Read the Docs build information Build id: 22680 Project: european-xfel-offline-calibration Version: latest Commit: 9559abb2f7d31d8046f2472b54f9196e9e8e6ab6 Date: 2021-11-22T12:55:32.667720Z State: finished Success: True [rtd-command-info] start-time: 2021-11-22T12:55:33.823352Z, end-time: 2021-11-22T12:55:58.267830Z, duration: 24, exit-code: 0 git clone --no-single-branch --depth 50 http://git.xfel.eu/gitlab/detectors/pycalibration.git . Cloning into '.'... 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[rtd-command-info] start-time: 2021-11-22T12:55:58.663063Z, end-time: 2021-11-22T12:55:59.090263Z, duration: 0, exit-code: 0 git checkout --force origin/doc/run_rtd Note: checking out 'origin/doc/run_rtd'. 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 HEAD is now at 9559abb put python check back [rtd-command-info] start-time: 2021-11-22T12:55:59.229573Z, end-time: 2021-11-22T12:55:59.320176Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-11-22T12:56:01.054287Z, end-time: 2021-11-22T12:56:06.880943Z, 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: 2021-11-22T12:56:07.024585Z, end-time: 2021-11-22T12:56:08.063236Z, duration: 1, 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 (21.3.1) [rtd-command-info] start-time: 2021-11-22T12:56:08.196444Z, end-time: 2021-11-22T12:56:41.761339Z, duration: 33, 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 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 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting Jinja2>=2.3 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting imagesize Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting idna<4,>=2.5 Downloading idna-3.3-py3-none-any.whl (61 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.6-py3-none-any.whl (97 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, pillow, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=98bc34a430c9fa0abfa9af31712d78be66620aded8d8cbe4646031c77297c902 Stored in directory: /tmp/pip-ephem-wheel-cache-032rr9cj/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260000 sha256=239bc4e1b4c4c9dcf958dbbd0de2727f065b555344f56403a755630bc9854f71 Stored in directory: /tmp/pip-ephem-wheel-cache-032rr9cj/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=6d619fce9bdb0e5c1f9f87c673a9e60614c974facd1956be2bf9329da742d83c Stored in directory: /tmp/pip-ephem-wheel-cache-032rr9cj/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 59.2.0 Uninstalling setuptools-59.2.0: Successfully uninstalled setuptools-59.2.0 Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.6 pytz-2021.3 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.26.0 setuptools-41.0.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-11-22T12:56:41.912684Z, end-time: 2021-11-22T12:59:41.410329Z, duration: 179, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting iCalibrationDB@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/cal_db_interactive.git@2.0.1 Cloning https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git (to revision 2.0.1) to /tmp/pip-install-vbtl8shu/icalibrationdb_f1a75d19a474476ea00b67b8c0d0e034 Running command git clone --filter=blob:none -q 'https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git' /tmp/pip-install-vbtl8shu/icalibrationdb_f1a75d19a474476ea00b67b8c0d0e034 Running command git checkout -q 65b3edf0aa2b59025d009301a3ba3bd078ffc8e4 Resolved https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/cal_db_interactive.git to commit 65b3edf0aa2b59025d009301a3ba3bd078ffc8e4 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting nbparameterise@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/nbparameterise.git@0.3 Cloning https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/nbparameterise.git (to revision 0.3) to /tmp/pip-install-vbtl8shu/nbparameterise_b649e4c5812f4ae8930d1f4f1d300c8b Running command git clone --filter=blob:none -q 'https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/nbparameterise.git' /tmp/pip-install-vbtl8shu/nbparameterise_b649e4c5812f4ae8930d1f4f1d300c8b Resolved https://xcalgitlab:****@git.xfel.eu/gitlab/detectors/nbparameterise.git to commit 8c92dbd7d37c9cac5bf58ab78730a3afea4127b1 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib Cloning https://xcalgitlab:****@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git (to revision 2.5.6-2.10.0) to /tmp/pip-install-vbtl8shu/xfeldetectoranalysis_7121ecc8128345049aa212ac4576a063 Running command git clone --filter=blob:none -q 'https://xcalgitlab:****@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git' /tmp/pip-install-vbtl8shu/xfeldetectoranalysis_7121ecc8128345049aa212ac4576a063 Running command git checkout -q 07626f2015c985e39bb80541db7d260affc1f574 Resolved https://xcalgitlab:****@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git to commit 07626f2015c985e39bb80541db7d260affc1f574 Installing build dependencies: started Installing build dependencies: still running... Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting h5py Downloading h5py-3.6.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting pyzmq Downloading pyzmq-22.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) Collecting python-dateutil Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) Collecting nbconvert Downloading nbconvert-6.3.0-py3-none-any.whl (556 kB) Collecting astsearch Downloading astsearch-0.2.0-py3-none-any.whl (6.5 kB) Collecting ipython Downloading ipython-7.29.0-py3-none-any.whl (790 kB) Collecting matplotlib>=2.0.0 Downloading matplotlib-3.