Read the Docs build information
Build id: 27592
Project: european-xfel-offline-calibration
Version: latest
Commit: 767ed427ae6efa0d1800640846dd84d1dc0c7632
Date: 2024-02-09T12:24:52.824488Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-02-09T12:27:44.215015Z, end-time: 2024-02-09T12:28:03.783653Z, duration: 19, exit-code: 0
git clone --no-single-branch --depth 50 http://git.xfel.eu/calibration/pycalibration .
Cloning into '.'...
warning: redirecting to https://git.xfel.eu/calibration/pycalibration.git/

[rtd-command-info] start-time: 2024-02-09T12:28:04.133406Z, end-time: 2024-02-09T12:28:05.022975Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 767ed427 Merge branch 'fix/avoid_nan_scale_disturbance' into 'master'

[rtd-command-info] start-time: 2024-02-09T12:28:05.113292Z, end-time: 2024-02-09T12:28:05.178968Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2024-02-09T12:28:07.047730Z, end-time: 2024-02-09T12:28:12.157875Z, duration: 5, exit-code: 0
python3.8 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest
Using base prefix '/home/docs/.pyenv/versions/3.8.0'
New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python3.8
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2024-02-09T12:28:12.248741Z, end-time: 2024-02-09T12:28:13.229845Z, duration: 0, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip
Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (24.0)

[rtd-command-info] start-time: 2024-02-09T12:28:13.318702Z, end-time: 2024-02-09T12:28:42.870650Z, duration: 29, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir jinja2==2.11.3 markupsafe==2.0.1 Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 mkdocs<1.1
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Collecting calibration-client==11.2.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting docutils==0.17.1 (from European-XFEL-Offline-Calibration==1.0)
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Collecting extra-data==1.15.1 (from European-XFEL-Offline-Calibration==1.0)
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Collecting extra-geom==1.10.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting jupyter-core==4.10.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting jupyter-client==7.3.4 (from European-XFEL-Offline-Calibration==1.0)
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Collecting kafka-python==2.0.2 (from European-XFEL-Offline-Calibration==1.0)
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Collecting lxml==4.5.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting nbformat==5.0.7 (from European-XFEL-Offline-Calibration==1.0)
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Collecting nbparameterise==0.6 (from European-XFEL-Offline-Calibration==1.0)
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Collecting notebook==6.1.5 (from European-XFEL-Offline-Calibration==1.0)
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Collecting numpy==1.20.3 (from European-XFEL-Offline-Calibration==1.0)
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Collecting pasha==0.1.1 (from European-XFEL-Offline-Calibration==1.0)
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Collecting prettytable==0.7.2 (from European-XFEL-Offline-Calibration==1.0)
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Collecting princess==0.5 (from European-XFEL-Offline-Calibration==1.0)
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Collecting pypandoc==1.4 (from European-XFEL-Offline-Calibration==1.0)
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Requirement already satisfied: python-dateutil==2.8.2 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from European-XFEL-Offline-Calibration==1.0) (2.8.2)
Collecting pyyaml==5.3 (from European-XFEL-Offline-Calibration==1.0)
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Collecting pyzmq==23.2.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting requests==2.22.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting scikit-learn==0.22.2.post1 (from European-XFEL-Offline-Calibration==1.0)
