Merge remote-tracking branch 'upstream/dev.qsystem' into add-jcm

Author: Vanshaj0429

.github/workflows/nightly_ci.yaml

@@ -65,6 +65,7 @@ jobs:
         cd ..
         python -m pip install git+https://github.com/qutip/qutip-qip
         python -m pip install --no-deps git+https://github.com/qutip/qutip-jax
+        python -m pip install --no-deps git+https://github.com/qutip/qutip-qoc
 
         git clone -b master https://github.com/qutip/qutip-qtrl.git
         cd qutip-qtrl
@@ -95,7 +96,7 @@ jobs:
       run: |
         jupyter kernel &
         cd notebooks
-        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=600 {} +
+        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=900 {} +
         rm template.ipynb
 
     - name: Create Notebook Artifact

.github/workflows/notebook_ci.yaml

@@ -29,7 +29,7 @@ jobs:
         folder-path: tutorials-v${{ matrix.qutip-version }}
         #use config file to define 403 and 405 errors as valid links
         #(APS blocks this link check)
-        config-file: mlc_config.json
+        config-file: mlc_external_config.json
 
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
@@ -59,14 +59,15 @@ jobs:
     - name: Install QuTiP
       run: |
         pip install --upgrade pip
-        python -m pip install jax jax[cpu] equinox diffrax
+        python -m pip install "jax<0.7.0" "jax[cpu]<0.7.0" equinox diffrax
         git clone -b ${{ matrix.qutip-branch }} https://github.com/qutip/qutip.git
         cd qutip
         pip install -r requirements.txt
         pip install .
         cd ..
         python -m pip install git+https://github.com/qutip/qutip-qip
         python -m pip install --no-deps git+https://github.com/qutip/qutip-jax
+        python -m pip install --no-deps git+https://github.com/qutip/qutip-qoc
 
         git clone -b master https://github.com/qutip/qutip-qtrl.git
         cd qutip-qtrl
@@ -97,7 +98,7 @@ jobs:
       run: |
         jupyter kernel &
         cd notebooks
-        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=600 {} +
+        find . -name '*.ipynb' -exec pytest --nbmake --overwrite --nbmake-timeout=900 {} +
         rm template.ipynb
 
     - name: Create Notebook Artifact
@@ -107,6 +108,15 @@ jobs:
         path: |
           notebooks/*.ipynb
           notebooks/**/*.ipynb
+   
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+      with:
+        use-quiet-mode: 'yes'
+        folder-path: tutorials-v${{ matrix.qutip-version }}
+        #use config file to define 403 and 405 errors as valid links
+        #(APS blocks this link check)
+        config-file: mlc_config.json
+
   publish:
     needs: pytests
     runs-on: ubuntu-latest
@@ -133,20 +143,21 @@ jobs:
           # Download resources from qutip.github.io repository
           mkdir css
           cd css
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/css/bootstrap.css
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/css/site.css
           cd ..
 
           mkdir _includes
           cd _includes
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/footer.html
-          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/header.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/head.html
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/navbar.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/footer.html
+          wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/_includes/scripts.html
           cd ..
 
           mkdir images
           cd images
           wget https://raw.githubusercontent.com/qutip/qutip.github.io/master/images/favicon.ico
+          wget https://raw.githubusercontent.com/langhaarzombie/langhaarzombie.github.io/develop/images/logo_small.png
           cd ..
 
           # build the website

mlc_external_config.json

@@ -0,0 +1,14 @@
+{
+    "projectBaseUrl":"${workspaceFolder}",
+    "timeout": "20s",
+    "retryOn429": true,
+    "retryCount": 5,
+    "fallbackRetryDelay": "30s",
+    "aliveStatusCodes": [200, 206, 403, 405],
+    "ignorePatterns": [
+    {
+      "pattern": "^(/|\\.\\/|\\.\\./)"  
+    }
+    ]
+}
+  

tutorials-v4/heom/heom-5a-fermions-single-impurity-model.md

@@ -20,7 +20,7 @@ kernelspec:
 
 ## Introduction
 
-Here we model a single fermion coupled to two electronic leads or reservoirs (e.g.,  this can describe a single quantum dot, a molecular transistor, etc).  Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his dissertation https://opus4.kobv.de/opus4-fau/files/10984/DissertationChristianSchinabeck.pdf and related publications.
+Here we model a single fermion coupled to two electronic leads or reservoirs (e.g.,  this can describe a single quantum dot, a molecular transistor, etc).  Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his dissertation https://open.fau.de/items/36fdd708-a467-4b59-bf4e-4a2110fbc431 and related publications.
 
 Notation:
 

tutorials-v4/heom/heom-5b-fermions-discrete-boson-model.md

@@ -20,7 +20,7 @@ kernelspec:
 
 Here we model a single fermion coupled to two electronic leads or reservoirs (e.g.,  this can describe a single quantum dot, a molecular transistor, etc), also coupled to a discrete bosonic (vibronic) mode.
 
-Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his Dissertation https://opus4.kobv.de/opus4-fau/files/10984/DissertationChristianSchinabeck.pdf and related publications. In particular this example reproduces some results from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.94.201407
+Note that in this implementation we primarily follow the definitions used by Christian Schinabeck in his Dissertation https://open.fau.de/items/36fdd708-a467-4b59-bf4e-4a2110fbc431 and related publications. In particular this example reproduces some results from https://journals.aps.org/prb/abstract/10.1103/PhysRevB.94.201407
 
 Notation: