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Update pandas to 3.0.2 #619

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5a5b642
Update pyproject.toml
jan-janssen Jan 25, 2026
ec5bc42
Update environment.yml
jan-janssen Jan 25, 2026
80c6b73
Update environment-docs.yml
jan-janssen Jan 25, 2026
d1dae9a
Update environment.yml
jan-janssen Jan 25, 2026
17e208e
use StringIO
jan-janssen Jan 25, 2026
a1ad2e4
Update environment-lammps.yml
jan-janssen Jan 25, 2026
9dcb967
Update environment-docs.yml
jan-janssen Jan 26, 2026
d9a827e
Update environment-lammps.yml
jan-janssen Jan 26, 2026
92b10dd
Update environment.yml
jan-janssen Jan 26, 2026
04b8e2c
Update pyproject.toml
jan-janssen Jan 26, 2026
8dc445e
Update environment-notebooks.yml
jan-janssen Jan 26, 2026
2badb7a
Merge branch 'main' into pandas
jan-janssen Apr 20, 2026
dcf8888
Update pyproject.toml
jan-janssen Apr 20, 2026
336cc5c
Update environment.yml
jan-janssen Apr 20, 2026
1fe4ec3
Update environment-docs.yml
jan-janssen Apr 20, 2026
9d5e966
Update vaspparser version to 0.0.3
jan-janssen Apr 20, 2026
a5659ef
Update lammpsparser version to 0.0.3
jan-janssen Apr 20, 2026
a076745
Update lammpsparser version to 0.0.3
jan-janssen Apr 20, 2026
528fc4f
Update environment-notebooks.yml
jan-janssen Apr 20, 2026
225072b
Update lammpsparser version to 0.0.3
jan-janssen Apr 20, 2026
2d70847
Update lammpsparser version to 0.0.3
jan-janssen Apr 20, 2026
3791200
Update pandas version to 3.0.2
jan-janssen Apr 20, 2026
2e01306
Merge branch 'main' into pandas
jan-janssen Apr 28, 2026
01a5fa9
Merge branch 'main' into pandas
jan-janssen Apr 28, 2026
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2 changes: 1 addition & 1 deletion .ci_support/environment-docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ dependencies:
- structuretoolkit =0.0.42
- seekpath =2.2.1
- lammps =2024.08.29
- pandas =2.3.3
- pandas =3.0.2
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- jupyter-book =1.0.0
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2 changes: 1 addition & 1 deletion .ci_support/environment-lammps.yml
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Expand Up @@ -2,7 +2,7 @@ channels:
- conda-forge
dependencies:
- lammps =2024.08.29=*openmpi*
- pandas =2.3.3
- pandas =3.0.2
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- iprpy-data =2023.07.25
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2 changes: 1 addition & 1 deletion .ci_support/environment-notebooks.yml
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Expand Up @@ -5,7 +5,7 @@ dependencies:
- papermill
- gpaw =25.7.0
- lammps =2024.08.29
- pandas =2.3.3
- pandas =3.0.2
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- dynaphopy =1.18.0
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2 changes: 1 addition & 1 deletion .ci_support/environment.yml
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Expand Up @@ -6,7 +6,7 @@ dependencies:
- lxml =6.0.2
- mendeleev =1.1.0
- numpy =2.4.3
- pandas =2.3.3
- pandas =3.0.2
- phonopy =3.2.0
- requests =2.32.5
- scipy =1.17.1
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2 changes: 1 addition & 1 deletion binder/environment.yml
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Expand Up @@ -10,7 +10,7 @@ dependencies:
- seekpath =2.2.1
- gpaw =25.7.0
- lammps =2024.08.29
- pandas =2.3.3
- pandas =3.0.2
- pylammpsmpi =0.3.12
- jinja2 =3.1.6
- dynaphopy =1.18.0
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6 changes: 3 additions & 3 deletions pyproject.toml
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Expand Up @@ -49,20 +49,20 @@ gpaw = [
lammps = [
"pylammpsmpi==0.3.12",
"jinja2==3.1.6",
"pandas==2.3.3",
"pandas==3.0.2",
"lammpsparser==0.0.3",
]
lammps_phonons = [
"pylammpsmpi==0.3.12",
"jinja2==3.1.6",
"pandas==2.3.3",
"pandas==3.0.2",
"dynaphopy==1.18.0",
"lammpsparser==0.0.3",
]
experimental = [
"lxml==6.0.2",
"mendeleev==1.1.0",
"pandas==2.3.3",
"pandas==3.0.2",
"requests==2.32.5",
Comment on lines 49 to 66
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@coderabbitai coderabbitai Bot Jan 25, 2026

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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check pandas 3.0.0 Python requirement from PyPI metadata
python3 <<'PY'
import json, urllib.request
try:
    data = json.load(urllib.request.urlopen("https://pypi.org/pypi/pandas/3.0.0/json"))
    print("Requires-Python:", data["info"]["requires_python"])
    print("Version:", data["info"]["version"])
    print("Release Date:", data["info"]["release_url"])
except Exception as e:
    print(f"Error: {e}")
PY

Repository: pyiron/atomistics

Length of output: 195

🏁 Script executed:

# Also check the pyproject.toml to confirm the Python range
cat pyproject.toml | grep -A 5 "python"

Repository: pyiron/atomistics

Length of output: 301

🏁 Script executed:

# Check if there are tests for optional dependencies
git ls-files | grep -E "test.*lammps|test.*pandas" | head -20

Repository: pyiron/atomistics

Length of output: 933

🌐 Web query:

pandas 3.0.0 python version requirements support

💡 Result:

pandas 3.0.0 supports (and effectively requires) Python 3.11 or newer (i.e., Python 3.10 and earlier are not supported). [1]

Source: pandas 3.0.0 release notes (“Increased minimum version for Python”). [1]

🏁 Script executed:

# Check if there are any existing compatibility or version constraint issues in the codebase
grep -r "pandas" pyproject.toml | head -10

Repository: pyiron/atomistics

Length of output: 123

🏁 Script executed:

# Check if there are any existing test markers or skip conditions for optional deps
grep -r "skipif\|mark.skip" tests/ --include="*.py" | grep -i "lammps\|pandas" | head -10

Repository: pyiron/atomistics

Length of output: 43

Downgrade pandas to a version compatible with Python 3.9-3.10.

pandas 3.0.0 requires Python 3.11+, which breaks compatibility with Python 3.9 and 3.10 that are within your project's declared support range (>=3.9,<3.15). This affects lines 52, 58, and 65 in the lammps, lammps_phonons, and experimental optional dependency groups. Use pandas 2.x instead.

🤖 Prompt for AI Agents 
In `@pyproject.toml` around lines 49 - 66, The pyproject optional dependency
groups lammps, lammps_phonons, and experimental currently pin pandas==3.0.0
which requires Python 3.11+; update those dependency entries in the lammps,
lammps_phonons, and experimental lists to a pandas 2.x release (e.g.,
pandas==2.1.3) that is compatible with Python 3.9–3.10 to restore declared
interpreter compatibility.

]
sphinxdft = [
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