From 25ffe4ba74f17a548c5a43f4094968580709b200 Mon Sep 17 00:00:00 2001
From: Theodore Chang <theodore.chang@physik.hu-berlin.de>
Date: Wed, 22 Mar 2023 03:24:28 +0000
Subject: [PATCH] Update some vulnerable and obsolete packages
---
CHANGELOG.md | 45 +++++++++++++++---------------------
nomad/app/v1/routers/auth.py | 2 +-
nomad/files.py | 9 +-------
pyproject.toml | 12 ++++------
requirements-dev.txt | 45 +++++++++++++++++++-----------------
requirements.txt | 39 ++++++++++++++++---------------
tests/conftest.py | 3 ++-
7 files changed, 72 insertions(+), 83 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b84088a737..10a0fd1bd1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,19 +1,7 @@
-## v1.1.6 (2022-12-23)
-### fixed (1 change)
-
-- [Fixed failing plot annotation valiation.](nomad-lab/nomad-FAIR@3cd5d0635566d9882e1c44cd922e113dfbeb1292) ([merge request](nomad-lab/nomad-FAIR!1005))
-
-### feature (1 change)
-
-- [Added a way to define formal models for metainfo annotations.](nomad-lab/nomad-FAIR@6a84b55e17dd5cd41cb5ba571f2451d528dbe6a0) ([merge request](nomad-lab/nomad-FAIR!990))
-
-### added (1 change)
-
-- [Replaced config object with pydantic models.](nomad-lab/nomad-FAIR@b9c1e023d95d14fd337b98a7ac895f505d4715a9) ([merge request](nomad-lab/nomad-FAIR!981))
## 1.1.8 (2023-03-10)
-### Fixed (8 changes)
+### Fixed (9 changes)
- [Fixed a bug in handling UI load errors.](nomad-lab/nomad-FAIR@bc01f359fbd55048fff0c7213ba42ae53451add3) ([merge request](nomad-lab/nomad-FAIR!1143))
- [Add parsers](nomad-lab/nomad-FAIR@b1c177f75cd72dfabaea6137d93375357857b3a6) ([merge request](nomad-lab/nomad-FAIR!1136))
@@ -23,6 +11,7 @@
- [ability to reference to the other uploads properly](nomad-lab/nomad-FAIR@8befc8efe92218aa63a63c562ac8057de54e5ba2) ([merge request](nomad-lab/nomad-FAIR!1070))
- [Added the staging url](nomad-lab/nomad-FAIR@5a0b31a7cff12106a28f0fc02bba7fda764d4708) ([merge request](nomad-lab/nomad-FAIR!1086))
- [Workflow fix](nomad-lab/nomad-FAIR@75170b392d779cf9a27880fd83433c3d47a85b37) ([merge request](nomad-lab/nomad-FAIR!1113))
+- [Fixed the availability of the beta/test snack in the UI.](nomad-lab/nomad-FAIR@a3f29510858bf6ba6056f1c52af177e70d24eacc) ([merge request](nomad-lab/nomad-FAIR!1134))
### Added (10 changes)
@@ -43,13 +32,9 @@
- [Upgraded nomad-lab to Python 3.9 and bumped a few dependency version.](nomad-lab/nomad-FAIR@5cb6d4a46c5ac6c4809e66cc288dee32a68721de) ([merge request](nomad-lab/nomad-FAIR!1125))
- [Changed the config to use Pydantic models for UI aspects.](nomad-lab/nomad-FAIR@de1ed6ffb8db168f6f7ae4f6e9addd59879f552f) ([merge request](nomad-lab/nomad-FAIR!1104))
-### Fixed. (1 change)
-
-- [Fixed the availability of the beta/test snack in the UI.](nomad-lab/nomad-FAIR@a3f29510858bf6ba6056f1c52af177e70d24eacc) ([merge request](nomad-lab/nomad-FAIR!1134))
-
## 1.1.7 (2023-02-20)
-### Added (17 changes)
+### Added (18 changes)
- [Added a config switch to enable disable north tools.](nomad-lab/nomad-FAIR@37d9b6db1e8044ae28476488e8c3ae1896e149ad) ([merge request](nomad-lab/nomad-FAIR!1099))
- [Refactor NORTH and Jupyterhub deployment. Add a new north API endpoint. Mount...](nomad-lab/nomad-FAIR@b0e28fa7fd3f47fcd538f33bd84bad659ee6549a) ([merge request](nomad-lab/nomad-FAIR!996))
@@ -68,8 +53,9 @@
- [Added a automatically generated changelog to our git.](nomad-lab/nomad-FAIR@fe795eff97145e0e28d61ca840cbb3069217d24a) ([merge request](nomad-lab/nomad-FAIR!1016))
- [Added a glossary to the documentation.](nomad-lab/nomad-FAIR@aa42834ed51b3d231a8edc58b00ea1f2dddc21f5) ([merge request](nomad-lab/nomad-FAIR!1024))
- [Added dropdown list to select from sections.](nomad-lab/nomad-FAIR@a332abed1318f60078463e2ee71ae68b2086ef1a) ([merge request](nomad-lab/nomad-FAIR!992))
+- [Implement extended matching of h5 files.](nomad-lab/nomad-FAIR@96372aa26a0675a0bbae99b8e5059f5e0f1a5f3a) ([merge request](nomad-lab/nomad-FAIR!1023))
