From 1aa7f08a9f0306066e7d424abf63f6f2c93c491b Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Thu, 4 Jun 2020 16:51:00 +0200
Subject: [PATCH] Merged more parsers to support 40+ parsers. #331
---
.dockerignore | 1 +
.gitignore | 1 +
.gitmodules | 36 ++++++++++++++++++
.python-version | 2 +-
Dockerfile | 72 ++++++++++++++---------------------
dependencies/nomad-meta-info | 2 +-
dependencies/parsers/amber | 1 +
dependencies/parsers/asap | 1 +
dependencies/parsers/charmm | 1 +
dependencies/parsers/dftbplus | 1 +
dependencies/parsers/fplo | 1 +
dependencies/parsers/gamess | 2 +-
dependencies/parsers/gromacs | 1 +
dependencies/parsers/gromos | 1 +
dependencies/parsers/lammps | 1 +
dependencies/parsers/mopac | 1 +
dependencies/parsers/namd | 1 +
dependencies/parsers/openkim | 1 +
dependencies/parsers/tinker | 1 +
dependencies/python_common | 2 +-
docs/archive.rst | 2 +-
docs/dev/setup.md | 12 +++---
gui/src/searchQuantities.json | 20 ++++++++--
nomad/parsing/__init__.py | 66 ++++++++++++++++++++++++++++++++
nomad/processing/data.py | 14 +++++--
requirements.txt | 4 +-
setup.py | 2 +-
27 files changed, 183 insertions(+), 67 deletions(-)
create mode 160000 dependencies/parsers/amber
create mode 160000 dependencies/parsers/asap
create mode 160000 dependencies/parsers/charmm
create mode 160000 dependencies/parsers/dftbplus
create mode 160000 dependencies/parsers/fplo
create mode 160000 dependencies/parsers/gromacs
create mode 160000 dependencies/parsers/gromos
create mode 160000 dependencies/parsers/lammps
create mode 160000 dependencies/parsers/mopac
create mode 160000 dependencies/parsers/namd
create mode 160000 dependencies/parsers/openkim
create mode 160000 dependencies/parsers/tinker
diff --git a/.dockerignore b/.dockerignore
index 97f4f45f8c..4ca4d01cd1 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -5,6 +5,7 @@
**/*.pyc
**/NOMAD.egg-info
.*env/
+.pyenv*/
.pytest_cache
.vscode/
.volumes/
diff --git a/.gitignore b/.gitignore
index 493920a7ed..b8df0fecc6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
.DS_Store
.*env/
+.pyenv*/
.pytest/
.python-version
.ipynb_checkpoints/
diff --git a/.gitmodules b/.gitmodules
index b76dc3c1d5..6ffd31428e 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -155,3 +155,39 @@
[submodule "dependencies/parsers/eels"]
path = dependencies/parsers/eels
url = https://github.com/markus1978/eels.git
+[submodule "dependencies/parsers/namd"]
+ path = dependencies/parsers/namd
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-namd.git
+[submodule "dependencies/parsers/charmm"]
+ path = dependencies/parsers/charmm
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-charmm.git
+[submodule "dependencies/parsers/dftbplus"]
+ path = dependencies/parsers/dftbplus
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dftb-plus.git
+[submodule "dependencies/parsers/asap"]
+ path = dependencies/parsers/asap
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-asap.git
+[submodule "dependencies/parsers/fplo"]
+ path = dependencies/parsers/fplo
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fplo.git
+[submodule "dependencies/parsers/mopac"]
+ path = dependencies/parsers/mopac
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mopac.git
+[submodule "dependencies/parsers/amber"]
+ path = dependencies/parsers/amber
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-amber.git
+[submodule "dependencies/parsers/gromacs"]
+ path = dependencies/parsers/gromacs
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromacs.git
+[submodule "dependencies/parsers/gromos"]
+ path = dependencies/parsers/gromos
