search

nomad-coe / nomad

NOMAD lets you manage and share your materials science data in a way that makes it truly useful to you, your group, and the community.
https://nomad-lab.eu
Apache License 2.0
64 stars 14 forks source link

JOSS Review: importing `ArchiveQuery` gives `FileNotFoundError` #68

Closed sgbaird closed 11 months ago

sgbaird commented 1 year ago

Running on: Ubuntu 20.04.6 LTS (GNU/Linux 5.10.16.3-microsoft-standard-WSL2 x86_64)

(nomad-pypi) sgbaird@Dell-G7:~$ python
Python 3.9.16 (main, Mar  8 2023, 14:00:05)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from nomad.client.archive import ArchiveQuery
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/client/__init__.py", line 19, in <module>
    from .archive import ArchiveQuery
  File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/client/archive.py", line 28, in <module>
    from nomad import config, metainfo as mi
  File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/__init__.py", line 95, in <module>
    north = NORTH()
  File "pydantic/main.py", line 340, in pydantic.main.BaseModel.__init__
  File "pydantic/main.py", line 1077, in pydantic.main.validate_model
  File "pydantic/fields.py", line 867, in pydantic.fields.ModelField.validate
  File "pydantic/fields.py", line 1148, in pydantic.fields.ModelField._apply_validators
  File "pydantic/class_validators.py", line 285, in pydantic.class_validators._generic_validator_cls.lambda4
  File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/models.py", line 272, in load_tools
    with open(path, 'rt') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/../../dependencies/nomad-remote-tools-hub/tools.json'
Details

(base) sgbaird@Dell-G7:~$ conda create -n nomad-pypi python==3.9.* Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/sgbaird/miniconda3/envs/nomad-pypi added / updated specs: - python=3.9 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu ca-certificates pkgs/main/linux-64::ca-certificates-2023.01.10-h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 openssl pkgs/main/linux-64::openssl-1.1.1t-h7f8727e_0 pip pkgs/main/linux-64::pip-23.0.1-py39h06a4308_0 python pkgs/main/linux-64::python-3.9.16-h7a1cb2a_2 readline pkgs/main/linux-64::readline-8.2-h5eee18b_0 setuptools pkgs/main/linux-64::setuptools-66.0.0-py39h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 tzdata pkgs/main/noarch::tzdata-2023c-h04d1e81_0 wheel pkgs/main/linux-64::wheel-0.38.4-py39h06a4308_0 xz pkgs/main/linux-64::xz-5.4.2-h5eee18b_0 zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0 Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate nomad-pypi # # To deactivate an active environment, use # # $ conda deactivate (base) sgbaird@Dell-G7:~$ conda activate nomad-pypi (nomad-pypi) sgbaird@Dell-G7:~$ pip install nomad-lab Collecting nomad-lab Downloading nomad-lab-1.1.10.tar.gz (20.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 20.8/20.8 MB 4.1 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Installing backend dependencies ... done Preparing metadata (pyproject.toml) ... done [SKIPPING MOST INSTALLATION INFO DUE TO CHARACTER LENGTH LIMIT] Successfully installed Markdown-3.4.3 SecretStorage-3.3.3 astroid-2.11.7 asttokens-2.2.1 atomicwrites-1.4.1 bleach-6.0.0 build-0.10.0 colorama-0.4.6 coverage-7.2.6 devtools-0.8.0 dill-0.3.6 essential-generators-1.0 executing-0.10.0 ghp-import-2.1.0 isort-5.12.0 jaraco.classes-3.2.3 jeepney-0.8.0 keyring-23.13.1 lazy-object-proxy-1.9.0 mccabe-0.7.0 mergedeep-1.3.4 mkdocs-1.2.3 mkdocs-macros-plugin-0.6.3 mkdocs-material-8.1.1 mkdocs-material-extensions-1.0.3 more-itertools-9.1.0 mypy-1.3.0 mypy-extensions-1.0.0 names-0.3.0 pip-tools-6.13.0 pkginfo-1.9.6 platformdirs-3.5.1 pluggy-1.0.0 py-1.11.0 pycodestyle-2.8.0 pylint-2.13.9 pylint-mongoengine-0.4.0 pylint-plugin-utils-0.7 pymdown-extensions-10.0.1 pyproject_hooks-1.0.0 pytest-3.10.0 pytest-cov-2.7.1 pytest-timeout-1.4.2 python-gitlab-2.10.1 pyyaml-env-tag-0.1 readme-renderer-37.3 requests-toolbelt-1.0.0 rope-0.21.0 termcolor-2.3.0 tomli-2.0.1 twine-3.4.2 typed-ast-1.5.4 watchdog-3.0.0 (nomad-pypi) sgbaird@Dell-G7:~$ python Python 3.9.16 (main, Mar 8 2023, 14:00:05) [GCC 11.2.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. >>> from nomad.client.archive import ArchiveQuery Traceback (most recent call last): File "", line 1, in File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/client/__init__.py", line 19, in from .archive import ArchiveQuery File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/client/archive.py", line 28, in from nomad import config, metainfo as mi File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/__init__.py", line 95, in north = NORTH() File "pydantic/main.py", line 340, in pydantic.main.BaseModel.__init__ File "pydantic/main.py", line 1077, in pydantic.main.validate_model File "pydantic/fields.py", line 867, in pydantic.fields.ModelField.validate File "pydantic/fields.py", line 1148, in pydantic.fields.ModelField._apply_validators File "pydantic/class_validators.py", line 285, in pydantic.class_validators._generic_validator_cls.lambda4 File "/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/models.py", line 272, in load_tools with open(path, 'rt') as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/sgbaird/miniconda3/envs/nomad-pypi/lib/python3.9/site-packages/nomad/config/../../dependencies/nomad-remote-tools-hub/tools.json'

markus1978 commented 1 year ago

We are about to remove this file entirely and make it part of the configuration. The problem will be solved, once the new config is merged.

markus1978 commented 11 months ago

We just released nomad-lab==1.2.0 to PyPI. This should solve this issue. Please re-open, if you still run into problems.