From 5a5b6423b0198b65f486209f9c1d2568cf76fe91 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 25 Jan 2026 17:17:55 +0100 Subject: [PATCH 01/25] Update pyproject.toml --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c0fef190..7811a466 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,20 +49,20 @@ gpaw = [ lammps = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", - "pandas==2.3.3", + "pandas==3.0.0", "pyiron_lammps==0.5.3", ] lammps_phonons = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", - "pandas==2.3.3", + "pandas==3.0.0", "dynaphopy==1.18.0", "pyiron_lammps==0.5.3", ] experimental = [ "lxml==6.0.2", "mendeleev==1.1.0", - "pandas==2.3.3", + "pandas==3.0.0", "requests==2.32.5", ] sphinxdft = [ From ec5bc42d9a0e7f315f6a563ecdf42549ef979ab4 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 25 Jan 2026 17:18:15 +0100 Subject: [PATCH 02/25] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 6438e092..a7d124ba 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -10,7 +10,7 @@ dependencies: - seekpath =2.2.0 - gpaw =25.7.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - dynaphopy =1.18.0 From 80c6b73ff3276a13bda1ce05aece0eb68f1c0592 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 25 Jan 2026 17:18:33 +0100 Subject: [PATCH 03/25] Update environment-docs.yml --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index f49c7032..1843322b 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -15,7 +15,7 @@ dependencies: - structuretoolkit =0.0.39 - seekpath =2.2.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - jupyter-book =1.0.0 From d1dae9a26e0983d026114422f738b68644da16ad Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 25 Jan 2026 17:18:51 +0100 Subject: [PATCH 04/25] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index e6b9585a..0ca1aee3 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -6,7 +6,7 @@ dependencies: - lxml =6.0.2 - mendeleev =1.1.0 - numpy =2.3.5 -- pandas =2.3.3 +- pandas =3.0.0 - phonopy =2.47.1 - requests =2.32.5 - scipy =1.16.3 From 17e208e6392cf1603b4bead9082ba8e015c52b3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Sun, 25 Jan 2026 19:19:55 +0100 Subject: [PATCH 05/25] use StringIO --- src/atomistics/referencedata/wikipedia.py | 4 +++- src/atomistics/referencedata/wolframalpha.py | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/atomistics/referencedata/wikipedia.py b/src/atomistics/referencedata/wikipedia.py index 5a74bd23..9498bc1f 100644 --- a/src/atomistics/referencedata/wikipedia.py +++ b/src/atomistics/referencedata/wikipedia.py @@ -1,3 +1,5 @@ +from io import StringIO + import pandas import requests @@ -33,7 +35,7 @@ def get_elastic_properties(chemical_symbol: str) -> dict: "https://en.wikipedia.org/wiki/Elastic_properties_of_the_elements_(data_page)", headers={"User-Agent": "atomistics package"}, ) - df_lst = pandas.read_html(response.text) + df_lst = pandas.read_html(StringIO(response.text)) property_dict = {} for i, p in enumerate(property_lst): df_tmp = df_lst[i] diff --git a/src/atomistics/referencedata/wolframalpha.py b/src/atomistics/referencedata/wolframalpha.py index 9abe941c..864a7a0b 100644 --- a/src/atomistics/referencedata/wolframalpha.py +++ b/src/atomistics/referencedata/wolframalpha.py @@ -1,4 +1,5 @@ import os +from io import StringIO from typing import Callable, Optional, Union import numpy as np @@ -17,7 +18,7 @@ def _get_content_from_url(url: str) -> pandas.DataFrame: Returns: pandas.DataFrame: The content retrieved from the URL as a pandas DataFrame. """ - content = pandas.read_html(requests.get(url).text) + content = pandas.read_html(StringIO(requests.get(url).text)) if len(content[8]) > 1: return content[8] else: From a1ad2e4a97695a32daa0c4b66877fa47a2f984e2 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Sun, 25 Jan 2026 19:22:59 +0100 Subject: [PATCH 06/25] Update environment-lammps.yml --- .ci_support/environment-lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 33d79574..428c7a11 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -2,7 +2,7 @@ channels: - conda-forge dependencies: - lammps =2024.08.29=*openmpi* -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - iprpy-data =2023.07.25 From 9dcb96711504bda4341e35314654de745c937a2b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 26 Jan 2026 17:12:19 +0100 Subject: [PATCH 07/25] Update environment-docs.yml --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 1843322b..b29b439e 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -19,7 +19,7 @@ dependencies: - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - jupyter-book =1.0.