-### Fixed (16 changes)
+### Fixed (18 changes)
- [Fixed wrong property inheritance base section order in UI metainfo.](nomad-lab/nomad-FAIR@9cbd6d9c37d21f06cf9fc3f5d9fbde746d7873b3) ([merge request](nomad-lab/nomad-FAIR!1098))
- [Fixed the build-in schema entry create to use the right definitions.](nomad-lab/nomad-FAIR@8db7bb1be8ab502f4aef178107f50d27297123a2) ([merge request](nomad-lab/nomad-FAIR!1095))
@@ -87,21 +73,28 @@
- [Fixed the README batches and changed pipeline to push tags to github.](nomad-lab/nomad-FAIR@8c42e102387b2d0c5f0a55fd368b266306b705f1) ([merge request](nomad-lab/nomad-FAIR!1057))
- [Fixed issue with optimade filter menu performing premature API calls.](nomad-lab/nomad-FAIR@7c4ad789591ce6a30cb6236825798e440711ce21) ([merge request](nomad-lab/nomad-FAIR!1048))
- [Fixed generation of duplicated subsections on updating an entry that triggers tabular parser](nomad-lab/nomad-FAIR@e91176fe2a197f9d8450e29dc8b599f669ecad1d) ([merge request](nomad-lab/nomad-FAIR!1033))
+- [Fix the select feature of the Datatable component](nomad-lab/nomad-FAIR@8fd52ed7bccc14c13c6c83d90e3a931df3cf9d25) ([merge request](nomad-lab/nomad-FAIR!1060))
+- [Datafile quantity containing `tabular_parser` annotation can be referenced](nomad-lab/nomad-FAIR@8ad191bf7f37b9c1286200127f6f5b2f0cf3701a) ([merge request](nomad-lab/nomad-FAIR!1017))
### Changed (2 changes)
- [Small UX changes to the upload interface.](nomad-lab/nomad-FAIR@5e18b0e12d4ce4d608a5cd68efbeb02ee2d51f04) ([merge request](nomad-lab/nomad-FAIR!1085))
- [Refactored the overview UI code to optimise loading performance.](nomad-lab/nomad-FAIR@161051655e8b9406197247ed943e027fdd13771b) ([merge request](nomad-lab/nomad-FAIR!1075))
-### fixed (2 changes)
+### Feature (1 change)
-- [Fix the select feature of the Datatable component](nomad-lab/nomad-FAIR@8fd52ed7bccc14c13c6c83d90e3a931df3cf9d25) ([merge request](nomad-lab/nomad-FAIR!1060))
-- [Datafile quantity containing `tabular_parser` annotation can be referenced](nomad-lab/nomad-FAIR@8ad191bf7f37b9c1286200127f6f5b2f0cf3701a) ([merge request](nomad-lab/nomad-FAIR!1017))
+- [Adds an ELN schema that allows to create entries that clone data from a labfolder project.](nomad-lab/nomad-FAIR@166a8aaa65f63bf368453365689e1dab577fc94d) ([merge request](nomad-lab/nomad-FAIR!948))
-### added (1 change)
+## 1.1.6 (2022-12-23)
-- [Implement extended matching of h5 files.](nomad-lab/nomad-FAIR@96372aa26a0675a0bbae99b8e5059f5e0f1a5f3a) ([merge request](nomad-lab/nomad-FAIR!1023))
+### Fixed (1 change)
-### feature (1 change)
+- [Fixed failing plot annotation valiation.](nomad-lab/nomad-FAIR@3cd5d0635566d9882e1c44cd922e113dfbeb1292) ([merge request](nomad-lab/nomad-FAIR!1005))
-- [Adds an ELN schema that allows to create entries that clone data from a labfolder project.](nomad-lab/nomad-FAIR@166a8aaa65f63bf368453365689e1dab577fc94d) ([merge request](nomad-lab/nomad-FAIR!948))
+### Feature (1 change)
+
+- [Added a way to define formal models for metainfo annotations.](nomad-lab/nomad-FAIR@6a84b55e17dd5cd41cb5ba571f2451d528dbe6a0) ([merge request](nomad-lab/nomad-FAIR!990))
+
+### Added (1 change)
+
+- [Replaced config object with pydantic models.](nomad-lab/nomad-FAIR@b9c1e023d95d14fd337b98a7ac895f505d4715a9) ([merge request](nomad-lab/nomad-FAIR!981))
diff --git a/nomad/app/v1/routers/auth.py b/nomad/app/v1/routers/auth.py
index 0cb6910761..f5c88d6e6a 100644
--- a/nomad/app/v1/routers/auth.py
+++ b/nomad/app/v1/routers/auth.py
@@ -337,7 +337,7 @@ async def get_signature_token(user: User = Depends(create_user_dependency())):
expires_at = datetime.datetime.utcnow() + datetime.timedelta(seconds=10)
signature_token = jwt.encode(
dict(user=user.user_id, exp=expires_at),
- config.services.api_secret, 'HS256').decode('utf-8')
+ config.services.api_secret, 'HS256')
return {'signature_token': signature_token}
diff --git a/nomad/files.py b/nomad/files.py
index 0059926c4e..01446aad78 100644