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.3 MB) Collecting Cython Downloading Cython-0.29.24-cp38-cp38-manylinux1_x86_64.whl (1.9 MB) Collecting dill>=0.2.5 Downloading dill-0.3.4-py2.py3-none-any.whl (86 kB) Collecting seaborn>=0.7.1 Downloading seaborn-0.11.2-py3-none-any.whl (292 kB) Collecting pypandoc Downloading pypandoc-1.6.4.tar.gz (26 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting brewer2mpl>=1.4 Downloading brewer2mpl-1.4.1-py2.py3-none-any.whl (24 kB) Collecting ipyparallel Downloading ipyparallel-8.0.0-py3-none-any.whl (397 kB) Collecting tornado>=4.5 Downloading tornado-6.1-cp38-cp38-manylinux2010_x86_64.whl (427 kB) Collecting numpy>=1.13 Downloading numpy-1.21.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting cycler>=0.10 Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB) Requirement already satisfied: packaging>=20.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib>=2.0.0->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (21.3) Collecting fonttools>=4.22.0 Downloading fonttools-4.28.2-py3-none-any.whl (880 kB) Requirement already satisfied: pyparsing>=2.2.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib>=2.0.0->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (3.0.6) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB) Collecting setuptools-scm>=4 Downloading setuptools_scm-6.3.2-py3-none-any.whl (33 kB) Collecting pillow>=6.2.0 Downloading Pillow-8.4.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) Requirement already satisfied: six>=1.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from python-dateutil->iCalibrationDB@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/cal_db_interactive.git@2.0.1->-r docs/requirements.txt (line 1)) (1.16.0) Collecting scipy>=1.0 Downloading scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 MB) Collecting pandas>=0.23 Downloading pandas-1.3.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB) Collecting astcheck>=0.2.3 Downloading astcheck-0.3.0-py3-none-any.whl (4.9 kB) Collecting entrypoints Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting tqdm Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB) Collecting decorator Downloading decorator-5.1.0-py3-none-any.whl (9.1 kB) Collecting psutil Downloading psutil-5.8.0-cp38-cp38-manylinux2010_x86_64.whl (296 kB) Collecting ipykernel>=4.4 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matplotlib_inline-0.1.3-py3-none-any.whl (8.2 kB) Requirement already satisfied: pygments in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (2.3.1) Collecting jedi>=0.16 Downloading jedi-0.18.1-py2.py3-none-any.whl (1.6 MB) Collecting mistune<2,>=0.8.1 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting pygments Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Requirement already satisfied: jinja2>=2.4 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert->nbparameterise@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/nbparameterise.git@0.3->-r docs/requirements.txt (line 2)) (3.0.3) Collecting nbformat>=4.4 Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB) Collecting bleach Downloading bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting testpath Downloading testpath-0.5.0-py3-none-any.whl (84 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.9-py3-none-any.whl (69 kB) Collecting jupyter-core Downloading jupyter_core-4.9.1-py3-none-any.whl (86 kB) Requirement already satisfied: pip>=8.1.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from pypandoc->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (21.3.1) Requirement already satisfied: wheel>=0.25.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from pypandoc->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (0.37.0) Collecting debugpy<2.0,>=1.0.0 Downloading debugpy-1.5.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.9 MB) Collecting parso<0.9.0,>=0.8.0 Downloading parso-0.8.2-py2.py3-none-any.whl (94 kB) Requirement already satisfied: MarkupSafe>=2.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from jinja2>=2.4->nbconvert->nbparameterise@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/detectors/nbparameterise.git@0.3->-r docs/requirements.txt (line 2)) (2.0.1) Collecting nest-asyncio>=1.5 Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-4.2.1-py3-none-any.whl (69 kB) Requirement already satisfied: pytz>=2017.3 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from pandas>=0.23->seaborn>=0.7.1->XFELDetectorAnalysis@ git+https://xcalgitlab:dxh5vE8fFsEJHvatXjsV@git.xfel.eu/gitlab/karaboDevices/pyDetLib.git@2.5.6-2.10.0#subdirectory=lib->-r docs/requirements.txt (line 3)) (2021.3) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting wcwidth Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB) Collecting tomli>=1.0.0 Downloading tomli-1.2.2-py3-none-any.whl (12 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 Downloading pyrsistent-0.18.0-cp38-cp38-manylinux1_x86_64.whl (118 kB) Collecting attrs>=17.4.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting importlib-resources>=1.4.0 Downloading importlib_resources-5.4.0-py3-none-any.whl (28 kB) Collecting zipp>=3.1.0 Downloading zipp-3.6.0-py3-none-any.whl (5.3 kB) Building wheels for collected packages: iCalibrationDB, nbparameterise, XFELDetectorAnalysis, pypandoc Building wheel for iCalibrationDB (setup.py): started Building wheel for iCalibrationDB (setup.py): finished with status 'done' Created wheel for iCalibrationDB: filename=iCalibrationDB-2.0.1-py3-none-any.whl size=30882 sha256=3fd50d01a18a0e2cee37f07222fcfb83ac56fb9a4844be1b33b32b06d2bca8e6 Stored in directory: /tmp/pip-ephem-wheel-cache-nzw57i5q/wheels/55/8f/f1/79e5f9dc42da804e18fd54d1621f39b935fd8cb4a003e55a87 Building wheel for nbparameterise (pyproject.toml): started Building wheel for nbparameterise (pyproject.toml): finished with status 'done' Created wheel for nbparameterise: filename=nbparameterise-0.2-py3-none-any.whl size=5373 sha256=a3f62877e2cdc86e4ba0503482ea80ce72b97bbef5b17302aa05febebad5e36a Stored in directory: /tmp/pip-ephem-wheel-cache-nzw57i5q/wheels/ce/de/ab/8eb9a9b5c01421af38fa56aed6e0f260cf6dee5fc95d07f1b7 Building wheel for XFELDetectorAnalysis (pyproject.toml): started Building wheel for XFELDetectorAnalysis (pyproject.toml): finished with status 'done' Created wheel for XFELDetectorAnalysis: filename=XFELDetectorAnalysis-0.1-cp38-cp38-linux_x86_64.whl size=888956 sha256=66388fd532965c27c617ba4b25c1e0940b00029a3125bb4af2bc2550998fad44 Stored in directory: /tmp/pip-ephem-wheel-cache-nzw57i5q/wheels/3f/2f/c4/b6bf720ef99b9ea33158399c864ebd00aba3c9c524c793819f Building wheel for pypandoc (setup.py): started Building wheel for pypandoc (setup.py): finished with status 'done' Created wheel for pypandoc: filename=pypandoc-1.6.4-py3-none-any.whl size=17417 sha256=ee82cf8203feef45c4d4935892a871dbbd366ab726ec561b8957b95cba52ed4a Stored in directory: /tmp/pip-ephem-wheel-cache-nzw57i5q/wheels/1d/e4/65/4bcca81dbf6dba03f945a3c3bbf04c348ac3f3894520eb1375 Successfully built iCalibrationDB nbparameterise XFELDetectorAnalysis pypandoc Installing collected packages: zipp, wcwidth, traitlets, pyrsistent, ptyprocess, parso, importlib-resources, attrs, tornado, tomli, pyzmq, python-dateutil, pygments, prompt-toolkit, pickleshare, pexpect, nest-asyncio, matplotlib-inline, jupyter-core, jsonschema, jedi, ipython-genutils, entrypoints, decorator, backcall, webencodings, setuptools-scm, pillow, numpy, nbformat, kiwisolver, jupyter-client, ipython, fonttools, debugpy, cycler, tqdm, testpath, scipy, psutil, pandocfilters, pandas, nbclient, mistune, matplotlib, jupyterlab-pygments, ipykernel, defusedxml, bleach, astcheck, seaborn, pypandoc, nbconvert, ipyparallel, h5py, dill, Cython, brewer2mpl, astsearch, XFELDetectorAnalysis, nbparameterise, iCalibrationDB Attempting uninstall: pygments Found existing installation: Pygments 2.3.1 Uninstalling Pygments-2.3.1: Successfully uninstalled Pygments-2.3.1 Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Successfully installed Cython-0.29.24 XFELDetectorAnalysis-0.1 astcheck-0.3.0 astsearch-0.2.0 attrs-21.2.0 backcall-0.2.0 bleach-4.1.0 brewer2mpl-1.4.1 cycler-0.11.0 debugpy-1.5.1 decorator-5.1.0 defusedxml-0.7.1 dill-0.3.4 entrypoints-0.3 fonttools-4.28.2 h5py-3.6.0 iCalibrationDB-2.0.1 importlib-resources-5.4.0 ipykernel-6.5.1 ipyparallel-8.0.0 ipython-7.29.0 ipython-genutils-0.2.0 jedi-0.18.1 jsonschema-4.2.1 jupyter-client-7.0.6 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 kiwisolver-1.3.2 matplotlib-3.5.0 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.5.9 nbconvert-6.3.0 nbformat-5.1.3 nbparameterise-0.2 nest-asyncio-1.5.1 numpy-1.21.4 pandas-1.3.4 pandocfilters-1.5.0 parso-0.8.2 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.4.0 prompt-toolkit-3.0.22 psutil-5.8.0 ptyprocess-0.7.0 pygments-2.10.0 pypandoc-1.6.4 pyrsistent-0.18.0 python-dateutil-2.8.2 pyzmq-22.3.0 scipy-1.7.2 seaborn-0.11.2 setuptools-scm-6.3.2 testpath-0.5.0 tomli-1.2.2 tornado-6.1 tqdm-4.62.3 traitlets-5.1.1 wcwidth-0.2.5 webencodings-0.5.1 zipp-3.6.0 [rtd-command-info] start-time: 2021-11-22T12:59:41.548659Z, end-time: 2021-11-22T13:00:55.470490Z, duration: 73, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs] Processing /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Requirement already satisfied: astsearch==0.2.0 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) (0.2.0) Collecting jupyter-core==4.6.1 Downloading jupyter_core-4.6.1-py2.py3-none-any.whl (82 kB) Collecting pyyaml==5.3 Downloading PyYAML-5.3.tar.gz (268 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting dynaconf==3.1.4 Downloading dynaconf-3.1.4-py2.py3-none-any.whl (197 kB) Collecting jupyter-client==6.1.7 Downloading jupyter_client-6.1.7-py3-none-any.whl (108 kB) Collecting kafka-python==2.0.2 Downloading kafka_python-2.0.2-py2.py3-none-any.whl (246 kB) Collecting numpy==1.20.3 Downloading numpy-1.20.3-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.4 MB) Collecting ipyparallel==6.2.4 Downloading ipyparallel-6.2.4-py2.py3-none-any.whl (198 kB) Collecting prettytable==0.7.2 Downloading prettytable-0.7.2.zip (28 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pypandoc==1.4 Downloading pypandoc-1.4.tar.gz (27 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting Jinja2==2.11.2 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting matplotlib==3.4.2 Downloading matplotlib-3.4.2-cp38-cp38-manylinux1_x86_64.whl (10.3 MB) Collecting python-dateutil==2.8.1 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting karabo-data==0.7.0 Downloading karabo_data-0.7.0-py3-none-any.whl (126 kB) Collecting iminuit==1.3.8 Downloading iminuit-1.3.8-cp38-cp38-manylinux2010_x86_64.whl (4.3 MB) Collecting nbconvert==5.6.1 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) Collecting sphinx==1.8.5 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting cfelpyutils==1.0.1 Downloading cfelpyutils-1.0.1-py3-none-any.whl (23 kB) Collecting pasha==0.1.0 Downloading pasha-0.1.0-py3-none-any.whl (11 kB) Collecting princess==0.5 Downloading princess-0.5-py3-none-any.whl (4.2 kB) Collecting notebook==6.1.5 Downloading notebook-6.1.5-py3-none-any.whl (9.5 MB) Collecting ipython==7.12.0 Downloading ipython-7.12.0-py3-none-any.whl (777 kB) Collecting tabulate==0.8.6 Downloading tabulate-0.8.6.tar.gz (45 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting gitpython==3.1.0 Downloading GitPython-3.1.0-py3-none-any.whl (450 kB) Collecting scikit-learn==0.22.2.post1 Downloading scikit_learn-0.22.2.post1-cp38-cp38-manylinux1_x86_64.whl (7.0 MB) Collecting scipy==1.7.0 Downloading scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.4 MB) Collecting astcheck==0.2.5 Downloading astcheck-0.2.5-py2.py3-none-any.whl (10 kB) Collecting nbclient==0.5.1 Downloading nbclient-0.5.1-py3-none-any.whl (65 kB) Collecting h5py==3.5.0 Downloading h5py-3.5.