From 70530ea3a782b524f801172c963c8ecb45b56154 Mon Sep 17 00:00:00 2001
From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com>
Date: Mon, 13 Oct 2025 16:14:42 +0200
Subject: [PATCH 1/5] env from jan-janssen/shared-conda-environment/

---
 mpie_cmti/environment.yml | 112 ++++++++++++++++++++++----------------
 1 file changed, 65 insertions(+), 47 deletions(-)

diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml
index 9f99ff17..64df03fb 100644
--- a/mpie_cmti/environment.yml
+++ b/mpie_cmti/environment.yml
@@ -1,49 +1,67 @@
+name: base
 channels:
-- conda-forge
-- nodefaults
+  - conda-forge
 dependencies:
-- aimsgb =1.1.1
-- atomicrex =1.0.4
-- bader =1.0.5
-- bokeh =3.8.0
-- calphy =1.4.3
-- fitsnap3 =3.1.0.4
-- flux-core =0.64.0
-- git =2.46.0
-- gpaw =24.6.0=*openmpi*
-- gpaw-data =0.9.20000
-- jupyter-server-proxy =4.4.0
-- jupyterhub =5.2.1
-- lammps =2023.08.02=*openmpi*
-- llama-index =0.14.4
-- matgl =1.1.2
-- maxvolpy =0.3.8
-- nbgitpuller =1.2.2
-- netcdf4 =1.7.2
-- nglview =3.1.4
-- mkl =2023.2.0
-- mlip =3.0
-- numba =0.60.0
-- openkim-models =2021.01.28
-- psycopg2 =2.9.9
-- pyiron =0.5.2
-- pyiron-data =0.0.30
-- pyiron_atomistics =0.7.20
-- pyiron_base =0.15.1
-- pyiron_contrib =0.1.19
-- pyiron_potentialfit =0.3.12
-- pyiron_workflow =0.13.3
-- pyiron_gui =0.0.12
-- pyironflow =0.0.20
-- python-ace =0.3.0
-- pytorch =2.1.2
-- pyxtal =1.0.9
-- runner =1.3
-- 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
+  - ase =3.26.0
+  - assyst =0.8.0  # [unix]
+  - atomistics =0.3.0
+  - black =25.1.0
+  - calphy =1.4.3  # [unix]
+  - conda =25.7.0
+  - conda-smithy =3.52.2
+  - coverage =7.10.7
+  - custodian =2025.8.13
+  - dynaphopy =1.18.0  # [unix]
+  - executorlib =1.7.1
+  - ffmpeg =7.1.1  # [unix]
+  - flux-core =0.64.0  # [linux]
+  - flux-sched =0.38.0  # [linux]
+  - git =2.51.0
+  - git-filter-repo =2.38.0
+  - gmailsorter =0.1.3
+  - grace-tensorpotential =0.5.3  # [unix]
+  - graphviz =12.0.0
+  - grayskull =2.9.1
+  - gunicorn =23.0.0  # [unix]
+  - h5io =0.2.5
+  - h5io_browser =0.2.3
+  - iprpy-data =2023.07.25
+  - jupyterlab =4.4.9
+  - lammps =2024.08.29=*openmpi*  # [unix]
+  - landau =1.4
+  - langchain =0.3.27
+  - langchain-anthropic =0.3.22
+  - langchain-experimental =0.3.4
+  - langchain-openai =0.3.35
+  - lxml =5.4.0
+  - 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
+  - pre-commit =4.3.0
+  - psycopg2 =2.9.10
+  - pyauthenticator =0.2.1  # [unix]
+  - pygraphviz =1.14
+  - pyiron =0.5.2
+  - pyiron-data =0.0.30
+  - pyiron_atomistics =0.8.1
+  - pyiron_base =0.15.4
+  - pyiron_snippets =1.0.1
+  - pylammpsmpi =0.3.3
+  - pymace =0.3.14  # [unix]
+  - pymov2gif =0.0.2  # [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]
+  - seaborn =0.13.2
+  - sphinxdft =3.1  # [linux]
+  - sqsgenerator =0.3
+  - sysroot_linux-64 =2.17  # [linux]
+  - tensorflow =2.18.0  # [unix]
+  - wget =1.21.4  # [unix]

From 86a06e27e7e6106361a7d5c749fbb415ee3c7a6f Mon Sep 17 00:00:00 2001
From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com>
Date: Mon, 13 Oct 2025 17:25:28 +0200
Subject: [PATCH 2/5] add -nodefaults

---
 mpie_cmti/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mpie_cmti/environment.yml b/mpie_cmti/environment.yml
index 64df03fb..48f30fd3 100644
--- a/mpie_cmti/environment.yml
+++ b/mpie_cmti/environment.yml
@@ -1,6 +1,7 @@
 name: base
 channels:
   - conda-forge
+  - nodefaults
 dependencies:
   - ase =3.26.0
   - assyst =0.8.0  # [unix]

From 0b0a721ea780eafa55ec23341300f16b7df92bed Mon Sep 17 00:00:00 2001
From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com>
Date: Mon, 13 Oct 2025 17:32:38 +0200
Subject: [PATCH 3/5] apply changes to other envs

---
 base/environment.yml              | 10 +++++-----
 md/environment.yml                | 15 +++++++--------
 potentialworkshop/environment.yml | 15 +++++----------
 pyiron/environment.yml            |  8 +++-----
 4 files changed, 20 insertions(+), 28 deletions(-)

diff --git a/base/environment.yml b/base/environment.yml
index 4366b44b..1b84eb53 100644
--- a/base/environment.yml
+++ b/base/environment.yml
@@ -1,7 +1,7 @@
 channels:
-- conda-forge
-- nodefaults
+  - 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..2faf72be 100644
--- a/md/environment.yml
+++ b/md/environment.yml
@@ -1,10 +1,9 @@
 channels:
-- conda-forge
-- nodefaults
+  - conda-forge
+  - nodefaults
 dependencies:
-- pyiron =0.5.2
-- pyiron_atomistics =0.7.20
-- pyiron-data =0.0.30
-- nglview =3.1.4
-- lammps =2023.08.02=*openmpi*
-- openkim-models =2021.01.28
+  - lammps =2024.08.29=*openmpi*  # [unix]
+  - nglview =3.1.4
+  - pyiron =0.5.2
+  - pyiron-data =0.0.30
+  - pyiron_atomistics =0.8.1
diff --git a/potentialworkshop/environment.yml b/potentialworkshop/environment.yml
index cd0c27d3..1dcad8e0 100644
--- a/potentialworkshop/environment.yml
+++ b/potentialworkshop/environment.yml
@@ -1,12 +1,7 @@
 channels:
-- conda-forge
-- nodefaults
+  - 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
-- calphy =1.4.3
-- pyxtal =1.0.9
+  - calphy =1.4.3  # [unix]
+  - python-ace =0.3.1 # [unix]
+  - pyxtal =1.1.1
diff --git a/pyiron/environment.yml b/pyiron/environment.yml
index 41862185..b230bbf5 100644
--- a/pyiron/environment.yml
+++ b/pyiron/environment.yml
@@ -1,7 +1,5 @@
 channels:
-- conda-forge
-- nodefaults
+  - conda-forge
+  - nodefaults
 dependencies:
-- sphinxdft =3.1
-- gpaw =24.6.0=*openmpi*
-- gpaw-data = 0.9.20000
+  - sphinxdft =3.1  # [linux]

From 147c173b0ade11f952db0a55dcef755a40262d08 Mon Sep 17 00:00:00 2001
From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com>
Date: Mon, 13 Oct 2025 17:41:07 +0200
Subject: [PATCH 4/5] Update testing.yml

---
 .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 6939bba445e9425c414e87109a23153451899d8d Mon Sep 17 00:00:00 2001
From: Niklas Siemer <70580458+niklassiemer@users.noreply.github.com>
Date: Tue, 14 Oct 2025 15:02:20 +0200
Subject: [PATCH 5/5] Add gpaw 25.7.0

---
 pyiron/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyiron/environment.yml b/pyiron/environment.yml
index b230bbf5..26729262 100644
--- a/pyiron/environment.yml
+++ b/pyiron/environment.yml
@@ -3,3 +3,4 @@ channels:
   - nodefaults
 dependencies:
   - sphinxdft =3.1  # [linux]
+  - gpaw =25.7.0=*openmpi*