Started by upstream project "Trigger" build number 132 originally caused by: Started by timer [Pipeline] Start of Pipeline [Pipeline] node Running on testintegration in /home/omero/workspace/OMERO-guides-push [Pipeline] { [Pipeline] library Loading library recursiveMerge@master Attempting to resolve master from remote references... > git --version # timeout=10 > git --version # 'git version 2.47.3' > git ls-remote -- https://github.com/ome/jenkins-library-recursivemerge.git # timeout=10 Found match: refs/heads/master revision af267baf738bf563fa6d26d1f37a3717d679c59f The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /var/jenkins_home/jobs/OMERO-guides-push/workspace@libs/e9d96de4efbb3e39a2ce24824e54985c7c2760a6ed46c5415ea0aa1fd1e18d41/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/ome/jenkins-library-recursivemerge.git # timeout=10 Fetching without tags Fetching upstream changes from https://github.com/ome/jenkins-library-recursivemerge.git > git --version # timeout=10 > git --version # 'git version 2.47.3' > git fetch --no-tags --force --progress -- https://github.com/ome/jenkins-library-recursivemerge.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Checking out Revision af267baf738bf563fa6d26d1f37a3717d679c59f (master) > git config core.sparsecheckout # timeout=10 > git checkout -f af267baf738bf563fa6d26d1f37a3717d679c59f # timeout=10 Commit message: "Merge pull request #19 from will-moore/readme" > git rev-list --no-walk af267baf738bf563fa6d26d1f37a3717d679c59f # timeout=10 [Pipeline] checkout The recommended git tool is: NONE No credentials specified Fetching changes from the remote Git repository > git rev-parse --resolve-git-dir /home/omero/workspace/OMERO-guides-push/.git # timeout=10 > git config remote.origin.url https://github.com/ome/omero-guides.git # timeout=10 Fetching upstream changes from https://github.com/ome/omero-guides.git > git --version # timeout=10 > git --version # 'git version 2.52.0' > git fetch --tags --force --progress -- https://github.com/ome/omero-guides.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Checking out Revision a1269029831376087e38a5f4e73ec27a95339faf (refs/remotes/origin/master) > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f a1269029831376087e38a5f4e73ec27a95339faf # timeout=10 Commit message: "Merge pull request #309 from ome/dependabot/submodules/download-a27d196" > git rev-list --no-walk a1269029831376087e38a5f4e73ec27a95339faf # timeout=10 Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 > git clean -fdx # timeout=10 > git submodule foreach --recursive git reset --hard # timeout=10 > git submodule foreach --recursive git clean -fdx # timeout=10 > git remote # timeout=10 > git submodule init # timeout=10 > git submodule sync # timeout=10 > git config --get remote.origin.url # timeout=10 > git submodule init # timeout=10 > git config -f .gitmodules --get-regexp ^submodule\.(.+)\.url # timeout=10 > git config --get submodule.cellprofiler.url # timeout=10 > git config -f .gitmodules --get submodule.cellprofiler.path # timeout=10 > git config --get submodule.matlab.url # timeout=10 > git config -f .gitmodules --get submodule.matlab.path # timeout=10 > git config --get submodule.qupath.url # timeout=10 > git config -f .gitmodules --get submodule.qupath.path # timeout=10 > git config --get submodule.fiji.url # timeout=10 > git config -f .gitmodules --get submodule.fiji.path # timeout=10 > git config --get submodule.orbit.url # timeout=10 > git config -f .gitmodules --get submodule.orbit.path # timeout=10 > git config --get submodule.r.url # timeout=10 > git config -f .gitmodules --get submodule.r.path # timeout=10 > git config --get submodule.figure.url # timeout=10 > git config -f .gitmodules --get submodule.figure.path # timeout=10 > git config --get submodule.trackmate.url # timeout=10 > git config -f .gitmodules --get submodule.trackmate.path # timeout=10 > git config --get submodule.python.url # timeout=10 > git config -f .gitmodules --get submodule.python.path # timeout=10 > git config --get submodule.parade.url # timeout=10 > git config -f .gitmodules --get submodule.parade.path # timeout=10 > git config --get submodule.fpbioimage.url # timeout=10 > git config -f .gitmodules --get submodule.fpbioimage.path # timeout=10 > git config --get submodule.iviewer.url # timeout=10 > git config -f .gitmodules --get submodule.iviewer.path # timeout=10 > git config --get submodule.upload.url # timeout=10 > git config -f .gitmodules --get submodule.upload.path # timeout=10 > git config --get submodule.ilastik.url # timeout=10 > git config -f .gitmodules --get submodule.ilastik.path # timeout=10 > git config --get submodule.introduction.url # timeout=10 > git config -f .gitmodules --get submodule.introduction.path # timeout=10 > git config --get submodule.download.url # timeout=10 > git config -f .gitmodules --get submodule.download.path # timeout=10 > git config --get submodule.java.url # timeout=10 > git config -f .gitmodules --get submodule.java.path # timeout=10 > git config --get submodule.scripts.url # timeout=10 > git config -f .gitmodules --get submodule.scripts.path # timeout=10 > git config --get submodule.mde.url # timeout=10 > git config -f .gitmodules --get submodule.mde.path # timeout=10 > git submodule update --init --recursive cellprofiler # timeout=10 > git submodule update --init --recursive matlab # timeout=10 > git submodule update --init --recursive qupath # timeout=10 > git submodule update --init --recursive fiji # timeout=10 > git submodule update --init --recursive orbit # timeout=10 > git submodule update --init --recursive r # timeout=10 > git submodule update --init --recursive figure # timeout=10 > git submodule update --init --recursive trackmate # timeout=10 > git submodule update --init --recursive python # timeout=10 > git submodule update --init --recursive parade # timeout=10 > git submodule update --init --recursive fpbioimage # timeout=10 > git submodule update --init --recursive iviewer # timeout=10 > git submodule update --init --recursive upload # timeout=10 > git submodule update --init --recursive ilastik # timeout=10 > git submodule update --init --recursive introduction # timeout=10 > git submodule update --init --recursive download # timeout=10 [Pipeline] pwd [Pipeline] sh + mkdir -p build + echo build [Pipeline] sh + pushd build ~/workspace/OMERO-guides-push/build ~/workspace/OMERO-guides-push + tar -zxf - + curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz + popd ~/workspace/OMERO-guides-push + python3.11 -m venv build/venv > git submodule update --init --recursive java # timeout=10 > git submodule update --init --recursive scripts # timeout=10 > git submodule update --init --recursive mde # timeout=10 + . build/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-guides-push/build/venv ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/OMERO-guides-push/build/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(venv) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(venv) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + python3.11 -m pip install -U pip Requirement already satisfied: pip in ./build/venv/lib64/python3.11/site-packages (22.3.1) Collecting pip Using cached pip-26.2.1-py3-none-any.whl (1.8 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 22.3.1 Uninstalling pip-22.3.1: Successfully uninstalled pip-22.3.1 Successfully installed pip-26.2.1 + python3.11 -m pip install scc Collecting scc Using cached scc-0.20.0-py3-none-any.whl.metadata (3.6 kB) Collecting PyGithub>=1.54 (from scc) Using cached pygithub-2.10.0-py3-none-any.whl.metadata (3.9 kB) Collecting PyYAML>=5.1 (from scc) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Collecting future (from scc) Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) Collecting ruamel.yaml (from scc) Using cached ruamel_yaml-0.19.1-py3-none-any.whl.metadata (16 kB) Collecting ruamel.yaml.jinja2 (from scc) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl.metadata (2.9 kB) Collecting six (from scc) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting urllib3<2 (from scc) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting yaclifw<0.3,>=0.2.0 (from scc) Using cached yaclifw-0.2.0-py3-none-any.whl Collecting pynacl>=1.4.0 (from PyGithub>=1.54->scc) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl.metadata (10.0 kB) Collecting requests>=2.14.0 (from PyGithub>=1.54->scc) Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pyjwt-2.15.1-py3-none-any.whl.metadata (3.5 kB) Collecting typing-extensions>=4.5.0 (from PyGithub>=1.54->scc) Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl.metadata (4.4 kB) Collecting cffi>=2.0.0 (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.5 kB) Collecting pycparser (from cffi>=2.0.0->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pycparser-3.11-py3-none-any.whl.metadata (8.2 kB) Collecting charset_normalizer<4,>=2 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (46 kB) Collecting idna<4,>=2.5 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached idna-3.20-py3-none-any.whl.metadata (7.2 kB) Collecting certifi>=2023.5.7 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB) Using cached scc-0.20.0-py3-none-any.whl (48 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached pygithub-2.10.0-py3-none-any.whl (455 kB) Using cached pyjwt-2.15.1-py3-none-any.whl (33 kB) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl (4.8 MB) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (217 kB) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl (1.4 MB) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB) Using cached requests-2.34.2-py3-none-any.whl (73 kB) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (269 kB) Using cached idna-3.20-py3-none-any.whl (69 kB) Using cached certifi-2026.7.22-py3-none-any.whl (136 kB) Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Using cached pycparser-3.11-py3-none-any.whl (51 kB) Using cached ruamel_yaml-0.19.1-py3-none-any.whl (118 kB) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Installing collected packages: urllib3, typing-extensions, six, ruamel.yaml, PyYAML, pyjwt, pycparser, idna, future, charset_normalizer, certifi, yaclifw, ruamel.yaml.jinja2, requests, cffi, pynacl, cryptography, PyGithub, scc Successfully installed PyGithub-2.10.0 PyYAML-6.0.3 certifi-2026.7.22 cffi-2.1.1 charset_normalizer-3.5.2 cryptography-50.0.2 future-1.0.0 idna-3.20 pycparser-3.11 pyjwt-2.15.1 pynacl-1.6.2 requests-2.34.2 ruamel.yaml-0.19.1 ruamel.yaml.jinja2-0.2.7 scc-0.20.0 six-1.17.0 typing-extensions-4.16.0 urllib3-1.26.20 yaclifw-0.2.0 [Pipeline] sh + export BASE_REPO=omero-guides.git + BASE_REPO=omero-guides.git + export BASE_BRANCH=master + BASE_BRANCH=master + export VERSION_LOG=/home/omero/workspace/OMERO-guides-push/build/version.tsv + VERSION_LOG=/home/omero/workspace/OMERO-guides-push/build/version.tsv + . build/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-guides-push/build/venv ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/OMERO-guides-push/build/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(venv) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(venv) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + '[' merge_ci '!=' null ']' + export PUSH_BRANCH=merge_ci + PUSH_BRANCH=merge_ci + '[' null '!=' null ']' + export STATUS=success-only 'MERGE_OPTIONS=-vvv --no-ask --reset --comment' + STATUS=success-only + MERGE_OPTIONS='-vvv --no-ask --reset --comment' + bash build/build-infra-master/recursive-merge Merge base repository (no submodule updates) 2026-10-17 00:23:01,798 [ scc.config] DEBUG Found github.token 2026-10-17 00:23:01,799 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443 2026-10-17 00:23:02,036 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:23:02,483 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:23:02,946 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None 2026-10-17 00:23:02,947 [ scc.gh] DEBUG 4222 remaining from 5000 (Reset at 00:10 2026-10-17 00:23:02,947 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:02,958 [ scc.git] DEBUG Check current status 2026-10-17 00:23:02,958 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:02,993 [ scc.git] DEBUG a126902 Merge pull request #309 from ome/dependabot/submodules/download-a27d196 2026-10-17 00:23:02,994 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:03,187 [ scc.git] DEBUG 248e8cbfb0372b3d3be2d82cfe9234dd2e25c140 cellprofiler (v0.4.0-32-g248e8cb) 2026-10-17 00:23:03,305 [ scc.git] DEBUG a27d196bee4a96b586246dc5d94ef07db7c5c0f8 download (heads/master) 2026-10-17 00:23:03,364 [ scc.git] DEBUG 654d43b5ef64f56bd6a99c69a9c98cbb5c8f76a7 figure (v0.1.0-55-g654d43b) 2026-10-17 00:23:03,447 [ scc.git] DEBUG 86f00e3e570d62226b02da1dc0cc639c389c7104 fiji (v0.2.1-89-g86f00e3) 2026-10-17 00:23:03,577 [ scc.git] DEBUG 8f4b1035592a83dacf55e5cb585fd6ebe775f7f4 fpbioimage (heads/master) 2026-10-17 00:23:03,635 [ scc.git] DEBUG c0bbd4292f8e5141db088fe9a5a5eef41a61e602 ilastik (v0.3.4-14-gc0bbd42) 2026-10-17 00:23:03,761 [ scc.git] DEBUG d9033638b26778db35de1c77428190ac4cad1936 introduction (heads/master) 2026-10-17 00:23:03,870 [ scc.git] DEBUG 6ed80b33e8ddc97c930e3ea8ba00702f34e0a8ed iviewer (heads/master) 2026-10-17 00:23:03,933 [ scc.git] DEBUG a4b6b55205d0588c48baa8177aa7608fd40b3f85 java (v0.1.1-17-ga4b6b55) 2026-10-17 00:23:03,986 [ scc.git] DEBUG ecbd07c31df9b103937f4803aa35f104480365f2 matlab (v0.1.0-26-gecbd07c) 2026-10-17 00:23:04,097 [ scc.git] DEBUG d43e17feb8400f35a51d20e050b8a87bcdbcd1eb mde (heads/master) 2026-10-17 00:23:04,227 [ scc.git] DEBUG 4ef1eaaf315bbb8ae56e9ea780971735dc406f46 orbit (heads/master) 2026-10-17 00:23:04,356 [ scc.git] DEBUG 908b3356722bb23aafe103d87f8675f80fbaa5ed parade (heads/master) 2026-10-17 00:23:04,425 [ scc.git] DEBUG 41e4ded95c4caa46ecaa8caea4a1c488587e5c31 python (v0.3.0-118-g41e4ded) 2026-10-17 00:23:04,564 [ scc.git] DEBUG e2982075e2ff9f583bbd6b09f1d70285cc016905 qupath (remotes/origin/HEAD) 2026-10-17 00:23:04,666 [ scc.git] DEBUG a770a1048469668b66f5bde686d5b6d84d021e6d r (v0.1.0-24-ga770a10) 2026-10-17 00:23:04,802 [ scc.git] DEBUG 6133d50509750bccdb809e0089bd5c717357d379 scripts (heads/master) 2026-10-17 00:23:04,926 [ scc.git] DEBUG ffe98a8835c0f1bf345cb9ec0cfd2ba4aa304bd1 trackmate (heads/master) 2026-10-17 00:23:04,963 [ scc.git] DEBUG 6a5e0152c1b372ebb146803c7421c95b42474200 upload (v0.1.0-98-g6a5e015) 2026-10-17 00:23:04,979 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:05,268 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guides HTTP/1.1" 200 None 2026-10-17 00:23:05,805 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:06,261 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:06,711 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:07,184 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:07,185 [ scc.git] DEBUG Resetting... 2026-10-17 00:23:07,185 [ scc.git] DEBUG Calling 'git reset --hard HEAD' 2026-10-17 00:23:07,699 [ scc.git] DEBUG HEAD is now at a126902 Merge pull request #309 from ome/dependabot/submodules/download-a27d196 2026-10-17 00:23:07,702 [ scc.git] DEBUG Calling 'git submodule update --recursive' 2026-10-17 00:23:09,249 [ scc.git] DEBUG Check current status 2026-10-17 00:23:09,249 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:09,276 [ scc.git] DEBUG a126902 Merge pull request #309 from ome/dependabot/submodules/download-a27d196 2026-10-17 00:23:09,277 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:09,457 [ scc.git] DEBUG 248e8cbfb0372b3d3be2d82cfe9234dd2e25c140 cellprofiler (v0.4.0-32-g248e8cb) 2026-10-17 00:23:09,613 [ scc.git] DEBUG a27d196bee4a96b586246dc5d94ef07db7c5c0f8 download (heads/master) 2026-10-17 00:23:09,677 [ scc.git] DEBUG 654d43b5ef64f56bd6a99c69a9c98cbb5c8f76a7 figure (v0.1.0-55-g654d43b) 2026-10-17 00:23:09,747 [ scc.git] DEBUG 86f00e3e570d62226b02da1dc0cc639c389c7104 fiji (v0.2.1-89-g86f00e3) 2026-10-17 00:23:09,904 [ scc.git] DEBUG 8f4b1035592a83dacf55e5cb585fd6ebe775f7f4 fpbioimage (heads/master) 2026-10-17 00:23:09,969 [ scc.git] DEBUG c0bbd4292f8e5141db088fe9a5a5eef41a61e602 ilastik (v0.3.4-14-gc0bbd42) 2026-10-17 00:23:10,125 [ scc.git] DEBUG d9033638b26778db35de1c77428190ac4cad1936 introduction (heads/master) 2026-10-17 00:23:10,291 [ scc.git] DEBUG 6ed80b33e8ddc97c930e3ea8ba00702f34e0a8ed iviewer (heads/master) 2026-10-17 00:23:10,360 [ scc.git] DEBUG a4b6b55205d0588c48baa8177aa7608fd40b3f85 java (v0.1.1-17-ga4b6b55) 2026-10-17 00:23:10,434 [ scc.git] DEBUG ecbd07c31df9b103937f4803aa35f104480365f2 matlab (v0.1.0-26-gecbd07c) 2026-10-17 00:23:10,591 [ scc.git] DEBUG d43e17feb8400f35a51d20e050b8a87bcdbcd1eb mde (heads/master) 2026-10-17 00:23:10,761 [ scc.git] DEBUG 4ef1eaaf315bbb8ae56e9ea780971735dc406f46 orbit (heads/master) 2026-10-17 00:23:10,931 [ scc.git] DEBUG 908b3356722bb23aafe103d87f8675f80fbaa5ed parade (heads/master) 2026-10-17 00:23:10,992 [ scc.git] DEBUG 41e4ded95c4caa46ecaa8caea4a1c488587e5c31 python (v0.3.0-118-g41e4ded) 2026-10-17 00:23:11,139 [ scc.git] DEBUG e2982075e2ff9f583bbd6b09f1d70285cc016905 qupath (remotes/origin/HEAD) 2026-10-17 00:23:11,195 [ scc.git] DEBUG a770a1048469668b66f5bde686d5b6d84d021e6d r (v0.1.0-24-ga770a10) 2026-10-17 00:23:11,326 [ scc.git] DEBUG 6133d50509750bccdb809e0089bd5c717357d379 scripts (heads/master) 2026-10-17 00:23:11,462 [ scc.git] DEBUG ffe98a8835c0f1bf345cb9ec0cfd2ba4aa304bd1 trackmate (heads/master) 2026-10-17 00:23:11,496 [ scc.git] DEBUG 6a5e0152c1b372ebb146803c7421c95b42474200 upload (v0.1.0-98-g6a5e015) 2026-10-17 00:23:11,498 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-10-17 00:23:11,498 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-10-17 00:23:11,498 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-10-17 00:23:11,498 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-10-17 00:23:11,498 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-10-17 00:23:11,498 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:23:11,833 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guides/pulls HTTP/1.1" 200 None 2026-10-17 00:23:11,834 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:23:11,834 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:23:11,834 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:23:11,851 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:23:11,876 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:23:11,876 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:23:11,917 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:23:11,977 [ scc.git] DEBUG Already up to date. 2026-10-17 00:23:11,977 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:23:11,977 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:23:11,977 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:23:11,996 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:23:12,977 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:23:12,977 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:23:12,993 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:23:15,152 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7fdb2e7cae90> has no local changes 2026-10-17 00:23:15,153 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Snone Repository: ome/omero-guides Excluded PRs: - PR 23 jburel 'Remove submodules' (exclude comment) Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:23:16,631 [ scc.git] DEBUG [detached HEAD 3f0f859] merge master -Dorg -Snone 2026-10-17 00:23:16,633 [ scc.merge] INFO Repository: ome/omero-guides 2026-10-17 00:23:16,633 [ scc.merge] INFO Excluded PRs: 2026-10-17 00:23:16,633 [ scc.merge] INFO - PR 23 jburel 'Remove submodules' (exclude comment) 2026-10-17 00:23:16,633 [ scc.merge] INFO Already up to date. 2026-10-17 00:23:16,633 [ scc.merge] INFO 2026-10-17 00:23:16,633 [ scc.merge] INFO 2026-10-17 00:23:16,633 [ scc.merge] DEBUG Cleaning remote branches created for merging 2026-10-17 00:23:16,633 [ scc.git] DEBUG Calling 'git remote' Synchronizing submodule url for 'cellprofiler' Synchronizing submodule url for 'download' Synchronizing submodule url for 'figure' Synchronizing submodule url for 'fiji' Synchronizing submodule url for 'fpbioimage' Synchronizing submodule url for 'ilastik' Synchronizing submodule url for 'introduction' Synchronizing submodule url for 'iviewer' Synchronizing submodule url for 'java' Synchronizing submodule url for 'matlab' Synchronizing submodule url for 'mde' Synchronizing submodule url for 'orbit' Synchronizing submodule url for 'parade' Synchronizing submodule url for 'python' Synchronizing submodule url for 'qupath' Synchronizing submodule url for 'r' Synchronizing submodule url for 'scripts' Synchronizing submodule url for 'trackmate' Synchronizing submodule url for 'upload' Merge all submodules2026-10-17 00:23:29,761 [ scc.config] DEBUG Found github.token 2026-10-17 00:23:29,762 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443 2026-10-17 00:23:30,000 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:23:30,452 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:23:30,892 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None 2026-10-17 00:23:30,893 [ scc.gh] DEBUG 4190 remaining from 5000 (Reset at 00:10 2026-10-17 00:23:30,893 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:30,904 [ scc.git] DEBUG Check current status 2026-10-17 00:23:30,904 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:30,923 [ scc.git] DEBUG 3f0f859 merge master -Dorg -Snone 2026-10-17 00:23:30,924 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:31,066 [ scc.git] DEBUG 248e8cbfb0372b3d3be2d82cfe9234dd2e25c140 cellprofiler (v0.4.0-32-g248e8cb) 2026-10-17 00:23:31,142 [ scc.git] DEBUG a27d196bee4a96b586246dc5d94ef07db7c5c0f8 download (heads/master) 2026-10-17 00:23:31,180 [ scc.git] DEBUG 654d43b5ef64f56bd6a99c69a9c98cbb5c8f76a7 figure (v0.1.0-55-g654d43b) 2026-10-17 00:23:31,216 [ scc.git] DEBUG 86f00e3e570d62226b02da1dc0cc639c389c7104 fiji (v0.2.1-89-g86f00e3) 2026-10-17 00:23:31,302 [ scc.git] DEBUG 8f4b1035592a83dacf55e5cb585fd6ebe775f7f4 fpbioimage (heads/master) 2026-10-17 00:23:31,346 [ scc.git] DEBUG c0bbd4292f8e5141db088fe9a5a5eef41a61e602 ilastik (v0.3.4-14-gc0bbd42) 2026-10-17 00:23:31,443 [ scc.git] DEBUG d9033638b26778db35de1c77428190ac4cad1936 introduction (heads/master) 2026-10-17 00:23:31,529 [ scc.git] DEBUG 6ed80b33e8ddc97c930e3ea8ba00702f34e0a8ed iviewer (heads/master) 2026-10-17 00:23:31,567 [ scc.git] DEBUG a4b6b55205d0588c48baa8177aa7608fd40b3f85 java (v0.1.1-17-ga4b6b55) 2026-10-17 00:23:31,610 [ scc.git] DEBUG ecbd07c31df9b103937f4803aa35f104480365f2 matlab (v0.1.0-26-gecbd07c) 2026-10-17 00:23:31,712 [ scc.git] DEBUG d43e17feb8400f35a51d20e050b8a87bcdbcd1eb mde (heads/master) 2026-10-17 00:23:31,801 [ scc.git] DEBUG 4ef1eaaf315bbb8ae56e9ea780971735dc406f46 orbit (heads/master) 2026-10-17 00:23:31,889 [ scc.git] DEBUG 908b3356722bb23aafe103d87f8675f80fbaa5ed parade (heads/master) 2026-10-17 00:23:31,926 [ scc.git] DEBUG 41e4ded95c4caa46ecaa8caea4a1c488587e5c31 python (v0.3.0-118-g41e4ded) 2026-10-17 00:23:32,028 [ scc.git] DEBUG e2982075e2ff9f583bbd6b09f1d70285cc016905 qupath (remotes/origin/HEAD) 2026-10-17 00:23:32,063 [ scc.git] DEBUG a770a1048469668b66f5bde686d5b6d84d021e6d r (v0.1.0-24-ga770a10) 2026-10-17 00:23:32,146 [ scc.git] DEBUG 6133d50509750bccdb809e0089bd5c717357d379 scripts (heads/master) 2026-10-17 00:23:32,231 [ scc.git] DEBUG ffe98a8835c0f1bf345cb9ec0cfd2ba4aa304bd1 trackmate (heads/master) 2026-10-17 00:23:32,255 [ scc.git] DEBUG 6a5e0152c1b372ebb146803c7421c95b42474200 upload (v0.1.0-98-g6a5e015) 2026-10-17 00:23:32,267 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:32,560 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guides HTTP/1.1" 200 None 2026-10-17 00:23:33,058 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:33,519 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:33,983 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:34,437 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:34,438 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:34,613 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/cellprofiler 2026-10-17 00:23:34,613 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:34,625 [ scc.git] DEBUG Check current status 2026-10-17 00:23:34,625 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:34,644 [ scc.git] DEBUG 248e8cb Merge pull request #23 from jburel/rtd_build 2026-10-17 00:23:34,644 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:34,764 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:35,041 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler HTTP/1.1" 200 None 2026-10-17 00:23:35,680 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:36,135 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:36,604 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:37,081 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:37,083 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:37,206 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:37,206 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/download 2026-10-17 00:23:37,207 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:37,220 [ scc.git] DEBUG Check current status 2026-10-17 00:23:37,220 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:37,238 [ scc.git] DEBUG a27d196 Fix build failure on rtd 2026-10-17 00:23:37,239 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:37,355 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:37,710 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-download HTTP/1.1" 200 None 2026-10-17 00:23:38,221 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:38,700 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:39,169 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:39,638 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:39,640 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:39,778 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:39,781 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/figure 2026-10-17 00:23:39,781 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:39,808 [ scc.git] DEBUG Check current status 2026-10-17 00:23:39,808 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:39,836 [ scc.git] DEBUG 654d43b Merge pull request #16 from jburel/rtd_build 2026-10-17 00:23:39,837 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:40,010 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:40,359 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure HTTP/1.1" 200 None 2026-10-17 00:23:40,889 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:41,380 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:41,831 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:42,293 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:42,294 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:42,409 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:42,410 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fiji 2026-10-17 00:23:42,410 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:42,424 [ scc.git] DEBUG Check current status 2026-10-17 00:23:42,424 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:42,443 [ scc.git] DEBUG 86f00e3 Merge pull request #33 from will-moore/bdv_mobie_update 