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromos.git
+[submodule "dependencies/parsers/lammps"]
+ path = dependencies/parsers/lammps
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps.git
+[submodule "dependencies/parsers/openkim"]
+ path = dependencies/parsers/openkim
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-openkim.git
+[submodule "dependencies/parsers/tinker"]
+ path = dependencies/parsers/tinker
+ url = https://gitlab.mpcdf.mpg.de/nomad-lab/parser-tinker.git
diff --git a/.python-version b/.python-version
index cff2619cfb..bec3a35ee8 100644
--- a/.python-version
+++ b/.python-version
@@ -1 +1 @@
-3.6.9
+system
diff --git a/Dockerfile b/Dockerfile
index 7bbf82b123..7b2271ad8e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,8 +19,10 @@
# The dockerfile is multistaged to use a fat, more convinient build image and
# copy only necessities to a slim final image
-# We use slim for the final image
-FROM python:3.6-slim as final
+# We use stretch instead of slim to allow compoilation of some dependencies. We
+# do not bother to have an additional copy to a final slim image, because the space
+# savings are minimal
+FROM python:3.7-stretch as final
# First built the GUI in a gui build image
FROM node:latest as gui_build
@@ -32,11 +34,15 @@ COPY gui/yarn.lock /app/yarn.lock
RUN yarn
COPY gui /app
RUN yarn run build
-# RUN yarn run --silent react-docgen src/components --pretty > react-docgen.out
# Second, build all python stuff in a python build image
-FROM python:3.6-stretch as build
-RUN mkdir /install
+FROM final
+RUN mkdir /app
+
+# Install linux package dependencies
+RUN apt-get update
+RUN apt-get install -y --no-install-recommends libgomp1
+RUN apt-get install -y libmagic-dev curl vim make cmake swig libnetcdf-dev
# Install some specific dependencies necessary for the build process
RUN pip install --upgrade pip
@@ -54,55 +60,33 @@ RUN pip install scikit-learn==0.20.2
RUN pip install ase==3.19.0
RUN pip install Pint
RUN pip install matid
-RUN pip install mdtraj==1.9.1
-RUN pip install mdanalysis==0.16.2
+RUN pip install mdtraj
+RUN pip install mdanalysis
-# Make will be necessary to build the docs with sphynx
-RUN apt-get update && apt-get install -y make
-RUN apt-get update && apt-get install -y vim
+# Install pymolfile (required by some parsers)
+RUN git clone -b nomad-fair https://gitlab.mpcdf.mpg.de/nomad-lab/pymolfile.git
+WORKDIR /pymolfile/
+RUN python3 setup.py install
+RUN rm -rf /pymolfile
# Copy files and install nomad@FAIRDI
-WORKDIR /install
-COPY . /install
+WORKDIR /app
+COPY . /app
RUN python setup.py compile
RUN pip install .[all]
RUN python setup.py sdist
-WORKDIR /install/docs
-# COPY --from=gui_build /app/react-docgen.out /install/docs
-RUN make html
-RUN \
- find /usr/local/lib/python3.6/ -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + && \
- find /usr/local/lib/python3.6/ -name 'test' -exec rm -r '{}' + && \
- find /usr/local/lib/python3.6/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
-# Third, create a slim final image
-FROM final
-
-RUN apt-get update && apt-get install -y --no-install-recommends libgomp1 && apt-get install -y libmagic-dev curl
+WORKDIR /app/docs
+RUN make html
-# copy the sources for tests, coverage, qa, etc.
-COPY . /app
+# Remove unnessesary files
WORKDIR /app
-# transfer installed packages from dependency stage
-COPY --from=build /usr/local/lib/python3.6/site-packages /usr/local/lib/python3.6/site-packages
-RUN echo "copy 1"
-# copy the meta-info, since it files are loaded via relative paths. TODO that should change.