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 - pyiron_vasp =0.2.19 - hatchling =1.28.0 - hatch-vcs =0.5.0 From d9a827ec4f2c1a9865b9319b646eaf4baeec012b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 26 Jan 2026 17:12:34 +0100 Subject: [PATCH 08/25] Update environment-lammps.yml --- .ci_support/environment-lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 428c7a11..d8172f47 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -7,4 +7,4 @@ dependencies: - jinja2 =3.1.6 - iprpy-data =2023.07.25 - dynaphopy =1.18.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 From 92b10dd8058ab8758291d18882eed67774e0f80c Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 26 Jan 2026 17:12:53 +0100 Subject: [PATCH 09/25] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index a7d124ba..1fc8a7d1 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -15,7 +15,7 @@ dependencies: - jinja2 =3.1.6 - dynaphopy =1.18.0 - tqdm =4.67.1 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 - pyiron_vasp =0.2.19 - hatchling =1.28.0 - hatch-vcs =0.5.0 From 04b8e2cc574e11986997d5bf9323bc70f80ab42e Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 26 Jan 2026 17:13:23 +0100 Subject: [PATCH 10/25] Update pyproject.toml --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7811a466..af0c7b82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,14 +50,14 @@ lammps = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", "pandas==3.0.0", - "pyiron_lammps==0.5.3", + "pyiron_lammps==0.5.4", ] lammps_phonons = [ "pylammpsmpi==0.3.9", "jinja2==3.1.6", "pandas==3.0.0", "dynaphopy==1.18.0", - "pyiron_lammps==0.5.3", + "pyiron_lammps==0.5.4", ] experimental = [ "lxml==6.0.2", From 8dc445e4b3eeac41ea2babb1b34b9165651d5c9a Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 26 Jan 2026 17:26:25 +0100 Subject: [PATCH 11/25] Update environment-notebooks.yml --- .ci_support/environment-notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 4dd14386..06d648aa 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,8 +5,8 @@ dependencies: - papermill - gpaw =25.7.0 - lammps =2024.08.29 -- pandas =2.3.3 +- pandas =3.0.0 - pylammpsmpi =0.3.9 - jinja2 =3.1.6 - dynaphopy =1.18.0 -- pyiron_lammps =0.5.3 +- pyiron_lammps =0.5.4 From dcf888848585161c7f23aa68e6f33a01f4640062 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:17:28 +0200 Subject: [PATCH 12/25] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0af620e8..63e4ed27 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -75,7 +75,7 @@ tqdm = [ "tqdm==4.67.3" ] vasp = [ - "vaspparser==0.0.2" + "vaspparser==0.0.3" ] [tool.hatch.build] From 336cc5c297740cbbe752b7c63b4336b7ff5efc7b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:17:49 +0200 Subject: [PATCH 13/25] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index be30882f..24d931df 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -15,6 +15,6 @@ dependencies: - structuretoolkit =0.0.42 - sphinx_parser =0.1.7 - tqdm =4.67.3 -- vaspparser =0.0.2 +- vaspparser =0.0.3 - hatchling =1.29.0 - hatch-vcs =0.5.0 From 1fe4ec3a25059632fde42f1b10ac745b50cc450d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:19:40 +0200 Subject: [PATCH 14/25] Update environment-docs.yml --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 57b3126e..c22e62c3 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -20,6 +20,6 @@ dependencies: - jinja2 =3.1.6 - jupyter-book =1.0.0 - lammpsparser =0.0.2 -- vaspparser =0.0.2 +- vaspparser =0.0.3 - hatchling =1.29.0 - hatch-vcs =0.5.0 From 9d5e966aee49fabe835d864d02870de0133b396b Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:20:19 +0200 Subject: [PATCH 15/25] Update vaspparser version to 0.0.3 --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 28f39376..3fb65463 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -16,6 +16,6 @@ dependencies: - dynaphopy =1.18.0 - tqdm =4.67.3 - lammpsparser =0.0.2 -- vaspparser =0.0.2 +- vaspparser =0.0.3 - hatchling =1.29.0 - hatch-vcs =0.5.0 From a5659ef8a1b119bc7686e3615a7a176d313fa76d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:22:06 +0200 Subject: [PATCH 16/25] Update lammpsparser version to 0.0.3 --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index c22e62c3..2eb76556 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -19,7 +19,7 @@ dependencies: - pylammpsmpi =0.3.12 - jinja2 =3.1.6 - jupyter-book =1.0.0 -- lammpsparser =0.0.2 +- lammpsparser =0.0.3 - vaspparser =0.0.3 - hatchling =1.29.0 - hatch-vcs =0.5.0 From a076745539c37eb76ef67b5c42e72ccc4e9596b4 