Fix/resource UUID and doc fix (#109)

* Fix ResourceTreeSet load error

* Raise error when using unsupported type to create ResourceTreeSet

* Fix children key error

* Fix children key error

* Fix workstation resource not tracking

* Fix workstation deck & children resource dupe

* Fix workstation deck & children resource dupe

* Fix multiple resource error

* Fix resource tree update

* Fix resource tree update

* Force confirm uuid

* Tip more error log

* Refactor Bioyond workstation and experiment workflow (#105)

Refactored the Bioyond workstation classes to improve parameter handling and workflow management. Updated experiment.py to use BioyondReactionStation with deck and material mappings, and enhanced workflow step parameter mapping and execution logic. Adjusted JSON experiment configs, improved workflow sequence handling, and added UUID assignment to PLR materials. Removed unused station_config and material cache logic, and added detailed docstrings and debug output for workflow methods.

* Fix resource get.
Fix resource parent not found.
Mapping uuid for all resources.

* mount parent uuid

* Add logging configuration based on BasicConfig in main function

* fix workstation node error

* fix workstation node error

* Update boot example

* temp fix for resource get

* temp fix for resource get

* provide error info when cant find plr type

* pack repo info

* fix to plr type error

* fix to plr type error

* Update regular container method

* support no size init

* fix comprehensive_station.json

* fix comprehensive_station.json

* fix type conversion

* fix state loading for regular container

* Update deploy-docs.yml

* Update deploy-docs.yml

---------

Co-authored-by: ZiWei <131428629+ZiWei09@users.noreply.github.com>

.github/workflows/conda-pack-build.yml

@@ -242,6 +242,10 @@ jobs:
           echo Adding: verify_installation.py
           copy scripts\verify_installation.py dist-package\
 
+          rem Copy source code repository (including .git)
+          echo Adding: Uni-Lab-OS source repository
+          robocopy . dist-package\Uni-Lab-OS /E /XD dist-package /NFL /NDL /NJH /NJS /NC /NS || if %ERRORLEVEL% LSS 8 exit /b 0
+
           rem Create README using Python script
           echo Creating: README.txt
           python scripts\create_readme.py ${{ matrix.platform }} ${{ github.event.inputs.branch }} dist-package\README.txt
@@ -274,6 +278,10 @@ jobs:
           echo "Adding: verify_installation.py"
           cp scripts/verify_installation.py dist-package/
 
+          # Copy source code repository (including .git)
+          echo "Adding: Uni-Lab-OS source repository"
+          rsync -a --exclude='dist-package' . dist-package/Uni-Lab-OS
+
           # Create README using Python script
           echo "Creating: README.txt"
           python scripts/create_readme.py ${{ matrix.platform }} ${{ github.event.inputs.branch }} dist-package/README.txt

.github/workflows/deploy-docs.yml

@@ -39,24 +39,39 @@ jobs:
         uses: actions/checkout@v4
         with:
           ref: ${{ github.event.inputs.branch || github.ref }}
+          fetch-depth: 0
 
-      - name: Setup Python environment
-        uses: actions/setup-python@v5
+      - name: Setup Miniforge (with mamba)
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: '3.10'
+          miniforge-version: latest
+          use-mamba: true
+          python-version: '3.11.11'
+          channels: conda-forge,robostack-staging,uni-lab,defaults
+          channel-priority: flexible
+          activate-environment: unilab
+          auto-update-conda: false
+          show-channel-urls: true
 
-      - name: Install system dependencies
+      - name: Install unilabos and dependencies
         run: |
-          sudo apt-get update
-          sudo apt-get install -y pandoc
+          echo "Installing unilabos and dependencies to unilab environment..."
+          echo "Using mamba for faster and more reliable dependency resolution..."
+          mamba install -n unilab uni-lab::unilabos -c uni-lab -c robostack-staging -c conda-forge -y
 
-      - name: Install Python dependencies
+      - name: Install latest unilabos from source
         run: |
-          python -m pip install --upgrade pip
-          # Install package in development mode to get version info
-          pip install -e .
-          # Install documentation dependencies
-          pip install -r docs/requirements.txt
+          echo "Uninstalling existing unilabos..."
+          mamba run -n unilab pip uninstall unilabos -y || echo "unilabos not installed via pip"
+          echo "Installing unilabos from source..."
+          mamba run -n unilab pip install .
+          echo "Verifying installation..."
+          mamba run -n unilab pip show unilabos
+
+      - name: Install documentation dependencies
+        run: |
+          echo "Installing documentation build dependencies..."
+          mamba run -n unilab pip install -r docs/requirements.txt
 
       - name: Setup Pages
         id: pages
@@ -68,8 +83,8 @@ jobs:
           cd docs
           # Clean previous builds
           rm -rf _build
-          # Build HTML documentation
-          python -m sphinx -b html . _build/html -v
+          # Build HTML documentation in conda environment
+          mamba run -n unilab python -m sphinx -b html . _build/html -v
 
       - name: Check build results
         run: |