Merge pull request #1 from AnyBody/pixi

Add pixi package manager

Author: melund

.gitattributes

@@ -0,0 +1,3 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/workflows/build.yaml

@@ -14,11 +14,6 @@ on:
         required: false
         default: ""
 
-defaults:
-  run:
-    shell: bash -leo pipefail {0} {0}
-
-
 jobs:
 
   find-tag:
@@ -40,12 +35,12 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Install mamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.4.1
         with:
-          environment-file: environment.yaml
-
-      - run: sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
+        
+      - run: pixi run sphinx-build -M linkcheck . _build -W --keep-going -a -q 
 
 
   link-check-last-tagged:
@@ -57,15 +52,30 @@ jobs:
         with:
           ref: ${{ needs.find-tag.outputs.latest-tag }}
 
+      - uses: prefix-dev/setup-pixi@v0.4.1
+        continue-on-error: true
+        id: pixisetup
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
+  
+      - if: steps.pixisetup.outcome == 'success'
+        run: pixi sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+          
       - name: Install mamba
+        if: steps.pixisetup.outcome == 'failure'
         uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment.yaml
+            
+      - name: build with mamba
+        if: steps.pixisetup.outcome == 'failure'
+        shell: bash -leo pipefail {0} {0}
+        run: sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+
 
-      - run: sphinx-build -M linkcheck . _build -W --keep-going -a -q 
-          
 
-  build:
+  build-latest:
 
     runs-on: ubuntu-latest
     needs: [find-tag, link-check]
@@ -75,41 +85,80 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Install mamba
-        uses: mamba-org/setup-micromamba@v1
+      - uses: prefix-dev/setup-pixi@v0.4.1
         with:
-          environment-file: environment.yaml
-
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
+  
       - name: Build Documentation
-        run:  |
-          sphinx-build -M html . _build-beta -W --keep-going -a -t draft
+        run: pixi run sphinx-build -M html . _build -W --keep-going -a -t draft
 
-      - name: Checkout last tagged
-        run: |
-          git checkout ${{ needs.find-tag.outputs.latest-tag }}
+      - uses: actions/upload-artifact@v3
+        with:
+          name: beta-version
+          path: _build/html
+
+
+  build-tagged:
+
+    runs-on: ubuntu-latest
+    needs: [find-tag, link-check]
 
-      - name: Build environment for last tagged version
-        run: micromamba create -n tutorial-tagged -y -f environment.yaml
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ needs.find-tag.outputs.latest-tag }}
+          fetch-depth: 0
 
-      - name: Build last tagged version
-        run: |
-          micromamba activate tutorial-tagged
-          sphinx-build -M html . _build -W --keep-going -a
+      - uses: prefix-dev/setup-pixi@v0.4.1
+        continue-on-error: true
+        id: pixisetup
+        with:
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
+    
+      - name: Build Documentation
+        if: steps.pixisetup.outcome == 'success'
+        run: pixi run sphinx-build -M html . _build -W --keep-going -a
+            
 
-      - name: Prepare html for upload
-        run: | 
-          mkdir -p gh-pages/beta
-          cp -rT _build-beta/html gh-pages/beta
-          cp -rT _build/html gh-pages
+      - name: Install mamba
+        if: steps.pixisetup.outcome == 'failure'
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yaml
+            
+      - name: build with mamba
+        if: steps.pixisetup.outcome == 'failure'
+        shell: bash -leo pipefail {0} {0}
+        run: sphinx-build -M html . _build -W --keep-going -a
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: tagged-version
+          path: _build/html
 
+  prepare-pages:
+    needs: [build-latest, build-tagged]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: tagged-version
+          path: public
+      - uses: actions/download-artifact@v3
+        with:
+          name: beta-version
+          path: public/beta
       - uses: actions/upload-pages-artifact@v2
         with: 
-          path: gh-pages
+          path: public
+          
 
 
   deploy:
-    needs: [build, link-check-last-tagged]
-    if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
+    needs: prepare-pages
+    if: github.ref == 'refs/heads/master'
     runs-on: ubuntu-latest
     permissions:
       pages: write    
@@ -124,5 +173,4 @@ jobs:
         id: deployment
         uses: actions/deploy-pages@v2
 
-        
-
+     

.gitignore

@@ -1,4 +1,6 @@
 _build/
 .vscode/
 *.docx
-*.pyc
+*.pyc# pixi environments
+.pixi
+

Finite_element_analysis/lesson1.md

@@ -264,7 +264,7 @@ getting lost in the jungle of meshing.
 
 In the following, we will make use of two freely available tools.
 Preprocessing (meshing and applying boundary conditions) is done using
-[IA-FEMesh](http://www.ccad.uiowa.edu/mimx) provided by the
+[IA-FEMesh](https://ctpr.github.io/IA-FEMesh/) provided by the
 University of Iowa. [Calculix](http://www.calculix.de) is used as
 solver and post-processor. This fine piece of software is written and
 maintained by Guido Dhondt and Klaus Wittig. Calculix v1.8 and

conf.py

@@ -119,6 +119,7 @@ def tagged_commit():
     ".github",
     "README.md",
     "galleries/*",
+    ".pixi",
 ]
 
 
@@ -276,7 +277,6 @@ def tagged_commit():
 
 html_theme_options = {
     # "logo_only": True,
-    
     "repository_url": "https://github.com/anybody/tutorials",
     "use_repository_button": False,
     # "extra_navbar": 'Tutorials by <a href="https://anybodytech.com">AnyBody Technology</a>',
@@ -288,9 +288,7 @@ def tagged_commit():
     "show_navbar_depth": 2,
     "search_bar_text": "",
     "pygment_light_style": "AnyScript",
-    "pygment_dark_style": "stata-dark"
-
-
+    "pygment_dark_style": "stata-dark",
 }
 
 
@@ -442,9 +440,9 @@ def tagged_commit():
     "https://doi.org/10.1115/1.4052115",  # asme.org prevents the linkcheck
     "https://dx.doi.org/10.1115/1.4001678",  # asme.org prevents the linkcheck
     "https://dx.doi.org/10.1115/1.4029258",  # asme.org prevents the linkcheck
-    "https://doi.org/10.1080/10255840802459412", # tandfonline sometimes blocks linkcheck
-    "https://doi.org/10.1080/23335432.2014.993706", # tandfonline sometimes blocks linkcheck
-    "https://anyscript.org/tutorials/dev/", # The dev sides can sometimes be missing.
+    "https://doi.org/10.1080/10255840802459412",  # tandfonline sometimes blocks linkcheck
+    "https://doi.org/10.1080/23335432.2014.993706",  # tandfonline sometimes blocks linkcheck
+    "https://anyscript.org/tutorials/dev/",  # The dev sides can sometimes be missing.
 ]
 
 linkcheck_allowed_redirects = {
@@ -457,4 +455,4 @@ def tagged_commit():
 
 
 def setup(app):
-    ... 
+    ...

environment.yaml

@@ -4,10 +4,9 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - pip
-  - sphinx<6
-  - myst-parser>=0.18
-  - pydata-sphinx-theme>=0.13
+  - sphinx<7
+  - myst-parser
+  - pydata-sphinx-theme
   - make
   - sphinx-togglebutton
   - pygments_anyscript
@@ -17,7 +16,7 @@ dependencies:
   - tomli
   - sphinx-copybutton
   - sphinxext-opengraph
-  - sphinx-book-theme>=1.0
+  - sphinx-book-theme
   - sphinx-design
   - sphinxcontrib-youtube