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Collecting scipy==1.7.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting sharedmem==0.3.8 (from European-XFEL-Offline-Calibration==1.0)
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Collecting sphinx==1.8.5 (from European-XFEL-Offline-Calibration==1.0)
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Collecting tabulate==0.8.6 (from European-XFEL-Offline-Calibration==1.0)
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Collecting traitlets==4.3.3 (from European-XFEL-Offline-Calibration==1.0)
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Collecting xarray==2022.3.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting EXtra-redu==0.0.8 (from European-XFEL-Offline-Calibration==1.0)
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Collecting rich==12.6.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting httpx==0.23.0 (from European-XFEL-Offline-Calibration==1.0)
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Collecting oauth2-xfel-client>=6.1 (from calibration-client==11.2.0->European-XFEL-Offline-Calibration==1.0)
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Collecting oauthlib (from calibration-client==11.2.0->European-XFEL-Offline-Calibration==1.0)
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Collecting requests-oauthlib (from calibration-client==11.2.0->European-XFEL-Offline-Calibration==1.0)
  Downloading requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB)
Collecting mypy-extensions>=0.4.3 (from cfelpyutils==2.0.6->European-XFEL-Offline-Calibration==1.0)
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Collecting pandas>=1.1.5 (from cfelpyutils==2.0.6->European-XFEL-Offline-Calibration==1.0)
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Collecting euxfel-bunch-pattern>=0.6 (from EXtra-redu==0.0.8->European-XFEL-Offline-Calibration==1.0)
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Collecting gitdb<5,>=4.0.1 (from gitpython==3.1.0->European-XFEL-Offline-Calibration==1.0)
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Collecting rfc3986<2,>=1.3 (from rfc3986[idna2008]<2,>=1.3->httpx==0.23.0->European-XFEL-Offline-Calibration==1.0)
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Collecting httpcore<0.16.0,>=0.15.0 (from httpx==0.23.0->European-XFEL-Offline-Calibration==1.0)
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Building wheels for collected packages: European-XFEL-Offline-Calibration, dill, prettytable, pypandoc, pyyaml, sharedmem, tabulate
  Building wheel for European-XFEL-Offline-Calibration (pyproject.toml): started
  Building wheel for European-XFEL-Offline-Calibration (pyproject.toml): finished with status 'done'
  Created wheel for European-XFEL-Offline-Calibration: filename=European_XFEL_Offline_Calibration-1.0-cp38-cp38-linux_x86_64.whl size=1639830 sha256=1862d15eda26c2d0b932bdef59964b1a00c65f2f41dbca8f0864fd5493697f1b
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/22/7d/09/eb4f2a2bc8741186a0b6a6c96994f65acdd8e2af144db3f698
  Building wheel for dill (setup.py): started
  Building wheel for dill (setup.py): finished with status 'done'
  Created wheel for dill: filename=dill-0.3.0-py3-none-any.whl size=77508 sha256=01dfc9f16252d62bc44211d6e8cc5a955ba0eabae92ccde871e4d6b43f6b8e3a
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/ec/e7/fb/9b59e2dbda9eeefab51f7cb41df434ff463c4afe1985abff24
  Building wheel for prettytable (setup.py): started
  Building wheel for prettytable (setup.py): finished with status 'done'
  Created wheel for prettytable: filename=prettytable-0.7.2-py3-none-any.whl size=13699 sha256=f6ba4960b115420b7d656a6fe77436cfccfdea866672777da7db576be72e4682
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/48/6d/77/9517cb933af254f51a446f1a5ec9c2be3e45f17384940bce68
