Fixed yamllint problems

rhfogh · Jul 8, 2024 · b335287 · b335287
1 parent ba6e55c
commit b335287
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diff --git a/.github/workflows/coverage_report.yml b/.github/workflows/coverage_report.yml
@@ -1,4 +1,4 @@
-# %YAML 1.2
+%YAML 1.2
 ---
 
 name: Coverage Report

diff --git a/.github/workflows/create-tag.yml b/.github/workflows/create-tag.yml
@@ -1,4 +1,4 @@
-# %YAML 1.2
+%YAML 1.2
 ---
 
 name: Create/Update Tag

diff --git a/.github/workflows/pages.yaml b/.github/workflows/pages.yaml
@@ -1,4 +1,4 @@
-# %YAML 1.2
+%YAML 1.2
 ---
 
 

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -1,4 +1,4 @@
-# %YAML 1.2
+%YAML 1.2
 ---
 
 name: Linting & Code Quality

diff --git a/mxcubecore/configuration/mockup/gphl/gphl-workflow.yml b/mxcubecore/configuration/mockup/gphl/gphl-workflow.yml
@@ -44,12 +44,12 @@ settings:
   # NB Temporary developer option. Defaults to 1
   allow_duplicate_orientations: 0
 
-    # TEST ONLY developer option. Use preset SPOT.XDS file and skip characterisation.
-    # Only works for GPhL test samples with SPOT.XDS  file
-    # NB to get sensible results you should use the default values for resolution and
-    # wavelength, and the default Eiger 16M detector
-    # Otherwise the UI may still work, but the indexing solutions will be weird
-    # use_preset_spotdir: true
+  # TEST ONLY developer option. Use preset SPOT.XDS file and skip characterisation.
+  # Only works for GPhL test samples with SPOT.XDS  file
+  # NB to get sensible results you should use the default values for resolution and
+  # wavelength, and the default Eiger 16M detector
+  # Otherwise the UI may still work, but the indexing solutions will be weird
+  # use_preset_spotdir: true
 
 
   defaults:
@@ -96,12 +96,12 @@ settings:
     # Any other true value reads from auto_acq_parameters below
     # automation_mode: TEST_FROM_FILE
 
-      # Default parameters for fully automated strategies
-      # Multiple acquisitions in order - characterisation then main
-      # passed to set_pre_strategy_params and set_pre_acquisition_params
-      # NB as long as we only acquire either characterisation+main or diffractcal
-      # the code will use list[0] for the first acquisition
-      # and list[-1] for the main one
+    # Default parameters for fully automated strategies
+    # Multiple acquisitions in order - characterisation then main
+    # passed to set_pre_strategy_params and set_pre_acquisition_params
+    # NB as long as we only acquire either characterisation+main or diffractcal
+    # the code will use list[0] for the first acquisition
+    # and list[-1] for the main one
     auto_acq_parameters:
       # For characterisation acquisition
       - exposure_time: 0.02
@@ -113,35 +113,35 @@ settings:
         # For acquisition or diffractcal
         # Expectation for crystal classes - needed for indexing selection.
 
-      # crystal_classes:
-      #   - 222P
-      #   - 222C
-      #   - 222I
-      # space_group: I222
-    - exposure_time: 0.02
-      image_width: 1.0
-      resolution: 1.5
-      snapshot_count: 2
-      wedge_width: 15.0
-      strategy: full
-      repetition_count: 1
-      strategy_options:
-      # Program options passed directly to stratcal - not needed normally
-      # Override default settings
-      # angular_tolerance, maximum_chi, and clip_kappa are defined in
-      # settings (above) and strategy_type and variant by program
-      # maximum_chi: 48.0
-      # angular_tolerance: 1.0
-      # option_name: 999.999
+        # crystal_classes:
+        #   - 222P
+        #   - 222C
+        #   - 222I
+        # space_group: I222
+      - exposure_time: 0.02
+        image_width: 1.0
+        resolution: 1.5
+        snapshot_count: 2
+        wedge_width: 15.0
+        strategy: full
+        repetition_count: 1
+        # strategy_options:
+        # # Program options passed directly to stratcal - not needed normally
+        #   Override default settings
+        #   angular_tolerance, maximum_chi, and clip_kappa are defined in
+        #   settings (above) and strategy_type and variant by program
+        #   maximum_chi: 48.0
+        #   angular_tolerance: 1.0
+        #   option_name: 999.999
 
