Merge branch 'main' into feature/generate-notebook-index

Author: hodgestar

.github/workflows/nightly_ci.yaml

@@ -20,27 +20,28 @@ jobs:
           - qutip-version: '5'
             qutip-branch: 'master'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - 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
 
-    - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Setup Conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        miniforge-variant: Mambaforge
         miniforge-version: latest
-        activate-environment: test-environment
-        use-mamba: true
+        activate-environment: test-environment-v${{ matrix.qutip-version }}
 
     - name: Get Date
       id: get-date
       run: echo "::set-output name=today::$(/bin/date -u '+%Y%m%d')"
       shell: bash
 
     - name: Cache Conda env
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.CONDA }}/envs
         key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('test_environment.yml') }}-${{ env.CACHE_NUMBER }}-qutip-${{ matrix.qutip-version }}
@@ -51,7 +52,7 @@ jobs:
 
     - name: Install environment
       if: steps.cache.outputs.cache-hit != 'true'
-      run: mamba env update -n test-environment -f test_environment.yml
+      run: conda env update -n test-environment-v${{ matrix.qutip-version }} -f test_environment-v${{ matrix.qutip-version }}.yml
 
     - name: Install QuTiP
       run: |
@@ -104,3 +105,20 @@ jobs:
         path: |
           notebooks/*.ipynb
           notebooks/**/*.ipynb
+
+
+  finalise:
+    needs: pytests
+    if: failure()
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Open Issue on Failure
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          if [[ -z "${{ inputs.open_issue }}" ]] || [[ "${{ inputs.open_issue }}" != "False" ]];
+          then
+            pip install requests
+            python tools/report_failing_tests.py $GITHUB_TOKEN
+          fi

.github/workflows/notebook_ci.yaml

@@ -21,28 +21,29 @@ jobs:
           - qutip-version: '5'
             qutip-branch: 'master'
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - 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
 
-    - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+    - name: Setup Conda
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        miniforge-variant: Mambaforge
         miniforge-version: latest
-        activate-environment: test-environment
-        use-mamba: true
+        activate-environment: test-environment-v${{ matrix.qutip-version }}
 
     - name: Get Date
       id: get-date
       run: echo "::set-output name=today::$(/bin/date -u '+%Y%m%d')"
       shell: bash
 
     - name: Cache Conda env
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.CONDA }}/envs
         key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('test_environment.yml') }}-${{ env.CACHE_NUMBER }}-qutip-${{ matrix.qutip-version }}
@@ -53,7 +54,7 @@ jobs:
 
     - name: Install environment
       if: steps.cache.outputs.cache-hit != 'true'
-      run: mamba env update -n test-environment -f test_environment.yml
+      run: conda env update -n test-environment-v${{ matrix.qutip-version }} -f test_environment-v${{ matrix.qutip-version }}.yml
 
     - name: Install QuTiP
       run: |
@@ -111,7 +112,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'qutip/qutip-tutorials' && github.ref == 'refs/heads/main' }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
           name: executed-notebooks-v4

mlc_config.json

@@ -0,0 +1,8 @@
+{
+  "projectBaseUrl":"${workspaceFolder}",
+  "timeout": "20s",
+  "retryOn429": true,
+  "retryCount": 5,
+  "fallbackRetryDelay": "30s",
+  "aliveStatusCodes": [200, 206, 403, 405]
+}

test_environment.yml test_environment-v4.ymltest_environment.yml renamed to test_environment-v4.yml

@@ -1,4 +1,4 @@
-name: test-environment
+name: test-environment-v4
 channels:
 - conda-forge
 dependencies:

test_environment-v5.yml

@@ -0,0 +1,16 @@
+name: test-environment-v5
+channels:
+- conda-forge
+dependencies:
+- python==3.12
+- pip>=22.1.2
+- numpy>=2.0.0
+- scipy>=1.9
+- matplotlib>=3.9
+- imagemagick>=7.1.0_36
+- mpmath>=1.2.1
+- pytest>=7.1.2
+- nbmake>=1.3.4
+- jupytext>=1.13.8
+- jupyter>=1.0.0
+- ipykernel>=6.17.1  # 6.18.0 was yanked but is still present on conda-forge

tools/report_failing_tests.py

@@ -0,0 +1,46 @@
+
+import requests
+import json
+import sys
+import argparse
+from datetime import date
+
+def open_issue(token):
+    url = "https://api.github.com/repos/qutip/qutip-jax/issues"
+    data = json.dumps({
+        "title": f"Automated tests failed on {date.today()}",
+        "labels": ["bug"],
+        "body": "Scheduled test failed!"
+    })
+
+    headers = {
+        "Accept": "application/vnd.github.v3+json",
+        "Authorization" : f"token {token}",
+    }
+
+    post_request = requests.post(url=url, data=data, headers=headers)
+
+    if post_request.status_code == 201:
+        print("Success")
+
+    else:
+        print(
+            "Fail:",
+            post_request.status_code,
+            post_request.reason,
+            post_request.content
+        )
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="""Open an issue on failed tests."""
+    )
+    parser.add_argument("token")
+    args = parser.parse_args()
+    print(args.token)
+    open_issue(args.token)
+
+
+if __name__ == "__main__":
+    sys.exit(main())

tutorials-v4/lectures/Lecture-11-Charge-Qubits.md

@@ -39,7 +39,7 @@ where $E_C$ is the charge energy, $E_J$ is the Josephson energy, and $\left| n\r
 
 #### References
 
- * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](http://link.aps.org/doi/10.1103/PhysRevA.76.042319)
+ * [J. Koch et al, Phys. Rec. A 76, 042319 (2007)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.76.042319)
  * [Y.A. Pashkin et al, Quantum Inf Process 8, 55 (2009)](http://dx.doi.org/10.1007/s11128-009-0101-5)
 
 

tutorials-v4/lectures/Lecture-2B-Single-Atom-Lasing.md

@@ -63,9 +63,9 @@ in units where $\hbar = 1$.
 
 References:
 
- * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](http://dx.doi.org/10.1103/PhysRevA.46.5944)
+ * [Yi Mu, C.M. Savage, Phys. Rev. A 46, 5944 (1992)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.46.5944)
 
- * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](http://dx.doi.org/10.1103/PhysRevLett.98.067204)
+ * [D.A. Rodrigues, J. Imbers, A.D. Armour, Phys. Rev. Lett. 98, 067204 (2007)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.98.067204)
 
  * [S. Ashhab, J.R. Johansson, A.M. Zagoskin, F. Nori, New J. Phys. 11, 023030 (2009)](http://dx.doi.org/10.1088/1367-2630/11/2/023030)
 

tutorials-v4/lectures/Lecture-3A-Dicke-model.md

@@ -49,7 +49,7 @@ $\displaystyle J_\pm = \sum_{i=1}^N \sigma_\pm^{(i)}$
 
 ### References
 
- * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](http://dx.doi.org/10.1103/PhysRev.93.99)
+ * [R.H. Dicke, Phys. Rev. 93, 99–110 (1954)](https://journals.aps.org/pr/abstract/10.1103/PhysRev.93.99)
 
 
 ## Setup problem in QuTiP
@@ -198,7 +198,7 @@ fig.tight_layout()
 
 ### References
 
-* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](http://dx.doi.org/10.1103/PhysRevLett.92.073602).
+* [Lambert et al., Phys. Rev. Lett. 92, 073602 (2004)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.92.073602).
 
 ```python
 def calulcate_entropy(M, N, g_vec):

tutorials-v4/lectures/Lecture-3B-Jaynes-Cumming-model-with-ultrastrong-coupling.md

@@ -51,11 +51,11 @@ The regime $g$ is large compared with all other energy scales in the Hamiltonian
 
 References:
 
- * [P. Nataf et al., Phys. Rev. Lett. 104, 023601 (2010)](http://dx.doi.org/10.1103/PhysRevLett.104.023601)
+ * [P. Nataf et al., Phys. Rev. Lett. 104, 023601 (2010)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.104.023601)
 
- * [J. Casanova et al., Phys. Rev. Lett. 105, 26360 (2010)](http://dx.doi.org/10.1103/PhysRevLett.105.263603).
+ * [J. Casanova et al., Phys. Rev. Lett. 105, 26360 (2010)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.263603).
 
- * [S. Ashhab et al., Phys. Rev. A 81, 042311 (2010)](http://dx.doi.org/10.1103/PhysRevA.81.042311)
+ * [S. Ashhab et al., Phys. Rev. A 81, 042311 (2010)](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.81.042311)
 <!-- #endregion -->
 
 <!-- #region -->