From 0a44d59c7af6d35eaf6e5ffdab81081994ae78d0 Mon Sep 17 00:00:00 2001 From: fabcor Date: Mon, 1 Jul 2024 16:33:38 +0200 Subject: [PATCH] Set 2 characters indentation level for YAML files --- .yamllint.yaml | 3 + .../gphl/gphl-setup.yml | 136 +++++++++--------- 2 files changed, 71 insertions(+), 68 deletions(-) diff --git a/.yamllint.yaml b/.yamllint.yaml index bd66e95b6..102df9db6 100644 --- a/.yamllint.yaml +++ b/.yamllint.yaml @@ -6,6 +6,9 @@ ignore: | ui/pnpm-lock.yaml rules: + indentation: + spaces: 2 + # Match line length to the one set by `black` the Python formatter line-length: max: 88 diff --git a/test/HardwareObjectsMockup.xml/gphl/gphl-setup.yml b/test/HardwareObjectsMockup.xml/gphl/gphl-setup.yml index 6b5c8c351..d92a0690b 100644 --- a/test/HardwareObjectsMockup.xml/gphl/gphl-setup.yml +++ b/test/HardwareObjectsMockup.xml/gphl/gphl-setup.yml @@ -1,95 +1,95 @@ --- -# yamllint disable rule:comments -# yamllint disable rule:comments-indentation -# yamllint disable rule:line-length - _initialise_class: - class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection + class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection directory_locations: - # Directory locations. Can also be used with ${} syntax in this file - GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/gphl_release - # GPHL_WRAPPERS: /data/users/p3l-gleb1/gphl/ + # Directory locations. Can also be used with ${} syntax in this file + GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/gphl_release + # GPHL_WRAPPERS: /data/users/p3l-gleb1/gphl/ # If set, run workflow through ssh with selected options # and quote parameters as appropriate # NB The Host option is mandatory # ConfigFile is the ssh configuration file, passed to ssh with the -F option -#ssh_options: -# Host: lonsdale -# IdentityFile: /home/rhfogh/.ssh/wf_test_id -# User: rhfogh -# StrictHostKeyChecking: no -# ConfigFile: /path/to/ssh/config/file - -# Directory used for GPhL workflow persistence data and workflow logs: -# Used to set the wdir workflow option -# If relative designates a subdirectory under Session.get_process_directory() -# If absolute taken as it stands +# ssh_options: +# Host: lonsdale +# IdentityFile: /home/rhfogh/.ssh/wf_test_id +# User: rhfogh +# StrictHostKeyChecking: no +# ConfigFile: /path/to/ssh/config/file + +# Directory used for GPhL workflow persistence data and workflow logs: +# Used to set the wdir workflow option +# If relative designates a subdirectory under Session.get_process_directory() +# If absolute taken as it stands gphl_subdir: GPHL -# root name of persistence layer file; suffix'.xml. is added +# root name of persistence layer file; suffix'.xml. is added gphl_persistname: persistence -#Hosts and ports for py4j java-python gateway, all OPTIONAL -#If not set will use py4j default values, which are as given below -#NB python_host is set automatically to localhost or socket.gethostname() -#NB java_host is not needed as all communication is effectively one-way -#connection_parameters: -# python_port: 25334 -# java_port: 25333 +# Hosts and ports for py4j java-python gateway, all OPTIONAL +# If not set will use py4j default values, which are as given below +# NB python_host is set automatically to localhost or socket.gethostname() +# NB java_host is not needed as all communication is effectively one-way +# connection_parameters: +# python_port: 25334 +# java_port: 25333 -#NB Non-absolute file names are interpreted relative to one of the -#HardwareRepository directories on the lookup path +# NB Non-absolute file names are interpreted relative to one of the +# HardwareRepository directories on the lookup path software_paths: - # Mandatory. Directory with workflow config input, e.g. instrumentation.nml - gphl_beamline_config: gphl/config_esrf_id30b + # Mandatory. Directory with workflow config input, e.g. instrumentation.nml + gphl_beamline_config: gphl/config_esrf_id30b - # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, - # unless already sourced in environment - GPHL_CCP4_PATH: /alt/rhfogh/Software/CCP4/latest/bin + # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, + # unless already sourced in environment + GPHL_CCP4_PATH: /alt/rhfogh/Software/CCP4/latest/bin - # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par - # unless already sourced in environment - GPHL_XDS_PATH: /alt/rhfogh/Software/XDS/latest + # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par + # unless already sourced in environment + GPHL_XDS_PATH: /alt/rhfogh/Software/XDS/latest - # OPTIONAL for java binary => defaults to just 'java' -# java_binary: "/alt/rhfogh/Software/GPhL/mxcube_setup/java-11-openjdk-11/bin/java" + # OPTIONAL for java binary => defaults to just 'java' + # java_binary: "/alt/rhfogh/Software/GPhL/mxcube_setup/java-11-openjdk-11/bin/java" - # gphl test samples directory - for collection emulation - gphl_test_samples: gphl/test_samples + # gphl test samples directory - for collection emulation + gphl_test_samples: gphl/test_samples - #Location of installation used for processing queue (if not reachable from BCS computer. - #Passed as environmental variable GPHL_PROC_INSTALLATION. Optional -# gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe + # Location of installation used for processing queue + # (if not reachable from BCS computer). + # Passed as environmental variable GPHL_PROC_INSTALLATION. Optional + # gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe # Software paths that are passed to global phasing workflow as java properties # Used to specify locations of alternative executables (wrappers) # More (unused) properties are described in the ASTRA workflow documentation software_properties: - #Location of GPhL .license directory - #defaults to GPHL_INSTALLATION - #Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : - # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" - - # MANDATORY pending change in workflow - co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" - - # OPTIONAL location of alternative executables (wrappers) supported by the workflow - # Each has an option (rarely used) to specify a specific license directory --> - # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process - # co.gphl.wf.process.bdg_licence_dir/fill/me/in - # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal - # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict - # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in - # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal - # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen - # co.gphl.wf.recen.bdg_licence_dir/fill/me/in - - # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow - co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240206/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal - co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240206/Files_workflow_TRUNK_alpha-bdg + # Location of GPhL .license directory + # defaults to GPHL_INSTALLATION + # Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : + # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" + + # MANDATORY pending change in workflow + co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" + + # OPTIONAL location of alternative executables (wrappers) supported by the workflow + # Each has an option (rarely used) to specify a specific license directory --> + # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process + # co.gphl.wf.process.bdg_licence_dir/fill/me/in + # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal + # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict + # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in + # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal + # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen + # co.gphl.wf.recen.bdg_licence_dir/fill/me/in + + # OPTIONAL. simcal *binary* For Mock collection emulation only. + # Not used by ASTRA workflow + # yamllint disable-line rule:line-length + co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240206/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal + # yamllint disable-line rule:line-length + co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240206/Files_workflow_TRUNK_alpha-bdg