Read the Docs build information Build id: 25810 Project: test-pycalibration Version: latest Commit: ca97c492a0b90387241c2cd4e04a0e019d1cc6b2 Date: 2023-03-30T07:42:52.575719Z State: finished Success: True [rtd-command-info] start-time: 2023-03-30T07:42:53.676984Z, end-time: 2023-03-30T07:43:10.904529Z, duration: 17, exit-code: 0 git clone --no-single-branch --depth 50 http://git.xfel.eu/calibration/pycalibration.git . Cloning into '.'... [rtd-command-info] start-time: 2023-03-30T07:43:11.273665Z, end-time: 2023-03-30T07:43:12.134195Z, duration: 0, exit-code: 0 git checkout --force origin/doc/writing_new_notebook Note: checking out 'origin/doc/writing_new_notebook'. 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 ca97c492 add calcat screenshots [rtd-command-info] start-time: 2023-03-30T07:43:12.221665Z, end-time: 2023-03-30T07:43:12.284234Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-03-30T07:43:13.852998Z, end-time: 2023-03-30T07:43:18.748298Z, duration: 4, exit-code: 0 python3.8 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest Using base prefix '/home/docs/.pyenv/versions/3.8.0' New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/bin/python3.8 Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2023-03-30T07:43:18.837046Z, end-time: 2023-03-30T07:43:19.753954Z, duration: 0, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/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/test-pycalibration/envs/latest/lib/python3.8/site-packages (23.0.1) [rtd-command-info] start-time: 2023-03-30T07:43:19.837537Z, end-time: 2023-03-30T07:43:44.401125Z, duration: 24, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/bin/python -m pip install --upgrade --no-cache-dir jinja2==2.11.3 markupsafe==2.0.1 Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting jinja2==2.11.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.7/125.7 kB 3.3 MB/s eta 0:00:00 Collecting markupsafe==2.0.1 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 Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 849.5/849.5 kB 18.2 MB/s eta 0:00:00 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 576.0/576.0 kB 181.9 MB/s eta 0:00:00 Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 543.2/543.2 kB 200.0 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 178.0 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 152.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.13-py3-none-any.whl (13 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 152.5 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 196.3 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 138.9 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.3.tar.gz (840 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 227.9 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting requests>=2.0.0 Downloading requests-2.28.2-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 160.0 MB/s eta 0:00:00 Collecting babel!=2.0,>=1.3 Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 119.0 MB/s eta 0:00:00 Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting packaging Downloading packaging-23.0-py3-none-any.whl (42 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 150.6 MB/s eta 0:00:00 Collecting imagesize Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 194.5 MB/s eta 0:00:00 Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting pytz>=2015.7 Downloading pytz-2023.3-py2.py3-none-any.whl (502 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.3/502.3 kB 221.9 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 163.5 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.12.7-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 187.8 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.15-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.9/140.9 kB 196.9 MB/s eta 0:00:00 Collecting charset-normalizer<4,>=2 Downloading charset_normalizer-3.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (195 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 195.9/195.9 kB 211.6 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 164.4 MB/s eta 0:00:00 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=23753 sha256=3f3b56ac07382ecbc4682295d70a05c0d456143f629cde95d0b685e9216eb668 Stored in directory: /tmp/pip-ephem-wheel-cache-ada4ytnc/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=1262646 sha256=0f8842d0a3760efc5ea09826c7f877fac00c35a9581926e9ca51ca51416c7b16 Stored in directory: /tmp/pip-ephem-wheel-cache-ada4ytnc/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-0.18.3-py3-none-any.whl size=492022 sha256=c1f3a3017ff29918a1a592cc8af290e64998da41c4c8e57e79a5f6725ebd4687 Stored in directory: /tmp/pip-ephem-wheel-cache-ada4ytnc/wheels/a0/0b/ee/e6994fadb42c1354dcccb139b0bf2795271bddfe6253ccdf11 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, Pygments, mock, docutils, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pillow, packaging, markupsafe, imagesize, idna, future, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Successfully