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Bump numpy to 2.4.3, ase to 3.28.0, scipy to 1.17.1 and structuretoolkit to 0.0.41 #605

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Merged
github-actions merged 25 commits into from
Apr 20, 2026
Merged

Bump numpy to 2.4.3, ase to 3.28.0, scipy to 1.17.1 and structuretoolkit to 0.0.41 #605

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e048d98
Bump numpy from 2.3.5 to 2.4.0
dependabot[bot] Jan 5, 2026
014622a
[dependabot skip] Update environment
github-actions[bot] Jan 5, 2026
15e44fe
Merge branch 'main' into dependabot/pip/numpy-2.4.0
jan-janssen Mar 27, 2026
cb352dd
Update package versions in environment.yml
jan-janssen Mar 27, 2026
b5d4ad2
Update structuretoolkit dependency version to 0.0.41
jan-janssen Mar 27, 2026
dab0c68
Update lammpsparser and vaspparser versions
jan-janssen Mar 27, 2026
3834616
Update vaspparser version to 0.0.2
jan-janssen Mar 27, 2026
ec7dcdb
Update lammpsparser and vaspparser versions
jan-janssen Mar 27, 2026
acaa94a
Update lammpsparser and vaspparser versions
jan-janssen Mar 27, 2026
a233e40
Update environment-lammps.yml
jan-janssen Mar 27, 2026
1d38133
Merge branch 'main' into dependabot/pip/numpy-2.4.0
jan-janssen Mar 27, 2026
de30593
Apply suggestion from @Copilot
jan-janssen Mar 27, 2026
8b5254a
Merge branch 'main' into dependabot/pip/numpy-2.4.0
jan-janssen Mar 27, 2026
3a300ab
Update sphinx-parser version to 0.1.7
jan-janssen Apr 20, 2026
84282e9
Update environment.yml
jan-janssen Apr 20, 2026
0e3996d
Update environment.yml
jan-janssen Apr 20, 2026
92c686b
Update structuretoolkit version to 0.0.42
jan-janssen Apr 20, 2026
a58f65c
Update environment-docs.yml
jan-janssen Apr 20, 2026
56d4dc4
Update environment.yml
jan-janssen Apr 20, 2026
1fa602c
Update pyproject.toml
jan-janssen Apr 20, 2026
4e5ed34
Update pylammpsmpi version to 0.3.12
jan-janssen Apr 20, 2026
b50fb60
Update pylammpsmpi version to 0.3.12
jan-janssen Apr 20, 2026
49aadc7
Update pylammpsmpi version to 0.3.12
jan-janssen Apr 20, 2026
558bd8c
Merge branch 'main' into dependabot/pip/numpy-2.4.0
jan-janssen Apr 20, 2026
0736ca0
Update environment-notebooks.yml
jan-janssen Apr 20, 2026
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10 changes: 5 additions & 5 deletions .ci_support/environment-docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,17 +6,17 @@ dependencies:
- sphinx
- sphinx_rtd_theme
- myst-parser
- ase =3.27.0
- ase =3.28.0
- coverage
- numpy =2.3.5
- scipy =1.17.0
- numpy =2.4.3
- scipy =1.17.1
- spglib =2.7.0
- phonopy =3.2.0
- structuretoolkit =0.0.40
- structuretoolkit =0.0.42
- seekpath =2.2.1
- lammps =2024.08.29
- pandas =2.3.3
- pylammpsmpi =0.3.11
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- jupyter-book =1.0.0
- lammpsparser =0.0.2
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2 changes: 1 addition & 1 deletion .ci_support/environment-lammps.yml
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Expand Up @@ -3,7 +3,7 @@ channels:
dependencies:
- lammps =2024.08.29=*openmpi*
- pandas =2.3.3
- pylammpsmpi =0.3.11
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- iprpy-data =2023.07.25
- dynaphopy =1.18.0
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2 changes: 1 addition & 1 deletion .ci_support/environment-notebooks.yml
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Expand Up @@ -6,7 +6,7 @@ dependencies:
- gpaw =25.7.0
- lammps =2024.08.29
- pandas =2.3.3
- pylammpsmpi =0.3.11
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- dynaphopy =1.18.0
- lammpsparser =0.0.2
10 changes: 5 additions & 5 deletions .ci_support/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
channels:
- conda-forge
dependencies:
- ase =3.27.0
- ase =3.28.0
- coverage
- lxml =6.0.2
- mendeleev =1.1.0
- numpy =2.3.5
- numpy =2.4.3
- pandas =2.3.3
- phonopy =3.2.0
- requests =2.32.5
- scipy =1.17.0
- scipy =1.17.1
- seekpath =2.2.1
- spglib =2.7.0
- structuretoolkit =0.0.40
- sphinx_parser =0.1.6
- structuretoolkit =0.0.42
- sphinx_parser =0.1.7
- tqdm =4.67.3
- vaspparser =0.0.2
- hatchling =1.29.0
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10 changes: 5 additions & 5 deletions binder/environment.yml
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@@ -1,17 +1,17 @@
channels:
- conda-forge
dependencies:
- ase =3.27.0
- numpy =2.3.5
- scipy =1.17.0
- ase =3.28.0
- numpy =2.4.3
- scipy =1.17.1
- spglib =2.7.0
- phonopy =3.2.0
- structuretoolkit =0.0.40
- structuretoolkit =0.0.42
- seekpath =2.2.1
- gpaw =25.7.0
- lammps =2024.08.29
- pandas =2.3.3
- pylammpsmpi =0.3.11
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- dynaphopy =1.18.0
- tqdm =4.67.3
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14 changes: 7 additions & 7 deletions pyproject.toml
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Expand Up @@ -25,9 +25,9 @@ classifiers = [
"Programming Language :: Python :: 3.13",
]
dependencies = [
"ase==3.27.0",
"numpy==2.3.5",
"scipy==1.17.0",
"ase==3.28.0",
"numpy==2.4.3",
"scipy==1.17.1",
Comment on lines +28 to +30
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Copilot AI Mar 27, 2026

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PR description/release notes text references bumping NumPy to 2.4.0, but this PR pins numpy==2.4.3. Please update the PR description (or align the pinned version) so reviewers and downstream automation aren’t misled about which version is being introduced.

Copilot uses AI. Check for mistakes.
"spglib==2.7.0",
]
dynamic = ["version"]
Expand All @@ -41,19 +41,19 @@ Repository = "https://github.com/pyiron/atomistics"
phonopy = [
"phonopy==3.2.0",
"seekpath==2.2.1",
"structuretoolkit==0.0.40",
"structuretoolkit==0.0.42",
]
gpaw = [
"gpaw==25.7.0",
]
lammps = [
"pylammpsmpi==0.3.11",
"pylammpsmpi==0.3.12",
"jinja2==3.1.6",
"pandas==2.3.3",
"lammpsparser==0.0.2",
]
lammps_phonons = [
"pylammpsmpi==0.3.11",
"pylammpsmpi==0.3.12",
"jinja2==3.1.6",
"pandas==2.3.3",
"dynaphopy==1.18.0",
Expand All @@ -66,7 +66,7 @@ experimental = [
"requests==2.32.5",
]
sphinxdft = [
"sphinx-parser==0.1.6"
"sphinx-parser==0.1.7"
]
qe = [
"pwtools==1.3.0"
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