--- a/nomad/files.py
+++ b/nomad/files.py
@@ -44,7 +44,6 @@ original mainfile, and vice versa.
'''
from abc import ABCMeta
-import sys
from typing import IO, Set, Dict, Iterable, Iterator, List, Tuple, Any, NamedTuple
from functools import lru_cache
from pydantic import BaseModel
@@ -59,18 +58,12 @@ import io
import json
import yaml
import magic
+import zipfile
from nomad import config, utils, datamodel
from nomad.config.models import BundleImportSettings, BundleExportSettings
from nomad.archive import write_archive, read_archive, ArchiveReader
-# TODO this should become obsolete, once we are going beyong python 3.6. For now
-# python 3.6's zipfile does not allow to seek/tell within a file-like opened from a
-# file in a zipfile.
-if sys.version_info >= (3, 7):
- import zipfile
-else:
- import zipfile37 as zipfile
decompress_file_extensions = ('.zip', '.tgz', '.gz', '.tar.gz', '.tar.bz2', '.tar')
bundle_info_filename = 'bundle_info.json'
diff --git a/pyproject.toml b/pyproject.toml
index 2f39ca01aa..e8040fc41a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ dependencies = [
'orjson==3.6.0',
'click>=7.1.2',
'requests==2.28.2',
- 'pytz==2021.1',
+ 'pytz==2022.7.1',
'aniso8601==7.0.0',
'ase==3.19.0',
'python-keycloak==0.26.1',
@@ -28,7 +28,7 @@ dependencies = [
'pydantic==1.10.5',
'jmespath==0.10.0',
'h5grove>=1.0.0',
- 'httpx==0.22.0',
+ 'httpx==0.23.3',
'memoization==0.4.0',
'rfc3161ng==2.1.3',
'lxml~=4.6',
@@ -66,7 +66,7 @@ infrastructure = [
'structlog',
'elasticsearch==7.17.1',
'msgpack',
- 'celery[redis]==4.4.7',
+ 'celery[redis]==5.2.7',
'asgiref~=3.5',
'mongoengine>=0.20',
'pymongo==3.12.1',
@@ -79,14 +79,13 @@ infrastructure = [
'bagit==1.8.1',
'bcrypt==3.2.0',
'filelock==3.3.1',
- 'pyjwt[crypto]==1.7.1',
+ 'pyjwt[crypto]==2.6.0',
'cryptography',
'jsonschema[format]==4.1.2',
'runstats==2.0.0',
'tabulate==0.8.9',
'bs4==0.0.1',
'html5lib==1.1',
- 'zipfile37==0.1.3',
'basicauth==0.4.1',
'inflection==0.5.1',
'unidecode==1.3.2',
@@ -99,9 +98,8 @@ infrastructure = [
'python-multipart==0.0.5',
'jupyterhub==1.4.2',
'dockerspawner==12.1.0',
- 'oauthenticator==14.2.0',
+ 'oauthenticator==15.1.0',
'validators==0.18.2',
- 'aiofiles==0.8.0',
'joblib>=1.1.0',
'importlib-metadata~=4.13.0' # Needed because of https://github.com/python/importlib_metadata/issues/411
]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index b44223e29c..a21d7fb8ad 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -4,10 +4,9 @@
#
# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt dependencies/matid/pyproject.toml dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/atomistic/pyproject.toml dependencies/parsers/database/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml dependencies/parsers/electronic/pyproject.toml dependencies/parsers/nexus/pyproject.toml dependencies/parsers/workflow/pyproject.toml pyproject.toml requirements.txt
#
-aiofiles==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
alabaster==0.7.12 # via -r requirements.txt, sphinx
alembic==1.9.1 # via -r requirements.txt, jupyterhub
-amqp==2.6.1 # via -r requirements.txt, kombu
+amqp==5.1.1 # via -r requirements.txt, kombu
aniso8601==7.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
anyio==3.6.2 # via -r requirements.txt, httpcore, jupyter-server, starlette, watchfiles
appnope==0.1.3 # via -r requirements.txt, ipykernel, ipython
@@ -38,18 +37,21 @@ bleach==5.0.1 # via -r requirements.txt, nbconvert, readme-renderer
bs4==0.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
build==0.9.0 # via nomad-lab (pyproject.toml), pip-tools
cachetools==4.2.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-celery[redis]==4.4.7 # via -r requirements.txt, nomad-lab (pyproject.toml)
+celery[redis]==5.2.7 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2022.12.7 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via -r requirements.txt, jupyterhub