installed Pygments-2.3.1 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.8.1 docutils-0.14 future-0.18.3 idna-3.4 imagesize-1.4.1 jinja2-2.11.3 markupsafe-2.0.1 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.28.2 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 urllib3-1.26.15 [rtd-command-info] start-time: 2023-03-30T07:43:44.488894Z, end-time: 2023-03-30T07:43:52.496706Z, duration: 8, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting iCalibrationDB@ git+https://ahmedk:rdBwfkjjZr1eVDyAqpYa@git.xfel.eu/detectors/cal_db_interactive.git@2.4.0 Cloning https://ahmedk:****@git.xfel.eu/detectors/cal_db_interactive.git (to revision 2.4.0) to /tmp/pip-install-sohqmpd1/icalibrationdb_44bd401b459b42a2a4a0982bc07893d5 Running command git clone --filter=blob:none --quiet 'https://ahmedk:****@git.xfel.eu/detectors/cal_db_interactive.git' /tmp/pip-install-sohqmpd1/icalibrationdb_44bd401b459b42a2a4a0982bc07893d5 Resolved https://ahmedk:****@git.xfel.eu/detectors/cal_db_interactive.git to commit a94aafeda7a9567645ac72f1e82bd9d849a6361f Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting h5py Downloading h5py-3.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 35.4 MB/s eta 0:00:00 Collecting pyzmq Downloading pyzmq-25.0.2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 234.6 MB/s eta 0:00:00 Collecting python-dateutil Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 224.1 MB/s eta 0:00:00 Collecting numpy>=1.14.5 Downloading numpy-1.24.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 137.8 MB/s eta 0:00:00 Requirement already satisfied: six>=1.5 in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from python-dateutil->iCalibrationDB@ git+https://ahmedk:rdBwfkjjZr1eVDyAqpYa@git.xfel.eu/detectors/cal_db_interactive.git@2.4.0->-r docs/requirements.txt (line 1)) (1.16.0) Building wheels for collected packages: iCalibrationDB Building wheel for iCalibrationDB (setup.py): started Building wheel for iCalibrationDB (setup.py): finished with status 'done' Created wheel for iCalibrationDB: filename=iCalibrationDB-2.4.0-py3-none-any.whl size=33836 sha256=e8c6d4f76363bdc4b0258216669d3ec1e9625d337b1139f3ff15b367491c63c2 Stored in directory: /tmp/pip-ephem-wheel-cache-o8p0p21s/wheels/ea/cb/4c/d1dbe0abb7db270f4319cba95be368eb5157ec89fea1d21c2c Successfully built iCalibrationDB Installing collected packages: pyzmq, python-dateutil, numpy, h5py, iCalibrationDB Successfully installed h5py-3.8.0 iCalibrationDB-2.4.0 numpy-1.24.2 python-dateutil-2.8.2 pyzmq-25.0.2 [rtd-command-info] start-time: 2023-03-30T07:43:52.577952Z, end-time: 2023-03-30T07:44:56.617491Z, duration: 64, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/bin/python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs] Processing /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/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' Collecting nbparameterise==0.6 Downloading nbparameterise-0.6-py3-none-any.whl (7.7 kB) Collecting xarray==2022.3.0 Downloading xarray-2022.3.0-py3-none-any.whl (870 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 870.9/870.9 kB 11.0 MB/s eta 0:00:00 Collecting jupyter-client==7.3.4 Downloading jupyter_client-7.3.4-py3-none-any.whl (132 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 132.1/132.1 kB 196.8 MB/s eta 0:00:00 Collecting nbclient==0.5.1 Downloading nbclient-0.5.1-py3-none-any.whl (65 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.7/65.7 kB 156.7 MB/s eta 0:00:00 Collecting pasha==0.1.1 Downloading pasha-0.1.1-py3-none-any.whl (11 kB) Collecting calibration-client==11.2.0 Downloading calibration_client-11.2.0-py3-none-any.whl (80 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.4/80.4 kB 196.3 MB/s eta 0:00:00 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 ipython==7.12.0 Downloading ipython-7.12.0-py3-none-any.whl (777 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 777.3/777.3 kB 152.4 MB/s eta 0:00:00 Collecting Cython==0.29.21 Downloading Cython-0.29.21-cp38-cp38-manylinux1_x86_64.whl (1.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 102.3 MB/s eta 0:00:00 Collecting scikit-learn==0.22.2.post1 Downloading scikit_learn-0.22.2.post1-cp38-cp38-manylinux1_x86_64.whl (7.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.0/7.0 MB 140.4 MB/s eta 0:00:00 Collecting Jinja2==2.11.2 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.8/125.8 kB 206.3 MB/s eta 0:00:00 Collecting extra-data==1.12.0 Downloading EXtra_data-1.12.0-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 204.9 MB/s eta 0:00:00 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 nbconvert==5.6.1 Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 455.1/455.1 kB 214.6 MB/s eta 0:00:00 Collecting tabulate==0.8.6 Downloading tabulate-0.8.6.tar.gz (45 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.5/45.5 kB 147.8 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.6/5.6 MB 139.0 MB/s eta 0:00:00 Collecting h5py==3.5.0 Downloading h5py-3.5.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 159.5 MB/s eta 0:00:00 Collecting pyzmq==23.2.0 Downloading pyzmq-23.2.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 208.1 MB/s eta 0:00:00 Collecting gitpython==3.1.0 Downloading GitPython-3.1.0-py3-none-any.whl (450 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 450.7/450.7 kB 167.5 MB/s eta 0:00:00 Collecting jupyter-console==6.1.0 Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting sphinx==1.8.5 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 201.3 MB/s eta 0:00:00 Collecting requests==2.22.0 Downloading requests-2.22.0-py2.py3-none-any.whl (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.0/58.0 kB 141.4 MB/s eta 0:00:00 Requirement already satisfied: python-dateutil==2.8.2 in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from European-XFEL-Offline-Calibration==1.0) (2.8.2) Collecting cfelpyutils==2.0.6 Downloading cfelpyutils-2.0.6-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (511 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 511.2/511.2 kB 198.9 MB/s eta 0:00:00 Collecting scipy==1.7.0 Downloading scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 28.4/28.4 MB 152.4 MB/s eta 0:00:00 Collecting matplotlib==3.4.2 Downloading matplotlib-3.4.2-cp38-cp38-manylinux1_x86_64.whl (10.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 144.1 MB/s eta 0:00:00 Collecting ipython-genutils==0.2.0 Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Collecting extra-geom==1.8.0 Downloading EXtra_geom-1.8.0-py3-none-any.whl (83 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.3/83.3 kB 168.5 MB/s eta 0:00:00 Collecting docutils==0.17.1 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 232.2 MB/s eta 0:00:00 Collecting princess==0.5 Downloading princess-0.5-py3-none-any.whl (4.2 kB) Collecting jupyter-core==4.10.0 Downloading jupyter_core-4.10.0-py3-none-any.whl (87 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.3/87.3 kB 200.7 MB/s eta 0:00:00 Collecting dill==0.3.0 Downloading dill-0.3.0.tar.gz (151 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 151.4/151.4 kB 212.0 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting nbformat==5.0.7 Downloading nbformat-5.0.7-py3-none-any.whl (170 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.6/170.6 kB 198.8 MB/s eta 0:00:00 Collecting EXtra-redu==0.0.7 Downloading EXtra_redu-0.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (460 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 460.9/460.9 kB 204.4 MB/s eta 0:00:00 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 notebook==6.1.5 Downloading notebook-6.1.5-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 154.2 MB/s eta 0:00:00 Collecting kafka-python==2.0.2 Downloading kafka_python-2.0.2-py2.py3-none-any.whl (246 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 246.5/246.5 kB 213.8 MB/s eta 0:00:00 Collecting ipykernel==5.1.4 Downloading ipykernel-5.1.4-py3-none-any.whl (116 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 116.8/116.8 kB 190.8 MB/s eta 0:00:00 Collecting traitlets==4.3.3 Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 75.7/75.7 kB 188.9 MB/s eta 0:00:00 Collecting astcheck==0.3.0 Downloading astcheck-0.3.0-py3-none-any.whl (4.9 kB) Collecting pyyaml==5.3 Downloading PyYAML-5.3.tar.gz (268 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 268.2/268.2 kB 205.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting env-cache==0.1 Downloading env_cache-0.1-py2.py3-none-any.whl (4.7 kB) Collecting ipyparallel==6.2.4 Downloading ipyparallel-6.2.4-py2.py3-none-any.whl (198 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 198.6/198.6 kB 198.6 MB/s eta 0:00:00 Collecting metadata-client==3.0.8 Downloading metadata_client-3.0.8-py3-none-any.whl (109 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 109.9/109.9 kB 175.2 MB/s eta 0:00:00 Requirement already satisfied: markupsafe==2.0.1 in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from European-XFEL-Offline-Calibration==1.0) (2.0.1) Collecting iminuit==1.3.8 Downloading iminuit-1.3.8-cp38-cp38-manylinux2010_x86_64.whl (4.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 170.7 MB/s eta 0:00:00 Collecting dynaconf==3.1.4 Downloading dynaconf-3.1.4-py2.py3-none-any.whl (197 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 197.5/197.5 kB 201.0 MB/s eta 0:00:00 Collecting numpy==1.20.3 Downloading numpy-1.20.3-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.4/15.4 MB 135.4 MB/s eta 0:00:00 Collecting nbsphinx Downloading nbsphinx-0.9.1-py3-none-any.whl (30 kB) Collecting oauthlib Downloading oauthlib-3.2.2-py3-none-any.whl (151 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 151.7/151.7 kB 189.1 MB/s eta 0:00:00 Requirement already satisfied: pytz in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from calibration-client==11.2.0->European-XFEL-Offline-Calibration==1.0) (2023.3) Collecting oauth2-xfel-client>=6.1 Downloading oauth2_xfel_client-6.1.1-py3-none-any.whl (9.8 kB) Collecting requests-oauthlib Downloading requests_oauthlib-1.3.1-py2.py3-none-any.whl (23 kB) Collecting pandas>=1.1.5 Downloading pandas-1.5.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 130.0 MB/s eta 0:00:00 Collecting mypy-extensions>=0.4.3 Downloading mypy_extensions-1.0.0-py3-none-any.whl (4.7 kB) Collecting euxfel-bunch-pattern>=0.6 Downloading euxfel_bunch_pattern-0.6-py3-none-any.whl (5.3 kB) Collecting gitdb<5,>=4.0.1 Downloading gitdb-4.0.10-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.7/62.7 kB 174.4 MB/s eta 0:00:00 Collecting tornado>=4.2 Downloading tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (423 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 424.0/424.0 kB 225.3 MB/s eta 0:00:00 Collecting decorator Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.38-py3-none-any.whl (385 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.8/385.8 kB 228.6 MB/s eta 0:00:00 Requirement already satisfied: pygments in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from ipython==7.12.0->European-XFEL-Offline-Calibration==1.0) (2.3.1) Collecting pygments Downloading Pygments-2.14.0-py3-none-any.whl (1.1 MB) 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Collecting pkgutil-resolve-name>=1.3.10 Downloading pkgutil_resolve_name-1.3.10-py3-none-any.whl (4.7 kB) Collecting wcwidth Downloading wcwidth-0.2.6-py2.py3-none-any.whl (29 kB) Collecting ptyprocess Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Collecting argon2-cffi-bindings Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.2/86.2 kB 173.5 MB/s eta 0:00:00 Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Requirement already satisfied: sphinxcontrib-serializinghtml in /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/envs/latest/lib/python3.8/site-packages (from sphinxcontrib-websupport->sphinx==1.8.5->European-XFEL-Offline-Calibration==1.0) (1.1.5) Collecting zipp>=3.1.0 Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB) Collecting cffi>=1.0.1 Downloading cffi-1.15.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (442 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 442.7/442.7 kB 221.0 MB/s eta 0:00:00 Collecting pycparser Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 184.4 MB/s eta 0:00:00 Building wheels for collected packages: dill, prettytable, pypandoc, pyyaml, sharedmem, tabulate, European-XFEL-Offline-Calibration 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=79fd803a9bf020b5e9eb153f575bf82c305f86c37dd732cb5c60a58eb9e67a0d Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=02f4639bbd46382286161b359a8c005adfdcfaa7fb4c398695d28953a6f6779e Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=53e6e9f4a12645f20591b8079623b122e0c1fa6cc0429b26a5423da0b82f9cee Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=07a1d68b9edce2f380d2dc5d053cb3b759f626c849b0b947d1e8415bfe835843 Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=1b31b08355d5f9069a0efca3b2187c0d9b3b7cc9cc280232fc6f916f2c263f51 Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=3522285f9abbe7b1bc7c6b86882cbae0c5ffe91bd53d7d4a57a6c797db9d2436 Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/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=1622287 sha256=6899b89ebe02403e5b28cbaf4bea0ef664eb5296fdc5fe154ff5670966ac3c65 Stored in directory: /tmp/pip-ephem-wheel-cache-wa7ghbyx/wheels/72/93/0a/52bfcaf2aa78260765507f5ca61897968faedf7c76a31dba2d Successfully built dill prettytable pypandoc pyyaml sharedmem tabulate European-XFEL-Offline-Calibration Installing collected packages: webencodings, wcwidth, tabulate, Send2Trash, ptyprocess, prettytable, pickleshare, mistune, kafka-python, ipython-genutils, env-cache, dynaconf, chardet, backcall, zipp, urllib3, tornado, testpath, smmap, setuptools, pyzmq, pyyaml, pyrsistent, pyparsing, pygments, pycparser, prompt-toolkit, prometheus-client, pkgutil-resolve-name, pillow, pexpect, parso, pandocfilters, oauthlib, numpy, nest-asyncio, mypy-extensions, lxml, kiwisolver, joblib, Jinja2, idna, entrypoints, docutils, dill, defusedxml, decorator, Cython, cycler, bleach, attrs, async-generator, astcheck, traitlets, terminado, sharedmem, scipy, requests, pypandoc, pasha, pandas, matplotlib, jedi, importlib-resources, iminuit, h5py, gitdb, euxfel-bunch-pattern, cffi, xarray, sphinx, scikit-learn, requests-oauthlib, jupyter-core, jsonschema, 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, nbsphinx, 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: pyzmq Found existing installation: pyzmq 25.0.2 Uninstalling pyzmq-25.0.2: Successfully uninstalled pyzmq-25.0.2 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 Attempting uninstall: numpy Found existing