Merge pull request #476 from BradyAJohnston/4.1

Upgrade for Blender 4.1

.github/workflows/docs.yml

@@ -14,23 +14,30 @@ jobs:
     runs-on: ubuntu-latest
     permissions: write-all
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11.7"
           cache: pip
-      - name: Install dependencies
-        run: |
-          make template
-          pip install quartodoc
-          pip install .
+
       - uses: quarto-dev/quarto-actions/setup@v2
         with:
           version: "1.4.549"
-      - name: Build docs
+      - name: Build docs using blender
         run: |
-          python docs/build_node_docs.py
-          make docs-build
+          wget -nv https://download.blender.org/release/Blender4.1/blender-4.1.0-linux-x64.tar.xz
+          tar -xf blender-4.1.0-linux-x64.tar.xz
+
+          blender-4.1.0-linux-x64/blender --version
+          blender-4.1.0-linux-x64/blender -b --python docs/install.py
+          blender-4.1.0-linux-x64/blender -b --python docs/build_node_docs.py
+
+
+      
+
+      - name: Build Docs
+        run: make docs-build
+
       # push to netlify -------------------------------------------------------
 
       # set release name ----

.github/workflows/test-addon.yml

@@ -0,0 +1,77 @@
+name: Test in Blender
+
+on: 
+    push:
+      branches: ["main"]
+    pull_request:
+      branches: ["main", "4.1"]
+
+jobs:
+    build:
+        runs-on: ${{ matrix.os }}
+        strategy:
+            max-parallel: 4
+            fail-fast: false
+            matrix:
+              blender-version: ["4.1"]
+              os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+              # os: [macos-13]
+        steps:
+            - uses: actions/checkout@v4
+            - uses: actions/setup-python@v5
+              with:
+                python-version: 3.11.7
+
+            - name: Test in Blender MacOS Intel
+              if: matrix.os == 'macos-13'
+              run: |
+                curl -L -o blender.dmg https://download.blender.org/release/Blender4.1/blender-4.1.0-macos-x64.dmg
+                hdiutil attach blender.dmg
+                cp -R /Volumes/Blender/Blender.app /Applications/
+                hdiutil detach /Volumes/Blender
+                /Applications/Blender.app/Contents/MacOS/Blender --version
+                /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/install.py
+                /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/run.py -- -v 
+            
+            - name: Test in Blender MacOS ARM
+              if: matrix.os == 'macos-14'
+              run: |
+                curl -L -o blender.dmg https://download.blender.org/release/Blender4.1/blender-4.1.0-macos-arm64.dmg
+                hdiutil attach blender.dmg
+                cp -R /Volumes/Blender/Blender.app /Applications/
+                hdiutil detach /Volumes/Blender
+                /Applications/Blender.app/Contents/MacOS/Blender --version
+                /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/install.py
+                /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/run.py -- -v 
+                
+            - name: Test in Blender Windows
+              if: matrix.os == 'windows-latest'
+              shell: pwsh
+              run: |
+                Invoke-WebRequest -Uri "https://download.blender.org/release/Blender4.1/blender-4.1.0-windows-x64.zip" -OutFile "blender.zip"
+                Expand-Archive -Path "blender.zip" -DestinationPath "blender"
+                .\blender\blender-4.1.0-windows-x64\blender.exe --version
+                .\blender\blender-4.1.0-windows-x64\blender.exe -b --python tests/install.py
+                .\blender\blender-4.1.0-windows-x64\blender.exe -b --python tests/run.py -- -v tests/
+            
+            - name: Test in Blender Linux
+              if: matrix.os == 'ubuntu-latest'
+              run: |
+                wget -nv https://download.blender.org/release/Blender4.1/blender-4.1.0-linux-x64.tar.xz
+                tar -xf blender-4.1.0-linux-x64.tar.xz
+
+                blender-4.1.0-linux-x64/blender --version
+                blender-4.1.0-linux-x64/blender -b --python tests/install.py
+                blender-4.1.0-linux-x64/blender -b --python tests/run.py -- -v tests/ --cov=molecularnodes --cov-report=xml:coverage.xml --ignore=molecularnodes/ui/panel.py
+            
+            - name: Expose coverage as a CI download 
+              uses: actions/upload-artifact@v1
+              if: matrix.os == 'ubuntu-latest'
+              with:
+                name: coverage.xml
+                path: coverage.xml
+
+            - name: Upload coverage reports to Codecov
+              if: matrix.os == 'ubuntu-latest'
+              uses: codecov/codecov-action@v3
+