cffi==1.15.1 # via -r requirements.txt, argon2-cffi-bindings, bcrypt, cryptography
cftime==1.6.2 # via -r requirements.txt, netcdf4
-charset-normalizer==2.0.12 # via -r requirements.txt, httpx, requests
-click==8.1.3 # via -r requirements.txt, asr, flask, mkdocs, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pip-tools, uvicorn
+charset-normalizer==2.0.12 # via -r requirements.txt, requests
+click==8.1.3 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, flask, mkdocs, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pip-tools, uvicorn
+click-didyoumean==0.3.0 # via -r requirements.txt, celery
+click-plugins==1.1.1 # via -r requirements.txt, celery
+click-repl==0.2.0 # via -r requirements.txt, celery
cloudpickle==2.2.0 # via -r requirements.txt, dask
colorama==0.4.6 # via twine
commonmark==0.9.1 # via -r requirements.txt, recommonmark
coverage==6.5.0 # via pytest-cov
-cryptography==39.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng
+cryptography==39.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng, secretstorage
cycler==0.11.0 # via -r requirements.txt, matplotlib
dask[array]==2022.2.0 # via -r requirements.txt, hyperspy
debugpy==1.6.5 # via -r requirements.txt, ipykernel
@@ -88,16 +90,16 @@ gitpython==3.1.24 # via -r requirements.txt, nomad-lab (pyproject.toml)
greenlet==2.0.1 # via -r requirements.txt, sqlalchemy
griddataformats==0.7.0 # via -r requirements.txt, mdanalysis
gsd==2.7.0 # via -r requirements.txt, mdanalysis
-h11==0.12.0 # via -r requirements.txt, httpcore, uvicorn
+h11==0.14.0 # via -r requirements.txt, httpcore, uvicorn
h5grove==1.2.0 # via -r requirements.txt, jupyterlab-h5web, nomad-lab (pyproject.toml)
h5py==3.6.0 # via -r requirements.txt, electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, h5py-wrapper, hyperspy, jupyterlab-h5web, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), phonopy, pyscf, workflowparsers (dependencies/parsers/workflow/pyproject.toml)
h5py-wrapper==1.1.0 # via -r requirements.txt, hdfdict
hdfdict @ git+https://github.com/shabihsherjeel/hdfdict@f48a586 # via -r requirements.txt, nexusutils (dependencies/parsers/nexus/pyproject.toml)
hjson==3.0.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
html5lib==1.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-httpcore==0.14.7 # via -r requirements.txt, httpx
+httpcore==0.16.3 # via -r requirements.txt, httpx
httptools==0.5.0 # via -r requirements.txt, uvicorn
-httpx==0.22.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+httpx==0.23.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
hyperspy==1.7.3 # via -r requirements.txt, nexusutils (dependencies/parsers/nexus/pyproject.toml)
idna==3.4 # via -r requirements.txt, anyio, email-validator, jsonschema, requests, rfc3986
imageio==2.24.0 # via -r requirements.txt, hyperspy, scikit-image
@@ -113,11 +115,12 @@ isort==4.3.21 # via pylint
itsdangerous==2.0.1 # via -r requirements.txt, flask, nomad-lab (pyproject.toml)
jaraco-classes==3.2.3 # via keyring
jedi==0.18.2 # via -r requirements.txt, ipython
+jeepney==0.8.0 # via keyring, secretstorage
jinja2==3.0.3 # via -r requirements.txt, flask, hyperspy, jupyter-server, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, nbconvert, nomad-lab (pyproject.toml), sphinx
jmespath==0.10.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
joblib==1.1.0 # via -r requirements.txt, mdanalysis, nomad-lab (pyproject.toml), scikit-learn
jsonpointer==2.3 # via -r requirements.txt, jsonschema
-jsonschema[format]==4.1.2 # via -r requirements.txt, jupyter-telemetry, nbformat, nomad-lab (pyproject.toml)
+jsonschema[format]==4.1.2 # via -r requirements.txt, jupyter-telemetry, nbformat, nomad-lab (pyproject.toml), oauthenticator
jupyter-client==7.4.8 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-server, nbclient
jupyter-core==4.12.0 # via -r requirements.txt, jupyter-client, jupyter-server, nbclient, nbconvert, nbformat