-COPY --from=build /install/dependencies/nomad-meta-info /app/dependencies/nomad-meta-info
-RUN echo "copy 2"
-# copy the documentation, its files will be served by the API
-COPY --from=build /install/docs/.build /app/docs/.build
-RUN echo "copy 3"
-# copy the source distribution, its files will be served by the API
-COPY --from=build /install/dist /app/dist
-RUN echo "copy 4"
-# copy the nomad command
-COPY --from=build /usr/local/bin/nomad /usr/bin/nomad
-RUN echo "copy 5"
-# copy the gui
-RUN mkdir -p /app/gui
-COPY --from=gui_build /app/build /app/gui/build
-RUN echo "copy 6"
+RUN \
+ find /usr/local/lib/python3.7/ -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + && \
+ find /usr/local/lib/python3.7/ -name 'test' -exec rm -r '{}' + && \
+ find /usr/local/lib/python3.7/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
+# Setup directories, users, rights
RUN mkdir -p /app/.volumes/fs
RUN useradd -ms /bin/bash nomad
RUN chown -R nomad /app
diff --git a/dependencies/nomad-meta-info b/dependencies/nomad-meta-info
index c424e75671..a2df84b2df 160000
--- a/dependencies/nomad-meta-info
+++ b/dependencies/nomad-meta-info
@@ -1 +1 @@
-Subproject commit c424e75671e8c09c2f29c90ec63feafd0a2a706e
+Subproject commit a2df84b2dfc2c96344e7261580a40d655c904047
diff --git a/dependencies/parsers/amber b/dependencies/parsers/amber
new file mode 160000
index 0000000000..09b52a7494
--- /dev/null
+++ b/dependencies/parsers/amber
@@ -0,0 +1 @@
+Subproject commit 09b52a7494b9655c53bbe3dcab2719823e5f2e27
diff --git a/dependencies/parsers/asap b/dependencies/parsers/asap
new file mode 160000
index 0000000000..dd555aad1c
--- /dev/null
+++ b/dependencies/parsers/asap
@@ -0,0 +1 @@
+Subproject commit dd555aad1ce925b5b56be7e55b6650f959ea5261
diff --git a/dependencies/parsers/charmm b/dependencies/parsers/charmm
new file mode 160000
index 0000000000..dc2b8d5a08
--- /dev/null
+++ b/dependencies/parsers/charmm
@@ -0,0 +1 @@
+Subproject commit dc2b8d5a08fb27e53057f27d9854b22ffee28f06
diff --git a/dependencies/parsers/dftbplus b/dependencies/parsers/dftbplus
new file mode 160000
index 0000000000..c447c6b07d
--- /dev/null
+++ b/dependencies/parsers/dftbplus
@@ -0,0 +1 @@
+Subproject commit c447c6b07d8528210975337571c98096caf26770
diff --git a/dependencies/parsers/fplo b/dependencies/parsers/fplo
new file mode 160000
index 0000000000..e4bd0a1bd7
--- /dev/null
+++ b/dependencies/parsers/fplo
@@ -0,0 +1 @@
+Subproject commit e4bd0a1bd72092de4f41c88ebf843265c162a84c
diff --git a/dependencies/parsers/gamess b/dependencies/parsers/gamess
index 2b49f65218..b830cf96f3 160000
--- a/dependencies/parsers/gamess
+++ b/dependencies/parsers/gamess
@@ -1 +1 @@
-Subproject commit 2b49f652182adb2139f9bc7503c25212c5ad35a7
+Subproject commit b830cf96f325c521c232ce8ccba83073eb5f3bab
diff --git a/dependencies/parsers/gromacs b/dependencies/parsers/gromacs
new file mode 160000
index 0000000000..ae0068cd75
--- /dev/null
+++ b/dependencies/parsers/gromacs
@@ -0,0 +1 @@
+Subproject commit ae0068cd75c1b0f6bb818e8cbd5a6a72fe7722f4
diff --git a/dependencies/parsers/gromos b/dependencies/parsers/gromos
new file mode 160000
index 0000000000..4a74602f7d
--- /dev/null
+++ b/dependencies/parsers/gromos
@@ -0,0 +1 @@
+Subproject commit 4a74602f7dd287da835cf6a64228b5ad53fd09be
