Read the Docs build information
Build id: 25744
Project: european-xfel-offline-calibration
Version: doc-mkdocs_new_documentations
Commit: e94b073da44e8d7368a385489d50ad2858d2f13d
Date: 2023-03-21T09:36:50.034178Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-03-21T09:36:51.130180Z, end-time: 2023-03-21T09:37:08.501535Z, duration: 17, 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: 2023-03-21T09:37:08.809583Z, end-time: 2023-03-21T09:37:09.597965Z, duration: 0, exit-code: 0
git checkout --force origin/doc/mkdocs_new_documentations
Note: checking out 'origin/doc/mkdocs_new_documentations'.

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 e94b073d add images and references

[rtd-command-info] start-time: 2023-03-21T09:37:09.689164Z, end-time: 2023-03-21T09:37:09.753032Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-03-21T09:37:11.301385Z, end-time: 2023-03-21T09:37:16.207875Z, duration: 4, exit-code: 0
python3.8 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations
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/doc-mkdocs_new_documentations/bin/python3.8
Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-03-21T09:37:16.296160Z, end-time: 2023-03-21T09:37:17.244008Z, duration: 0, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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/doc-mkdocs_new_documentations/lib/python3.8/site-packages (23.0.1)

[rtd-command-info] start-time: 2023-03-21T09:37:17.332528Z, end-time: 2023-03-21T09:37:44.438775Z, duration: 27, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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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Building wheels for collected packages: mock, pillow, future
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Successfully built mock pillow future
Installing collected packages: snowballstemmer, pytz, Pygments, mock, docutils, zipp, urllib3, tornado, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, six, setuptools, PyYAML, pillow, packaging, markupsafe, imagesize, idna, future, click, charset-normalizer, certifi, babel, alabaster, requests, livereload, jinja2, importlib-metadata, commonmark, sphinx, Markdown, recommonmark, mkdocs
  Attempting uninstall: setuptools
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Requirement already satisfied: zipp>=3.1.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/lib/python3.8/site-packages (from importlib-resources>=1.4.0->jsonschema!=2.5.0,>=2.4->nbformat==5.0.7->European-XFEL-Offline-Calibration==1.0) (3.15.0)
Collecting cffi>=1.0.1
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Collecting pycparser
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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=1598716 sha256=cae89f2943c6f8b875cb1c58105e1b38289c440e0b2056c951d1cd0a0d9cc5bb
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/wheels/1d/8e/2b/dcedca7f2ac9a173c60e54d723e1d361570bb0c374714b3976
  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=77512 sha256=1ebb87b80b4850798f67496cd7224c15b9e408bfc1bfd8aab25b4d0fe17cd6de
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/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=8e6e5b57888e71ed49bac802caa2337c38f7212be5a50b4ebd702f57b7dfc3b5
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/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=16716 sha256=2385aab6a669b6ffd6b037830d81ece1b7fb9b7d276a49fbf7b37724d52a423a
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/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=d7eaf9fc6bd0e1cfdedb0e85cd133324e9c2c340f96e9d5c1ab1486136cb91d3
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/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=18342 sha256=c81850fba0db7faacc3a86d435a8ed4b9a73f2286fae54533809d0f1c0d095a5
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/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=23273 sha256=60ddda2dcdc62d4b6a870357d97f3a51b05b86a504684018b685290b7702bcc3
  Stored in directory: /tmp/pip-ephem-wheel-cache-mjmhh5fh/wheels/86/8c/d9/3b6c2f55efaefe656c52b725d2fdc5669085c83444979db8b3
Successfully built European-XFEL-Offline-Calibration dill prettytable pypandoc pyyaml sharedmem tabulate
Installing collected packages: webencodings, wcwidth, tabulate, Send2Trash, ptyprocess, prettytable, pickleshare, mistune, kafka-python, ipython-genutils, env-cache, dynaconf, chardet, backcall, urllib3, testpath, terminado, sphinxcontrib-websupport, smmap, setuptools, pyzmq, pyyaml, pyrsistent, pyparsing, pycparser, prompt-toolkit, prometheus-client, pkgutil-resolve-name, pillow, pexpect, parso, pandocfilters, oauthlib, numpy, nest-asyncio, mypy-extensions, lxml, kiwisolver, joblib, Jinja2, importlib-resources, idna, entrypoints, docutils, dill, defusedxml, decorator, Cython, cycler, bleach, attrs, async-generator, astcheck, traitlets, sharedmem, scipy, requests, pypandoc, pasha, pandas, matplotlib, jsonschema, jedi, iminuit, h5py, gitdb, euxfel-bunch-pattern, cffi, xarray, sphinx, scikit-learn, requests-oauthlib, jupyter-core, ipython, gitpython, cfelpyutils, argon2-cffi-bindings, oauth2-xfel-client, nbformat, jupyter-client, extra-geom, extra-data, argon2-cffi, nbconvert, nbclient, metadata-client, ipykernel, EXtra-redu, calibration-client, princess, notebook, nbparameterise, jupyter-console, ipyparallel, European-XFEL-Offline-Calibration
  Attempting uninstall: urllib3
    Found existing installation: urllib3 1.26.15
    Uninstalling urllib3-1.26.15:
      Successfully uninstalled urllib3-1.26.15
  Attempting uninstall: setuptools
    Found existing installation: setuptools 41.0.1
    Uninstalling setuptools-41.0.1:
      Successfully uninstalled setuptools-41.0.1
  Attempting uninstall: pyyaml
    Found existing installation: PyYAML 6.0
    Uninstalling PyYAML-6.0:
      Successfully uninstalled PyYAML-6.0
  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 3.1.2
    Uninstalling Jinja2-3.1.2:
      Successfully uninstalled Jinja2-3.1.2
  Attempting uninstall: idna
    Found existing installation: idna 3.4
    Uninstalling idna-3.4:
      Successfully uninstalled idna-3.4
  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 2.28.2
    Uninstalling requests-2.28.2:
      Successfully uninstalled requests-2.28.2
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 5.1.1
    Uninstalling Sphinx-5.1.1:
      Successfully uninstalled Sphinx-5.1.1
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.
mkdocs-material 8.5.11 requires jinja2>=3.0.2, but you have jinja2 2.11.2 which is incompatible.
mkdocs-material 8.5.11 requires requests>=2.26, but you have requests 2.22.0 which is incompatible.
Successfully installed Cython-0.29.21 EXtra-redu-0.0.7 European-XFEL-Offline-Calibration-1.0 Jinja2-2.11.2 Send2Trash-1.8.0 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 astcheck-0.3.0 async-generator-1.10 attrs-22.2.0 backcall-0.2.0 bleach-6.0.0 calibration-client-11.2.0 cfelpyutils-2.0.6 cffi-1.15.1 chardet-3.0.4 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 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-1.12.0 extra-geom-1.8.0 gitdb-4.0.10 gitpython-3.1.0 h5py-3.5.0 idna-2.8 iminuit-1.3.8 importlib-resources-5.12.0 ipykernel-5.1.4 ipyparallel-6.2.4 ipython-7.12.0 ipython-genutils-0.2.0 jedi-0.18.2 joblib-1.2.0 jsonschema-4.17.3 jupyter-client-7.3.4 jupyter-console-6.1.0 jupyter-core-4.10.0 kafka-python-2.0.2 kiwisolver-1.4.4 lxml-4.5.0 matplotlib-3.4.2 metadata-client-3.0.8 mistune-0.8.4 mypy-extensions-1.0.0 nbclient-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 nbparameterise-0.6 nest-asyncio-1.5.6 notebook-6.1.5 numpy-1.20.3 oauth2-xfel-client-6.1.1 oauthlib-3.2.2 pandas-1.5.3 pandocfilters-1.5.0 parso-0.8.3 pasha-0.1.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-9.4.0 pkgutil-resolve-name-1.3.10 prettytable-0.7.2 princess-0.5 prometheus-client-0.16.0 prompt-toolkit-3.0.38 ptyprocess-0.7.0 pycparser-2.21 pypandoc-1.4 pyparsing-3.0.9 pyrsistent-0.19.3 pyyaml-5.3 pyzmq-23.2.0 requests-2.22.0 requests-oauthlib-1.3.1 scikit-learn-0.22.2.post1 scipy-1.7.0 setuptools-67.6.0 sharedmem-0.3.8 smmap-5.0.0 sphinx-1.8.5 sphinxcontrib-websupport-1.2.4 tabulate-0.8.6 terminado-0.17.1 testpath-0.6.0 traitlets-4.3.3 urllib3-1.25.11 wcwidth-0.2.6 webencodings-0.5.1 xarray-2022.3.0

[rtd-command-info] start-time: 2023-03-21T09:38:55.202768Z, end-time: 2023-03-21T09:38:55.261123Z, 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/doc-mkdocs_new_documentations/docs
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:
- pymdownx.highlight:
    anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.tasklist
- pymdownx.arithmatex:
    generic: true
- pymdownx.tabbed:
    alternate_style: true
- pymdownx.details
- pymdownx.superfences
- pymdownx.mark
- pymdownx.emoji: null
- attr_list
- def_list
- footnotes
- md_in_html
- toc:
    permalink: true
- admonition
- tables
- codehilite
nav:
- index.md
- Operation:
  - Calibration database: calibration_database.md
  - myMDC: myMDC.md
  - Troubleshooting:
    - Correcting detector RAW data: troubleshooting_correction.md
    - Calibration constant generation: troubleshooting_calibration_generation.md
- Development:
  - Installation: installation.md
  - Workflow: workflow.md
  - How to write a notebook: how_to_write_xfel_calibrate_notebook_NBC.md
  - Advanced topics: advanced.md
- Code Reference:
  - CALCAT Interface: calcat_interface.md
  - Calibration Tools: cal_tools.md
- Reference:
  - FAQ: references/faq.md
  - Changelog: references/changelog.md
  - Glossary: glossary.md
plugins:
- glightbox
- literate-nav
- mkdocstrings:
    custom_templates: templates
    default_handler: python
- search
- autorefs
repo_url: https://git.xfel.eu/calibration/pycalibration
site_name: EuXFEL Offline calibration
theme:
  features:
  - navigation.tabs
  - navigation.sections
  - toc.integrate
  - navigation.top
  - search.suggest
  - search.highlight
  - content.tabs.link
  - content.code.annotation
  - content.code.copy
  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: 2023-03-21T09:38:55.349323Z, end-time: 2023-03-21T09:39:04.784657Z, duration: 9, exit-code: 0
/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/doc-mkdocs_new_documentations/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/doc-mkdocs_new_documentations/_build/html
INFO     -  The following pages exist in the docs directory, but are not included in the "nav" configuration:
  - available_notebooks.md
  - cal_tools_algorithms.md
  - configuration.md
  - operation.md
  - xfel_calibrate_conf.md
  - references/glossary.md
WARNING  -  A relative path to 'glossary.md' is included in the 'nav' configuration, which is not found in the documentation files
WARNING  -  griffe: cal_tools/files.py:480: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:407: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:436: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:232: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at cal_tools/files.py:1
WARNING  -  griffe: cal_tools/files.py:179: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:249: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:295: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:135: Parameter 'args,' does not appear in the function signature
WARNING  -  griffe: cal_tools/files.py:140: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:555: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:525: No type or annotation for parameter 'kwargs'
WARNING  -  griffe: cal_tools/files.py:529: No type or annotation for returned value 1
WARNING  -  griffe: cal_tools/files.py:23: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'BoolOp' node at cal_tools/files.py:1
WARNING  -  griffe: cal_tools/files.py:70: No type or annotation for yielded value 1
WARNING  -  griffe: cal_tools/files.py:43: No type or annotation for yielded value 1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at cal_tools/calcat_interface.py:1
WARNING  -  griffe: cal_tools/calcat_interface.py:566: No type or annotation for returned value 1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at cal_tools/calcat_interface.py:1
ERROR    -  griffe: Failed to parse annotation from 'Tuple' node at cal_tools/calcat_interface.py:1
WARNING  -  griffe: cal_tools/calcat_interface.py:851: No type or annotation for returned value 1
INFO     -  Documentation built in 8.84 seconds