jupyter-server==1.23.4 # via -r requirements.txt, jupyterlab-h5web
@@ -127,7 +130,7 @@ jupyterlab-h5web==6.5.0 # via -r requirements.txt, nexusutils (dependencies/pa
jupyterlab-pygments==0.2.2 # via -r requirements.txt, nbconvert
keyring==23.11.0 # via twine
kiwisolver==1.4.4 # via -r requirements.txt, matplotlib
-kombu==4.6.11 # via -r requirements.txt, celery
+kombu==5.2.4 # via -r requirements.txt, celery
lark==1.1.5 # via -r requirements.txt, optimade
latexcodec==2.0.1 # via -r requirements.txt, pybtex
lazy-object-proxy==1.9.0 # via astroid
@@ -154,7 +157,7 @@ mmtf-python==1.1.3 # via -r requirements.txt, mdanalysis
mongoengine==0.25.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mongomock==4.1.2 # via -r requirements.txt, optimade
monty==2022.9.9 # via -r requirements.txt, emmet-core, mp-api, pymatgen
-more-itertools==9.0.0 # via pytest
+more-itertools==9.0.0 # via jaraco-classes, pytest
mp-api==0.30.10 # via -r requirements.txt, pymatgen
mpmath==1.2.1 # via -r requirements.txt, sympy
mrcfile==1.4.3 # via -r requirements.txt, griddataformats
@@ -174,7 +177,7 @@ numba==0.56.4 # via -r requirements.txt, hyperspy, sparse
numcodecs==0.10.2 # via -r requirements.txt, zarr
numexpr==2.8.4 # via -r requirements.txt, hyperspy
numpy==1.21.6 # via -r requirements.txt, ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
-oauthenticator==14.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via -r requirements.txt, jupyterhub
openpyxl==3.0.9 # via -r requirements.txt, nomad-lab (pyproject.toml)
optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -202,7 +205,7 @@ plotly==5.11.0 # via -r requirements.txt, asr, pymatgen
pluggy==1.0.0 # via pytest
prettytable==3.6.0 # via -r requirements.txt, hyperspy
prometheus-client==0.15.0 # via -r requirements.txt, jupyter-server, jupyterhub
-prompt-toolkit==3.0.36 # via -r requirements.txt, ipython
+prompt-toolkit==3.0.36 # via -r requirements.txt, click-repl, ipython
psutil==5.9.4 # via -r requirements.txt, ipykernel, ipyparallel
ptyprocess==0.7.0 # via -r requirements.txt, pexpect, terminado
py==1.11.0 # via pytest
@@ -213,7 +216,7 @@ pycodestyle==2.8.0 # via nexusutils (dependencies/parsers/nexus/pyproject
pycparser==2.21 # via -r requirements.txt, cffi
pydantic==1.10.5 # via -r requirements.txt, emmet-core, fastapi, nomad-lab (pyproject.toml), optimade
pygments==2.14.0 # via -r requirements.txt, ipython, mkdocs-material, nbconvert, readme-renderer, sphinx
-pyjwt[crypto]==1.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+pyjwt[crypto]==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
pylint==2.13.9 # via nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pylint-mongoengine, pylint-plugin-utils
pylint-mongoengine==0.4.0 # via nomad-lab (pyproject.toml)
pylint-plugin-utils==0.7 # via nomad-lab (pyproject.toml), pylint-mongoengine
@@ -237,7 +240,7 @@ python-keycloak==0.26.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-logstash==0.4.6 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-magic==0.4.24 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-multipart==0.0.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pytz==2021.1 # via -r requirements.txt, babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pandas
+pytz==2022.7.1 # via -r requirements.txt, babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pandas
pywavelets==1.3.0 # via -r requirements.txt, scikit-image
pyyaml==6.0 # via -r requirements.txt, dask, hdfdict, hyperspy, mkdocs, mkdocs-macros-plugin, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), phonopy, pybtex, pyyaml-env-tag, uvicorn
pyyaml-env-tag==0.1 # via mkdocs
@@ -246,7 +249,7 @@ rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
readme-renderer==37.3 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
redis==4.4.2 # via -r requirements.txt, celery
-requests==2.28.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), optimade, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine
+requests==2.28.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), oauthenticator, optimade, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine
requests-toolbelt==0.10.1 # via python-gitlab, twine
rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via -r requirements.txt, jsonschema
@@ -254,15 +257,16 @@ rfc3986[idna2008]==1.5.0 # via -r requirements.txt, httpx, twine
rfc3987==1.3.8 # via -r requirements.txt, jsonschema
rope==0.21.0 # via nomad-lab (pyproject.toml)
rsa==4.9 # via -r requirements.txt, python-jose
-ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, pymatgen
+ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, oauthenticator, pymatgen
ruamel-yaml-clib==0.2.7 # via -r requirements.txt, ruamel-yaml
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via -r requirements.txt, hyperspy
scikit-learn==1.0.2 # via -r requirements.txt, matid (dependencies/matid/pyproject.toml)
scipy==1.7.1 # via -r requirements.txt, ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
+secretstorage==3.3.3 # via keyring
send2trash==1.8.0 # via -r requirements.txt, jupyter-server
sentinels==1.0.0 # via -r requirements.txt, mongomock
-six==1.16.0 # via -r requirements.txt, asttokens, astunparse, basicauth, bcrypt, bleach, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, pytest, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
+six==1.16.0 # via -r requirements.txt, asttokens, astunparse, basicauth, bcrypt, bleach, click-repl, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, pytest, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
smmap==5.0.0 # via -r requirements.txt, gitdb
sniffio==1.3.0 # via -r requirements.txt, anyio, httpcore, httpx
snowballstemmer==2.2.0 # via -r requirements.txt, sphinx
@@ -307,7 +311,7 @@ urllib3==1.26.14 # via -r requirements.txt, docker, elasticsearch, requ
uvicorn[standard]==0.20.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
uvloop==0.17.0 # via -r requirements.txt, uvicorn
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-vine==1.3.0 # via -r requirements.txt, amqp, celery
+vine==5.0.0 # via -r requirements.txt, amqp, celery, kombu
watchdog==2.1.9 # via mkdocs
watchfiles==0.18.1 # via -r requirements.txt, uvicorn
wcwidth==0.2.5 # via -r requirements.txt, prettytable, prompt-toolkit
@@ -321,7 +325,6 @@ wrapt==1.12.1 # via -r requirements.txt, astroid, nomad-lab (pyproje
xarray==0.20.2 # via -r requirements.txt, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
xrdtools==0.1.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
zarr==2.12.0 # via -r requirements.txt, hyperspy
-zipfile37==0.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
zipp==3.11.0 # via -r requirements.txt, importlib-metadata
zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
diff --git a/requirements.txt b/requirements.txt
index 46e3dda812..892cb1a622 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,10 +4,9 @@
#
# pip-compile --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/matid/pyproject.toml dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/atomistic/pyproject.toml dependencies/parsers/database/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml dependencies/parsers/electronic/pyproject.toml dependencies/parsers/nexus/pyproject.toml dependencies/parsers/workflow/pyproject.toml pyproject.toml
#
-aiofiles==0.8.0 # via nomad-lab (pyproject.toml)
alabaster==0.7.12 # via sphinx
alembic==1.9.1 # via jupyterhub
-amqp==2.6.1 # via kombu
+amqp==5.1.1 # via kombu
aniso8601==7.0.0 # via nomad-lab (pyproject.toml)
anyio==3.6.2 # via httpcore, jupyter-server, starlette, watchfiles
appnope==0.1.3 # via ipykernel, ipython
@@ -34,13 +33,16 @@ bitarray==2.3.5 # via nomad-dos-fingerprints (dependencies/nomad-dos-f
bleach==5.0.1 # via nbconvert
bs4==0.0.1 # via nomad-lab (pyproject.toml)
cachetools==4.2.4 # via nomad-lab (pyproject.toml)