diff --git a/dependencies/parsers/lammps b/dependencies/parsers/lammps
new file mode 160000
index 0000000000..433f848030
--- /dev/null
+++ b/dependencies/parsers/lammps
@@ -0,0 +1 @@
+Subproject commit 433f848030759d28bacb780d800877445490da70
diff --git a/dependencies/parsers/mopac b/dependencies/parsers/mopac
new file mode 160000
index 0000000000..aac03d990b
--- /dev/null
+++ b/dependencies/parsers/mopac
@@ -0,0 +1 @@
+Subproject commit aac03d990b7823776c51a1976b2d5a304e4a1cce
diff --git a/dependencies/parsers/namd b/dependencies/parsers/namd
new file mode 160000
index 0000000000..3d225e6858
--- /dev/null
+++ b/dependencies/parsers/namd
@@ -0,0 +1 @@
+Subproject commit 3d225e6858fc449e12c5ca45d9597562011f6589
diff --git a/dependencies/parsers/openkim b/dependencies/parsers/openkim
new file mode 160000
index 0000000000..e38d2615a2
--- /dev/null
+++ b/dependencies/parsers/openkim
@@ -0,0 +1 @@
+Subproject commit e38d2615a243c775a378e47a461c731babebf3e6
diff --git a/dependencies/parsers/tinker b/dependencies/parsers/tinker
new file mode 160000
index 0000000000..f9822b6611
--- /dev/null
+++ b/dependencies/parsers/tinker
@@ -0,0 +1 @@
+Subproject commit f9822b6611dc5c8f816c76405923d4973e797d93
diff --git a/dependencies/python_common b/dependencies/python_common
index 5023497ce1..5c98d3fc34 160000
--- a/dependencies/python_common
+++ b/dependencies/python_common
@@ -1 +1 @@
-Subproject commit 5023497ce1651f41de44cb35e953432d450b29f5
+Subproject commit 5c98d3fc345beb43ecb8c163fb2f1ad9678f45a2
diff --git a/docs/archive.rst b/docs/archive.rst
index 06d321811b..258d09ea58 100644
--- a/docs/archive.rst
+++ b/docs/archive.rst
@@ -7,4 +7,4 @@ Of course, you can access the NOMAD Archive directly via the NOMAD API (see the
and `API reference <api.html>`_). But, it is more effective and convenient to use NOMAD's Python client
library.
-.. automodule:: nomad.client
\ No newline at end of file
+.. automodule:: nomad.client
diff --git a/docs/dev/setup.md b/docs/dev/setup.md
index 31cc96fd98..9bee9630a4 100644
--- a/docs/dev/setup.md
+++ b/docs/dev/setup.md
@@ -38,7 +38,7 @@ cd nomad-FAIR
### C libs
Even though the NOMAD infrastructure is written in python, there is a C library
-required by one of our pyhton dependencies.
+required by one of our python dependencies.
#### libmagic
@@ -52,11 +52,9 @@ brew install libmagic
### Virtual environment
#### pyenv
-The nomad code currently targets python 3.6. If you host machine has 3.7 or later installed,
-you can use [pyenv](https://github.com/pyenv/pyenv) to use python 3.6 in parallel.
-To use 3.7 there is a slight issue about the `enum34` which fails the compilation of the
-`mdtraj` and `mdanalysis` packages. A possible work arround is to uninstall and tham re-install
-`enum34` once the other packages are installed.
+The nomad code currently targets python 3.7. If you host machine has an older version installed,
+you can use [pyenv](https://github.com/pyenv/pyenv) to use python 3.7 in parallel to your
+system's python.
#### virtualenv
We strongly recommend to use *virtualenv* to create a virtual environment. It will allow you
@@ -73,7 +71,7 @@ source .pyenv/bin/activate
If you are a conda user, there is an equivalent, but you have to install pip and the
right python version while creating the environment.
```
-conda create --name nomad_env pip python=3.6
+conda create --name nomad_env pip python=3.7
conda activate nomad_env
```
diff --git a/gui/src/searchQuantities.json b/gui/src/searchQuantities.json
index 15f889e986..b9853c22ba 100644
--- a/gui/src/searchQuantities.json
+++ b/gui/src/searchQuantities.json
@@ -71,17 +71,17 @@
},
"labels.label": {
"name": "labels.label",
- "description": null,
+ "description": "The label as a string",
"many": false
},
"labels.type": {
"name": "labels.type",
- "description": null,
+ "description": "The type of the label",
"many": false
},
"labels.source": {
"name": "labels.source",
- "description": null,
+ "description": "The source that this label was taken from.",
"many": false
},
"optimade.elements": {
@@ -234,16 +234,20 @@
"name": "dft.code_name",
"description": "The name of the used code.",
"many": false,
- "statistic_size": 34,
+ "statistic_size": 46,
"statistic_values": [
"ABINIT",
+ "Amber",
+ "ASAP",
"ATK",
"BAND",
"BigDFT",
"CASTEP",
+ "Charmm",
"CP2K",
"CPMD",
"Crystal",
+ "DFTb plus",
"DL_POLY",
"DMol3",
"elastic",
@@ -251,20 +255,28 @@
"exciting",
"FHI-aims",
"fleur",
+ "fplo",
"GAMESS",
"Gaussian",
"GPAW",
+ "Gromacs",
+ "Gromos",
"gulp",
+ "lammps",
"libAtoms",
"MOLCAS",
+ "MOPAC",
+ "Namd",
"NWChem",
"Octopus",
"ONETEP",
+ "OpenKIM",
"ORCA",
"Phonopy",
"qbox",
"Quantum Espresso",
"Siesta",
+ "TINKER",
"turbomole",
"VASP",
"WIEN2k",
diff --git a/nomad/parsing/__init__.py b/nomad/parsing/__init__.py
index 5ca0195a82..7edbc88cf0 100644
--- a/nomad/parsing/__init__.py
+++ b/nomad/parsing/__init__.py
@@ -464,6 +464,72 @@ parsers = [
name='parsers/onetep', code_name='ONETEP', code_homepage='https://www.onetep.org/', domain='dft',
parser_class_name='onetepparser.OnetepParser',
mainfile_contents_re=r'####### # # ####### ####### ####### ######'
+ ),
+ LegacyParser(
+ name='parsers/openkim', code_name='OpenKIM', domain='dft',
+ parser_class_name='openkimparser.OpenKIMParser',
+ mainfile_contents_re=r'OPENKIM'
+ ),
+ LegacyParser(
+ name='parsers/tinker', code_name='TINKER', domain='dft',
+ parser_class_name='tinkerparser.TinkerParser',
+ mainfile_contents_re=r'TINKER --- Software Tools for Molecular Design'
+ ),
+ LegacyParser(
+ name='parsers/lammps', code_name='lammps', domain='dft',
+ parser_class_name='lammpsparser.LammpsParser',
+ mainfile_contents_re=r'^LAMMPS'
+ ),
+ LegacyParser(
+ name='parsers/amber', code_name='Amber', domain='dft',
+ parser_class_name='amberparser.AMBERParser',
+ mainfile_contents_re=r'\s*Amber\s[0-9]+\s[A-Z]+\s*[0-9]+'
+ ),
+ LegacyParser(
+ name='parsers/gromacs', code_name='Gromacs', domain='dft',
+ parser_class_name='gromacsparser.GROMACSParser',
+ mainfile_contents_re=r'GROMACS - gmx mdrun'
+ ),
+ LegacyParser(
+ name='parsers/gromos', code_name='Gromos', domain='dft',
+ parser_class_name='gromosparser.GromosParser',
+ mainfile_contents_re=r'Bugreports to http://www.gromos.net'
+ ),
+ LegacyParser(
+ name='parsers/namd', code_name='Namd', domain='dft',
+ parser_class_name='namdparser.NamdParser',
+ mainfile_contents_re=r'\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*',
+ mainfile_mime_re=r'text/.*',
+ ),
+ LegacyParser(
+ name='parsers/charmm', code_name='Charmm', domain='dft',
+ parser_class_name='charmmparser.CharmmParser',
+ mainfile_contents_re=r'\s*Chemistry\s*at\s*HARvard\s*Macromolecular\s*Mechanics\s*',
+ mainfile_mime_re=r'text/.*',
+ ),
+ LegacyParser(
+ name='parsers/dftbplus', code_name='DFTb plus', domain='dft',
+ parser_class_name='dftbplusparser.DFTBPlusParser',
+ mainfile_contents_re=r'^ Fermi distribution function\s*',
+ mainfile_mime_re=r'text/.*',
+ ),
+ LegacyParser(
+ name='parsers/asap', code_name='ASAP', domain='dft',
+ parser_class_name='asapparser.AsapParser',
+ mainfile_name_re=r'.*.traj$',
+ mainfile_mime_re=r'application/octet-stream',
+ ),
+ LegacyParser(
+ name='parsers/fplo', code_name='fplo', domain='dft',
+ parser_class_name='fploparser.FploParser',
+ mainfile_contents_re=r'\s*\|\s*FULL-POTENTIAL LOCAL-ORBITAL MINIMUM BASIS BANDSTRUCTURE CODE\s*\|\s*',
+ mainfile_mime_re=r'text/.*',
+ ),
+ LegacyParser(
+ name='parsers/mopac', code_name='MOPAC', domain='dft',
+ parser_class_name='mopacparser.MopacParser',
+ mainfile_contents_re=r'\s*\*\*\s*MOPAC\s*([0-9a-zA-Z]*)\s*\*\*\s*',
+ mainfile_mime_re=r'text/.*',
)
]
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index fe60a55c05..b9782abff6 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -296,6 +296,12 @@ class Calc(Proc):
except Exception as e:
logger.error('could unload processing results', exc_info=e)
+ def _setup_fallback_metadata(self):
+ self._entry_metadata = self.create_metadata()
+ self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
+ self._entry_metadata.last_processing = datetime.utcnow()
+ self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)
+
@process
def process_calc(self):
'''
@@ -309,10 +315,7 @@ class Calc(Proc):
try:
# save preliminary minimum calc metadata in case processing fails
# successful processing will replace it with the actual metadata
- self._entry_metadata = self.create_metadata()
- self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
- self._entry_metadata.last_processing = datetime.utcnow()
- self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)
+ self._setup_fallback_metadata()
if len(self._entry_metadata.files) >= config.auxfile_cutoff:
self.warning(
@@ -334,6 +337,9 @@ class Calc(Proc):
# in case of failure, index a minimum set of metadata and mark
# processing failure
try:
+ if self._entry_metadata is None:
+ self._setup_fallback_metadata()
+
self._entry_metadata.processed = False
self.apply_entry_metadata(self._entry_metadata)
diff --git a/requirements.txt b/requirements.txt
index 41a323f7e4..b7199b04e6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -31,8 +31,8 @@ matid==0.6.0
python-magic
panedr==0.2
parmed==3.0.0
-mdtraj==1.9.1
-mdanalysis==0.16.2
+mdtraj
+mdanalysis
nomadcore
# [infrastructure]
diff --git a/setup.py b/setup.py
index c16a3817d2..07358a0ad4 100644
--- a/setup.py
+++ b/setup.py
@@ -250,7 +250,7 @@ def setup_kwargs():
if __name__ == '__main__':
if len(sys.argv) == 2 and sys.argv[1] == 'compile':
kwargs = compile_dependency_setup_kwargs(['dependencies'], **setup_kwargs())
- kwargs['packages'].remove('nomadcore.md_data_access')
+ # kwargs['packages'].remove('nomadcore.md_data_access')
with open('setup.json', 'wt') as f:
json.dump(kwargs, f, indent=2)
sys.exit(0)
--
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