From 22e8f1653a48b5f45e5d1a96d9d198faaa215adb Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 09:50:49 +0200 Subject: [PATCH 01/10] Use Quay.io for python 3.12 --- base/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/base/Dockerfile b/base/Dockerfile index 19a71048..39488957 100755 --- a/base/Dockerfile +++ b/base/Dockerfile @@ -1,8 +1,8 @@ -ARG ROOT_CONTAINER=jupyter/base-notebook:ubuntu-22.04@sha256:0ec801994602a53d3917d0f07ccf4474a1ddf5ae419483b24681a3c42abc4ce5 +ARG ROOT_CONTAINER=quay.io/jupyter/base-notebook:82d322f00937 ARG BASE_CONTAINER=$ROOT_CONTAINER FROM $BASE_CONTAINER -MAINTAINER Jan Janssen , Muhammad Hassani +MAINTAINER Jan Janssen , Niklas Siemer USER root From 9c4ff7e5f34a81855045b4c9d52202e295d93612 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 09:51:32 +0200 Subject: [PATCH 02/10] Update Dockerfile --- mpie_cmti/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mpie_cmti/Dockerfile b/mpie_cmti/Dockerfile index 73c74d95..b5cf971b 100755 --- a/mpie_cmti/Dockerfile +++ b/mpie_cmti/Dockerfile @@ -1,4 +1,4 @@ -ARG ROOT_IMAGE=jupyter/base-notebook:ubuntu-22.04@sha256:0ec801994602a53d3917d0f07ccf4474a1ddf5ae419483b24681a3c42abc4ce5 AS root_image +ARG ROOT_IMAGE=quay.io/jupyter/base-notebook:82d322f00937 AS root_image FROM $ROOT_IMAGE MAINTAINER Jan Janssen , Marian Bruns From 738add27cc699c60ed4f68883d2480d42c02aa34 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 10:06:10 +0200 Subject: [PATCH 03/10] libgl1-mesa-glx is deprecated Using libgl1 and libglx-mesa0 instead (https://askubuntu.com/a/1520333/178692) --- base/apt.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/base/apt.txt b/base/apt.txt index 36beaf27..597959dc 100644 --- a/base/apt.txt +++ b/base/apt.txt @@ -1,2 +1,3 @@ -libgl1-mesa-glx +libgl1 +libglx-mesa0 patch From e32fc2e03e7de52fabf4755c244a1f07c4797b88 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 10:10:52 +0200 Subject: [PATCH 04/10] Same for the cmti apt --- mpie_cmti/apt.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mpie_cmti/apt.txt b/mpie_cmti/apt.txt index 36beaf27..597959dc 100644 --- a/mpie_cmti/apt.txt +++ b/mpie_cmti/apt.txt @@ -1,2 +1,3 @@ -libgl1-mesa-glx +libgl1 +libglx-mesa0 patch From f9a471660c635545a93bc7479c8e3363b65260b1 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 10:12:39 +0200 Subject: [PATCH 05/10] Pip testing.yml with 3.12 --- .github/workflows/testing.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 842eebe4..bc463d6b 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -20,7 +20,7 @@ jobs: - name: Setup Mambaforge uses: conda-incubator/setup-miniconda@v3 with: - python-version: "3.11" + python-version: "3.12" miniforge-version: latest condarc-file: .condarc environment-file: environment.yml From b4c969df77eb5017fa9f2d0397b18b6e0c6f05a2 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 6 Oct 2025 10:13:04 +0200 Subject: [PATCH 06/10] weekly.yml with python 3.12 --- .github/workflows/weekly.