installation: numpy 1.24.2 Uninstalling numpy-1.24.2: Successfully uninstalled numpy-1.24.2 Attempting uninstall: Jinja2 Found existing installation: Jinja2 2.11.3 Uninstalling Jinja2-2.11.3: Successfully uninstalled Jinja2-2.11.3 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: h5py Found existing installation: h5py 3.8.0 Uninstalling h5py-3.8.0: Successfully uninstalled h5py-3.8.0 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 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 nbsphinx-0.8.8 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 pygments-2.14.0 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-67.6.1 sharedmem-0.3.8 smmap-5.0.0 sphinx-1.8.5 tabulate-0.8.6 terminado-0.17.1 testpath-0.6.0 tornado-6.2 traitlets-4.3.3 urllib3-1.25.11 wcwidth-0.2.6 webencodings-0.5.1 xarray-2022.3.0 zipp-3.15.0 [rtd-command-info] start-time: 2023-03-30T07:44:57.312566Z, end-time: 2023-03-30T07:44:57.372245Z, 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. import glob # 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('.')) import os import shutil import sys import textwrap from datetime import datetime from subprocess import Popen, check_output from textwrap import dedent, indent from uuid import uuid4 import nbformat import tabulate from dateutil.parser import parse from lxml import etree from nbconvert import RSTExporter # generate the list of available notebooks from xfel_calibrate import notebooks # -- 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 = [ 'nbsphinx', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', ] sys.path.append(os.path.abspath("../pycalibration/")) p = Popen(["./makeAllDocs.sh"]) p.communicate() # 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 = 'sphinx_rtd_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]) 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()): # Avoid having test notebooks in detector notebooks documentations. if "TEST" in detector.upper(): continue 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/legacy/artefacts") 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/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'test-pycalibration', 'name': u'test_pycalibration', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'http://rtd.xfel.eu/docs/test-pycalibration/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/writing_new_notebook', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'doc/writing_new_notebook', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'doc/writing_new_notebook', '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': 'ca97c492', } 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: 2023-03-30T07:44:57.464107Z, end-time: 2023-03-30T07:45:52.935995Z, duration: 55, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/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] Support files will be in calversion_files/ [NbConvertApp] Making directory ./calversion_files [NbConvertApp] Making directory ./calversion_files [NbConvertApp] Writing 3752 bytes to ./calversion.rst Matplotlib is building the font cache; this may take a moment. 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Text in column margin in table line 6. ================ =============================================================== ========================================================================================== Parameter name To be used for Special purpose ---------------- --------------------------------------------------------------- ------------------------------------------------------------------------------------------ in_folder the input path data resides in, usually without a run number out_folder path to write data out to, usually without a run number reports can be placed here metadata_folder directory path for calibration metadata file with local constants. run(s) which XFEL DAQ runs to use, often ranges are allowed karabo_id detector karabo name to access detector files and constants. karabo_da refers to detector's modules data aggregator names to process. modules refers to the detector's modules indices to process, ranges often ok. sequences sequence files for the XFEL DAQ system, ranges are often ok. local_output write calibration constant from file, not database db_output write calibration constant from database, not file saves the database from unintentional constant injections during developments or testing. ================ =============================================================== ========================================================================================== /usr/src/app/checkouts/readthedocs.org/user_builds/test-pycalibration/checkouts/latest/docs/source/workflow.rst:45: WARNING: Unknown target name: "how_to_write_xfel_calibrate_notebook_nbc". pickling environment... done checking consistency... done preparing documents... done writing output... 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