2026-10-17 00:23:42,445 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:42,568 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:42,950 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji HTTP/1.1" 200 None 2026-10-17 00:23:43,481 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:43,945 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:44,392 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:44,847 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:44,849 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:44,983 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:44,983 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fpbioimage 2026-10-17 00:23:44,983 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:45,004 [ scc.git] DEBUG Check current status 2026-10-17 00:23:45,004 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:45,039 [ scc.git] DEBUG 8f4b103 remove sphinx job following migration to rtd 2026-10-17 00:23:45,041 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:45,180 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:45,550 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fpbioimage HTTP/1.1" 200 None 2026-10-17 00:23:46,051 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:46,520 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:46,972 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:47,431 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:47,432 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:47,584 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:47,584 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/ilastik 2026-10-17 00:23:47,585 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:47,604 [ scc.git] DEBUG Check current status 2026-10-17 00:23:47,604 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:47,634 [ scc.git] DEBUG c0bbd42 Merge pull request #41 from pwalczysko/s3 2026-10-17 00:23:47,635 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:47,788 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:48,134 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-ilastik HTTP/1.1" 200 None 2026-10-17 00:23:48,701 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:49,158 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:49,631 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:50,274 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:50,275 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:50,427 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:50,427 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/introduction 2026-10-17 00:23:50,428 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:50,441 [ scc.git] DEBUG Check current status 2026-10-17 00:23:50,441 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:50,463 [ scc.git] DEBUG d903363 Merge pull request #26 from jburel/rtd_build 2026-10-17 00:23:50,465 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:50,623 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:50,986 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-introduction HTTP/1.1" 200 None 2026-10-17 00:23:51,480 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:51,941 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:52,390 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:52,838 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:52,839 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:53,025 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:53,026 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/iviewer 2026-10-17 00:23:53,026 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:53,053 [ scc.git] DEBUG Check current status 2026-10-17 00:23:53,053 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:53,091 [ scc.git] DEBUG 6ed80b3 Merge pull request #13 from jburel/rtd_build 2026-10-17 00:23:53,092 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:53,306 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:53,630 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-iviewer HTTP/1.1" 200 None 2026-10-17 00:23:54,139 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:54,581 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:55,233 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:55,746 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:55,748 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:55,912 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:55,912 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/java 2026-10-17 00:23:55,912 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:55,927 [ scc.git] DEBUG Check current status 2026-10-17 00:23:55,927 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:55,948 [ scc.git] DEBUG a4b6b55 Remove badge for sphinx 2026-10-17 00:23:55,949 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:56,126 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:56,453 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java HTTP/1.1" 200 None 2026-10-17 00:23:56,945 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:23:57,422 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:23:57,886 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:23:58,347 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:23:58,348 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:23:58,539 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:23:58,539 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/matlab 2026-10-17 00:23:58,540 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:23:58,558 [ scc.git] DEBUG Check current status 2026-10-17 00:23:58,558 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:23:58,593 [ scc.git] DEBUG ecbd07c Merge pull request #5 from pwalczysko/matlab-online 2026-10-17 00:23:58,595 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:23:58,779 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:23:59,103 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-matlab HTTP/1.1" 200 None 2026-10-17 00:23:59,608 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:00,069 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:00,543 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:01,007 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:01,009 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:01,141 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:01,142 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/mde 2026-10-17 00:24:01,142 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:01,157 [ scc.git] DEBUG Check current status 2026-10-17 00:24:01,157 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:01,179 [ scc.git] DEBUG d43e17f Merge pull request #5 from jburel/rtd_build 2026-10-17 00:24:01,180 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:01,338 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:01,768 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde HTTP/1.1" 200 None 2026-10-17 00:24:02,269 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:02,749 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:03,234 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:03,695 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:03,696 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:03,872 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:03,872 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/orbit 2026-10-17 00:24:03,872 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:03,892 [ scc.git] DEBUG Check current status 2026-10-17 00:24:03,893 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:03,923 [ scc.git] DEBUG 4ef1eaa Update actions to v3 and v4 2026-10-17 00:24:03,924 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:04,081 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:04,459 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-orbit HTTP/1.1" 200 None 2026-10-17 00:24:04,962 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:05,440 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:05,903 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:06,372 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:06,374 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:06,563 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:06,563 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/parade 2026-10-17 00:24:06,563 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:06,586 [ scc.git] DEBUG Check current status 2026-10-17 00:24:06,586 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:06,627 [ scc.git] DEBUG 908b335 Merge pull request #1 from ome/rtd_build 2026-10-17 00:24:06,628 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:06,878 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:07,275 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-parade HTTP/1.1" 200 None 2026-10-17 00:24:07,772 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:08,230 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:08,721 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:09,177 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:09,179 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:09,351 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:09,351 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/python 2026-10-17 00:24:09,351 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:09,369 [ scc.git] DEBUG Check current status 2026-10-17 00:24:09,370 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:09,396 [ scc.git] DEBUG 41e4ded Merge pull request #65 from pwalczysko/no-idr 2026-10-17 00:24:09,397 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:09,592 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:09,936 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-python HTTP/1.1" 200 None 2026-10-17 00:24:10,683 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:11,153 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:11,613 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:12,067 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:12,069 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:12,210 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:12,210 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/qupath 2026-10-17 00:24:12,210 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:12,231 [ scc.git] DEBUG Check current status 2026-10-17 00:24:12,231 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:12,270 [ scc.git] DEBUG e298207 Merge pull request #15 from pwalczysko/tweaks 2026-10-17 00:24:12,271 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:12,433 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:12,796 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-qupath HTTP/1.1" 200 None 2026-10-17 00:24:13,286 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:13,751 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:14,218 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:14,675 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:14,677 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:14,914 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:14,915 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/r 2026-10-17 00:24:14,915 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:14,944 [ scc.git] DEBUG Check current status 2026-10-17 00:24:14,944 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:14,982 [ scc.git] DEBUG a770a10 Remove sphinx badge 2026-10-17 00:24:14,983 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:15,256 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:15,630 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r HTTP/1.1" 200 None 2026-10-17 00:24:16,117 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:16,578 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:17,024 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:17,478 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:17,480 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:17,686 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:17,687 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/scripts 2026-10-17 00:24:17,687 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:17,706 [ scc.git] DEBUG Check current status 2026-10-17 00:24:17,706 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:17,737 [ scc.git] DEBUG 6133d50 Merge pull request #4 from Rdornier/import-from-csv-fix 2026-10-17 00:24:17,741 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:17,952 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:18,290 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-scripts HTTP/1.1" 200 None 2026-10-17 00:24:18,844 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:19,301 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:19,761 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:20,230 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:20,232 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:20,440 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:20,441 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/trackmate 2026-10-17 00:24:20,442 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:20,467 [ scc.git] DEBUG Check current status 2026-10-17 00:24:20,468 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:20,495 [ scc.git] DEBUG ffe98a8 Merge pull request #5 from jburel/rtd_build 2026-10-17 00:24:20,498 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:20,656 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:21,097 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-trackmate HTTP/1.1" 200 None 2026-10-17 00:24:21,595 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:22,047 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:22,510 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:22,955 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:22,956 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:23,096 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:23,097 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/upload 2026-10-17 00:24:23,098 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-17 00:24:23,110 [ scc.git] DEBUG Check current status 2026-10-17 00:24:23,110 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:23,132 [ scc.git] DEBUG 6a5e015 Merge pull request #19 from pwalczysko/update-insight-download 2026-10-17 00:24:23,133 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:23,287 [ scc.config] DEBUG Found remote.origin.url 2026-10-17 00:24:23,644 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-upload HTTP/1.1" 200 None 2026-10-17 00:24:24,142 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None 2026-10-17 00:24:24,601 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None 2026-10-17 00:24:25,061 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None 2026-10-17 00:24:25,512 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None 2026-10-17 00:24:25,514 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:25,676 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:25,676 [ scc.git] DEBUG Resetting... 2026-10-17 00:24:25,676 [ scc.git] DEBUG Calling 'git reset --hard HEAD' 2026-10-17 00:24:26,236 [ scc.git] DEBUG HEAD is now at 3f0f859 merge master -Dorg -Snone 2026-10-17 00:24:26,238 [ scc.git] DEBUG Calling 'git submodule update --recursive' 2026-10-17 00:24:28,107 [ scc.git] DEBUG Check current status 2026-10-17 00:24:28,107 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-17 00:24:28,146 [ scc.git] DEBUG 3f0f859 merge master -Dorg -Snone 2026-10-17 00:24:28,148 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-17 00:24:28,418 [ scc.git] DEBUG 248e8cbfb0372b3d3be2d82cfe9234dd2e25c140 cellprofiler (v0.4.0-32-g248e8cb) 2026-10-17 00:24:28,567 [ scc.git] DEBUG a27d196bee4a96b586246dc5d94ef07db7c5c0f8 download (heads/master) 2026-10-17 00:24:28,621 [ scc.git] DEBUG 654d43b5ef64f56bd6a99c69a9c98cbb5c8f76a7 figure (v0.1.0-55-g654d43b) 2026-10-17 00:24:28,680 [ scc.git] DEBUG 86f00e3e570d62226b02da1dc0cc639c389c7104 fiji (v0.2.1-89-g86f00e3) 2026-10-17 00:24:28,821 [ scc.git] DEBUG 8f4b1035592a83dacf55e5cb585fd6ebe775f7f4 fpbioimage (heads/master) 2026-10-17 00:24:28,883 [ scc.git] DEBUG c0bbd4292f8e5141db088fe9a5a5eef41a61e602 ilastik (v0.3.4-14-gc0bbd42) 2026-10-17 00:24:29,038 [ scc.git] DEBUG d9033638b26778db35de1c77428190ac4cad1936 introduction (heads/master) 2026-10-17 00:24:29,194 [ scc.git] DEBUG 6ed80b33e8ddc97c930e3ea8ba00702f34e0a8ed iviewer (heads/master) 2026-10-17 00:24:29,278 [ scc.git] DEBUG a4b6b55205d0588c48baa8177aa7608fd40b3f85 java (v0.1.1-17-ga4b6b55) 2026-10-17 00:24:29,333 [ scc.git] DEBUG ecbd07c31df9b103937f4803aa35f104480365f2 matlab (v0.1.0-26-gecbd07c) 2026-10-17 00:24:29,486 [ scc.git] DEBUG d43e17feb8400f35a51d20e050b8a87bcdbcd1eb mde (heads/master) 2026-10-17 00:24:29,644 [ scc.git] DEBUG 4ef1eaaf315bbb8ae56e9ea780971735dc406f46 orbit (heads/master) 2026-10-17 00:24:29,778 [ scc.git] DEBUG 908b3356722bb23aafe103d87f8675f80fbaa5ed parade (heads/master) 2026-10-17 00:24:29,822 [ scc.git] DEBUG 41e4ded95c4caa46ecaa8caea4a1c488587e5c31 python (v0.3.0-118-g41e4ded) 2026-10-17 00:24:30,013 [ scc.git] DEBUG e2982075e2ff9f583bbd6b09f1d70285cc016905 qupath (remotes/origin/HEAD) 2026-10-17 00:24:30,060 [ scc.git] DEBUG a770a1048469668b66f5bde686d5b6d84d021e6d r (v0.1.0-24-ga770a10) 2026-10-17 00:24:30,207 [ scc.git] DEBUG 6133d50509750bccdb809e0089bd5c717357d379 scripts (heads/master) 2026-10-17 00:24:30,360 [ scc.git] DEBUG ffe98a8835c0f1bf345cb9ec0cfd2ba4aa304bd1 trackmate (heads/master) 2026-10-17 00:24:30,383 [ scc.git] DEBUG 6a5e0152c1b372ebb146803c7421c95b42474200 upload (v0.1.0-98-g6a5e015) 2026-10-17 00:24:30,384 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-10-17 00:24:30,384 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-10-17 00:24:30,384 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-10-17 00:24:30,384 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-10-17 00:24:30,384 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-10-17 00:24:30,384 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-10-17 00:24:30,384 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:30,748 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guides/pulls HTTP/1.1" 200 None 2026-10-17 00:24:30,750 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:30,750 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:30,750 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:30,763 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:30,784 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:30,784 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:30,829 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:30,916 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:30,916 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:30,916 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:30,916 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:30,932 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:31,863 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:31,863 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:31,875 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:32,257 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/pulls HTTP/1.1" 200 None 2026-10-17 00:24:32,760 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/issues/25 HTTP/1.1" 200 None 2026-10-17 00:24:33,259 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/issues/25/comments HTTP/1.1" 200 None 2026-10-17 00:24:33,769 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/issues/24 HTTP/1.1" 200 None 2026-10-17 00:24:34,278 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/issues/24/comments HTTP/1.1" 200 None 2026-10-17 00:24:34,853 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/commits/647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:35,381 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/commits/647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:24:35,859 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/commits/647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:36,321 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-cellprofiler/statuses/647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:24:36,322 [ scc.repo] DEBUG - PR 24 jburel 'Remove binder' 2026-10-17 00:24:36,322 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:36,322 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/cellprofiler 2026-10-17 00:24:36,322 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:36,322 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:36,338 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:36,354 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:36,354 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:36,377 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:36,444 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:36,444 [ scc.git] DEBUG Calling 'git fetch origin pull/24/head' 2026-10-17 00:24:37,184 [ scc.git] DEBUG From https://github.com/ome/omero-guide-cellprofiler 2026-10-17 00:24:37,184 [ scc.git] DEBUG * branch refs/pull/24/head -> FETCH_HEAD 2026-10-17 00:24:37,210 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:37,210 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:37,210 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:37,238 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25' 2026-10-17 00:24:37,284 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:37,299 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 24 (Remove binder) 647d3d34fa15bd7aa6a1437fc63c92be3cbc8b25' 2026-10-17 00:24:37,542 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:24:37,625 [ scc.git] DEBUG .github/workflows/binder_badge.yml | 25 ------------------------- 2026-10-17 00:24:37,625 [ scc.git] DEBUG .github/workflows/build.yml | 27 +++++++++++++++++++++++++++ 2026-10-17 00:24:37,625 [ scc.git] DEBUG README.md | 15 ++++++--------- 2026-10-17 00:24:37,625 [ scc.git] DEBUG binder/environment.yml | 6 ++++-- 2026-10-17 00:24:37,625 [ scc.git] DEBUG 4 files changed, 37 insertions(+), 36 deletions(-) 2026-10-17 00:24:37,625 [ scc.git] DEBUG delete mode 100644 .github/workflows/binder_badge.yml 2026-10-17 00:24:37,625 [ scc.git] DEBUG create mode 100644 .github/workflows/build.yml 2026-10-17 00:24:37,821 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:24:37,821 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:37,964 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:37,964 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:37,979 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:38,101 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:38,158 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df5490b50> has no local changes 2026-10-17 00:24:38,158 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-cellprofiler Excluded PRs: - PR 25 pwalczysko 'Deprecate the non-save idr0002 notebook and redirect' (stage: draft) Already up to date. Merged PRs: - PR 24 jburel 'Remove binder' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:38,287 [ scc.git] DEBUG [detached HEAD 48355f3] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:38,289 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:38,289 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:38,555 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-download/pulls HTTP/1.1" 200 2 2026-10-17 00:24:38,555 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:38,556 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/download 2026-10-17 00:24:38,556 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:38,556 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:38,572 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:38,598 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:38,598 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:38,620 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:38,677 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:38,677 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:38,677 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:38,677 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:38,693 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:38,820 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:38,820 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:38,832 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:38,943 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:38,988 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df5403150> has no local changes 2026-10-17 00:24:38,989 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-download Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:39,123 [ scc.git] DEBUG [detached HEAD ad767a1] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:39,125 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:39,125 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:39,440 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/pulls HTTP/1.1" 200 None 2026-10-17 00:24:39,985 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/issues/17 HTTP/1.1" 200 None 2026-10-17 00:24:40,617 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/d142504a021b0e7f274520f08eb24796f0663404?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:41,212 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/d142504a021b0e7f274520f08eb24796f0663404/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:24:41,703 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/d142504a021b0e7f274520f08eb24796f0663404?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:42,153 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/statuses/d142504a021b0e7f274520f08eb24796f0663404?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:24:42,153 [ scc.repo] DEBUG - PR 17 will-moore 'Update inset workflow for OMERO.figure 7.2.0' 2026-10-17 00:24:42,657 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/issues/14 HTTP/1.1" 200 None 2026-10-17 00:24:43,156 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/issues/14/comments HTTP/1.1" 200 None 2026-10-17 00:24:43,703 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/c2e5919f88d844ffea560784b7a800c655ff0743?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:44,220 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/c2e5919f88d844ffea560784b7a800c655ff0743/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:24:44,713 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/commits/c2e5919f88d844ffea560784b7a800c655ff0743?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:45,170 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-figure/statuses/c2e5919f88d844ffea560784b7a800c655ff0743?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:24:45,170 [ scc.repo] DEBUG - PR 14 will-moore 'Table data by roi' 2026-10-17 00:24:45,171 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:45,171 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/figure 2026-10-17 00:24:45,171 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:45,171 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:45,188 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:45,208 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:45,208 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:45,234 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:45,299 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:45,299 [ scc.git] DEBUG Calling 'git fetch origin pull/14/head' 2026-10-17 00:24:45,944 [ scc.git] DEBUG From https://github.com/ome/omero-guide-figure 2026-10-17 00:24:45,944 [ scc.git] DEBUG * branch refs/pull/14/head -> FETCH_HEAD 2026-10-17 00:24:45,968 [ scc.git] DEBUG Calling 'git fetch origin pull/17/head' 2026-10-17 00:24:46,444 [ scc.git] DEBUG From https://github.com/ome/omero-guide-figure 2026-10-17 00:24:46,445 [ scc.git] DEBUG * branch refs/pull/17/head -> FETCH_HEAD 2026-10-17 00:24:46,468 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:46,468 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:46,468 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:46,485 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...c2e5919f88d844ffea560784b7a800c655ff0743' 2026-10-17 00:24:46,537 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:46,552 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 14 (Table data by roi) c2e5919f88d844ffea560784b7a800c655ff0743' 2026-10-17 00:24:46,814 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:24:46,891 [ scc.git] DEBUG docs/omero_figure_scripting.rst | 20 ++++++++++---------- 2026-10-17 00:24:46,891 [ scc.git] DEBUG scripts/figure_table_data_shapes.js | 12 ++++++++---- 2026-10-17 00:24:46,891 [ scc.git] DEBUG 2 files changed, 18 insertions(+), 14 deletions(-) 2026-10-17 00:24:47,143 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:24:47,144 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...d142504a021b0e7f274520f08eb24796f0663404' 2026-10-17 00:24:47,201 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:47,229 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 17 (Update inset workflow for OMERO.figure 7.2.0) d142504a021b0e7f274520f08eb24796f0663404' 2026-10-17 00:24:47,475 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:24:47,553 [ scc.git] DEBUG docs/omero_figure.rst | 15 ++++++++------- 2026-10-17 00:24:47,553 [ scc.git] DEBUG 1 file changed, 8 insertions(+), 7 deletions(-) 2026-10-17 00:24:47,755 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:24:47,756 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:47,905 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:47,905 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:47,919 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:48,041 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:48,105 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df54c46d0> has no local changes 2026-10-17 00:24:48,105 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-figure Already up to date. Merged PRs: - PR 14 will-moore 'Table data by roi' - PR 17 will-moore 'Update inset workflow for OMERO.figure 7.2.0' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:48,246 [ scc.git] DEBUG [detached HEAD 70b36a6] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:48,250 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:48,250 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:48,589 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/pulls HTTP/1.1" 200 None 2026-10-17 00:24:49,130 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/issues/35 HTTP/1.1" 200 None 2026-10-17 00:24:49,642 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/issues/35/comments HTTP/1.1" 200 None 2026-10-17 00:24:50,197 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/commits/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:50,688 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/commits/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:24:51,163 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/commits/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:51,639 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/statuses/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04?per_page=1 HTTP/1.1" 200 None 2026-10-17 00:24:52,112 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/commits/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04?page=1 HTTP/1.1" 200 None 2026-10-17 00:24:52,607 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/commits/5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04/status HTTP/1.1" 200 None 2026-10-17 00:24:52,608 [ scc.repo] DEBUG - PR 35 pwalczysko 'livingobjects' 2026-10-17 00:24:53,133 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/issues/24 HTTP/1.1" 200 None 2026-10-17 00:24:53,645 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fiji/issues/24/comments HTTP/1.1" 200 None 2026-10-17 00:24:53,646 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:53,646 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fiji 2026-10-17 00:24:53,646 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:53,646 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:53,662 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:53,682 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:53,683 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:53,703 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:53,755 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:53,755 [ scc.git] DEBUG Calling 'git fetch origin pull/35/head' 2026-10-17 00:24:54,286 [ scc.git] DEBUG From https://github.com/ome/omero-guide-fiji 2026-10-17 00:24:54,286 [ scc.git] DEBUG * branch refs/pull/35/head -> FETCH_HEAD 2026-10-17 00:24:54,311 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:54,311 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:54,311 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:54,324 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04' 2026-10-17 00:24:54,376 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:54,397 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 35 (livingobjects) 5cd76b1e65bf2e0b0a0c11b6eeffc6c036c23a04' 2026-10-17 00:24:54,726 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:24:54,831 [ scc.git] DEBUG .github/workflows/repo2docker.yml | 23 ----------------------- 2026-10-17 00:24:54,831 [ scc.git] DEBUG README.md | 19 +------------------ 2026-10-17 00:24:54,831 [ scc.git] DEBUG docs/headless_notebook.rst | 2 +- 2026-10-17 00:24:54,831 [ scc.git] DEBUG docs/view_mobie_zarr.rst | 4 ++-- 2026-10-17 00:24:54,831 [ scc.git] DEBUG notebooks/imagej_python_zarr.ipynb | 2 +- 2026-10-17 00:24:54,831 [ scc.git] DEBUG scripts/groovy/mobie_ome_zarr.groovy | 2 +- 2026-10-17 00:24:54,831 [ scc.git] DEBUG 6 files changed, 6 insertions(+), 46 deletions(-) 2026-10-17 00:24:54,831 [ scc.git] DEBUG delete mode 100644 .github/workflows/repo2docker.yml 2026-10-17 00:24:55,011 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:24:55,012 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:55,256 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:55,256 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:55,289 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:55,521 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:55,685 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df5433210> has no local changes 2026-10-17 00:24:55,686 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-fiji Excluded PRs: - PR 24 oeway 'Disable FilamentDetector in Fiji' (user: oeway) Already up to date. Merged PRs: - PR 35 pwalczysko 'livingobjects' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:55,982 [ scc.git] DEBUG [detached HEAD 0ae03e7] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:55,985 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:55,986 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:56,213 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-fpbioimage/pulls HTTP/1.1" 200 2 2026-10-17 00:24:56,214 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:56,214 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fpbioimage 2026-10-17 00:24:56,214 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:56,214 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:56,255 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:56,287 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:56,287 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:56,327 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:56,438 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:56,438 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:56,438 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:56,438 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:56,474 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:56,706 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:56,706 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:56,733 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:56,946 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:57,019 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df54c4d90> has no local changes 2026-10-17 00:24:57,019 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-fpbioimage Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:57,211 [ scc.git] DEBUG [detached HEAD c68e90d] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:57,213 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:57,213 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:57,428 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-ilastik/pulls HTTP/1.1" 200 2 2026-10-17 00:24:57,428 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:57,428 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/ilastik 2026-10-17 00:24:57,429 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:57,429 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:57,445 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:57,465 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:57,465 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:57,488 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:57,546 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:57,546 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:57,546 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:57,546 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:57,561 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:57,699 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:57,699 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:57,713 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:57,847 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:57,903 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df426ff10> has no local changes 2026-10-17 00:24:57,903 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-ilastik Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:58,037 [ scc.git] DEBUG [detached HEAD 289985f] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:58,039 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:58,040 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:58,260 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-introduction/pulls HTTP/1.1" 200 2 2026-10-17 00:24:58,261 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:58,261 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/introduction 2026-10-17 00:24:58,261 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:58,261 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:58,276 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:58,292 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:58,292 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:58,315 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:58,370 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:58,371 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:58,371 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:58,371 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:58,386 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:58,515 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:58,515 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:58,527 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:58,678 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:58,755 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df54b7650> has no local changes 2026-10-17 00:24:58,755 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-introduction Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:58,904 [ scc.git] DEBUG [detached HEAD d1c64d0] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:58,906 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:58,906 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:24:59,123 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-iviewer/pulls HTTP/1.1" 200 2 2026-10-17 00:24:59,124 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:24:59,124 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/iviewer 2026-10-17 00:24:59,124 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:59,124 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:59,139 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:24:59,158 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:24:59,158 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:24:59,178 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:24:59,248 [ scc.git] DEBUG Already up to date. 2026-10-17 00:24:59,249 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:24:59,249 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:59,249 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:59,265 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:24:59,399 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:24:59,399 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:24:59,411 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:24:59,526 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:24:59,589 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df545a6d0> has no local changes 2026-10-17 00:24:59,589 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-iviewer Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:24:59,740 [ scc.git] DEBUG [detached HEAD 798786a] merge master -Dorg -Ssuccess-only 2026-10-17 00:24:59,744 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:24:59,744 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:00,080 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/pulls HTTP/1.1" 200 None 2026-10-17 00:25:00,603 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/issues/3 HTTP/1.1" 200 None 2026-10-17 00:25:01,122 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/issues/3/comments HTTP/1.1" 200 None 2026-10-17 00:25:01,726 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/commits/31294bfa7f63d9dbaa984a386e6db9a945cc0fa5?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:02,231 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/commits/31294bfa7f63d9dbaa984a386e6db9a945cc0fa5/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:25:02,726 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/commits/31294bfa7f63d9dbaa984a386e6db9a945cc0fa5?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:03,194 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-java/statuses/31294bfa7f63d9dbaa984a386e6db9a945cc0fa5?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:25:03,194 [ scc.repo] DEBUG - PR 3 jburel 'fix build failure on rtd' 2026-10-17 00:25:03,194 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:03,194 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/java 2026-10-17 00:25:03,194 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:03,195 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:03,213 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:03,230 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:03,230 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:03,250 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:03,323 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:03,323 [ scc.git] DEBUG Calling 'git fetch origin pull/3/head' 2026-10-17 00:25:03,839 [ scc.git] DEBUG From https://github.com/ome/omero-guide-java 2026-10-17 00:25:03,839 [ scc.git] DEBUG * branch refs/pull/3/head -> FETCH_HEAD 2026-10-17 00:25:03,868 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:03,868 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:03,868 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:03,884 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...31294bfa7f63d9dbaa984a386e6db9a945cc0fa5' 2026-10-17 00:25:03,922 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:03,938 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 3 (fix build failure on rtd) 31294bfa7f63d9dbaa984a386e6db9a945cc0fa5' 2026-10-17 00:25:04,153 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:25:04,233 [ scc.git] DEBUG .readthedocs.yaml | 8 ++++---- 2026-10-17 00:25:04,233 [ scc.git] DEBUG 1 file changed, 4 insertions(+), 4 deletions(-) 2026-10-17 00:25:04,427 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:04,427 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:04,599 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:04,599 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:04,618 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:04,748 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:04,815 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df54b4c10> has no local changes 2026-10-17 00:25:04,815 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-java Already up to date. Merged PRs: - PR 3 jburel 'fix build failure on rtd' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:04,961 [ scc.git] DEBUG [detached HEAD ea8cd5b] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:04,962 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:04,962 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:05,184 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-matlab/pulls HTTP/1.1" 200 2 2026-10-17 00:25:05,185 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:05,185 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/matlab 2026-10-17 00:25:05,185 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:05,185 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:05,212 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:05,229 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:05,229 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:05,252 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:05,314 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:05,315 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:05,315 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:05,315 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:05,344 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:05,488 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:05,489 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:05,504 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:05,644 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:05,692 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df4262990> has no local changes 2026-10-17 00:25:05,693 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-matlab Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:05,835 [ scc.git] DEBUG [detached HEAD 889f49e] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:05,837 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:05,837 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:06,163 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/pulls HTTP/1.1" 200 None 2026-10-17 00:25:06,677 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/issues/4 HTTP/1.1" 200 None 2026-10-17 00:25:07,174 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/issues/4/comments HTTP/1.1" 200 None 2026-10-17 00:25:07,792 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/commits/4b6e2511fe820a323b2311e2b39910b6b79fcf6a?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:08,362 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/commits/4b6e2511fe820a323b2311e2b39910b6b79fcf6a/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:25:08,842 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/commits/4b6e2511fe820a323b2311e2b39910b6b79fcf6a?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:09,318 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-mde/statuses/4b6e2511fe820a323b2311e2b39910b6b79fcf6a?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:25:09,319 [ scc.repo] DEBUG - PR 4 pwalczysko 'Remove relative reference when it does not work' 2026-10-17 00:25:09,319 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:09,319 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/mde 2026-10-17 00:25:09,319 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:09,319 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:09,341 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:09,368 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:09,369 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:09,401 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:09,500 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:09,500 [ scc.git] DEBUG Calling 'git fetch origin pull/4/head' 2026-10-17 00:25:10,004 [ scc.git] DEBUG From https://github.com/ome/omero-guide-mde 2026-10-17 00:25:10,004 [ scc.git] DEBUG * branch refs/pull/4/head -> FETCH_HEAD 2026-10-17 00:25:10,037 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:10,037 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:10,037 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:10,057 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...4b6e2511fe820a323b2311e2b39910b6b79fcf6a' 2026-10-17 00:25:10,097 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:10,116 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 4 (Remove relative reference when it does not work) 4b6e2511fe820a323b2311e2b39910b6b79fcf6a' 2026-10-17 00:25:10,342 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:25:10,413 [ scc.git] DEBUG docs/mde_customizeObjects.rst | 4 ++-- 2026-10-17 00:25:10,414 [ scc.git] DEBUG docs/mde_customizeView.rst | 4 ++-- 2026-10-17 00:25:10,414 [ scc.git] DEBUG 2 files changed, 4 insertions(+), 4 deletions(-) 2026-10-17 00:25:10,606 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:10,607 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:10,762 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:10,762 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:10,779 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:10,924 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:11,014 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df53c0590> has no local changes 2026-10-17 00:25:11,014 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-mde Already up to date. Merged PRs: - PR 4 pwalczysko 'Remove relative reference when it does not work' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:11,224 [ scc.git] DEBUG [detached HEAD a168dcf] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:11,233 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:11,233 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:11,443 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-orbit/pulls HTTP/1.1" 200 2 2026-10-17 00:25:11,444 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:11,444 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/orbit 2026-10-17 00:25:11,444 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:11,444 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:11,472 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:11,498 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:11,498 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:11,533 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:11,639 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:11,639 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:11,639 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:11,639 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:11,672 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:11,927 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:11,927 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:11,955 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:12,113 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:12,187 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df536bb10> has no local changes 2026-10-17 00:25:12,187 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-orbit Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:12,369 [ scc.git] DEBUG [detached HEAD 481abb3] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:13,308 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:13,308 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:13,527 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-parade/pulls HTTP/1.1" 200 2 2026-10-17 00:25:13,528 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:13,528 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/parade 2026-10-17 00:25:13,528 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:13,528 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:13,547 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:13,567 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:13,567 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:13,604 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:13,663 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:13,663 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:13,663 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:13,663 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:13,685 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:13,839 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:13,839 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:13,857 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:14,003 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:14,066 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df42cbfd0> has no local changes 2026-10-17 00:25:14,066 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-parade Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:14,243 [ scc.git] DEBUG [detached HEAD e128016] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:14,245 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:14,245 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:14,469 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-python/pulls HTTP/1.1" 200 2 2026-10-17 00:25:14,470 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:14,470 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/python 2026-10-17 00:25:14,470 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:14,470 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:14,488 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:14,509 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:14,509 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:14,535 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:14,598 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:14,598 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:14,598 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:14,598 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:14,616 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:14,754 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:14,754 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:14,769 