Joss paper+ docs

.gitattributes

@@ -1,3 +1,10 @@
 assets/tslam-final_eval.tgz filter=lfs diff=lfs merge=lfs -text
 assets/ttool-v2.0.0-34-g96053edf.tgz filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
+f:/augmented-carpentry/assets/illustration/hardware_overview/hardware_overview_v9.3dm filter=lfs diff=lfs merge=lfs -text
+f:/augmented-carpentry/assets/illustration/hardware_overview/hardware_overview.3dm filter=lfs diff=lfs merge=lfs -text
+assets/illustration/hardware_overview/hardware_overview.3dm filter=lfs diff=lfs merge=lfs -text
+assets/illustration/hardware_overview/hardware_overview_v10.3dm filter=lfs diff=lfs merge=lfs -text
+assets/illustration/hardware_overview/hardware_overview_v9.3dm filter=lfs diff=lfs merge=lfs -text
+assets/illustration/hardware_overview/hardware_overview_v9.3dmbak filter=lfs diff=lfs merge=lfs -text
+assets/illustration/hardware_overview/hardware_overview_v9.3dm.rhl filter=lfs diff=lfs merge=lfs -text

.github/ISSUE_TEMPLATE/add_tool.md

@@ -0,0 +1,15 @@
+---
+name: Documentation issue
+about: Report an inconsistency or suggest an improvement in the documentation
+title: 'Tool/Mount: '
+labels: documentation
+assignees: 
+  - 9and3
+
+---
+
+**Description**
+<!-- Provide a clear and concise summary of whcih tool or mount you would like to see added to AC. -->
+
+**Related links**
+<!-- Add models and specs. -->

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: 'Bug: '
+labels: bug
+assignees:
+    - 9and3
+
+---
+
+**Describe the bug**
+<!-- A clear and concise description of what the bug is. -->
+
+**To Reproduce**
+<!-- Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error -->
+
+**Expected behavior**
+<!-- A clear and concise description of what you expected to happen. -->
+
+**Screenshots**
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+**Computing Machine:**
+ <!-- - OS: [e.g. Ubuntu LTS 22.04] -->

.github/ISSUE_TEMPLATE/doc_report.md

@@ -0,0 +1,20 @@
+---
+name: Documentation issue
+about: Report an inconsistency or suggest an improvement in the documentation
+title: 'Docs: '
+labels: documentation
+assignees: 
+  - 9and3
+
+---
+
+**Description**
+<!-- Provide a clear and concise summary of the inconsistency or issue you encountered in the documentation or the documentation section that needs improvement. Explain why you think the documentation should be adjusted and describe the severity of the issue:
+- Keep it short and concise.
+- One issue at a time. -->
+
+**Related links**
+<!-- Share the link to the specific documentation section and other possibly related sections. Use anchor links (permanent links) where possible. -->
+
+**Proposed change (optional)**
+<!-- Sketch out rough ideas or write a concrete proposal for the improvement. This field is optional but very helpful. -->

.github/workflows/changelog-build.yml

@@ -0,0 +1,21 @@
+name: changelog-build
+on:
+  release:
+    types: [published]
+
+jobs:
+  changelog:
+    name: Update changelog
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: main
+
+      - name: Update changelog
+        uses: rhysd/changelog-from-release/action@v3
+        with:
+            file: CHANGELOG.md
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            pull_request: true

.github/workflows/doc-build.yml

@@ -0,0 +1,47 @@
+name: doc-build
+
+on:
+  push:
+    paths:
+      - 'tests/**'
+      - 'src/**'
+      - 'cmake/**'
+      - 'CMakeLists.txt'
+      - 'Dockerfile'
+      - 'assets/**'
+      - 'deps/**'
+      - 'docs/**'
+      - 'materials/**'
+
+jobs:
+  build-doc:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Doxygen
+        run: sudo apt-get install -y doxygen
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.9.2
+
+      - name: Replace the changelog/index.md with the latest CHANGELOG.md but convert it to UTF8
+        run: iconv -f ISO-8859-1 -t UTF-8 CHANGELOG.md > docs/changelog/index.md
+
+      - name: Replace the CONTRIBUTING_copy.md with the latest CONTRIBUTING.md but convert it to UTF8
+        run: iconv -f ISO-8859-1 -t UTF-8 CONTRIBUTING.md > docs/contributing/index.md
+
+      - name: Create ac conda environment
+        run: conda env create -f environment.yml
+
+      - name: Build the documentation
+        run: conda run -n ac mkdocs build
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

.github/workflows/docker-ubuntu-build-and-test.yml

@@ -2,9 +2,14 @@ name: ubuntu-testsuite
 
 on:
   push:
-    branches: ["main"]
-  pull_request:
-    branches: ["main"]
+    paths:
+      - 'tests/**'
+      - 'src/**'
+      - 'cmake/**'
+      - 'CMakeLists.txt'
+      - 'Dockerfile'
+      - 'assets/**'
+      - 'deps/**'
 
 jobs:
   build-container:

.github/workflows/docker-ubuntu-build.yml

@@ -2,9 +2,13 @@ name: ubuntu-build
 
 on:
   push:
-    branches: ["main"]
-  pull_request:
-    branches: ["main"]
+    paths:
+      - 'src/**'
+      - 'cmake/**'
+      - 'CMakeLists.txt'
+      - 'Dockerfile'
+      - 'assets/**'
+      - 'deps/**'
 
 jobs:
   build-container:

.github/workflows/gh-build.yml

@@ -3,8 +3,12 @@ name: gh-build
 on:
   push:
     branches: ["main"]
+    paths:
+      - 'py/**'
   pull_request:
     branches: ["main"]
+    paths:
+      - 'py/**'
 
 jobs:
   build_ghuser_components:

.github/workflows/joss-pdf-build.yml

@@ -0,0 +1,86 @@
+name: joss-pdf-build
+
+on:
+  push:
+    paths:
+    - paper/**
+    - .github/workflows/joss-pdf-build.yml
+
+jobs:
+  paper-build:
+    runs-on: ubuntu-latest
+    name: JOSS-paper-build
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
+
+
+  paper-add-to-repo:
+    runs-on: ubuntu-latest
+    name: add-pdf-to-repo
+    needs: paper-build
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check if on protected branch
+        run: |
+          if [ "${GITHUB_REF##*/}" = "main" ]; then
+            echo "Warning: The pdf will not be commit to to the protected branch 'main'. You should do this manuallly if on main."
+            exit 1
+          fi
+        shell: bash
+
+      - name: If exists the paper file paper/paper.pdf, remove it
+        run: |
+          if [ -f paper/paper.pdf ]; then
+            rm paper/paper.pdf
+          else
+            echo "File paper/paper.pdf does not exist."
+          fi
+        shell: bash
+
+      - name: Download
+        uses: actions/download-artifact@v4
+        with:
+          name: paper
+          path: paper
+
+      - name: Install GitHub CLI
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gh
+
+      - name: Authenticate GitHub CLI
+        run: |
+          echo "${{ secrets.GITHUB_TOKEN }}" | gh auth login --with-token
+
+      - name: Get current branch name
+        run: |
+          current_branch=$(git branch --show-current)
+          echo "Current branch: $current_branch"
+        shell: bash
+
+      - name: Create new branch and commit pdf addtion/replacement
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "github-actions[bot]"
+          git add paper/paper.pdf
+          git commit -m "ACTION_BOT: AC JOSS paper draft PDF"
+          git push --set-upstream origin $current_branch
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}