Read the Docs build information
Build id: 25743
Project: european-xfel-offline-calibration
Version: doc-mkdocs_new_documentations
Commit: df34bf53a7f290a44db9c2f83e586b4156d58c95
Date: 2023-03-21T09:27:12.429238Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-03-21T09:27:13.486924Z, end-time: 2023-03-21T09:27:29.898551Z, duration: 16, 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: 2023-03-21T09:27:30.189514Z, end-time: 2023-03-21T09:27:31.023706Z, 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 df34bf53 remove emojis

[rtd-command-info] start-time: 2023-03-21T09:27:31.108497Z, end-time: 2023-03-21T09:27:31.168073Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-03-21T09:27:32.689467Z, end-time: 2023-03-21T09:27:37.541380Z, 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: 2023-03-21T09:27:37.628939Z, end-time: 2023-03-21T09:27:38.575899Z, 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: 2023-03-21T09:27:38.658184Z, end-time: 2023-03-21T09:28:05.894443Z, 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
  Downloading cffi-1.15.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (442 kB)
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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=1598721 sha256=4e7e49d542465f688250120fb0943119672065d0f9533fe40b5b8441647b4873
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=a99be1e69e4466ce05acd9eb1c343e4da6cfc16688af069b6a7d96f87c649776
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=7da6b913fa037419911613f62102a4987353902b51a87dfb54db92446150ec41
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=824493f6a0f3ea0ecef3ffadf9a0615298033ef9ce2e972a604d74f22fbfb725
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=3ab4172d2f0ca0650a918b4c90fbeaa79505902d30da8ac798cece2b9255905e
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=faac2d7a0c7f92c93448482794fcb2259b821f4f93521abe38e0c19e40c643db
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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=315f754cfa20f3466b71f4a267f58dc829218c2a097b8846087863c15eb050ae
  Stored in directory: /tmp/pip-ephem-wheel-cache-ap711z3v/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: 2023-03-21T09:29:16.152734Z, end-time: 2023-03-21T09:29:16.213580Z, 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: 2023-03-21T09:29:16.299902Z, end-time: 2023-03-21T09:29:25.521862Z, 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
WARNING  -  A relative path to 'references/faq.md' is included in the 'nav' configuration, which is not found in the documentation files
WARNING  -  A relative path to 'references/changelog.md' is included in the 'nav' configuration, which is not found in the documentation files
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
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_cc_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_ccv_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_conditions_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_pdu_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_detectors_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/home_reports_calcat.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/detector_mapping/AGIPD_modules_pic.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/detector_mapping/JUNGFRAU_PDU_pic.png' which is not found in the documentation files.
WARNING  -  Documentation file 'calibration_database.md' contains a link to 'static/detector_mapping/icalibrationdb_agipd_det_mapping.png' which is not found in the documentation files.
WARNING  -  Documentation file 'how_to_write_xfel_calibrate_notebook_NBC.md' contains a link to 'static/how_to_write_xfel_calibrate_notebook_NBC_14_0.png' which is not found in the documentation files.
WARNING  -  Documentation file 'myMDC.md' contains a link to 'static/myMDC/calibration_constants.png' which is not found in the documentation files.
INFO     -  Documentation built in 8.66 seconds