Updates for scipy, numpy 2, and Python 3.12 (#757)

* scipy.integrate.simps to scipy.integrate.simpson

* no more ragged arrays

* run black

* bump versions, update CHANGELOG

* fixes

* fix docs?

* run black

* use numpy 2

* allow older scipt as well

* fix docs?

* Apply suggestions from code review

* fix docs?

* fix test

* fix docs?

* fix docs?

* fix docs?

* fix docs?

* fix docs?

* fix docs?

* fix docs?

* fix docs?

* try to fix tests

* try to fix tests

* try to fix tests using latest thewalrus

* try to fix tests using latest thewalrus

* fix typo in test fix

* debug info

* xfail broken test

* codecov

* codecov

* test

* Update test_param.py

* Apply suggestions from code review

Co-authored-by: Luke Helt <31250931+heltluke@users.noreply.github.com>

* fmt

* Update requirements.txt

* Update requirements-ci.txt

* revert cosmetic changes

* more

* more

* even more

* and yet more

* Apply suggestions from code review

Still needs capitals

* Revert "Apply suggestions from code review
"

This reverts commit 01a1e58.

# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
#
# On branch updates-for-scipy-2
# Your branch is up to date with 'origin/updates-for-scipy-2'.
#
# Changes to be committed:
#	modified:   .github/workflows/tests.yaml
#

* black

---------

Co-authored-by: Luke Helt <luke.helt@gmail.com>
Co-authored-by: Luke Helt <31250931+heltluke@users.noreply.github.com>

Author: lneuhaus

.github/CHANGELOG.md

@@ -12,13 +12,16 @@
 
 <h3>Bug fixes</h3>
 
+* Updates `scipy.integrate.simps` to `scipy.integrate.simpson` when using newer scipy versions, such that SF continues working. Also makes numpy usage explicit about the creation of ragged numpy arrays. This patch furthermore fixes a number of CI issues, to get most test pipelines passing again. 
+[#757](https://github.com/XanaduAI/strawberryfields/pull/757)
+
 <h3>Documentation</h3>
 
 <h3>Contributors</h3>
 
 This release contains contributions from (in alphabetical order):
 
-Theodor Isacsson
+Leonhard Neuhaus, Luke Helt, Theodor Isacsson
 
 
 # Release 0.23.0 (current release)

.github/workflows/docs.yml

@@ -6,7 +6,7 @@ jobs:
   sphinx:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - uses: XanaduAI/sphinx-action@master
       with:
         docs-folder: "doc/"

.github/workflows/tests.yaml

@@ -37,14 +37,14 @@ jobs:
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install dependencies
         run: |
@@ -57,7 +57,7 @@ jobs:
         run: |
           pip install -r requirements-ci.txt
           python3 setup.py bdist_wheel
-          pip install dist/StrawberryFields*.whl
+          pip install dist/strawberryfields*.whl
 
       - name: Run tests
         run: python3 -m pytest tests --cov=strawberryfields --cov-report=term-missing --cov-report=xml -p no:warnings --randomly-seed=42 --tb=native -m "$OPTIONS"
@@ -66,6 +66,9 @@ jobs:
         run: bash <(sed -i 's/filename=\"/filename=\"strawberryfields\//g' coverage.xml)
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v5
         with:
-          file: ./coverage.xml
+          # token: ${{ secrets.CODECOV_TOKEN }}  # we currently do not have a token for SF
+          files: ./coverage.xml
+          disable_search: true
+          fail_ci_if_error: false

.readthedocs.yml

@@ -4,12 +4,12 @@ sphinx:
   configuration: doc/conf.py
 
 python:
-    version: 3.8
-    install:
-        - requirements: doc/requirements.txt
-        - method: pip
-          path: .
-    system_packages: true
+  install:
+      - requirements: doc/requirements.txt
+      - method: pip
+        path: .
 
 build:
-    image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"

doc/requirements.txt

@@ -5,19 +5,21 @@ jinja2==3.0.3
 sphinx==2.2.2
 m2r2==0.3.1
 mistune==0.8.4
-numba==0.53.1
+numba==0.56.4
 networkx==2.6.3
 numpy==1.19.2
 plotly==4.4.1
 protobuf<4.21.0  # remove when fix is released
 quantum-blackbird==0.4.0
+quantum-xir>=0.1.1
 scipy==1.7.1
 scikit-learn==1.0.2
 sphinx-autodoc-typehints==1.10.3
 sphinx-copybutton==0.4.0
 sphinx-automodapi==0.13
 sphinxcontrib-bibtex==0.4.2
 tensorflow==2.6.3
-thewalrus==0.18.0
+thewalrus==0.19.0
 toml==0.10.2
 xanadu-sphinx-theme==0.1.0
+xanadu-cloud-client>=0.2.1

requirements-ci.txt

@@ -6,9 +6,10 @@ tensorboard
 networkx
 quantum-blackbird
 python-dateutil
-thewalrus>=0.17.0
+thewalrus>=0.22.0
 toml
 numba
 requests
+setuptools
 urllib3
 plotly

requirements.txt

@@ -1,15 +1,15 @@
 networkx==2.7.1
 numba==0.55.1
-numpy==1.21.5
+numpy==1.26.4
 plotly==5.6.0
 python-dateutil==2.8.2
 quantum-blackbird==0.4.0
 requests==2.27.1
-scipy==1.8.0
+scipy==1.14.0
 sympy==1.10
 tensorflow==2.8.0
 tensorboard==2.8.0
-thewalrus==0.19.0
+thewalrus==0.22.0
 toml==0.10.2
 typing-extensions==4.1.1
 urllib3==1.26.8

setup.py

@@ -25,7 +25,7 @@
     "python-dateutil>=2.8.0",
     "quantum-blackbird>=0.4.0",
     "requests>=2.22.0",
-    "scipy>=1.0.0",
+    "scipy>=1.8.0",
     "sympy>=1.5",
     "thewalrus>=0.18.0",
     "toml",

strawberryfields/apps/data/sample.py

@@ -48,7 +48,8 @@ def _data_filename(self) -> str:
         ``scipy.sparse.csr_matrix`` saved in ``.npz`` format.
 
         For ``_data_filename = "example"``, the corresponding samples should be stored as
-        ``./sample_data/example.npz`` and the adjacency matrix as ``./sample_data/example_A.npz``."""
+        ``./sample_data/example.npz`` and the adjacency matrix as ``./sample_data/example_A.npz``.
+        """
         pass
 
     def __init__(self):

strawberryfields/apps/train/__init__.py

@@ -92,6 +92,7 @@
     <br>
 
 """
+
 from strawberryfields.apps.train.cost import KL, Stochastic
 from strawberryfields.apps.train.embed import Exp, ExpFeatures
 from strawberryfields.apps.train.param import (