Package setup (#2)

.JuliaFormatter.toml

@@ -1,2 +1,3 @@
+# See https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options
 style = "blue"
 indent = 2

.github/ISSUE_TEMPLATE/BUG_REPORT.md

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+---
+name: SparseArraysBase.jl bug report
+about: Create a bug report to help us improve SparseArraysBase.jl
+title: "[BUG] YOUR SHORT DESCRIPTION OF THE BUG HERE"
+labels: ["bug"]
+assignees: ''
+
+---
+
+**Description of bug**
+
+Please give a brief description of the bug or unexpected behavior here.
+
+**Minimal code demonstrating the bug or unexpected behavior**
+
+If applicable, provide a minimal code that can be run to demonstrate the bug or unexpected behavior.
+
+If you are unable to construct a minimal code that demonstrates the bug or unexpected behavior, provide detailed steps for how to reproduce the behavior you are seeing.
+
+<details><summary>Minimal runnable code</summary><p>
+
+```julia
+[YOUR MINIMAL RUNNABLE CODE HERE]
+```
+
+</p></details>
+
+
+**Expected output or behavior**
+
+Describe what you expected to happen.
+
+If you provided a minimal code that can be run to demonstrate the bug or unexpected behavior, describe what you expected the output would be.
+
+
+**Actual output or behavior**
+
+Describe what actually happened.
+
+If you provided a minimal code that demonstrates the bug or unexpected behavior, provide the output you get from that code. If the code leads to an error or warning, include the full error or warning below.
+
+<details><summary>Output of minimal runnable code</summary><p>
+
+```julia
+[OUTPUT OF YOUR MINIMAL RUNNABLE CODE HERE]
+```
+
+</p></details>
+
+
+**Version information**
+
+ - Output from `versioninfo()`:
+```julia
+julia> versioninfo()
+[YOUR OUTPUT HERE]
+```
+ - Output from `using Pkg; Pkg.status("SparseArraysBase")`:
+```julia
+julia> using Pkg; Pkg.status("SparseArraysBase")
+[YOUR OUTPUT HERE]
+```

.github/ISSUE_TEMPLATE/FEATURE_REQUEST.md

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+---
+name: SparseArraysBase.jl feature request
+about: Suggest an idea for SparseArraysBase.jl
+title: "[ENHANCEMENT] YOUR SHORT DESCRIPTION OF THE FEATURE REQUEST HERE"
+labels: ["enhancement"]
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+# Description
+
+Please include a summary of the change and which issue is fixed (if applicable). Please also include relevant motivation and context. List any dependencies that are required for this change.
+
+Fixes #(issue)
+
+If practical and applicable, please include a minimal demonstration of the previous behavior and new behavior below.
+
+<details><summary>Minimal demonstration of previous behavior</summary><p>
+
+```julia
+[YOUR MINIMAL DEMONSTRATION OF PREVIOUS BEHAVIOR]
+```
+
+</p></details>
+
+<details><summary>Minimal demonstration of new behavior</summary><p>
+
+```julia
+[YOUR MINIMAL DEMONSTRATION OF NEW BEHAVIOR]
+```
+
+</p></details>
+
+# How Has This Been Tested?
+
+Please add tests that verify your changes to a file in the `test` directory.
+
+Please give a summary of the tests that you added to verify your changes.
+
+- [ ] Test A
+- [ ] Test B
+
+# Checklist:
+
+- [ ] My code follows the style guidelines of this project. Please run `using JuliaFormatter; format(".")` in the base directory of the repository (`~/.julia/dev/SparseArraysBase`) to format your code according to our style guidelines.
+- [ ] I have performed a self-review of my own code.
+- [ ] I have commented my code, particularly in hard-to-understand areas.
+- [ ] I have added tests that verify the behavior of the changes I made.
+- [ ] I have made corresponding changes to the documentation.
+- [ ] My changes generate no new warnings.
+- [ ] Any dependent changes have been merged and published in downstream modules.

.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CI.yml

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+name: CI
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+  pull_request:
+  workflow_dispatch:
+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:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          # - 'lts' # TODO: Reenable once dependencies are registered.
+          - '1'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v5
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    permissions:
+      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      contents: write
+      statuses: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v2
+      - name: Configure doc environment
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - name: Run doctests
+        shell: julia --project=docs --color=yes {0}
+        run: |
+          using Documenter: DocMeta, doctest
+          using SparseArraysBase
+          DocMeta.setdocmeta!(SparseArraysBase, :DocTestSetup, :(using SparseArraysBase); recursive=true)
+          doctest(SparseArraysBase)

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - 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()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/FormatCheck.yml

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+name: Format check
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  format:
+    name: "Format Check"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 1
+      - name: Install JuliaFormatter and format
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Check format
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "The following files have not been formatted:"
+              write(stdout, out)
+              out_diff = Cmd(`git diff`) |> read |> String
+              @error "Diff:"
+              write(stdout, out_diff)
+              exit(1)
+              @error ""
+          end'

.github/workflows/LiterateCheck.yml

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+name: Literate check
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  literate:
+    name: "Literate Check"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 1
+      - name: Install Literate and generate docs
+        run: |
+          julia  -e '
+          using Pkg
+          # TODO: Delete once they are registered.
+          Pkg.add(url="https://github.com/ITensor/BroadcastMapConversion.jl")
+          Pkg.add(url="https://github.com/ITensor/NestedPermutedDimsArrays.jl")
+          Pkg.add(url="https://github.com/ITensor/TypeParameterAccessors.jl")
+          Pkg.develop(PackageSpec(path=pwd()))
+          Pkg.instantiate()
+          Pkg.add(PackageSpec(name="Literate"))'
+          julia  -e 'include("docs/make_readme.jl")'
+      - name: Check if docs need to be updated
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "The docs are outdated, rerun Literate to regenerate them."
+              write(stdout, out)
+              out_diff = Cmd(`git diff`) |> read |> String
+              @error "Diff:"
+              write(stdout, out_diff)
+              exit(1)
+              @error ""
+          end'

.github/workflows/Register.yml

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+name: Register Package
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Version to register or component to bump
+        required: true
+jobs:
+  register:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: write
+    steps:
+      - uses: julia-actions/RegisterAction@latest
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+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

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+*.jl.*.cov
+*.jl.cov
+*.jl.mem
+*.o
+*.swp
+.DS_Store
+.benchmarkci
+.tmp
+.vscode/
+Manifest.toml
+benchmark/*.json
+docs/Manifest.toml
+docs/build/
+docs/src/index.md

.pre-commit-config.yaml

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+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: check-merge-conflict
+  - id: check-toml
+  - id: check-yaml
+  - id: end-of-file-fixer
+    exclude_types: [markdown]  # incompatible with Literate.jl
+- repo: https://github.com/qiaojunfeng/pre-commit-julia-format
+  rev: v0.2.0
+  hooks:
+  - id: julia-format