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Update numpy to 2.4.1, matplotlib to 3.10.8 and pysqa to 0.3.4 #891

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Merged
jan-janssen merged 7 commits into from
Jan 25, 2026
Merged

Update numpy to 2.4.1, matplotlib to 3.10.8 and pysqa to 0.3.4 #891

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70e91ab
Update environment-integration.yml
jan-janssen Jan 25, 2026
1e56b13
Update environment-mini.yml
jan-janssen Jan 25, 2026
9d4a72e
Update environment-mpich.yml
jan-janssen Jan 25, 2026
6250337
Update environment-openmpi.yml
jan-janssen Jan 25, 2026
0f9ee04
Update environment-win.yml
jan-janssen Jan 25, 2026
ca66118
Update pyproject.toml
jan-janssen Jan 25, 2026
4e03f2a
Update environment-integration.yml
jan-janssen Jan 25, 2026
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6 changes: 3 additions & 3 deletions .ci_support/environment-integration.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ dependencies:
- h5py =3.15.1
- jupyter
- mpi4py =4.1.1
- numpy =2.3.3
- numpy =2.3.5
- openmpi
- papermill
- atomistics =0.3.4
Expand All @@ -15,9 +15,9 @@ dependencies:
- hatchling =1.28.0
- hatch-vcs =0.5.0
- ipython =9.9.0
- matplotlib =3.10.6
- matplotlib =3.10.8
- networkx =3.6.1
- pygraphviz =1.14
- pysqa =0.3.3
- pysqa =0.3.4
- pyzmq =27.1.0
- qe =7.5
2 changes: 1 addition & 1 deletion .ci_support/environment-mini.yml
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Expand Up @@ -2,7 +2,7 @@ channels:
- conda-forge
dependencies:
- python
- numpy =2.3.3
- numpy =2.4.1
- cloudpickle =3.1.0
- hatchling =1.28.0
- hatch-vcs =0.5.0
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4 changes: 2 additions & 2 deletions .ci_support/environment-mpich.yml
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Expand Up @@ -2,7 +2,7 @@ channels:
- conda-forge
dependencies:
- python
- numpy =2.3.3
- numpy =2.4.1
- mpich
- cloudpickle =3.1.2
- h5py =3.15.1
Expand All @@ -12,5 +12,5 @@ dependencies:
- mpi4py =4.1.1
- networkx =3.6.1
- pygraphviz =1.14
- pysqa =0.3.3
- pysqa =0.3.4
- pyzmq =27.1.0
4 changes: 2 additions & 2 deletions .ci_support/environment-openmpi.yml
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Expand Up @@ -2,7 +2,7 @@ channels:
- conda-forge
dependencies:
- python
- numpy =2.3.3
- numpy =2.4.1
- openmpi
- cloudpickle =3.1.2
- h5py =3.15.1
Expand All @@ -12,5 +12,5 @@ dependencies:
- mpi4py =4.1.1
- networkx =3.6.1
- pygraphviz =1.14
- pysqa =0.3.3
- pysqa =0.3.4
- pyzmq =27.1.0
2 changes: 1 addition & 1 deletion .ci_support/environment-win.yml
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Expand Up @@ -2,7 +2,7 @@ channels:
- conda-forge
dependencies:
- python
- numpy =2.3.3
- numpy =2.4.1
- msmpi
- cloudpickle =3.1.2
- h5py =3.15.1
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -52,12 +52,12 @@ graphnotebook = [
]
mpi = ["mpi4py==4.1.1"]
cluster = [
"pysqa==0.3.3",
"pysqa==0.3.4",
"h5py==3.15.1",
]
all = [
"mpi4py==4.1.1",
"pysqa==0.3.3",
"pysqa==0.3.4",
"h5py==3.15.1",
Comment on lines 54 to 61
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🌐 Web query:

pysqa 0.3.4 pypi python version requirements

💡 Result:

pysqa==0.3.4 is not available on PyPI (the latest PyPI release is 0.3.3, released Oct 20, 2025). For pysqa on PyPI, the declared Python requirement is:

  • Python >= 3.9, < 3.15. [1]

Replace pysqa 0.3.4 with the available version 0.3.3 (or remove if 0.3.4 is planned for future release).
pysqa 0.3.4 does not exist on PyPI; the latest release is 0.3.3 (Oct 20, 2025). The specification at lines 55 and 60 will fail installation. Update to pysqa==0.3.3 or document if this change is contingent on an upcoming release.

🤖 Prompt for AI Agents 
In `@pyproject.toml` around lines 54 - 61, The pyproject extras list references a
non-existent package version "pysqa==0.3.4" in the cluster and all extras;
update those entries (the strings "pysqa==0.3.4" inside the cluster and all
arrays) to the available version "pysqa==0.3.3" or remove the pysqa entries if
you intend to wait for a future release, ensuring both the cluster and all
extras are kept consistent.

"pygraphviz==1.14",
"networkx==3.6.1",
Expand Down