-celery[redis]==4.4.7 # via nomad-lab (pyproject.toml)
+celery[redis]==5.2.7 # via nomad-lab (pyproject.toml)
certifi==2022.12.7 # via elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via jupyterhub
cffi==1.15.1 # via argon2-cffi-bindings, bcrypt, cryptography
cftime==1.6.2 # via netcdf4
-charset-normalizer==2.0.12 # via httpx, requests
-click==8.1.3 # via asr, flask, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), uvicorn
+charset-normalizer==2.0.12 # via requests
+click==8.1.3 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), uvicorn
+click-didyoumean==0.3.0 # via celery
+click-plugins==1.1.1 # via celery
+click-repl==0.2.0 # via celery
cloudpickle==2.2.0 # via dask
commonmark==0.9.1 # via recommonmark
cryptography==39.0.0 # via nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng
@@ -78,16 +80,16 @@ gitpython==3.1.24 # via nomad-lab (pyproject.toml)
greenlet==2.0.1 # via sqlalchemy
griddataformats==0.7.0 # via mdanalysis
gsd==2.7.0 # via mdanalysis
-h11==0.12.0 # via httpcore, uvicorn
+h11==0.14.0 # via httpcore, uvicorn
h5grove==1.2.0 # via jupyterlab-h5web, nomad-lab (pyproject.toml)
h5py==3.6.0 # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, h5py-wrapper, hyperspy, jupyterlab-h5web, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), phonopy, pyscf, workflowparsers (dependencies/parsers/workflow/pyproject.toml)
h5py-wrapper==1.1.0 # via hdfdict
hdfdict @ git+https://github.com/shabihsherjeel/hdfdict@f48a586 # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
hjson==3.0.2 # via nomad-lab (pyproject.toml)
html5lib==1.1 # via nomad-lab (pyproject.toml)
-httpcore==0.14.7 # via httpx
+httpcore==0.16.3 # via httpx
httptools==0.5.0 # via uvicorn
-httpx==0.22.0 # via nomad-lab (pyproject.toml)
+httpx==0.23.3 # via nomad-lab (pyproject.toml)
hyperspy==1.7.3 # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
idna==3.4 # via anyio, email-validator, jsonschema, requests, rfc3986
imageio==2.24.0 # via hyperspy, scikit-image
@@ -105,7 +107,7 @@ jinja2==3.0.3 # via flask, hyperspy, jupyter-server, jupyterhub, nbc
jmespath==0.10.0 # via nomad-lab (pyproject.toml)
joblib==1.1.0 # via mdanalysis, nomad-lab (pyproject.toml), scikit-learn
jsonpointer==2.3 # via jsonschema
-jsonschema[format]==4.1.2 # via jupyter-telemetry, nbformat, nomad-lab (pyproject.toml)
+jsonschema[format]==4.1.2 # via jupyter-telemetry, nbformat, nomad-lab (pyproject.toml), oauthenticator
jupyter-client==7.4.8 # via ipykernel, ipyparallel, jupyter-server, nbclient
jupyter-core==4.12.0 # via jupyter-client, jupyter-server, nbclient, nbconvert, nbformat
jupyter-server==1.23.4 # via jupyterlab-h5web
@@ -114,7 +116,7 @@ jupyterhub==1.4.2 # via dockerspawner, nomad-lab (pyproject.toml), oauth
jupyterlab-h5web==6.5.0 # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
jupyterlab-pygments==0.2.2 # via nbconvert
kiwisolver==1.4.4 # via matplotlib
-kombu==4.6.11 # via celery
+kombu==5.2.4 # via celery
lark==1.1.5 # via optimade
latexcodec==2.0.1 # via pybtex
llvmlite==0.39.1 # via numba
@@ -149,7 +151,7 @@ numba==0.56.4 # via hyperspy, sparse
numcodecs==0.10.2 # via zarr
numexpr==2.8.4 # via hyperspy
numpy==1.21.6 # via ase, biopython, cftime, dask, griddataformats, gsd, h5grove, h5py, hyperspy, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, xrdtools, zarr
-oauthenticator==14.2.0 # via nomad-lab (pyproject.toml)
+oauthenticator==15.1.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.0.9 # via nomad-lab (pyproject.toml)
optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml)
@@ -172,7 +174,7 @@ pint==0.17 # via hyperspy, nomad-lab (pyproject.toml)
plotly==5.11.0 # via asr, pymatgen
prettytable==3.6.0 # via hyperspy
prometheus-client==0.15.0 # via jupyter-server, jupyterhub
-prompt-toolkit==3.0.36 # via ipython
+prompt-toolkit==3.0.36 # via click-repl, ipython
psutil==5.9.4 # via ipykernel, ipyparallel
ptyprocess==0.7.0 # via pexpect, terminado