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/weekly.yml b/.github/workflows/weekly.yml index 7014b214..5cf40a24 100644 --- a/.github/workflows/weekly.yml +++ b/.github/workflows/weekly.yml @@ -16,7 +16,7 @@ jobs: strategy: matrix: operating-system: [ubuntu-latest] - python-version: ["3.11"] + python-version: ["3.12"] steps: - uses: actions/checkout@v2 From 2da1ea51b8b678a112be5737582ce1136e687f86 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 13 Oct 2025 16:51:13 +0200 Subject: [PATCH 07/10] inpired by jans shared env --- mpie_cmti/environment.yml | 53 ++++++++++++++++++++++++++++----------- 1 file changed, 38 insertions(+), 15 deletions(-) diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml index 9f99ff17..2668345b 100644 --- a/mpie_cmti/environment.yml +++ b/mpie_cmti/environment.yml @@ -2,48 +2,71 @@ channels: - conda-forge - nodefaults dependencies: +- ase =3.26.0 - aimsgb =1.1.1 +- assyst =0.8.0 # [unix] +- atomistics =0.3.0 - atomicrex =1.0.4 - bader =1.0.5 +- black =25.1.0 - bokeh =3.8.0 - calphy =1.4.3 +- conda =25.7.0 +- conda-smithy =3.52.2 +- custodian =2025.8.13 +- executorlib =1.7.1 - fitsnap3 =3.1.0.4 - flux-core =0.64.0 -- git =2.46.0 +- git =2.51.0 - gpaw =24.6.0=*openmpi* - gpaw-data =0.9.20000 +- grace-tensorpotential =0.5.3 # [unix] +- graphviz =12.0.0 +- h5io =0.2.5 +- h5io_browser =0.2.3 +- iprpy-data =2023.07.25 - jupyter-server-proxy =4.4.0 - jupyterhub =5.2.1 -- lammps =2023.08.02=*openmpi* +- lammps =2024.08.29=*openmpi* # [unix] +- landau =1.4 - llama-index =0.14.4 - matgl =1.1.2 - maxvolpy =0.3.8 - nbgitpuller =1.2.2 - netcdf4 =1.7.2 +- mamba =2.2.0 +- matplotlib-base =3.10.6 +- mkl =2024.2.2 # [linux] +- mpi4py =4.1.0 +- mypy =1.18.2 - nglview =3.1.4 -- mkl =2023.2.0 - mlip =3.0 -- numba =0.60.0 - openkim-models =2021.01.28 -- psycopg2 =2.9.9 +- psycopg2 =2.9.10 +- pygraphviz =1.14 - pyiron =0.5.2 - pyiron-data =0.0.30 -- pyiron_atomistics =0.7.20 -- pyiron_base =0.15.1 +- pyiron_atomistics =0.8.1 +- pyiron_base =0.15.4 +- pyiron_snippets =1.0.1 - pyiron_contrib =0.1.19 - pyiron_potentialfit =0.3.12 -- pyiron_workflow =0.13.3 +- pyiron_workflow =0.15.3 - pyiron_gui =0.0.12 - pyironflow =0.0.20 -- python-ace =0.3.0 -- pytorch =2.1.2 -- pyxtal =1.0.9 +- pylammpsmpi =0.3.3 +- pymace =0.3.14 # [unix] +- pysqa =0.3.2 +- python =3.12.10 +- python-ace =0.3.1 # [unix] +- python-ternary =1.0.8 +- pytorch =2.5.1 # [unix] +- pyxtal =1.1.1 +- qe =7.5 # [unix64] - runner =1.3 +- seaborn =0.13.2 - sphinxdft =3.1 - sqsgenerator =0.3 - structdbrest =0.0.1 - sysroot_linux-64 =2.17 -- tensorflow =2.17.0 -- dscribe =2.1.2 -- landau =1.4 -- backports.tarfile +- tensorflow =2.18.0 From 4f6b6576b725da5af0565bfaa63af311044ddca9 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 13 Oct 2025 17:11:25 +0200 Subject: [PATCH 08/10] apply changes to all environment files --- base/environment.yml | 6 +++--- md/environment.yml | 6 +++--- potentialworkshop/environment.yml | 14 +++++++------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/base/environment.yml b/base/environment.yml index 4366b44b..f7e00f8a 100644 --- a/base/environment.yml +++ b/base/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - nodefaults dependencies: -- pyiron_base =0.15.1 -- git =2.46.0 -- mkl =2023.2.0 +- git =2.51.0 +- mkl =2024.2.2 # [linux] +- pyiron_base =0.15.4 diff --git a/md/environment.yml b/md/environment.yml index 1050756f..00fa1bd9 100644 --- a/md/environment.yml +++ b/md/environment.yml @@ -2,9 +2,9 @@ channels: - conda-forge - nodefaults dependencies: +- lammps =2024.08.29=*openmpi* # [unix] +- nglview =3.1.4 - pyiron =0.5.2 -- pyiron_atomistics =0.7.20 - pyiron-data =0.0.30 -- nglview =3.1.4 -- lammps =2023.08.02=*openmpi* +- pyiron_atomistics =0.8.1 - openkim-models =2021.01.28 diff --git a/potentialworkshop/environment.yml b/potentialworkshop/environment.yml index cd0c27d3..9f0aa81f 100644 --- a/potentialworkshop/environment.yml +++ b/potentialworkshop/environment.yml @@ -2,11 +2,11 @@ channels: - conda-forge - nodefaults dependencies: -- atomicrex =1.0.3 -- runner =1.2 -- structdbrest =0.0.1 -- pyiron_potentialfit =0.3.7 -- nbgitpuller =1.2.2 -- python-ace =0.3.0 +- atomicrex =1.0.4 - calphy =1.4.3 -- pyxtal =1.0.9 +- nbgitpuller =1.2.2 +- pyiron_potentialfit =0.3.12 +- python-ace =0.3.1 # [unix] +- pyxtal =1.1.1 +- runner =1.3 +- structdbrest =0.0.1 From 78f1e5df2a35e06c28a0840cd998dd302bf392c4 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 13 Oct 2025 17:19:57 +0200 Subject: [PATCH 09/10] update gpaw --- mpie_cmti/environment.yml | 3 +-- pyiron/environment.yml | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml index 2668345b..7462cf20 100644 --- a/mpie_cmti/environment.yml +++ b/mpie_cmti/environment.yml @@ -18,8 +18,7 @@ dependencies: - fitsnap3 =3.1.0.4 - flux-core =0.64.0 - git =2.51.0 -- gpaw =24.6.0=*openmpi* -- gpaw-data =0.9.20000 +- gpaw =25.1.0=*openmpi* - grace-tensorpotential =0.5.3 # [unix] - graphviz =12.0.0 - h5io =0.2.5 diff --git a/pyiron/environment.yml b/pyiron/environment.yml index 41862185..6f07278d 100644 --- a/pyiron/environment.yml +++ b/pyiron/environment.yml @@ -3,5 +3,4 @@ channels: - nodefaults dependencies: - sphinxdft =3.1 -- gpaw =24.6.0=*openmpi* -- gpaw-data = 0.9.20000 +- gpaw =25.1.0=*openmpi* From 7048760ea6f47b9655d7a2e8d711fca153fb7db4 Mon Sep 17 00:00:00 2001 From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com> Date: Mon, 13 Oct 2025 17:49:06 +0200 Subject: [PATCH 10/10] rm maxvolpy and gpaw --- mpie_cmti/environment.yml | 2 -- pyiron/environment.yml | 1 - 2 files changed, 3 deletions(-) diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml index 7462cf20..8da9ae8c 100644 --- a/mpie_cmti/environment.yml +++ b/mpie_cmti/environment.yml @@ -18,7 +18,6 @@ dependencies: - fitsnap3 =3.1.0.4 - flux-core =0.64.0 - git =2.51.0 -- gpaw =25.1.0=*openmpi* - grace-tensorpotential =0.5.3 # [unix] - graphviz =12.0.0 - h5io =0.2.5 @@ -30,7 +29,6 @@ dependencies: - landau =1.4 - llama-index =0.14.4 - matgl =1.1.2 -- maxvolpy =0.3.8 - nbgitpuller =1.2.2 - netcdf4 =1.7.2 - mamba =2.2.0 diff --git a/pyiron/environment.yml b/pyiron/environment.yml index 6f07278d..aa114825 100644 --- a/pyiron/environment.yml +++ b/pyiron/environment.yml @@ -3,4 +3,3 @@ channels: - nodefaults dependencies: - sphinxdft =3.1 -- gpaw =25.1.0=*openmpi*