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:14,895 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:14,967 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df427a5d0> has no local changes 2026-10-17 00:25:14,967 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-python Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:15,207 [ scc.git] DEBUG [detached HEAD 834fd0e] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:15,217 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:15,217 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:15,429 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-qupath/pulls HTTP/1.1" 200 2 2026-10-17 00:25:15,430 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:15,430 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/qupath 2026-10-17 00:25:15,431 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:15,431 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:16,237 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:16,254 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:16,254 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:16,293 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:16,354 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:16,354 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:16,354 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:16,354 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:16,371 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:16,490 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:16,490 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:16,505 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:16,628 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:16,683 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df40f7f10> has no local changes 2026-10-17 00:25:16,683 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-qupath Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:16,833 [ scc.git] DEBUG [detached HEAD 5c9b0fe] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:16,835 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:16,835 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:17,162 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/pulls HTTP/1.1" 200 None 2026-10-17 00:25:17,668 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/issues/11 HTTP/1.1" 200 None 2026-10-17 00:25:18,209 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/issues/11/comments HTTP/1.1" 200 None 2026-10-17 00:25:18,835 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/commits/990828ddac8bc276820c2fa5952182f56b0ab241?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:20,013 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/commits/990828ddac8bc276820c2fa5952182f56b0ab241/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-17 00:25:20,499 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/commits/990828ddac8bc276820c2fa5952182f56b0ab241?page=1 HTTP/1.1" 200 None 2026-10-17 00:25:20,951 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-r/statuses/990828ddac8bc276820c2fa5952182f56b0ab241?per_page=1 HTTP/1.1" 200 2 2026-10-17 00:25:20,952 [ scc.repo] DEBUG - PR 11 jburel 'fix build failure on rtd' 2026-10-17 00:25:20,952 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:20,952 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/r 2026-10-17 00:25:22,431 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:23,437 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:27,944 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:27,973 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:27,973 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:28,015 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:28,069 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:28,070 [ scc.git] DEBUG Calling 'git fetch origin pull/11/head' 2026-10-17 00:25:28,575 [ scc.git] DEBUG From https://github.com/ome/omero-guide-r 2026-10-17 00:25:28,575 [ scc.git] DEBUG * branch refs/pull/11/head -> FETCH_HEAD 2026-10-17 00:25:28,600 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:28,600 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:28,600 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:28,615 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...990828ddac8bc276820c2fa5952182f56b0ab241' 2026-10-17 00:25:28,640 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:28,654 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 11 (fix build failure on rtd) 990828ddac8bc276820c2fa5952182f56b0ab241' 2026-10-17 00:25:28,824 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-17 00:25:28,880 [ scc.git] DEBUG .readthedocs.yaml | 8 ++++---- 2026-10-17 00:25:28,880 [ scc.git] DEBUG 1 file changed, 4 insertions(+), 4 deletions(-) 2026-10-17 00:25:29,066 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:29,067 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:29,197 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:29,197 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:29,212 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:29,334 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:29,396 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df410ba90> has no local changes 2026-10-17 00:25:29,396 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-r Already up to date. Merged PRs: - PR 11 jburel 'fix build failure on rtd' Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:29,552 [ scc.git] DEBUG [detached HEAD fa8b3ba] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:29,554 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:29,554 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:29,786 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-scripts/pulls HTTP/1.1" 200 2 2026-10-17 00:25:29,787 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:29,787 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/scripts 2026-10-17 00:25:29,788 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:29,788 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:29,804 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:29,823 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:29,823 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:29,847 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:29,909 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:29,909 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:29,909 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:29,909 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:29,928 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:30,055 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:30,055 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:30,071 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:30,194 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:30,259 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df410be90> has no local changes 2026-10-17 00:25:30,259 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-scripts Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:30,389 [ scc.git] DEBUG [detached HEAD e1f747f] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:30,391 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:30,391 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:30,602 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-trackmate/pulls HTTP/1.1" 200 2 2026-10-17 00:25:30,603 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:30,603 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/trackmate 2026-10-17 00:25:30,603 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:30,604 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:30,623 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:30,646 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:30,646 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:30,668 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:30,733 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:30,733 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:30,733 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:30,733 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:30,750 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:30,888 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:30,888 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:30,905 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:31,022 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:31,091 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df41377d0> has no local changes 2026-10-17 00:25:31,091 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-trackmate Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:31,224 [ scc.git] DEBUG [detached HEAD e43ba1b] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:31,226 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:31,226 [ scc.repo] DEBUG ## PRs found: 2026-10-17 00:25:31,445 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-guide-upload/pulls HTTP/1.1" 200 2 2026-10-17 00:25:31,445 [ scc.repo] DEBUG ## Branches found: 2026-10-17 00:25:31,446 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/upload 2026-10-17 00:25:31,446 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:31,446 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:31,463 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-17 00:25:31,486 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-17 00:25:31,486 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-17 00:25:31,509 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-17 00:25:31,570 [ scc.git] DEBUG Already up to date. 2026-10-17 00:25:31,570 [ scc.git] DEBUG ## Unique users: [] 2026-10-17 00:25:31,570 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:31,570 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:31,586 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-17 00:25:31,713 [ scc.git] DEBUG Get sha1 of %s 2026-10-17 00:25:31,713 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-17 00:25:31,728 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:31,847 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:31,914 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df40eea90> has no local changes 2026-10-17 00:25:31,914 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guide-upload Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:32,073 [ scc.git] DEBUG [detached HEAD bb8906a] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:32,076 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:32,076 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-17 00:25:32,270 [ scc.config] DEBUG Found submodule.cellprofiler.url 2026-10-17 00:25:32,472 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:32,506 [ scc.config] DEBUG Found submodule.download.url 2026-10-17 00:25:32,910 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:32,949 [ scc.config] DEBUG Found submodule.figure.url 2026-10-17 00:25:33,355 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:33,399 [ scc.config] DEBUG Found submodule.fiji.url 2026-10-17 00:25:33,802 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:33,844 [ scc.config] DEBUG Found submodule.fpbioimage.url 2026-10-17 00:25:34,247 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:34,281 [ scc.config] DEBUG Found submodule.ilastik.url 2026-10-17 00:25:34,694 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:34,732 [ scc.config] DEBUG Found submodule.introduction.url 2026-10-17 00:25:35,120 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:35,156 [ scc.config] DEBUG Found submodule.iviewer.url 2026-10-17 00:25:35,571 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:35,608 [ scc.config] DEBUG Found submodule.java.url 2026-10-17 00:25:36,011 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:36,050 [ scc.config] DEBUG Found submodule.matlab.url 2026-10-17 00:25:36,440 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:36,483 [ scc.config] DEBUG Found submodule.mde.url 2026-10-17 00:25:36,882 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:36,917 [ scc.config] DEBUG Found submodule.orbit.url 2026-10-17 00:25:37,344 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:37,378 [ scc.config] DEBUG Found submodule.parade.url 2026-10-17 00:25:37,773 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:37,811 [ scc.config] DEBUG Found submodule.python.url 2026-10-17 00:25:38,251 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:38,287 [ scc.config] DEBUG Found submodule.qupath.url 2026-10-17 00:25:38,685 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:38,721 [ scc.config] DEBUG Found submodule.r.url 2026-10-17 00:25:39,117 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:39,184 [ scc.config] DEBUG Found submodule.scripts.url 2026-10-17 00:25:39,555 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:39,612 [ scc.config] DEBUG Found submodule.trackmate.url 2026-10-17 00:25:40,016 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:40,090 [ scc.config] DEBUG Found submodule.upload.url 2026-10-17 00:25:40,457 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-17 00:25:40,491 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-17 00:25:41,868 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f8df5487ad0> has local changes 2026-10-17 00:25:41,868 [ scc.git] DEBUG Calling 'git commit -a -n -m merge master -Dorg -Ssuccess-only Repository: ome/omero-guides Excluded PRs: - PR 23 jburel 'Remove submodules' (exclude comment) Already up to date. Repository: ome/omero-guide-cellprofiler Excluded PRs: - PR 25 pwalczysko 'Deprecate the non-save idr0002 notebook and redirect' (stage: draft) Already up to date. Merged PRs: - PR 24 jburel 'Remove binder' Repository: ome/omero-guide-download Already up to date. Repository: ome/omero-guide-figure Already up to date. Merged PRs: - PR 14 will-moore 'Table data by roi' - PR 17 will-moore 'Update inset workflow for OMERO.figure 7.2.0' Repository: ome/omero-guide-fiji Excluded PRs: - PR 24 oeway 'Disable FilamentDetector in Fiji' (user: oeway) Already up to date. Merged PRs: - PR 35 pwalczysko 'livingobjects' Repository: ome/omero-guide-fpbioimage Already up to date. Repository: ome/omero-guide-ilastik Already up to date. Repository: ome/omero-guide-introduction Already up to date. Repository: ome/omero-guide-iviewer Already up to date. Repository: ome/omero-guide-java Already up to date. Merged PRs: - PR 3 jburel 'fix build failure on rtd' Repository: ome/omero-guide-matlab Already up to date. Repository: ome/omero-guide-mde Already up to date. Merged PRs: - PR 4 pwalczysko 'Remove relative reference when it does not work' Repository: ome/omero-guide-orbit Already up to date. Repository: ome/omero-guide-parade Already up to date. Repository: ome/omero-guide-python Already up to date. Repository: ome/omero-guide-qupath Already up to date. Repository: ome/omero-guide-r Already up to date. Merged PRs: - PR 11 jburel 'fix build failure on rtd' Repository: ome/omero-guide-scripts Already up to date. Repository: ome/omero-guide-trackmate Already up to date. Repository: ome/omero-guide-upload Already up to date. Generated by OMERO-guides-push#98 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-guides-push/98/)' 2026-10-17 00:25:42,366 [ scc.git] DEBUG [detached HEAD abebeaa] merge master -Dorg -Ssuccess-only 2026-10-17 00:25:42,366 [ scc.git] DEBUG 20 files changed, 38 insertions(+), 38 deletions(-) 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guides 2026-10-17 00:25:42,368 [ scc.merge] INFO Excluded PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 23 jburel 'Remove submodules' (exclude comment) 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-cellprofiler 2026-10-17 00:25:42,368 [ scc.merge] INFO Excluded PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 25 pwalczysko 'Deprecate the non-save idr0002 notebook and redirect' (stage: draft) 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 24 jburel 'Remove binder' 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-download 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-figure 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 14 will-moore 'Table data by roi' 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 17 will-moore 'Update inset workflow for OMERO.figure 7.2.0' 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-fiji 2026-10-17 00:25:42,368 [ scc.merge] INFO Excluded PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 24 oeway 'Disable FilamentDetector in Fiji' (user: oeway) 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,368 [ scc.merge] INFO - PR 35 pwalczysko 'livingobjects' 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-fpbioimage 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-ilastik 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-introduction 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-iviewer 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Repository: ome/omero-guide-java 2026-10-17 00:25:42,368 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,368 [ scc.merge] INFO 2026-10-17 00:25:42,368 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,369 [ scc.merge] INFO - PR 3 jburel 'fix build failure on rtd' 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-matlab 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-mde 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,369 [ scc.merge] INFO - PR 4 pwalczysko 'Remove relative reference when it does not work' 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-orbit 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-parade 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-python 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-qupath 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-r 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Merged PRs: 2026-10-17 00:25:42,369 [ scc.merge] INFO - PR 11 jburel 'fix build failure on rtd' 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-scripts 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-trackmate 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO Repository: ome/omero-guide-upload 2026-10-17 00:25:42,369 [ scc.merge] INFO Already up to date. 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] INFO 2026-10-17 00:25:42,369 [ scc.merge] DEBUG Cleaning remote branches created for merging 2026-10-17 00:25:42,369 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,384 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/cellprofiler 2026-10-17 00:25:42,384 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,400 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,400 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/download 2026-10-17 00:25:42,401 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,417 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,417 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/figure 2026-10-17 00:25:42,417 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,433 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,433 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fiji 2026-10-17 00:25:42,433 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,450 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,450 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/fpbioimage 2026-10-17 00:25:42,450 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,466 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,466 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/ilastik 2026-10-17 00:25:42,466 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,482 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,482 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/introduction 2026-10-17 00:25:42,482 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,499 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,499 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/iviewer 2026-10-17 00:25:42,499 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,515 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,516 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/java 2026-10-17 00:25:42,516 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,532 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,532 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/matlab 2026-10-17 00:25:42,532 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,548 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,548 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/mde 2026-10-17 00:25:42,548 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,562 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,562 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/orbit 2026-10-17 00:25:42,562 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,578 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,578 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/parade 2026-10-17 00:25:42,578 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,593 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,593 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/python 2026-10-17 00:25:42,593 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,608 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,608 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/qupath 2026-10-17 00:25:42,608 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,624 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,625 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/r 2026-10-17 00:25:42,625 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,641 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,641 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/scripts 2026-10-17 00:25:42,641 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,659 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,659 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/trackmate 2026-10-17 00:25:42,660 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,677 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push 2026-10-17 00:25:42,677 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push/upload 2026-10-17 00:25:42,677 [ scc.git] DEBUG Calling 'git remote' 2026-10-17 00:25:42,693 [ scc.git] DEBUG cd /home/omero/workspace/OMERO-guides-push Update component versions python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/cellprofiler/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/cellprofiler/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/download/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/download/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/figure/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/figure/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/fiji/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/fiji/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/fpbioimage/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/fpbioimage/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/ilastik/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/ilastik/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/introduction/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/introduction/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/iviewer/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/iviewer/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/java/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/java/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/matlab/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/matlab/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/mde/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/mde/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/orbit/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/orbit/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/parade/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/parade/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/python/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/python/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/qupath/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/qupath/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/r/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/r/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/scripts/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/scripts/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/trackmate/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/trackmate/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/upload/setup.py': [Errno 2] No such file or directory python3.11: can't open file '/home/omero/workspace/OMERO-guides-push/upload/setup.py': [Errno 2] No such file or directory grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: grep: build.gradle: No such file or directory Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Up-to-date: Commit all component version changes Entering 'cellprofiler' Entering 'download' Entering 'figure' Entering 'fiji' Entering 'fpbioimage' Entering 'ilastik' Entering 'introduction' Entering 'iviewer' Entering 'java' Entering 'matlab' Entering 'mde' Entering 'orbit' Entering 'parade' Entering 'python' Entering 'qupath' Entering 'r' Entering 'scripts' Entering 'trackmate' Entering 'upload' Entering 'cellprofiler' HEAD detached from 248e8cb nothing to commit, working tree clean Entering 'download' HEAD detached from a27d196 nothing to commit, working tree clean Entering 'figure' HEAD detached from 654d43b nothing to commit, working tree clean Entering 'fiji' HEAD detached from 86f00e3 nothing to commit, working tree clean Entering 'fpbioimage' HEAD detached from 8f4b103 nothing to commit, working tree clean Entering 'ilastik' HEAD detached from c0bbd42 nothing to commit, working tree clean Entering 'introduction' HEAD detached from d903363 nothing to commit, working tree clean Entering 'iviewer' HEAD detached from 6ed80b3 nothing to commit, working tree clean Entering 'java' HEAD detached from a4b6b55 nothing to commit, working tree clean Entering 'matlab' HEAD detached from ecbd07c nothing to commit, working tree clean Entering 'mde' HEAD detached from d43e17f nothing to commit, working tree clean Entering 'orbit' HEAD detached from 4ef1eaa nothing to commit, working tree clean Entering 'parade' HEAD detached from 908b335 nothing to commit, working tree clean Entering 'python' HEAD detached from 41e4ded nothing to commit, working tree clean Entering 'qupath' HEAD detached from e298207 nothing to commit, working tree clean Entering 'r' HEAD detached from a770a10 nothing to commit, working tree clean Entering 'scripts' HEAD detached from 6133d50 nothing to commit, working tree clean Entering 'trackmate' HEAD detached from ffe98a8 nothing to commit, working tree clean Entering 'upload' HEAD detached from 6a5e015 nothing to commit, working tree clean HEAD detached from a126902 nothing to commit, working tree clean 2026-10-17 00:27:59,356 [ scc.push] INFO Merged branch pushed to https://github.com/snoopycrimecop/omero-guides/tree/merge_ci [Pipeline] archiveArtifacts Archiving artifacts [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline Finished: SUCCESS