Merge branch 'compile-default-plugins' into 'develop'

Lock plugin requirements

See merge request !2052

.gitlab-ci.yml

@@ -203,7 +203,7 @@ check python dependencies:
   before_script:
     - scripts/check_elastic.sh
     - uv pip install -e ".[dev]"
-    - uv pip install -r default_plugins.txt -c requirements-dev.txt # required until all legacy tests are removed
+    - uv pip install -r requirements-plugins.txt -c requirements-dev.txt # remove this after moving to distro
 
 generate pytest timings:
   extends: .base_test
@@ -314,7 +314,7 @@ check gui artifacts:
     GIT_SUBMODULE_PATHS: dependencies/*
   script:
     - uv pip install ".[dev,parsing,infrastructure]"
-    - uv pip install -r default_plugins.txt # remove this after moving to distro
+    - uv pip install -r requirements-plugins.txt -c requirements-dev.txt # remove this after moving to distro
     - scripts/check_gui_artifacts.sh
   after_script:
     - >

Dockerfile

@@ -196,8 +196,8 @@ RUN pip install nomad-lab-*.tar.gz
 
 # Install default plugins. TODO: This can be removed once we have a proper
 # distribution project.
-COPY default_plugins.txt .
-RUN uv pip install -r default_plugins.txt -c requirements.txt
+COPY requirements-plugins.txt .
+RUN uv pip install -r requirements-plugins.txt -c requirements.txt
 
 
 # ================================================================================

default_plugins.txt

@@ -3,11 +3,11 @@ git+https://github.com/FAIRmat-NFDI/nomad-porous-materials.git@522f4a3208077f534
 git+https://github.com/FAIRmat-NFDI/nomad-aitoolkit.git@b203f8eb28dc4b6771a39d5c5b7ad3d9d8583ac8
 nomad-simulations==0.0.1
 pynxtools[convert]==0.5.0
-git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@92d120d
-git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@c9bd20c
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-bandstructure.git@6521a2b
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-dos.git@dad7e2b
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-soap.git@1b0e60e
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-spectra.git@ec14732
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-system.git@01523dd
-git+https://github.com/nomad-coe/nomad-normalizer-plugin-simulation-workflow.git@22af484
+git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop
+git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-bandstructure.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-dos.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-soap.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-spectra.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-system.git@develop
+git+https://github.com/nomad-coe/nomad-normalizer-plugin-simulation-workflow.git@develop

pyproject.toml

@@ -211,3 +211,6 @@ disable_error_code = "import, annotation-unchecked"
 
 
 [tool.setuptools_scm]
+
+[tool.uv]
+index-url = "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple"

requirements-dev.txt

@@ -110,7 +110,7 @@ m2r==0.2.1                # via -r requirements.txt, nomad-lab (pyproject.toml)
 mako==1.3.5               # via alembic, -r requirements.txt
 markdown==3.7             # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
 markupsafe==2.1.5         # via jinja2, mako, mkdocs, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml)
-matid==2.1.0              # via -r requirements.txt, nomad-lab (pyproject.toml)
+matid==2.1.1              # via -r requirements.txt, nomad-lab (pyproject.toml)
 matplotlib==3.9.2         # via ase, asr, mdanalysis, phonopy, pymatgen, -r requirements.txt
 mda-xdrlib==0.2.0         # via mdanalysis, pyedr, -r requirements.txt
 mdanalysis==2.7.0         # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -215,10 +215,10 @@ rfc3987==1.3.8            # via jsonschema, -r requirements.txt
 rope==0.21.0              # via nomad-lab (pyproject.toml)
 ruamel-yaml==0.18.6       # via jupyter-telemetry, oauthenticator, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'  # via ruamel-yaml, -r requirements.txt
-ruff==0.6.1               # via nomad-lab (pyproject.toml)
+ruff==0.6.2               # via nomad-lab (pyproject.toml)
 runstats==2.0.0           # via -r requirements.txt, nomad-lab (pyproject.toml)
 scikit-learn==1.5.1       # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
-scipy==1.14.0             # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
+scipy==1.14.1             # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
 secretstorage==3.3.3 ; sys_platform == 'linux'  # via keyring
 sentinels==1.0.0          # via mongomock, -r requirements.txt
 six==1.16.0               # via asttokens, basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
@@ -251,7 +251,7 @@ tqdm==4.66.5              # via mdanalysis, pyedr, pymatgen, twine, -r requireme
 traitlets==5.14.3         # via jupyter-telemetry, jupyterhub, -r requirements.txt
 twine==3.4.2              # via nomad-lab (pyproject.toml)
 typed-ast==1.5.5          # via nomad-lab (pyproject.toml)
-types-python-dateutil==2.9.0.20240316  # via arrow, -r requirements.txt
+types-python-dateutil==2.9.0.20240821  # via arrow, -r requirements.txt
 typing-extensions==4.12.2  # via alembic, fastapi, jwcrypto, mypy, pydantic, sqlalchemy, -r requirements.txt
 typish==1.9.3             # via nptyping, -r requirements.txt
 tzdata==2024.1            # via celery, pandas, -r requirements.txt
@@ -259,7 +259,7 @@ uncertainties==3.2.2      # via pymatgen, -r requirements.txt
 unidecode==1.3.2          # via -r requirements.txt, nomad-lab (pyproject.toml)
 uri-template==1.3.0       # via jsonschema, -r requirements.txt
 urllib3==1.26.19          # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
-uv==0.3.0                 # via nomad-lab (pyproject.toml)
+uv==0.3.1                 # via nomad-lab (pyproject.toml)
 uvicorn==0.30.6           # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
 uvloop==0.20.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32'  # via uvicorn, -r requirements.txt
 validators==0.18.2        # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -270,7 +270,7 @@ wcwidth==0.2.13           # via prompt-toolkit, -r requirements.txt
 webcolors==24.8.0         # via jsonschema, -r requirements.txt
 webencodings==0.5.1       # via html5lib, -r requirements.txt
 websockets==13.0          # via uvicorn, -r requirements.txt
-werkzeug==3.0.3           # via flask, -r requirements.txt
+werkzeug==3.0.4           # via flask, -r requirements.txt
 wrapt==1.16.0             # via -r requirements.txt, nomad-lab (pyproject.toml)
 xarray==2024.7.0          # via -r requirements.txt, nomad-lab (pyproject.toml)
 zipp==3.20.0              # via importlib-metadata, -r requirements.txt

requirements.txt

@@ -91,7 +91,7 @@ lxml-html-clean==0.2.0    # via nomad-lab (pyproject.toml)
 m2r==0.2.1                # via nomad-lab (pyproject.toml)
 mako==1.3.5               # via alembic
 markupsafe==2.1.5         # via jinja2, mako, werkzeug
-matid==2.1.0              # via nomad-lab (pyproject.toml)
+matid==2.1.1              # via nomad-lab (pyproject.toml)
 matplotlib==3.9.2         # via ase, asr, mdanalysis, phonopy, pymatgen
 mda-xdrlib==0.2.0         # via mdanalysis, pyedr
 mdanalysis==2.7.0         # via nomad-lab (pyproject.toml)
@@ -162,7 +162,7 @@ ruamel-yaml==0.18.6       # via jupyter-telemetry, oauthenticator, pymatgen
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'  # via ruamel-yaml
 runstats==2.0.0           # via nomad-lab (pyproject.toml)
 scikit-learn==1.5.1       # via matid, nomad-lab (pyproject.toml)
-scipy==1.14.0             # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
+scipy==1.14.1             # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
 sentinels==1.0.0          # via mongomock
 six==1.16.0               # via basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
 smmap==5.0.1              # via gitdb
@@ -190,7 +190,7 @@ toposort==1.10            # via nomad-lab (pyproject.toml)
 tornado==6.4.1            # via jupyterhub
 tqdm==4.66.5              # via mdanalysis, pyedr, pymatgen
 traitlets==5.14.3         # via jupyter-telemetry, jupyterhub
-types-python-dateutil==2.9.0.20240316  # via arrow
+types-python-dateutil==2.9.0.20240821  # via arrow
 typing-extensions==4.12.2  # via alembic, fastapi, jwcrypto, pydantic, sqlalchemy
 typish==1.9.3             # via nptyping
 tzdata==2024.1            # via celery, pandas
@@ -207,7 +207,7 @@ wcwidth==0.2.13           # via prompt-toolkit
 webcolors==24.8.0         # via jsonschema
 webencodings==0.5.1       # via html5lib
 websockets==13.0          # via uvicorn
-werkzeug==3.0.3           # via flask
+werkzeug==3.0.4           # via flask
 wrapt==1.16.0             # via nomad-lab (pyproject.toml)
 xarray==2024.7.0          # via nomad-lab (pyproject.toml)
 zipp==3.20.0              # via importlib-metadata

scripts/generate_python_dependencies.sh

@@ -28,3 +28,9 @@ uv pip compile -U --universal -p 3.11 --annotation-style=line \
     requirements.txt \
     pyproject.toml
 
+uv pip compile --universal -p 3.11 --annotation-style=line \
+    --output-file=requirements-plugins.txt \
+    --unsafe-package nomad-lab \
+    -c requirements-dev.txt \
+    default_plugins.txt
+

scripts/setup_dev_env.sh

@@ -25,7 +25,7 @@ uv pip install -e ".[infrastructure,parsing,dev]" -c requirements-dev.txt
 
 # Install "default" plugins. TODO: This can be removed once we have proper
 # distributions projects.
-uv pip install -r default_plugins.txt -c requirements-dev.txt
+uv pip install -r requirements-plugins.txt # remove this after moving to distro
 
 # Build documentation
 sh scripts/generate_docs_artifacts.sh