Merge branch 'main' into bcif

.github/workflows/docs.yml

@@ -13,6 +13,8 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     permissions: write-all
+    env:
+      BLENDER_VERSION: blender-4.2.0-linux-x64
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -21,17 +23,29 @@ jobs:
           cache: pip
 
       - uses: quarto-dev/quarto-actions/setup@v2
-        with:
-          version: "1.4.549"
+      - name: Set derived environment variables
+        run: |
+          echo "BLENDER_FILENAME=${{ env.BLENDER_VERSION }}.tar.xz" >> $GITHUB_ENV
+          echo "BLENDER_URL=https://mirrors.iu13.net/blender/release/Blender4.2/${{ env.BLENDER_VERSION }}.tar.xz" >> $GITHUB_ENV
+      - name: Install Blender Dependencies
+        run: |
+          sudo apt-get install libxxf86vm-dev -y
+          sudo apt-get install libxfixes3 -y
+          sudo apt-get install libxi-dev -y
+          sudo apt-get install libxkbcommon-x11-0 -y
+          sudo apt-get install libgl1-mesa-glx -y
+      - name: Download & Extract Blender
+        run: |
+          wget -q $BLENDER_URL
+          tar -xf $BLENDER_FILENAME
+          rm -rf $BLENDER_FILENAME
+      - name: Add Blender executable to path
+        run: |
+          echo "${{ github.workspace }}/${{ env.BLENDER_VERSION }}/" >> $GITHUB_PATH
       - name: Build docs using blender
         run: |
-          wget -nv https://download.blender.org/release/Blender4.2/blender-4.2.0-linux-x64.tar.xz -O ./blender.tar.xz
-          mkdir -p ./blender
-          tar -xf ./blender.tar.xz -C ./blender --strip-components=1
-
-          blender/blender --version
-          blender/blender -b --python docs/install.py
-          blender/blender -b --python docs/build_node_docs.py
+          blender -b --python tests/python.py -- -m pip install .
+          blender -b --python docs/generate.py
 
       - name: Build Docs
         run: quarto render docs

CONTRIBUTING.md

@@ -247,13 +247,13 @@ To build the documentation, [`Quarto`](https://quarto.org) is used. The docs can
 
 ```bash
 conda activate mn
-python docs/build_node_docs.py
+python docs/generate.py
 quarto preview
 ```
 
 The long-form written documentation is all inside of `docs/`. Documentation is written in markdown (`.md`) or quarto-flavored markdown (`.qmd`) which allows to execute code when building the docs.
 
-The documentation for individual nodes which are shown [here](https://bradyajohnston.github.io/MolecularNodes/nodes/) are built by running the `docs/build_node_docs.py`, which extracts information from the relevent `.blend` data files inside of `molecularnodes/assets/`. Combining the information for the input / output types & tooltips with the summaries described in `molecularnodes/ui/node_info.py` we can then generate nice HTML documentation for each of the nodes.
+The documentation for individual nodes which are shown [here](https://bradyajohnston.github.io/MolecularNodes/nodes/) are built by running the `docs/generate.py`, which extracts information from the relevent `.blend` data files inside of `molecularnodes/assets/`. Combining the information for the input / output types & tooltips with the summaries described in `molecularnodes/ui/node_info.py` we can then generate nice HTML documentation for each of the nodes.
 
 This isn't currently the best implementation for this. I would prefer to just pull from those nodes which are defined in the `.blend` file, but we aren't able to include descriptions for the node groups currently inside of the `.blend`. `node_info.py` is also used for building the add menus as well as the documentation. To update the descriptions of inputs, outputs and data types the nodes themselves need to be updated inside of the `.blend` files. Relevant example videos should be updated when nodes are changed.
 

LICENSE.OLD

@@ -0,0 +1,24 @@
+This text is included pursuant to the obligations of an upstream licence and must be 
+retained in any derivatives, but it is not the licence applicable to this code
+
+MIT License
+
+Copyright (c) 2022 Brady Johnston
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docs/_quarto.yml

@@ -1,38 +1,46 @@
 project:
   type: website
   output-dir: _build
-  # render: 
-  #   - "*.qmd"
-  # pre-render: build_node_docs.py
 
 filters:
   - preview-colour
 
 website:
   title: "Molecular Nodes"
-  sidebar:
-    style: docked
-    search: true
-    collapse-level: 1
-    contents:
-      - href: index.md
-        text: About
-
-      - installation.md
-      - example_listings.qmd
-      - section: Tutorials
-        contents: tutorials/*
-      - section: Nodes
-        contents: nodes/*
-      # - section: API Reference
-      #   contents: reference/*
+  page-navigation: true
+  navbar:
+    left:
+      - file: installation.qmd
+        text: Installation
+      - file: tutorials/
+        text: Tutorials
+      - file: nodes/
+        text: Node Documentation
+      - file: examples/
+        text: Examples
     tools:
       - icon: github
         href: https://github.com/BradyAJohnston/MolecularNodes
       - icon: twitter
         href: https://twitter.com/bradyajohnston
       - icon: youtube
         href: https://youtube.com/c/bradyjohnston
+
+  sidebar:
+    - id: nodes
+      title: Nodes
+      style: floating
+      align: left
+      contents: nodes/
+
+    - id: tutorials
+      Title: Tutorials
+      align: left
+      style: floating
+      contents: tutorials/
+
+
+
   page-footer:
     left: "This site is built with ❤️ and [Quarto](https://quarto.org/)."
     background: "#F8F9FA"
@@ -42,27 +50,10 @@ format:
     page-layout: full
     theme: 
       light: yeti
-      dark: superhero
+      dark: darkly
     css: styles.css
     toc: true
     toc-depth: 2
     preview-colour:
       code: true
       text: true
-
-# # generate python API docs
-# quartodoc:
-#   package: molecularnodes
-#   # source_dir: ../molecularnodes
-#   dir: reference
-#   sections:
-#     - title: Importing Files
-#       desc: "Importing different data formats."
-#       contents:
-#         - name: io.pdb.load
-#         - name: io.local.load
-#         - name: io.cellpack.load
-#         - name: io.star.load
-
-
-

docs/examples/biologi-molecular/index.qmd

@@ -1,6 +1,6 @@
 ---
 title: Biologia Molecular
-date: "20240202"
+date: "20230202"
 image: https://imgur.com/nMBlLgk.png
 ---
 

docs/examples/clockwork/index.qmd

@@ -0,0 +1,11 @@
+---
+title: Clockwork
+image: https://img.youtube.com/vi/lv89fSt5jBY/0.jpg
+date: "20240804"
+---
+
+Clockwork is a YouTube channel about some of the really nitty-gritty biochemistry with great visuals and writing. They recently started posting videos again, having made the jump from 2D animations in After Effects to 3D animations inside of Blender using Molecular Nodes.
+
+You can see their work and sign up for their newsletter at [their website](https://watchclockwork.com).
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/lv89fSt5jBY?si=x4CXSBUAYLB_6Qfp" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

docs/example_listings.qmd → docs/examples/index.qmd

@@ -1,9 +1,9 @@
 ---
 title: Examples
 listing: 
-    contents: examples
+    contents: .
     type: grid
-    sort: date
+    sort: date desc
     sort-ui: true
 
 ---