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:22:20 +0200 Subject: [PATCH 17/25] Update lammpsparser version to 0.0.3 --- .ci_support/environment-lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 514c276b..41108054 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -7,4 +7,4 @@ dependencies: - jinja2 =3.1.6 - iprpy-data =2023.07.25 - dynaphopy =1.18.0 -- lammpsparser =0.0.2 +- lammpsparser =0.0.3 From 528fc4f54cd6c970fcff90b1311dd683b0498a53 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:22:37 +0200 Subject: [PATCH 18/25] Update environment-notebooks.yml --- .ci_support/environment-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 47fd0ee9..62668cf5 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -9,4 +9,4 @@ dependencies: - pylammpsmpi =0.3.12 - jinja2 =3.1.6 - dynaphopy =1.18.0 -- lammpsparser =0.0.2 +- lammpsparser =0.0.3 From 225072bde86df2ec31260995f68331faad0becb3 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:22:57 +0200 Subject: [PATCH 19/25] Update lammpsparser version to 0.0.3 --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 3fb65463..184b01dc 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -15,7 +15,7 @@ dependencies: - jinja2 =3.1.6 - dynaphopy =1.18.0 - tqdm =4.67.3 -- lammpsparser =0.0.2 +- lammpsparser =0.0.3 - vaspparser =0.0.3 - hatchling =1.29.0 - hatch-vcs =0.5.0 From 2d70847a30c68545fc1f5e28bad99c4f433b175a Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 12:23:24 +0200 Subject: [PATCH 20/25] Update lammpsparser version to 0.0.3 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 63e4ed27..ca2e3003 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,14 +50,14 @@ lammps = [ "pylammpsmpi==0.3.12", "jinja2==3.1.6", "pandas==3.0.2", - "lammpsparser==0.0.2", + "lammpsparser==0.0.3", ] lammps_phonons = [ "pylammpsmpi==0.3.12", "jinja2==3.1.6", "pandas==3.0.0", "dynaphopy==1.18.0", - "lammpsparser==0.0.2", + "lammpsparser==0.0.3", ] experimental = [ "lxml==6.0.2", From 3791200d58f2ab522f75ac9da3462cb866c198ba Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Mon, 20 Apr 2026 13:14:25 +0200 Subject: [PATCH 21/25] Update pandas version to 3.0.2 --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ca2e3003..b21c4698 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,14 +55,14 @@ lammps = [ lammps_phonons = [ "pylammpsmpi==0.3.12", "jinja2==3.1.6", - "pandas==3.0.0", + "pandas==3.0.2", "dynaphopy==1.18.0", "lammpsparser==0.0.3", ] experimental = [ "lxml==6.0.2", "mendeleev==1.1.0", - "pandas==3.0.0", + "pandas==3.0.2", "requests==2.32.5", ] sphinxdft = [ From 9f5421e5c2aebce111d3a17fd5c69d2a0a6bb38a Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 9 Jun 2026 13:41:01 +0200 Subject: [PATCH 22/25] Update environment.yml --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 0d8b082e..c78298cc 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -9,7 +9,7 @@ dependencies: - structuretoolkit =0.0.42 - seekpath =2.2.1 - gpaw =25.7.0 -- lammps =2024.08.29 +- lammps =2025.07.22 - pandas =3.0.3 - pylammpsmpi =0.4.0 - jinja2 =3.1.6 From 86a8b8dd65d6c24c80334c574a4754bdd1daa042 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 9 Jun 2026 13:48:20 +0200 Subject: [PATCH 23/25] Update LAMMPS version in environment file --- .ci_support/environment-lammps.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 05509dfa..f953c39d 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -1,7 +1,7 @@ channels: - conda-forge dependencies: -- lammps =2024.08.29=*openmpi* +- lammps =2025.07.22=*openmpi* - pandas =3.0.3 - pylammpsmpi =0.4.0 - jinja2 =3.1.6 From 3d3fbb7058fe76d93910a2c0213047e2c9b46d62 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 9 Jun 2026 13:48:43 +0200 Subject: [PATCH 24/25] Update LAMMPS version to 2025.07.22 --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index b2f51093..c346e0f7 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -14,7 +14,7 @@ dependencies: - phonopy =3.2.0 - structuretoolkit =0.0.44 - seekpath =2.2.1 -- lammps =2024.08.29 +- lammps =2025.07.22 - pandas =3.0.3 - pylammpsmpi =0.4.0 - jinja2 =3.1.6 From 59bdaa218c9d1376d7d21c399e2fd037e25f4bb9 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Tue, 9 Jun 2026 13:49:03 +0200 Subject: [PATCH 25/25] Update lammps version in environment-notebooks.yml --- .ci_support/environment-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 8246954a..84615ae5 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -4,7 +4,7 @@ dependencies: - jupyter - papermill - gpaw =25.7.0 -- lammps =2024.08.29 +- lammps =2025.07.22 - pandas =3.0.3 - pylammpsmpi =0.4.0 - jinja2 =3.1.6