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting dill==0.3.0 Downloading dill-0.3.0.tar.gz (151 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting lxml==4.5.0 Downloading lxml-4.5.0-cp38-cp38-manylinux1_x86_64.whl (5.6 MB) Collecting metadata-client==3.0.8 Downloading metadata_client-3.0.8-py3-none-any.whl (109 kB) Collecting pyzmq==19.0.0 Downloading pyzmq-19.0.0-cp38-cp38-manylinux1_x86_64.whl (1.1 MB) Collecting jupyter-console==6.1.0 Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting Cython==0.29.21 Downloading Cython-0.29.21-cp38-cp38-manylinux1_x86_64.whl (1.9 MB) Collecting extra-geom==1.6.0 Downloading EXtra_geom-1.6.0-py3-none-any.whl (77 kB) Collecting ipykernel==5.1.4 Downloading ipykernel-5.1.4-py3-none-any.whl (116 kB) Collecting extra-data==1.4.1 Downloading EXtra_data-1.4.1-py3-none-any.whl (102 kB) Collecting nbformat==5.0.7 Downloading nbformat-5.0.7-py3-none-any.whl (170 kB) Collecting requests==2.22.0 Downloading requests-2.22.0-py2.py3-none-any.whl (57 kB) Collecting docutils==0.17.1 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Requirement already satisfied: ipython-genutils==0.2.0 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) (0.2.0) Collecting sharedmem==0.3.8 Downloading sharedmem-0.3.8.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting traitlets==4.3.3 Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) Collecting nbparameterise==0.5 Downloading nbparameterise-0.5-py3-none-any.whl (6.0 kB) Collecting nbsphinx Downloading nbsphinx-0.8.7-py3-none-any.whl (25 kB) Requirement already satisfied: future in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from cfelpyutils==1.0.1->European-XFEL-Offline-Calibration==1.0) (0.18.2) Requirement already satisfied: pandas in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from extra-data==1.4.1->European-XFEL-Offline-Calibration==1.0) (1.3.4) Collecting karabo-bridge>=0.6 Downloading karabo_bridge-0.6.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting xarray Downloading xarray-0.20.1-py3-none-any.whl (835 kB) Collecting fabio Downloading fabio-0.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.0 MB) Requirement already satisfied: psutil in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from extra-data==1.4.1->European-XFEL-Offline-Calibration==1.0) (5.8.0) Collecting gitdb<5,>=4.0.1 Downloading gitdb-4.0.9-py3-none-any.whl (63 kB) Requirement already satisfied: tornado>=4.2 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipykernel==5.1.4->European-XFEL-Offline-Calibration==1.0) (6.1) Requirement already satisfied: decorator in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipyparallel==6.2.4->European-XFEL-Offline-Calibration==1.0) (5.1.0) Requirement already satisfied: pickleshare in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (0.7.5) Requirement already satisfied: setuptools>=18.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (41.0.1) Collecting setuptools>=18.5 Downloading setuptools-59.2.0-py3-none-any.whl (952 kB) Requirement already satisfied: jedi>=0.10 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (0.18.1) Requirement already satisfied: backcall in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (0.2.0) Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (3.0.22) Requirement already satisfied: pygments in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (2.10.0) Requirement already satisfied: pexpect in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (4.8.0) Requirement already satisfied: MarkupSafe>=0.23 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from Jinja2==2.11.2->European-XFEL-Offline-Calibration==1.0) (2.0.1) Collecting msgpack>=0.5.4 Downloading msgpack-1.0.2-cp38-cp38-manylinux1_x86_64.whl (302 kB) Collecting msgpack-numpy>=0.4.3 Downloading msgpack_numpy-0.4.7.1-py2.py3-none-any.whl (6.7 kB) Requirement already satisfied: cycler>=0.10 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib==3.4.2->European-XFEL-Offline-Calibration==1.0) (0.11.0) Requirement already satisfied: kiwisolver>=1.0.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib==3.4.2->European-XFEL-Offline-Calibration==1.0) (1.3.2) Requirement already satisfied: pillow>=6.2.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib==3.4.2->European-XFEL-Offline-Calibration==1.0) (8.4.0) Requirement already satisfied: pyparsing>=2.2.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from matplotlib==3.4.2->European-XFEL-Offline-Calibration==1.0) (3.0.6) Collecting oauthlib Downloading oauthlib-3.1.1-py2.py3-none-any.whl (146 kB) Requirement already satisfied: pytz in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from metadata-client==3.0.8->European-XFEL-Offline-Calibration==1.0) (2021.3) Collecting oauth2-xfel-client>=6.0 Downloading oauth2_xfel_client-6.0.0-py3-none-any.whl (8.7 kB) Collecting requests-oauthlib Downloading requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB) Requirement already satisfied: nest-asyncio in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbclient==0.5.1->European-XFEL-Offline-Calibration==1.0) (1.5.1) Collecting async-generator Downloading async_generator-1.10-py3-none-any.whl (18 kB) Requirement already satisfied: mistune<2,>=0.8.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (0.8.4) Requirement already satisfied: entrypoints>=0.2.2 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (0.3) Requirement already satisfied: testpath in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (0.5.0) Requirement already satisfied: pandocfilters>=1.4.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (1.5.0) Requirement already satisfied: bleach in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (4.1.0) Requirement already satisfied: defusedxml in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (0.7.1) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from nbformat==5.0.7->European-XFEL-Offline-Calibration==1.0) (4.2.1) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Collecting prometheus-client Downloading prometheus_client-0.12.0-py2.py3-none-any.whl (57 kB) Collecting terminado>=0.8.3 Downloading terminado-0.12.1-py3-none-any.whl (15 kB) Collecting argon2-cffi Downloading argon2_cffi-21.1.0-cp35-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.whl (96 kB) Requirement already satisfied: pip>=8.1.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from pypandoc==1.4->European-XFEL-Offline-Calibration==1.0) (21.3.1) Requirement already satisfied: wheel>=0.25.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from pypandoc==1.4->European-XFEL-Offline-Calibration==1.0) (0.37.0) Requirement already satisfied: six>=1.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from python-dateutil==2.8.1->European-XFEL-Offline-Calibration==1.0) (1.16.0) Collecting idna<2.9,>=2.5 Downloading idna-2.8-py2.py3-none-any.whl (58 kB) Requirement already 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Requirement already satisfied: packaging in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (21.3) Requirement already satisfied: sphinxcontrib-websupport in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (1.2.4) Requirement already satisfied: alabaster<0.8,>=0.7 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (0.7.12) Requirement already satisfied: babel!=2.0,>=1.3 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (2.9.1) Collecting smmap<6,>=3.0.1 Downloading smmap-5.0.0-py3-none-any.whl (24 kB) Requirement already satisfied: parso<0.9.0,>=0.8.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from jedi>=0.10->ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (0.8.2) Requirement already satisfied: importlib-resources>=1.4.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat==5.0.7->European-XFEL-Offline-Calibration==1.0) (5.4.0) Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat==5.0.7->European-XFEL-Offline-Calibration==1.0) (0.18.0) Requirement already satisfied: attrs>=17.4.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat==5.0.7->European-XFEL-Offline-Calibration==1.0) (21.2.0) Requirement already satisfied: wcwidth in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (0.2.5) Requirement already satisfied: ptyprocess in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from terminado>=0.8.3->notebook==6.1.5->European-XFEL-Offline-Calibration==1.0) (0.7.0) Collecting cffi>=1.0.0 Downloading cffi-1.15.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (446 kB) Requirement already satisfied: webencodings in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from bleach->nbconvert==5.6.1->European-XFEL-Offline-Calibration==1.0) (0.5.1) Requirement already satisfied: sphinxcontrib-serializinghtml in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/lib/python3.8/site-packages (from sphinxcontrib-websupport->sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (1.1.5) Collecting pycparser Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB) Requirement already satisfied: zipp>=3.1.0 in /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/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) (3.6.0) Building wheels for collected packages: dill, prettytable, pypandoc, pyyaml, sharedmem, tabulate, European-XFEL-Offline-Calibration, karabo-bridge 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=63b36407621c4e8236b0e4bd92b54422512b62c8da67002c7ef5539fbcbeee5a Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/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=af383a8223ce17158fd280fdfd6870eb02090b90f888e56845c205e32d2f56f5 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/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=16715 sha256=a4eec686aa5adf9573b52e1aa55f9510e15929d9b704a89dce06a7b09bb536a6 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/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=4f161da1cdcd60a4b25e260585748154fa96f24f8f6d07a8f72a88c829d67ee5 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/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=aa8719de61f0255e4ac00add93d7b81569e4737bfe3a3e2a2a0925eab809dda0 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/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=23271 sha256=4064f125609602a4533917c836254d789224ddd93f48268116ba4c4b592f8a81 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/wheels/86/8c/d9/3b6c2f55efaefe656c52b725d2fdc5669085c83444979db8b3 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=945740 sha256=55b1d9281a1964b939eec55cde4f1c609c01174e2f29f61a7744ecc799fa3ae2 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/wheels/22/7d/09/eb4f2a2bc8741186a0b6a6c96994f65acdd8e2af144db3f698 Building wheel for karabo-bridge (setup.py): started Building wheel for karabo-bridge (setup.py): finished with status 'done' Created wheel for karabo-bridge: filename=karabo_bridge-0.6.1-py3-none-any.whl size=23572 sha256=eb074f7eb181ca9b510153502944a581246442cc5d733feb56d969f3ac151165 Stored in directory: /tmp/pip-ephem-wheel-cache-k21rd2ad/wheels/2a/a0/2b/f52b06d2c14fbb8bdcb82677deaa7a5c4d40277f87aab8058c Successfully built dill prettytable pypandoc pyyaml sharedmem tabulate European-XFEL-Offline-Calibration karabo-bridge Installing collected packages: urllib3, traitlets, idna, chardet, setuptools, requests, pyzmq, python-dateutil, pycparser, oauthlib, numpy, msgpack, jupyter-core, smmap, requests-oauthlib, nbformat, msgpack-numpy, jupyter-client, Jinja2, ipython, cffi, async-generator, astcheck, xarray, terminado, Send2Trash, scipy, prometheus-client, oauth2-xfel-client, nbconvert, nbclient, matplotlib, karabo-bridge, joblib, ipykernel, h5py, gitdb, fabio, docutils, cfelpyutils, argon2-cffi, tabulate, sphinx, sharedmem, scikit-learn, pyyaml, pypandoc, princess, prettytable, pasha, notebook, nbparameterise, metadata-client, lxml, karabo-data, kafka-python, jupyter-console, ipyparallel, iminuit, gitpython, extra-geom, extra-data, dynaconf, dill, Cython, nbsphinx, European-XFEL-Offline-Calibration Attempting uninstall: urllib3 Found existing installation: urllib3 1.26.7 Uninstalling urllib3-1.26.7: Successfully uninstalled urllib3-1.26.7 Attempting uninstall: traitlets Found existing installation: traitlets 5.1.1 Uninstalling traitlets-5.1.1: Successfully uninstalled traitlets-5.1.1 Attempting uninstall: idna Found existing installation: idna 3.3 Uninstalling idna-3.3: Successfully uninstalled idna-3.3 Attempting uninstall: setuptools Found existing installation: setuptools 41.0.1 Uninstalling setuptools-41.0.1: Successfully uninstalled setuptools-41.0.1 Attempting uninstall: requests Found existing installation: requests 2.26.0 Uninstalling requests-2.26.0: Successfully uninstalled requests-2.26.0 Attempting uninstall: pyzmq Found existing installation: pyzmq 22.3.0 Uninstalling pyzmq-22.3.0: Successfully uninstalled pyzmq-22.3.0 Attempting uninstall: python-dateutil Found existing installation: python-dateutil 2.8.2 Uninstalling python-dateutil-2.8.2: Successfully uninstalled python-dateutil-2.8.2 Attempting uninstall: numpy Found existing installation: numpy 1.21.4 Uninstalling numpy-1.21.4: Successfully uninstalled numpy-1.21.4 Attempting uninstall: jupyter-core Found existing installation: jupyter-core 4.9.1 Uninstalling jupyter-core-4.9.1: Successfully uninstalled jupyter-core-4.9.1 Attempting uninstall: nbformat Found existing installation: nbformat 5.1.3 Uninstalling nbformat-5.1.3: Successfully uninstalled nbformat-5.1.3 Attempting uninstall: jupyter-client Found existing installation: jupyter-client 7.0.6 Uninstalling jupyter-client-7.0.6: Successfully uninstalled jupyter-client-7.0.6 Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: ipython Found existing installation: ipython 7.29.0 Uninstalling ipython-7.29.0: Successfully uninstalled ipython-7.29.0 Attempting uninstall: astcheck Found existing installation: astcheck 0.3.0 Uninstalling astcheck-0.3.0: Successfully uninstalled astcheck-0.3.0 Attempting uninstall: scipy Found existing installation: scipy 1.7.2 Uninstalling scipy-1.7.2: Successfully uninstalled scipy-1.7.2 Attempting uninstall: nbconvert Found existing installation: nbconvert 6.3.0 Uninstalling nbconvert-6.3.0: Successfully uninstalled nbconvert-6.3.0 Attempting uninstall: nbclient Found existing installation: nbclient 0.5.9 Uninstalling nbclient-0.5.9: Successfully uninstalled nbclient-0.5.9 Attempting uninstall: matplotlib Found existing installation: matplotlib 3.5.0 Uninstalling matplotlib-3.5.0: Successfully uninstalled matplotlib-3.5.0 Attempting uninstall: ipykernel Found existing installation: ipykernel 6.5.1 Uninstalling ipykernel-6.5.1: Successfully uninstalled ipykernel-6.5.1 Attempting uninstall: h5py Found existing installation: h5py 3.6.0 Uninstalling h5py-3.6.0: Successfully uninstalled h5py-3.6.0 Attempting uninstall: docutils Found existing installation: docutils 0.14 Uninstalling docutils-0.14: Successfully uninstalled docutils-0.14 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: pypandoc Found existing installation: pypandoc 1.6.4 Uninstalling pypandoc-1.6.4: Successfully uninstalled pypandoc-1.6.4 Attempting uninstall: nbparameterise Found existing installation: nbparameterise 0.2 Uninstalling nbparameterise-0.2: Successfully uninstalled nbparameterise-0.2 Attempting uninstall: ipyparallel Found existing installation: ipyparallel 8.0.0 Uninstalling ipyparallel-8.0.0: Successfully uninstalled ipyparallel-8.0.0 Attempting uninstall: dill Found existing installation: dill 0.3.4 Uninstalling dill-0.3.4: Successfully uninstalled dill-0.3.4 Attempting uninstall: Cython Found existing installation: Cython 0.29.24 Uninstalling Cython-0.29.24: Successfully uninstalled Cython-0.29.24 Successfully installed Cython-0.29.21 European-XFEL-Offline-Calibration-1.0 Jinja2-2.11.2 Send2Trash-1.8.0 argon2-cffi-21.1.0 astcheck-0.2.5 async-generator-1.10 cfelpyutils-1.0.1 cffi-1.15.0 chardet-3.0.4 dill-0.3.0 docutils-0.17.1 dynaconf-3.1.4 extra-data-1.4.1 extra-geom-1.6.0 fabio-0.12.0 gitdb-4.0.9 gitpython-3.1.0 h5py-3.5.0 idna-2.8 iminuit-1.3.8 ipykernel-5.1.4 ipyparallel-6.2.4 ipython-7.12.0 joblib-1.1.0 jupyter-client-6.1.7 jupyter-console-6.1.0 jupyter-core-4.6.1 kafka-python-2.0.2 karabo-bridge-0.6.1 karabo-data-0.7.0 lxml-4.5.0 matplotlib-3.4.2 metadata-client-3.0.8 msgpack-1.0.2 msgpack-numpy-0.4.7.1 nbclient-0.5.1 nbconvert-5.6.1 nbformat-5.0.7 nbparameterise-0.5 nbsphinx-0.8.7 notebook-6.1.5 numpy-1.20.3 oauth2-xfel-client-6.0.0 oauthlib-3.1.1 pasha-0.1.0 prettytable-0.7.2 princess-0.5 prometheus-client-0.12.0 pycparser-2.21 pypandoc-1.4 python-dateutil-2.8.1 pyyaml-5.3 pyzmq-19.0.0 requests-2.22.0 requests-oauthlib-1.3.0 scikit-learn-0.22.2.post1 scipy-1.7.0 setuptools-59.2.0 sharedmem-0.3.8 smmap-5.0.0 sphinx-1.8.5 tabulate-0.8.6 terminado-0.12.1 traitlets-4.3.3 urllib3-1.25.11 xarray-0.20.1 [rtd-command-info] start-time: 2021-11-22T13:00:56.516913Z, end-time: 2021-11-22T13:00:56.609009Z, duration: 0, exit-code: 0 cat docs/source/conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # European XFEL Offline Calibration documentation build configuration file, created by # sphinx-quickstart on Sun Jun 10 17:32:30 2018. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # # import os # import sys # sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', ] import glob import os import sys from subprocess import Popen sys.path.append(os.path.abspath("../pycalibration/")) p = Popen(["./makeAllDocs.sh"]) p.communicate() import mock autodoc_mock_imports = ['Cython'] MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot','Cython'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = mock.Mock() # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = 'European XFEL Offline Calibration' copyright = '2018, The European XFEL Detector Group' author = 'The European XFEL Detector Group' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = '1.0' # The full version, including alpha/beta/rc tags. release = '1.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # # html_theme = '' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] # The name for this set of Sphinx documents. # " v documentation" by default. # # html_title = 'European XFEL Offline Calibration v1.0' # A shorter title for the navigation bar. Default is the same as html_title. # # html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. # # html_logo = None # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # # html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # # html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # # html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # # html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'EuropeanXFELOfflineCalibrationdoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', 'extraclassoptions': 'openany, oneside', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'EuropeanXFELOfflineCalibration.tex', 'European XFEL Offline Calibration Documentation', 'The European XFEL Detector Group', 'manual', True), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'europeanxfelofflinecalibration', 'European XFEL Offline Calibration Documentation', [author], 1) ] # If true, show URL addresses after external links. # # man_show_urls = False # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'EuropeanXFELOfflineCalibration', 'European XFEL Offline Calibration Documentation', author, 'EuropeanXFELOfflineCalibration', 'One line description of project.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = {'https://docs.python.org/': None} # first install pandoc if necessary, this is mainly meant for the RTD builds try: from nbconvert.utils.pandoc import check_pandoc_version check_pandoc_version() print("Pandoc was found!") except: print("Installing Pandoc!") from subprocess import check_call pandoc_url = "https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb" pandoc_pack = "pandoc-2.2.1-1-amd64.deb" check_call(["wget", pandoc_url]) check_call(["dpkg", "-i", pandoc_pack]) import os from subprocess import check_output from textwrap import dedent, indent import nbformat from nbconvert import RSTExporter # generate the list of available notebooks from xfel_calibrate import notebooks rst_exporter = RSTExporter() ''' with open("available_notebooks.rst", "w") as f: f.write(dedent(""" .. _available_notebooks: Available Notebooks =================== The following notebooks are currently integrated into the European XFEL Offline Calibration tool chain. """)) for detector in sorted(notebooks.notebooks.keys()): values = notebooks.notebooks[detector] f.write("{}\n".format(detector)) f.write("{}\n".format("-"*len(detector))) f.write("\n") for caltype in sorted(values.keys()): data = values[caltype] nbpath = os.path.abspath("{}/../../../{}".format(__file__, data["notebook"])) with open(nbpath, "r") as nf: nb = nbformat.read(nf, as_version=4) def first_markdown_cell(nb): for cell in nb.cells: if cell.cell_type == 'markdown': return cell mdcell = first_markdown_cell(nb) nb.cells = [mdcell] # we only want this single cell body, _ = rst_exporter.from_notebook_node(nb) adjusted = [] # adjust titles for line in body.split("\n"): if line.startswith("=="): line = line.replace("=", "+") if line.startswith("--"): line = line.replace("-", "~") adjusted.append(line) f.write("\n".join(adjusted)) f.write("\n") f.write("To invoke this notebook and display help use:\n\n") f.write(".. code-block:: bash\n\n") f.write(" xfel-calibrate {} {} --help\n\n".format(detector, caltype)) f.write("The full parameter list of this notebook (with defaults is): \n\n") f.write(".. code-block:: bash\n\n") nb_help = ["xfel-calibrate", detector, caltype, "--help"] output = check_output(nb_help).decode('utf8') f.write(indent(output.replace("DETECTOR", detector).replace("TYPE", caltype), " "*4)) f.write("\n\n") ''' # add test results test_artefact_dir = os.path.realpath("../../tests/artefacts") import shutil import textwrap from datetime import datetime from uuid import uuid4 import tabulate from dateutil.parser import parse from lxml import etree def xml_to_rst_report(xml, git_tag, reports=[]): e = etree.fromstring(xml.encode()) rst = [""] rst += ["Test execution for {test_name} on {ex_date}"] test_name, ex_date = e.get("name").split("-") ex_date = parse(ex_date) rst[-1] = rst[-1].format(test_name=test_name, ex_date=ex_date) rst += ["="*len(rst[-1])] rst += [""] num_tests = e.get("tests") num_err = int(e.get("errors")) num_fail = int(e.get("failures")) num_skip = int(e.get("skipped")) # create a summary header if num_err + num_fail == 0: rst += [":header-passed:`✓`"] else: rst += [":header-failed:`❌`"] if num_skip > 0: rst[-1] += ":header-skipped:`⚠`" rst += [""] # give a summary rst += [":Git tag: {git_tag}".format(git_tag=git_tag)] rst += [":Tests: {num_tests}".format(num_tests=num_tests)] rst += [":Errors: {num_err}".format(num_err=num_err)] rst += [":Failures: {num_fail}".format(num_fail=num_fail)] rst += [":Skipped: {num_skip}".format(num_skip=num_skip)] rst += [":Duration: {duration}s".format(duration=e.get("time"))] for rname, rpath in reports: rst += [":Report: `{} <{}>`_".format(rname, rpath)] rst += [""] # now the details rst += ["Detailed Results"] rst += ["-"*len(rst[-1])] rst += [""] detailed_failures = [] rows = [] for child in e: if child.tag != "testcase": continue name = child.get("name") extime = child.get("time") status = ":passed:`passed`" msg = "" etype = "" if len(child): # children are pressent so test failed or skipped detail = child[0] etype = detail.get("type") msg = detail.get("message") if etype == "skip": status = ":skipped:`skipped`" else: status= ":failed:`failed`" detailed_failures.append((name, detail.text)) msg = "\n".join(textwrap.wrap(msg, 20)) row = [status, name, etype, msg, extime ] rows.append(row) header = ["Result", "Test", "Error", "Message", "Duration (s)"] tblrst = tabulate.tabulate(rows, headers=header, tablefmt="rst") rst += tblrst.split("\n") rst += [""] for test, report in detailed_failures: rst += ["Failure report for: {}".format(test)] rst += ["~"*len(rst[-1])] rst += [""] rst += [".. code-block:: python"] rst += textwrap.indent(report, " "*4).split("\n") rst += [""] do_console = False for child in e: if child.tag == "system-out" and len(child.text.strip()): do_console = True break if do_console: # console output rst += ["Console Output"] rst += ["-"*len(rst[-1])] rst += [""] for child in e: if child.tag != "system-out": continue rst += [".. code-block:: console"] rst += textwrap.indent(child.text, " "*4).split("\n") return "\n".join(rst) def sorted_dir(folder): def getmtime(name): path = os.path.join(folder, name) return os.path.getmtime(path) sort = sorted(os.listdir(folder), key=getmtime, reverse=True) return [(s, datetime.fromtimestamp(getmtime(s))) for s in sort] header = """ Test Results ++++++++++++ Results are organized by git commit, and sorted descending by date. Contents: .. toctree:: :maxdepth: 2 """ if not os.path.exists("./test_rsts"): os.makedirs("./test_rsts") ''' with open("test_results.rst", "w") as f: f.write(header) for commit, modtime in sorted_dir(test_artefact_dir): with open("./test_rsts/{}.rst".format(commit), "w") as fr: rst = [".. include:: roles.rst"] rst += [""] rst += ["{} - {}".format(commit[:8], modtime)] rst += ["+"*len(rst[-1])] rst += [""] fr.write("\n".join(rst)) # copy reports pdfs = glob.glob("{}/{}/*/*.pdf".format(test_artefact_dir, commit)) if not os.path.exists("./_static/reports/{}".format(commit)): os.makedirs("./_static/reports/{}".format(commit)) reports = {} for pdf in pdfs: ppath = "{}/{}.pdf".format(commit, uuid4()) shutil.copyfile(pdf, "./_static/reports/{}".format(ppath)) rloc = pdf.split("/")[-2] rlist = reports.get(rloc, []) rname = os.path.basename(pdf).split(".")[0] rlist.append((rname, "../_static/reports/{}".format(ppath))) reports[rloc] = rlist xmls = glob.glob("{}/{}/*/TEST*.xml".format(test_artefact_dir, commit)) for xml in xmls: rloc = xml.split("/")[-2] with open(xml, "r") as xf: xs = xf.read() rst = xml_to_rst_report(xs, commit, reports=reports.get(rloc, [])) fr.write(rst) f.write(" test_rsts/{}\n".format(commit)) ''' def setup(app): app.add_stylesheet('css/test_decorators.css') ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'http://rtd.xfel.eu/websupport' websupport2_static_url = '/static/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "media/", 'STATIC_URL': "/static/", 'PRODUCTION_DOMAIN': "rtd.xfel.eu", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("doc-commonspace", "/en/doc-commonspace/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'european-xfel-offline-calibration', 'name': u'European XFEL Offline Calibration', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'http://rtd.xfel.eu/docs/european-xfel-offline-calibration/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'http://rtd.xfel.eu', 'github_user': 'None', 'proxied_api_host': '/_', 'github_repo': 'None', 'github_version': 'doc/run_rtd', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'doc/run_rtd', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'doc/run_rtd', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'None', 'commit': '9559abb2', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-11-22T13:00:56.746969Z, end-time: 2021-11-22T13:01:00.021887Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/envs/latest/bin/sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 [NbConvertApp] Converting notebook ../../../notebooks/Tutorial/calversion.ipynb to rst [NbConvertApp] Writing 4434 bytes to ./calversion.rst Pandoc was found! loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... [ 9%] _notebooks/calversion reading sources... [ 18%] _notebooks/index reading sources... [ 27%] advanced reading sources... [ 36%] configuration reading sources... [ 45%] how_it_works reading sources... [ 54%] index reading sources... [ 63%] installation reading sources... [ 72%] test_rsts/roles reading sources... [ 81%] testing reading sources... [ 90%] tutorial reading sources... [100%] workflow /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/_notebooks/calversion.rst:2: WARNING: Explicit markup ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/advanced.rst:46: WARNING: Literal block expected; none found. /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/how_it_works.rst:6: WARNING: Unknown target name: "nbconvert". /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/index.rst:11: WARNING: toctree contains reference to nonexisting document 'available_notebooks' /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/testing.rst:116: WARNING: Problems with "include" directive path: InputError: [Errno 2] No such file or directory: 'test_results.rst'. looking for now-outdated files... none found pickling environment... done checking consistency... /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/test_rsts/roles.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[100%] workflow generating indices... genindex/usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/how_it_works.rst:17: WARNING: undefined label: available_notebooks (if the link has no caption the label must precede a section header) /usr/src/app/checkouts/readthedocs.org/user_builds/european-xfel-offline-calibration/checkouts/latest/docs/source/workflow.rst:291: WARNING: undefined label: available_notebooks (if the link has no caption the label must precede a section header) writing additional pages... search copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 8 warnings. The HTML pages are in _build/html.