.sh -o -)"
+  build_script:
+    - cirrusjl build
+  test_script:
+    - cirrusjl test

.copier-answers.yml

@@ -0,0 +1,39 @@
+# Changes here will be overwritten by Copier
+AddAllcontributors: false
+AddCitationCFF: true
+AddCodeOfConduct: false
+AddCompatHelperCI: true
+AddCopierCI: true
+AddDependabot: true
+AddDocs: false
+AddDocsCI: true
+AddFormatterAndLinterConfigFiles: true
+AddGitHubPRTemplate: true
+AddGitHubTemplates: false
+AddLintCI: true
+AddLychee: true
+AddMacToCI: true
+AddPrecommit: true
+AddTagBotCI: true
+AddTestCI: true
+AddWinToCI: true
+Authors: Chris Damour
+AutoIncludeTests: true
+CheckExplicitImports: true
+ConfigIndentation: 2
+ExplicitImportsChecklist: exclude_all_qualified_accesses_are_public
+JuliaIndentation: 4
+JuliaMinCIVersion: lts
+JuliaMinVersion: 1.6.7
+License: MIT
+LicenseCopyrightHolders: Chris Damour
+MarkdownIndentation: 2
+PackageName: ExpressionData
+PackageOwner: damourChris
+PackageUUID: 479be80e-0d6f-4501-bee0-9ae8a09d31d3
+RunJuliaNightlyOnCI: true
+StrategyConfirmIncluded: true
+StrategyLevel: 2
+StrategyReviewExcluded: false
+UseCirrusCI: true
+_src_path: /home/damourchris/.julia/packages/BestieTemplate/jdG8v

.devcontainer/devcontainer.json

@@ -7,4 +7,4 @@
         "ghcr.io/julialang/devcontainer-features/julia:1": {}
     },
     "postCreateCommand": "julia --project= -e 'using Pkg; Pkg.Registry.add(RegistrySpec(url=\"https://github.com/damourChris/SysBioRegistry.jl\")); Pkg.instantiate();'"
-}
+}

.editorconfig

@@ -0,0 +1,18 @@
+# https://editorconfig.org
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+trim_trailing_whitespace = true
+
+[*.jl]
+indent_size = 4
+
+[*.md]
+indent_size = 2
+
+[*.{yml,toml,json}]
+indent_size = 2

.github/ISSUE_TEMPLATE/bug_report.md

@@ -31,19 +31,19 @@ Without MRE, we would only be able to help you to a limited extent, and attentio
 
 **Environment (please complete the following information):**
 
-  - Output of `using Pkg; Pkg.status()`
+- Output of `using Pkg; Pkg.status()`
 
 ```julia
 
 ```
 
-  - Output of `using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)`
+- Output of `using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)`
 
 ```julia
 
 ```
 
-  - Output of `versioninfo()`
+- Output of `versioninfo()`
 
 ```julia
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,25 @@
+<!--
+Thanks for making a pull request to ExpressionData.jl.
+We have added this PR template to help you help us.
+See the comments below, fill the required fields, and check the items.
+-->
+
+## Related issues
+
+<!-- We normally work with (i) create issue; (ii) discussion if necessary; (iii) create PR. So, at least one of the following should be true:-->
+
+<!-- Option 1, this closes an existing issue. Fill the number below-->
+Closes #
+
+<!-- Option 2, this is a small fix that arguably won't need an issue. Uncomment below -->
+<!--
+There is no related issue.
+-->
+
+## Checklist
+
+<!-- mark true if NA -->
+<!-- leave PR as draft until all is checked -->
+- [ ] Tests are passing
+- [ ] Lint workflow is passing
+- [ ] Docs were updated and workflow is passing

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -7,7 +7,8 @@ Fixes ...
 - [] Appropriate tests were added
 - [] The new feature was added in a way that does not break public API
 - [] New documentation related to the new feature was added
-- 
+-
+
 **Additional context**
 
 Add any other context about the problem here.

.github/workflows/CompatHelper.yml

@@ -1,11 +1,15 @@
+# CompatHelper v3.5.0
 name: CompatHelper
+
 on:
   schedule:
-    - cron: 0 0 * * *
+    - cron: 0 0 * * * # Every day at 00:00 UTC
   workflow_dispatch:
+
 permissions:
   contents: write
   pull-requests: write
+
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
@@ -17,9 +21,11 @@ jobs:
       - name: Install Julia, but only if it is not already available in the PATH
         uses: julia-actions/setup-julia@v2
         with:
-          version: '1'
+          version: "1"
           arch: ${{ runner.arch }}
         if: steps.julia_in_path.outcome != 'success'
+      - name: Use Julia cache
+        uses: julia-actions/cache@v2
       - name: "Add the General registry via Git"
         run: |
           import Pkg

.github/workflows/Copier.yml

@@ -0,0 +1,59 @@
+name: Copier Update
+
+on:
+  schedule:
+    - cron: 0 7 1/7 * *  # Every 7 days at 7:00 UTC
+  workflow_dispatch:
+
+jobs:
+  Copier:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.COPIER_PAT }}
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: "1"
+      - name: Use Julia cache
+        uses: julia-actions/cache@v2
+      - name: Install JuliaFormatter.jl
+        run: julia -e 'using Pkg; pkg"add JuliaFormatter"'
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: touch requirements.txt
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          cache: 'pip'
+          python-version: "3.11"
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: rm requirements.txt
+      - name: Check for update in the template
+        run: |
+          pip install copier
+          copier update -A -o rej
+          echo -e "Automated changed by Copier.yml workflow\n" > /tmp/body.md
+          echo -e 'Rejected changes (if any):\n```diff\n' >> /tmp/body.md
+          find . -name "*.rej" | xargs cat >> /tmp/body.md
+          find . -name "*.rej" | xargs rm -f
+          echo -e '```' >> /tmp/body.md
+          git diff
+      - name: Run pre-commit to run the formatters
+        run: |
+          pip install pre-commit
+          pre-commit run -a || true # Ignore pre-commit errors
+      - name: Create Pull Request
+        id: cpr
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.COPIER_PAT }}
+          commit-message: ":robot: BestieTemplate.jl update"
+          title: "[AUTO] BestieTemplate.jl update"
+          body-path: /tmp/body.md
+          branch: auto-copier-template-update
+          delete-branch: true
+          labels: configuration, automated pr, no changelog
+      - name: Check outputs
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

.github/workflows/Docs.yml

@@ -0,0 +1,57 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "src/**"
+      - "*.toml"
+    tags: ["*"]
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "docs/**"
+      - "src/**"
+      - "*.toml"
+    types: [opened, synchronize, reopened]
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: "1"
+      - name: Use Julia cache
+        uses: julia-actions/cache@v2
+      - name: Instantiate environment with development version of the package
+        run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - name: Run doctest
+        run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using ExpressionData
+            DocMeta.setdocmeta!(ExpressionData, :DocTestSetup, :(using ExpressionData); recursive=true)
+            doctest(ExpressionData)'
+      - name: Generate and deploy documentation
+        run: julia --project=docs docs/make.jl
+        env:
+          JULIA_PKG_SERVER: ""
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988