.github/workflows/tests.yml

@@ -2,11 +2,9 @@ name: test-addon
 
 on: 
   push:
-    branches: 
-      - main
+    branches: ["main"]
   pull_request:
-    branches:
-      - main
+    branches: ["main", "4.1"]
 
 jobs:
   build:
@@ -15,15 +13,16 @@ jobs:
       max-parallel: 4
       fail-fast: false
       matrix:
-        blender-version: ["4.0.0"]
+        blender-version: ["4.1.0"]
+        python-version: ['3.11.7']
         os: [ubuntu-latest, windows-latest, macos-13, macos-14]
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: ${{ matrix.python-version }}
           cache: 'pip'
-      - run: pip install bpy==${{ matrix.blender-version }}
+      # - run: pip install bpy==${{ matrix.blender-version }}
       - name: Install
         run: |
           pip install poetry
@@ -38,7 +37,7 @@ jobs:
           patchelf --set-rpath '$ORIGIN/bpy/lib' pyopenvdb.so
           
       - name: Run Tests
-        run: poetry run python -m pytest --verbose --cov=molecularnodes --cov-report=xml:coverage.xml --ignore=molecularnodes/ui/panel.py
+        run: poetry run python -m pytest --verbose --cov=molecularnodes --cov-report=xml:coverage.xml --ignore=molecularnodes/ui/panel.py -k "not star"
 
       - name: Expose coverage as a CI download # Related to test_addon_blender_advanced.py
         uses: actions/upload-artifact@v1

docs/install.py

@@ -0,0 +1,20 @@
+import subprocess
+import sys
+import os
+
+
+def main():
+
+    python = os.path.realpath(sys.executable)
+
+    commands = [
+        f'{python} -m pip install .',
+        f'{python} -m pip install quartodoc'
+    ]
+
+    for command in commands:
+        subprocess.run(command.split(' '))
+
+
+if __name__ == "__main__":
+    main()

docs/tutorials/01_importing.qmd

@@ -7,7 +7,7 @@ Molecules, simulations and other file formats can all be imported via the `Molec
 
 ![The panel location.](images/panel-location.png)
 
-You can download a structure directly from the PDB, just from the accession code. Molecular Nodes will download the file as a `.mmtf` file and cache it locally on your computer, then open the file in to Blender. This is the quickest way to import structures that are already available via the wwPDB. Currently this downloads via the RCSB.
+You can download a structure directly from the PDB, just from the accession code. Molecular Nodes will download the file as a `.bcif` file and cache it locally on your computer, then open the file in to Blender. This is the quickest way to import structures that are already available via the wwPDB. Currently this downloads via the RCSB.
 
 To download directly from the PDB, you can use the <kbd>PDB</kbd> tab.
 

molecularnodes/__init__.py

@@ -63,10 +63,12 @@ def unregister():
     except RuntimeError:
         pass
 
+
+# can't register the add-on when these are uncommnted, but they do fix the issue
+# of having to call register() when running a script
 # unregister()
 # register()
 
-
 # # register won't be called when MN is run as a module
 bpy.app.handlers.load_post.append(_rejuvenate_universe)
 bpy.app.handlers.load_post.append(_rehydrate_ensembles)

molecularnodes/blender/node.py

@@ -0,0 +1,37 @@
+from abc import ABCMeta
+from typing import Optional, Any
+import warnings
+import time
+import numpy as np
+import bpy
+
+
+class Node(metaclass=ABCMeta):
+    def __init__(self, node: bpy.types.Node, chain=[]):
+
+        self.node = node
+        self.group = node.id_data
+        self.chain = chain
+
+    @property
+    def location(self):
+        return np.array(self.node.location)
+
+    def new(self, name):
+        "Add a new node to the node group."
+        try:
+            return self.group.nodes.new(f'GeometryNode{name}')
+        except RuntimeError:
+            return self.group.nodes.new(f'ShaderNode{name}')
+
+    def link(self, name, linkto=0, linkfrom=0):
+        "Create a new node along in the chain and create a link to it. Return the new node."
+        new_node = self.new(name)
+        new_node.location = self.location + np.array((200, 0))
+
+        self.group.links.new(
+            self.node.outputs[linkfrom],
+            new_node.inputs[linkto]
+        )
+
+        return Node(new_node, chain=self.chain + [self])