   # Java invocation properties - syntax is e.g. '-Dfile.encoding=UTF-8'
   invocation_properties:
 
     # File name prefix for workflow log files
     co.gphl.wf.persistName: wf
 
-      # Switch to pass log to stdout. Defaults to true
-      # co.gphl.wf.logStdout: false
+    # Switch to pass log to stdout. Defaults to true
+    # co.gphl.wf.logStdout: false
 
   # Properties applied after the java command - syntax as above-->
   # Note that irrelevant properties are simply ignored.-->
@@ -157,11 +157,11 @@ settings:
     # Chcks for data processing directory tree
     # co.gphl.wf.procRootCheck: false
 
-      # Parameters to individual applications
-      # Switch devMod to true to activate development parameters
-      # NB needed as of 20231116 no longer in active use
-      # co.gphl.wf.devMode: true
-      # For stratcal configuration switches edit run_stratcal_wrap.py script instead
+    # Parameters to individual applications
+    # Switch devMod to true to activate development parameters
+    # NB needed as of 20231116 no longer in active use
+    # co.gphl.wf.devMode: true
+    # For stratcal configuration switches edit run_stratcal_wrap.py script instead
 
     # Dummy sample properties.
     # Choose values for these to make spot predictions for the characterisation

diff --git a/mxcubecore/configuration/mockup/gphl/gphl_wf_automation_interface.yml b/mxcubecore/configuration/mockup/gphl/gphl_wf_automation_interface.yml
@@ -12,110 +12,109 @@
 
 task:
 
-parameters:
-  # Process control and ???
-  wfpath: Gphl  # Mandatory – specifies  GΦL workflow
-  automation_mode: MASSIF1  # Optional,  defaults to None (manual)
-  shape: some_shape_name  # Used for EDNA workflow, I do not know  what for
+  parameters:
+    # Process control and ???
+    wfpath: Gphl  # Mandatory – specifies  GΦL workflow
+    automation_mode: MASSIF1  # Optional,  defaults to None (manual)
+    shape: some_shape_name  # Used for EDNA workflow, I do not know  what for
 
-  # Strategy control
-  strategy_name: "Native data collection"  # (str) Mandatory.
-  # Options are: ‘Native data collection’, ‘Phasing (SAD)’
-  # ‘Two-wavelength MAD’, ‘Three-wavelength MAD’, ‘Diffractometer calibration’
+    # Strategy control
+    strategy_name: "Native data collection"  # (str) Mandatory.
+    # Options are: ‘Native data collection’, ‘Phasing (SAD)’
+    # ‘Two-wavelength MAD’, ‘Three-wavelength MAD’, ‘Diffractometer calibration’
 
-  # directory and file names. All optional, default to session default
-  # See File Locations in manual
-  prefix: <path_template.base_prefix>  # (str)
-  suffix: <path_template.suffix>  # (str) Optional
-  subdir: <Image path subdirectory>  # (str) Optional
+    # directory and file names. All optional, default to session default
+    # See File Locations in manual
+    prefix: <path_template.base_prefix>  # (str)
+    suffix: <path_template.suffix>  # (str) Optional
+    subdir: <Image path subdirectory>  # (str) Optional
 
-  # Optional, overriding configured defaults:
-  decay_limit: 25  # (%).
-  # Minimum % intensity remaining at target resolution using recommended dose budget
-  # dose_budget = 2 * resolution**2 * log(100. / decay_limit) / relative_sensitivity
-  maximum_dose_budget: 20  # (MGy). Maximum when calculating budget from resolution
-  characterisation_budget_fraction: 0.05  # dose fraction used for characterisation
+    # Optional, overriding configured defaults:
+    decay_limit: 25  # (%).
+    # Minimum % intensity remaining at target resolution using recommended dose budget
+    # dose_budget = 2 * resolution**2 * log(100. / decay_limit) / relative_sensitivity
+    maximum_dose_budget: 20  # (MGy). Maximum when calculating budget from resolution
+    characterisation_budget_fraction: 0.05  # dose fraction used for characterisation
 
-  # Strategy name, matching strategylib.nml.
-  auto_acq_parameters:  # (list of dict) automation parameters for acquisitions.
-    # Optional.
-    # The standard workflows have two acquisitions, characterisation and main;
-    # diffractometer calibration has only one, and future workflows may have more.
-    # The dictionaries are applied to the acquisitions in order;
-    # if there is only one dictionary in the list, it applies to all acquisitions.
-    # The following appear in task dictionaries in interactive MXCuBE3,
-    # but are NOT used by the  GΦL workflow: wfname, wftype, strategies, type
+    # Strategy name, matching strategylib.nml.
+    auto_acq_parameters:  # (list of dict) automation parameters for acquisitions.
+      # Optional.
+      # The standard workflows have two acquisitions, characterisation and main;
+      # diffractometer calibration has only one, and future workflows may have more.
+      # The dictionaries are applied to the acquisitions in order;
+      # if there is only one dictionary in the list, it applies to all acquisitions.
+      # The following appear in task dictionaries in interactive MXCuBE3,
+      # but are NOT used by the  GΦL workflow: wfname, wftype, strategies, type
 
-    # The first dictionary are the parameters needed for MASSIF1 characterisation
-    # where characterisation and first XDS run are done BEFORE starting the workflow
-    # init_spot_dir can be set ONLY for characterisation
-    # init_spot_dir, if set, turns off the workflow-driven characterisation
-    # resolution, energies, and transmission are taken from the current values
-    # in this case unless explicitly set
-    - exposure_time: 0.04  # (s) Optional, default configured.
-      # Mandatory if init_spot_dir is set
-      image_width: 0.1    # (°) Optional, default configured.
-      # Mandatory if init_spot_dir is set
-      # use_dose: 20.0 # (MGy) Total dose. Optional. Overrides dose budget
-      # transmission: 100.0 # (%) Nptional  Overrides use_dose.
-      # Defaults to current valuee if init_spot_dir is set
-      init_spot_dir: "/where/ever/dict"   # Directory containing SPOTS.XDS file
-      # from preliminary XDS calculation
-      # When init_spot_dir is set, strategy must be the name of the strategy
-      # (specified in stragegylib.nml) that was actually used for characterisation.
-      strategy: “Char_6_5_multitrigger”
-      # Optional: Arithmetic crystal classes expected for the symmetry.
-      # Will be used to select a matching indexing solution,
-      # and to determine acquisition strategy.
-      # If no matching indexing solution is found, these will be ignored.
-      # Must be given in first (characterisation) set of auto_acq_parameters
-      # crystal_classes:
-      #   - 4I
-      #   - 422I
-      # Pass input cell and symmetry to XDS and processing and force their use as
-      # starting point. Used to override XDS cell, symmetry determination
-      use_cell_for_processing: false
+      # The first dictionary are the parameters needed for MASSIF1 characterisation
+      # where characterisation and first XDS run are done BEFORE starting the workflow
+      # init_spot_dir can be set ONLY for characterisation
+      # init_spot_dir, if set, turns off the workflow-driven characterisation
+      # resolution, energies, and transmission are taken from the current values
+      # in this case unless explicitly set
+      - exposure_time: 0.04  # (s) Optional, default configured.
+        # Mandatory if init_spot_dir is set
+        image_width: 0.1    # (°) Optional, default configured.
+        # Mandatory if init_spot_dir is set
+        # use_dose: 20.0 # (MGy) Total dose. Optional. Overrides dose budget
+        # transmission: 100.0 # (%) Nptional  Overrides use_dose.
+        # Defaults to current valuee if init_spot_dir is set
+        init_spot_dir: "/where/ever/dict"   # Directory containing SPOTS.XDS file
+        # from preliminary XDS calculation
+        # When init_spot_dir is set, strategy must be the name of the strategy
+        # (specified in stragegylib.nml) that was actually used for characterisation.
+        strategy: “Char_6_5_multitrigger”
+        # Optional: Arithmetic crystal classes expected for the symmetry.
+        # Will be used to select a matching indexing solution,
+        # and to determine acquisition strategy.
+        # If no matching indexing solution is found, these will be ignored.
+        # Must be given in first (characterisation) set of auto_acq_parameters
+        # crystal_classes:
+        #   - 4I
+        #   - 422I
+        # Pass input cell and symmetry to XDS and processing and force their use as
+        # starting point. Used to override XDS cell, symmetry determination
+        use_cell_for_processing: false
 