pyasn1==0.4.8 # via pyasn1-modules, python-jose, rfc3161ng, rsa
@@ -181,7 +183,7 @@ pybtex==0.24.0 # via emmet-core, pymatgen
pycparser==2.21 # via cffi
pydantic==1.10.5 # via emmet-core, fastapi, nomad-lab (pyproject.toml), optimade
pygments==2.14.0 # via ipython, nbconvert, sphinx
-pyjwt[crypto]==1.7.1 # via nomad-lab (pyproject.toml)
+pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml)
pymatgen==2023.2.28 # via asr, emmet-core, mp-api, nomad-lab (pyproject.toml)
pymongo==3.12.1 # via mongoengine, nomad-lab (pyproject.toml), optimade
pyopenssl==23.0.0 # via certipy
@@ -197,20 +199,20 @@ python-keycloak==0.26.1 # via nomad-lab (pyproject.toml)
python-logstash==0.4.6 # via nomad-lab (pyproject.toml)
python-magic==0.4.24 # via nomad-lab (pyproject.toml)
python-multipart==0.0.5 # via nomad-lab (pyproject.toml)
-pytz==2021.1 # via babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pandas
+pytz==2022.7.1 # via babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pandas
pywavelets==1.3.0 # via scikit-image
pyyaml==6.0 # via dask, hdfdict, hyperspy, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), phonopy, pybtex, uvicorn
pyzmq==25.0.0 # via ipykernel, ipyparallel, jupyter-client, jupyter-server
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
recommonmark==0.7.1 # via nomad-lab (pyproject.toml)
redis==4.4.2 # via celery
-requests==2.28.2 # via docker, hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), optimade, pymatgen, python-keycloak, rfc3161ng, sphinx
+requests==2.28.2 # via docker, hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), oauthenticator, optimade, pymatgen, python-keycloak, rfc3161ng, sphinx
rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via jsonschema
rfc3986[idna2008]==1.5.0 # via httpx
rfc3987==1.3.8 # via jsonschema
rsa==4.9 # via python-jose
-ruamel-yaml==0.17.21 # via jupyter-telemetry, pymatgen
+ruamel-yaml==0.17.21 # via jupyter-telemetry, oauthenticator, pymatgen
ruamel-yaml-clib==0.2.7 # via ruamel-yaml
runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via hyperspy
@@ -218,7 +220,7 @@ scikit-learn==1.0.2 # via matid (dependencies/matid/pyproject.toml)
scipy==1.7.1 # via ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, scikit-image, scikit-learn, sparse
send2trash==1.8.0 # via jupyter-server
sentinels==1.0.0 # via mongomock
-six==1.16.0 # via astunparse, basicauth, bcrypt, bleach, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
+six==1.16.0 # via astunparse, basicauth, bcrypt, bleach, click-repl, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
smmap==5.0.0 # via gitdb
sniffio==1.3.0 # via anyio, httpcore, httpx
snowballstemmer==2.2.0 # via sphinx
@@ -257,7 +259,7 @@ urllib3==1.26.14 # via docker, elasticsearch, requests
uvicorn[standard]==0.20.0 # via nomad-lab (pyproject.toml)
uvloop==0.17.0 # via uvicorn
validators==0.18.2 # via nomad-lab (pyproject.toml)
-vine==1.3.0 # via amqp, celery
+vine==5.0.0 # via amqp, celery, kombu
watchfiles==0.18.1 # via uvicorn
wcwidth==0.2.5 # via prettytable, prompt-toolkit
webcolors==1.12 # via jsonschema
@@ -270,7 +272,6 @@ wrapt==1.12.1 # via nomad-lab (pyproject.toml)
xarray==0.20.2 # via nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
xrdtools==0.1.1 # via nomad-lab (pyproject.toml)
zarr==2.12.0 # via hyperspy
-zipfile37==0.1.3 # via nomad-lab (pyproject.toml)
zipp==3.11.0 # via importlib-metadata
zipstream-new==1.1.5 # via nomad-lab (pyproject.toml)
diff --git a/tests/conftest.py b/tests/conftest.py
index 79593cb47c..cffde080ba 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -70,10 +70,11 @@ indices = [elastic_test_entries_index, elastic_test_materials_index]
warnings.simplefilter("ignore")
-
structlogging.ConsoleFormatter.short_format = True
setattr(logging, 'Formatter', structlogging.ConsoleFormatter)
+pytest_plugins = ("celery.contrib.pytest", )
+
@pytest.fixture(scope='function')
def tmp():
--
GitLab