  Building wheel for pypandoc (setup.py): started
  Building wheel for pypandoc (setup.py): finished with status 'done'
  Created wheel for pypandoc: filename=pypandoc-1.4-py3-none-any.whl size=16714 sha256=68b16b7db8ceb7246cc632664cdfb2aab1f77d9c715899143a1c6e2065819edb
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/f7/d9/a0/ef1fe56c058e41d6271a4935caaeae89d43e2280504690a329
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3-cp38-cp38-linux_x86_64.whl size=44227 sha256=b61aec337f50c4108e07a184c5101ed5efb965c74d51d871ced90d3dc00269f9
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/e4/94/ec/65e430f66fda7a86c08f61ce59455581adc269a65881b4ffeb
  Building wheel for sharedmem (setup.py): started
  Building wheel for sharedmem (setup.py): finished with status 'done'
  Created wheel for sharedmem: filename=sharedmem-0.3.8-py3-none-any.whl size=18341 sha256=89d8a72d0e70814e4fd1efbb27e122560f4cc53ef72cdec3281678034fff0a40
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/ee/ef/25/9562dc56f11d2b55824c1b1547eff68b75f1a0117d3b0867dd
  Building wheel for tabulate (setup.py): started
  Building wheel for tabulate (setup.py): finished with status 'done'
  Created wheel for tabulate: filename=tabulate-0.8.6-py3-none-any.whl size=23272 sha256=8e835b36d551cd0a108c37d0d29a8f0cff77b4e2bea483e337ade18e2feea698
  Stored in directory: /tmp/pip-ephem-wheel-cache-wij0ndx8/wheels/86/8c/d9/3b6c2f55efaefe656c52b725d2fdc5669085c83444979db8b3
Successfully built European-XFEL-Offline-Calibration dill prettytable pypandoc pyyaml sharedmem tabulate
Installing collected packages: tabulate, rfc3986, prettytable, mistune, kafka-python, ipython-genutils, env-cache, dynaconf, commonmark, chardet, urllib3, tzdata, traitlets, testpath, sphinxcontrib-websupport, smmap, setuptools, rich, pyzmq, pyyaml, pyparsing, pillow, oauthlib, numpy, mypy-extensions, lxml, kiwisolver, joblib, Jinja2, idna, h11, entrypoints, docutils, dill, Cython, cycler, async-generator, astcheck, sharedmem, scipy, requests, pypandoc, pasha, pandas, matplotlib, jupyter-core, ipython, iminuit, h5py, gitdb, euxfel-bunch-pattern, anyio, xarray, sphinx, scikit-learn, requests-oauthlib, jupyter-client, httpcore, gitpython, cfelpyutils, oauth2-xfel-client, nbformat, ipykernel, httpx, extra-geom, extra-data, nbconvert, nbclient, metadata-client, jupyter-console, ipyparallel, EXtra-redu, calibration-client, princess, notebook, nbparameterise, European-XFEL-Offline-Calibration
  Attempting uninstall: mistune
    Found existing installation: mistune 3.0.2
    Uninstalling mistune-3.0.2:
      Successfully uninstalled mistune-3.0.2
  Attempting uninstall: commonmark
    Found existing installation: commonmark 0.8.1
    Uninstalling commonmark-0.8.1:
      Successfully uninstalled commonmark-0.8.1
  Attempting uninstall: urllib3
    Found existing installation: urllib3 2.2.0
    Uninstalling urllib3-2.2.0:
      Successfully uninstalled urllib3-2.2.0
  Attempting uninstall: traitlets
    Found existing installation: traitlets 5.14.1
    Uninstalling traitlets-5.14.1:
      Successfully uninstalled traitlets-5.14.1
  Attempting uninstall: setuptools
    Found existing installation: setuptools 41.0.1
    Uninstalling setuptools-41.0.1:
      Successfully uninstalled setuptools-41.0.1
  Attempting uninstall: pyzmq
    Found existing installation: pyzmq 25.1.2
    Uninstalling pyzmq-25.1.2:
      Successfully uninstalled pyzmq-25.1.2
  Attempting uninstall: pyyaml
    Found existing installation: PyYAML 6.0.1
    Uninstalling PyYAML-6.0.1:
      Successfully uninstalled PyYAML-6.0.1
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
  Attempting uninstall: Jinja2
    Found existing installation: Jinja2 3.1.3
    Uninstalling Jinja2-3.1.3:
      Successfully uninstalled Jinja2-3.1.3
  Attempting uninstall: idna
    Found existing installation: idna 3.6
    Uninstalling idna-3.6:
      Successfully uninstalled idna-3.6
  Attempting uninstall: h11
    Found existing installation: h11 0.14.0
    Uninstalling h11-0.14.0:
      Successfully uninstalled h11-0.14.0
  Attempting uninstall: docutils
    Found existing installation: docutils 0.14
    Uninstalling docutils-0.14:
      Successfully uninstalled docutils-0.14
  Attempting uninstall: requests
    Found existing installation: requests 2.31.0
    Uninstalling requests-2.31.0:
      Successfully uninstalled requests-2.31.0
  Attempting uninstall: jupyter-core
    Found existing installation: jupyter_core 5.7.1
    Uninstalling jupyter_core-5.7.1:
      Successfully uninstalled jupyter_core-5.7.1
  Attempting uninstall: ipython
    Found existing installation: ipython 8.12.3
    Uninstalling ipython-8.12.3:
      Successfully uninstalled ipython-8.12.3
  Attempting uninstall: anyio
    Found existing installation: anyio 4.2.0
    Uninstalling anyio-4.2.0:
      Successfully uninstalled anyio-4.2.0
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 5.1.1
    Uninstalling Sphinx-5.1.1:
      Successfully uninstalled Sphinx-5.1.1
  Attempting uninstall: jupyter-client
    Found existing installation: jupyter_client 8.6.0
    Uninstalling jupyter_client-8.6.0:
      Successfully uninstalled jupyter_client-8.6.0
  Attempting uninstall: httpcore
    Found existing installation: httpcore 1.0.2
    Uninstalling httpcore-1.0.2:
      Successfully uninstalled httpcore-1.0.2
  Attempting uninstall: nbformat
    Found existing installation: nbformat 5.9.2
    Uninstalling nbformat-5.9.2:
      Successfully uninstalled nbformat-5.9.2
  Attempting uninstall: ipykernel
    Found existing installation: ipykernel 6.29.2
    Uninstalling ipykernel-6.29.2:
      Successfully uninstalled ipykernel-6.29.2
  Attempting uninstall: httpx
    Found existing installation: httpx 0.26.0
    Uninstalling httpx-0.26.0:
      Successfully uninstalled httpx-0.26.0
  Attempting uninstall: nbconvert
    Found existing installation: nbconvert 7.16.0
    Uninstalling nbconvert-7.16.0:
      Successfully uninstalled nbconvert-7.16.0
  Attempting uninstall: nbclient
    Found existing installation: nbclient 0.9.0
    Uninstalling nbclient-0.9.0:
      Successfully uninstalled nbclient-0.9.0
  Attempting uninstall: jupyter-console
    Found existing installation: jupyter-console 6.6.3
    Uninstalling jupyter-console-6.6.3:
      Successfully uninstalled jupyter-console-6.6.3
  Attempting uninstall: notebook
    Found existing installation: notebook 7.0.7
    Uninstalling notebook-7.0.7:
      Successfully uninstalled notebook-7.0.7
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
jupyter-events 0.9.0 requires traitlets>=5.3, but you have traitlets 4.3.3 which is incompatible.
jupyter-server 2.12.5 requires jupyter-client>=7.4.4, but you have jupyter-client 7.3.4 which is incompatible.
jupyter-server 2.12.5 requires jupyter-core!=5.0.*,>=4.12, but you have jupyter-core 4.10.0 which is incompatible.
jupyter-server 2.12.5 requires nbconvert>=6.4.4, but you have nbconvert 5.6.1 which is incompatible.
jupyter-server 2.12.5 requires nbformat>=5.3.0, but you have nbformat 5.0.7 which is incompatible.
jupyter-server 2.12.5 requires pyzmq>=24, but you have pyzmq 23.2.0 which is incompatible.
jupyter-server 2.12.5 requires traitlets>=5.6.0, but you have traitlets 4.3.3 which is incompatible.
jupyterlab 4.1.0 requires httpx>=0.25.0, but you have httpx 0.23.0 which is incompatible.
jupyterlab 4.1.0 requires jinja2>=3.0.3, but you have jinja2 2.11.2 which is incompatible.
jupyterlab-server 2.25.2 requires jinja2>=3.0.3, but you have jinja2 2.11.2 which is incompatible.
jupyterlab-server 2.25.2 requires requests>=2.31, but you have requests 2.22.0 which is incompatible.
mkdocs-material 9.0.15 requires jinja2>=3.0, but you have jinja2 2.11.2 which is incompatible.
mkdocs-material 9.0.15 requires requests>=2.26, but you have requests 2.22.0 which is incompatible.
Successfully installed Cython-0.29.21 EXtra-redu-0.0.8 European-XFEL-Offline-Calibration-1.0 Jinja2-2.11.2 anyio-3.7.1 astcheck-0.3.0 async-generator-1.10 calibration-client-11.2.0 cfelpyutils-2.0.6 chardet-3.0.4 commonmark-0.9.1 cycler-0.12.1 dill-0.3.0 docutils-0.17.1 dynaconf-3.1.4 entrypoints-0.4 env-cache-0.1 euxfel-bunch-pattern-0.6 extra-data-1.15.1 extra-geom-1.10.0 gitdb-4.0.11 gitpython-3.1.0 h11-0.12.0 h5py-3.5.0 httpcore-0.15.0 httpx-0.23.0 idna-2.8 iminuit-1.3.8 ipykernel-5.1.4 ipyparallel-6.2.4 ipython-7.12.0 ipython-genutils-0.2.0 joblib-1.3.2 jupyter-client-7.3.4 jupyter-console-6.1.0 jupyter-core-4.10.0 kafka-python-2.0.2 kiwisolver-1.4.5 lxml-4.5.0 matplotlib-3.4.2 metadata-client-4.0.0 mistune-0.8.4 mypy-extensions-1.0.0 nbclient-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 nbparameterise-0.6 notebook-6.1.5 numpy-1.20.3 oauth2-xfel-client-6.1.1 oauthlib-3.2.2 pandas-2.0.3 pasha-0.1.1 pillow-10.2.0 prettytable-0.7.2 princess-0.5 pypandoc-1.4 pyparsing-3.1.1 pyyaml-5.3 pyzmq-23.2.0 requests-2.22.0 requests-oauthlib-1.3.1 rfc3986-1.5.0 rich-12.6.0 scikit-learn-0.22.2.post1 scipy-1.7.0 setuptools-69.0.3 sharedmem-0.3.8 smmap-5.0.1 sphinx-1.8.5 sphinxcontrib-websupport-1.2.4 tabulate-0.8.6 testpath-0.6.0 traitlets-4.3.3 tzdata-2023.4 urllib3-1.25.11 xarray-2022.3.0

[rtd-command-info] start-time: 2024-02-09T12:30:20.248846Z, end-time: 2024-02-09T12:30:20.312765Z, duration: 0, exit-code: 0
cat mkdocs.yml
copyright: '&copy; 2018 <a href="https://www.xfel.eu/"  target="_blank" rel="noopener">European
  XFEL</a>'
docs_dir: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs
extra_css:
- css/extra.css
- css/custom.css
- http://rtd.xfel.eu/static/css/badge_only.css
- http://rtd.xfel.eu/static/css/readthedocs-doc-embed.css
extra_javascript:
- readthedocs-data.js
- http://rtd.xfel.eu/static/core/js/readthedocs-doc-embed.js
- http://rtd.xfel.eu/static/javascript/readthedocs-analytics.js
google_analytics: null
markdown_extensions:
- abbr
- pymdownx.highlight:
    anchor_linenums: true
    linenums_style: pymdownx-inline
- pymdownx.superfences
- pymdownx.inlinehilite
- pymdownx.snippets:
    auto_append:
    - docs/includes/abbreviations.md
- pymdownx.tasklist
- pymdownx.arithmatex:
    generic: true
- pymdownx.tabbed:
    alternate_style: true
- pymdownx.details
- pymdownx.mark
- pymdownx.emoji: null
- attr_list
- def_list
- footnotes
- md_in_html
- toc:
    permalink: true
- admonition
- tables
- codehilite
nav:
- index.md
- Operation:
  - CALCAT: operation/calibration_database.md
  - myMDC: operation/myMDC.md
  - Available Calibration notebooks: operation/available_notebooks.md
  - Calibration webservice:
    - The webservice: operation/webservice.md
    - Calibration Configuration: operation/calibration_configurations.md
- Development:
  - Installation: development/installation.md
  - Workflow: development/workflow.md
  - How to write a notebook: development/how_to_write_xfel_calibrate_notebook_NBC.md
  - Configuration: development/configuration.md
  - Automated tests: development/testing_pipeline.md
- Code Reference: reference/
- Reference:
  - FAQ: references/faq.md
  - Changelog: references/changelog.md
plugins:
- glightbox
- search
- autorefs
- gen-files:
    scripts:
    - docs/gen_ref_pages.py
- literate-nav:
    nav_file: SUMMARY.md
- section-index
- mkdocstrings:
    handlers:
      python:
        docstring_section_style: list
        docstring_style: sphinx
        import:
        - https://docs.python-requests.org/en/master/objects.inv
repo_url: https://git.xfel.eu/calibration/pycalibration
site_name: EuXFEL Offline calibration
theme:
  features:
  - navigation.tabs
  - navigation.tabs.sticky
  - navigation.sections
  - navigation.top
  - navigation.instant
  - navigation.tracking
  - search.suggest
  - search.highlight
  - content.tabs.link
  - content.code.annotation
  - content.code.copy
  - navigation.indexes
  - content.tooltips
  - toc.follow
  language: en
  name: material
  palette:
  - scheme: light
    toggle:
      icon: material/lightbulb
      name: Switch to dark mode
  - scheme: slate
    toggle:
      icon: material/lightbulb-outline
      name: Switch to light mode

[rtd-command-info] start-time: 2024-02-09T12:30:20.401415Z, end-time: 2024-02-09T12:30:29.531798Z, duration: 9, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m mkdocs build --clean --site-dir _build/html --config-file mkdocs.yml
INFO     -  Cleaning site directory
INFO     -  Building documentation to directory: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/_build/html
INFO     -  The following pages exist in the docs directory, but are not included in the "nav" configuration:
  - overview.md
  - development/advanced.md
  - development/contributing_to_gitlab.md
  - includes/abbreviations.md
WARNING  -  Documentation file 'development/configuration.md' contains a link to 'reference/xfel-calibrate/calibrate.md' which is not found in the documentation files.
WARNING  -  Documentation file 'development/workflow.md' contains a link to 'development/SUMMARY.md' which is not found in the documentation files.
WARNING  -  Documentation file 'development/workflow.md' contains a link to 'reference/src/cal_tools/files.md' which is not found in the documentation files.
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:43: No type or annotation for parameter 'run'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:43: Parameter 'run' does not appear in the function signature
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:389: No type or annotation for returned value 'bool'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:453: No type or annotation for returned value 'float'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:420: No type or annotation for returned value 'int'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:401: No type or annotation for returned value 'list'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:443: No type or annotation for returned value 'float'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:407: No type or annotation for returned value 'float'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/agipdlib.py:430: No type or annotation for returned value 'int'
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:247: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:116: Parameter 'caldata' does not appear in the function signature
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:120: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:528: No type or annotation for returned value 'DICT'
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:401: No type or annotation for parameter '**condition_params'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:401: Parameter '**condition_params' does not appear in the function signature
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:577: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:469: Failed to get 'name: description' pair from 'Any further keyword arguments are passed on to'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:470: Failed to get 'name: description' pair from 'CalibrationClient.__init__().'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:473: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/calcat_interface.py:928: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:484: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:411: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:440: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:232: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:179: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:249: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:295: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:135: Parameter 'args,' does not appear in the function signature
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:140: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:559: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:529: No type or annotation for parameter 'kwargs'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:533: No type or annotation for returned value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:23: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:70: No type or annotation for yielded value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/files.py:43: No type or annotation for yielded value 1
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/tools.py:1059: No type or annotation for returned value 'str'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/gotthard2/gotthard2lib.py:54: No type or annotation for returned value 'str'
WARNING  -  griffe: /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages/cal_tools/jungfrau/jfstrixel.py:75: No type or annotation for returned value 1
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