-    # acquisition parameters, for successive steps (characterisation or main).
-    # This example lists all options, for documentation purposes
-    # All are optional (except when init_spot_dir is set) and should normally
-    # be left empty so the default is used.
-    - resolution: 1.7  # (Å) Optional. Defaults to current value,
-      # or to diffraction plan aimed_resolution
-      energies: (12.4,)  # tuple(keV) List of energies to use in experiment.
-      # two or three for MAD (only).
-      # First wavelength will be used for calculating strategies, dose budget, etc.
-      # Optional, except for MAD - will default to current beamline energy.
-      exposure_time: 0.04  # (s) Optional, default configured.
-      # Mandatory if init_spot_dir is set
-      image_width: 0.1  # (°) Optional, default configured.
-      # Mandatory if init_spot_dir is set
-      wedge_width: 30.0  # (°) Wedge width (for interleaving)
-      #  Optional, default configured.
-      snapshot_count: 2  # Optional, default configured.
-      use_dose: 20.0  # (MGy) NB Optional, for entire experiment.
-      # Defaults to calculated dose budget. Resets transmission, exposure time
-      transmission: 80.0  # (%) NB Optional  Overrides use_dose.
-      # Defaults to current valuee if init_spot_dir is set
-      # Otherwise is set from dose budget and resolution.
-      # If set this value will reset the dose budget
-      # Strategy variant
-      # Default is “quick” for MAD, “full” for native or SAD
-      strategy: full
-      # Number of repetitions of entire strategy
-      repetition_count: 1
-      # Pass input cell and symmetry to XDS and processing and force their use as
-      # startign point. Used to override XDS cell, symmetry determination
-      use_cell_for_processing: false
+      # acquisition parameters, for successive steps (characterisation or main).
+      # This example lists all options, for documentation purposes
+      # All are optional (except when init_spot_dir is set) and should normally
+      # be left empty so the default is used.
+      - resolution: 1.7  # (Å) Optional. Defaults to current value,
+        # or to diffraction plan aimed_resolution
+        energies: (12.4,)  # tuple(keV) List of energies to use in experiment.
+        # two or three for MAD (only).
+        # First wavelength will be used for calculating strategies, dose budget, etc.
+        # Optional, except for MAD - will default to current beamline energy.
+        exposure_time: 0.04  # (s) Optional, default configured.
+        # Mandatory if init_spot_dir is set
+        image_width: 0.1  # (°) Optional, default configured.
+        # Mandatory if init_spot_dir is set
+        wedge_width: 30.0  # (°) Wedge width (for interleaving)
+        #  Optional, default configured.
+        snapshot_count: 2  # Optional, default configured.
+        use_dose: 20.0  # (MGy) NB Optional, for entire experiment.
+        # Defaults to calculated dose budget. Resets transmission, exposure time
+        transmission: 80.0  # (%) NB Optional  Overrides use_dose.
+        # Defaults to current valuee if init_spot_dir is set
+        # Otherwise is set from dose budget and resolution.
+        # If set this value will reset the dose budget
+        # Strategy variant
+        # Default is “quick” for MAD, “full” for native or SAD
+        strategy: full
+        # Number of repetitions of entire strategy
+        repetition_count: 1
+        # Pass input cell and symmetry to XDS and processing and force their use as
+        # startign point. Used to override XDS cell, symmetry determination
+        use_cell_for_processing: false
 
-      strategy_options:  # (dict) strategy calculation parameters. See below
-
-        # strategy options. Control the stratcal strategy calculation program.
-        # maximum_chi is automaticaly reduced to match kappa motor limits.
-        maximum_chi: 48.0  # (°) Optional. Maximum chi value allowed for strategies.
-        # Default 48
-        angular tolerance: 1.0  # (°) Optional.
-        # Tolerance to distinguish strategy orientations
+        strategy_options:  # (dict) strategy calculation parameters. See below
+          # strategy options. Control the stratcal strategy calculation program.
+          # maximum_chi is automaticaly reduced to match kappa motor limits.
+          maximum_chi: 48.0  # (°) Optional. Maximum chi value allowed for strategies.
+          # Default 48
+          angular tolerance: 1.0  # (°) Optional.
+          # Tolerance to distinguish strategy orientations
 
 # Other parameters are set (ultimately) from ISPyB. These are all optional:
 # From crystal description: