Restyle repository to 80 columns.

Documentation/source/conf.py

@@ -88,7 +88,8 @@
 html_static_path = ['_static']
 
 
-# Don't sort module contents alphabetically, we want to order them in a helpful way for the user to read.
+# Don't sort module contents alphabetically, we want to order them in a
+# helpful way for the user to read.
 autodoc_member_order = 'bysource'
 
 

run_configs/gcom/grab_gcom.py

@@ -20,7 +20,11 @@
 if __name__ == '__main__':
 
     # note: we can add arguments to grab_config.arg_parser here
-    # todo: do a real example of this in one of the configs, or at least in the docs.
+    # todo: do a real example of this in one of the configs, or at least in
+    #       the docs.
 
     with grab_config:
-        fcm_export(grab_config, src='fcm:gcom.xm_tr/build', revision=revision, dst_label="gcom")
+        fcm_export(grab_config,
+                   src='fcm:gcom.xm_tr/build',
+                   revision=revision,
+                   dst_label="gcom")

run_configs/jules/build_jules.py

@@ -43,9 +43,16 @@ def __init__(self):
 
     with BuildConfig(project_label=f'jules {revision} $compiler',
                      tool_box=tool_box) as state:
-        # grab the source. todo: use some checkouts instead of exports in these configs.
-        fcm_export(state, src='fcm:jules.xm_tr/src', revision=revision, dst_label='src')
-        fcm_export(state, src='fcm:jules.xm_tr/utils', revision=revision, dst_label='utils')
+        # grab the source. todo: use some checkouts instead of exports in
+        #                        these configs.
+        fcm_export(state,
+                   src='fcm:jules.xm_tr/src',
+                   revision=revision,
+                   dst_label='src')
+        fcm_export(state,
+                   src='fcm:jules.xm_tr/utils',
+                   revision=revision,
+                   dst_label='utils')
 
         grab_pre_build(state, path='/not/a/real/folder', allow_fail=True),
 
@@ -61,9 +68,15 @@ def __init__(self):
         # move inc files to the root for easy tool use
         root_inc_files(state)
 
-        preprocess_fortran(state, common_flags=['-P', '-DMPI_DUMMY', '-DNCDF_DUMMY', '-I$output'])
+        preprocess_fortran(state,
+                           common_flags=['-P',
+                                         '-DMPI_DUMMY',
+                                         '-DNCDF_DUMMY',
+                                         '-I$output'])
 
-        analyse(state, root_symbol='jules', unreferenced_deps=['imogen_update_carb'])
+        analyse(state,
+                root_symbol='jules',
+                unreferenced_deps=['imogen_update_carb'])
 
         compile_fortran(state)
 

run_configs/lfric/grab_lfric.py

@@ -16,18 +16,30 @@
 # these configs are interrogated by the build scripts
 # todo: doesn't need two separate configs, they use the same project workspace
 tool_box = ToolBox()
-lfric_source_config = BuildConfig(project_label=f'lfric source {LFRIC_REVISION}',
-                                  tool_box=tool_box)
-gpl_utils_source_config = BuildConfig(project_label=f'lfric source {LFRIC_REVISION}',
-                                      tool_box=tool_box)
+lfric_source_config = BuildConfig(
+    project_label=f'lfric source {LFRIC_REVISION}',
+    tool_box=tool_box
+)
+gpl_utils_source_config = BuildConfig(
+    project_label=f'lfric source {LFRIC_REVISION}',
+    tool_box=tool_box
+)
 
 
 if __name__ == '__main__':
 
     with lfric_source_config:
         fcm_export(
-            lfric_source_config, src='fcm:lfric.xm_tr', revision=LFRIC_REVISION, dst_label='lfric')
+            lfric_source_config,
+            src='fcm:lfric.xm_tr',
+            revision=LFRIC_REVISION,
+            dst_label='lfric'
+        )
 
     with gpl_utils_source_config:
         fcm_export(
-            gpl_utils_source_config, src='fcm:lfric_gpl_utils.xm-tr', revision=LFRIC_REVISION, dst_label='gpl_utils')
+            gpl_utils_source_config,
+            src='fcm:lfric_gpl_utils.xm-tr',
+            revision=LFRIC_REVISION,
+            dst_label='gpl_utils'
+        )

run_configs/lfric/gungho.py

@@ -34,7 +34,8 @@ def get_transformation_script(fpath, config):
             relative_path = fpath.relative_to(base_path)
         except ValueError:
             pass
-    local_transformation_script = optimisation_path / (relative_path.with_suffix('.py'))
+    local_transformation_script = optimisation_path \
+        / (relative_path.with_suffix('.py'))
     if local_transformation_script.exists():
         return local_transformation_script
     global_transformation_script = optimisation_path / 'global.py'
@@ -49,15 +50,28 @@ def get_transformation_script(fpath, config):
 
     with BuildConfig(project_label='gungho $compiler $two_stage',
                      tool_box=ToolBox()) as state:
-        grab_folder(state, src=lfric_source / 'infrastructure/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'components/driver/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'components' / 'inventory' / 'source', dst_label='')
-        grab_folder(state, src=lfric_source / 'components/science/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'components/lfric-xios/source/', dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'infrastructure/source/',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'components/driver/source/',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'components' / 'inventory' / 'source',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'components/science/source/',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'components/lfric-xios/source/',
+                    dst_label='')
         grab_folder(state, src=lfric_source / 'gungho/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'um_physics/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'miniapps' / 'gungho_model' / 'source', dst_label='')
-        grab_folder(state, src=lfric_source / 'miniapps' / 'gungho_model' / 'optimisation',
+        grab_folder(state,
+                    src=lfric_source / 'um_physics' / 'source',
+                    dst_label='')
+        gungho_model_path = lfric_source / 'miniapps' / 'gungho_model'
+        grab_folder(state, src=gungho_model_path / 'source', dst_label='')
+        grab_folder(state, src=gungho_model_path / 'optimisation',
                     dst_label='optimisation')
         grab_folder(state, src=lfric_source / 'jules/source/', dst_label='')
         grab_folder(state, src=lfric_source / 'socrates/source/', dst_label='')
@@ -77,10 +91,15 @@ def get_transformation_script(fpath, config):
         preprocess_fortran(
             state,
             common_flags=[
-                '-DRDEF_PRECISION=64', '-DR_SOLVER_PRECISION=64', '-DR_TRAN_PRECISION=64', '-DUSE_XIOS',
+                '-DRDEF_PRECISION=64',
+                '-DR_SOLVER_PRECISION=64',
+                '-DR_TRAN_PRECISION=64',
+                '-DUSE_XIOS',
             ])
 
-        preprocess_x90(state, common_flags=['-DRDEF_PRECISION=64', '-DUSE_XIOS', '-DCOUPLED'])
+        preprocess_x90(state, common_flags=['-DRDEF_PRECISION=64',
+                                            '-DUSE_XIOS',
+                                            '-DCOUPLED'])
 
         psyclone(
             state,
@@ -94,7 +113,12 @@ def get_transformation_script(fpath, config):
         analyse(
             state,
             root_symbol='gungho_model',
-            ignore_mod_deps=['netcdf', 'MPI', 'yaxt', 'pfunit_mod', 'xios', 'mod_wait'],
+            ignore_mod_deps=['netcdf',
+                             'MPI',
+                             'yaxt',
+                             'pfunit_mod',
+                             'xios',
+                             'mod_wait'],
         )
 
         compile_fortran(
@@ -105,10 +129,15 @@ def get_transformation_script(fpath, config):
                 '-g',
                 '-std=f2008',
 
-                '-Wall', '-Werror=conversion', '-Werror=unused-variable', '-Werror=character-truncation',
+                '-Wall',
+                '-Werror=conversion',
+                '-Werror=unused-variable',
+                '-Werror=character-truncation',
                 '-Werror=unused-value', '-Werror=tabs',
 
-                '-DRDEF_PRECISION=64', '-DR_SOLVER_PRECISION=64', '-DR_TRAN_PRECISION=64',
+                '-DRDEF_PRECISION=64',
+                '-DR_SOLVER_PRECISION=64',
+                '-DR_TRAN_PRECISION=64',
                 '-DUSE_XIOS', '-DUSE_MPI=YES',
             ],
         )
@@ -119,9 +148,10 @@ def get_transformation_script(fpath, config):
             state,
             flags=[
                 '-fopenmp',
-
-                '-lyaxt', '-lyaxt_c', '-lnetcdff', '-lnetcdf', '-lhdf5',  # EXTERNAL_DYNAMIC_LIBRARIES
-                '-lxios',  # EXTERNAL_STATIC_LIBRARIES
+                # EXTERNAL_DYNAMIC_LIBRARIES
+                '-lyaxt', '-lyaxt_c', '-lnetcdff', '-lnetcdf', '-lhdf5',
+                # EXTERNAL_STATIC_LIBRARIES
+                '-lxios',
                 '-lstdc++',
             ],
         )

run_configs/lfric/lfric_common.py

@@ -23,12 +23,17 @@ def check_available(self):
 
 # todo: is this part of psyclone? if so, put  it in the psyclone step module?
 @step
-def configurator(config, lfric_source: Path, gpl_utils_source: Path, rose_meta_conf: Path, config_dir=None):
-
+def configurator(config,
+                 lfric_source: Path,
+                 gpl_utils_source: Path,
+                 rose_meta_conf: Path,
+                 config_dir=None):
     rose_picker_tool = gpl_utils_source / 'rose_picker/rose_picker'
-    gen_namelist_tool = lfric_source / 'infrastructure/build/tools/GenerateNamelist'
-    gen_loader_tool = lfric_source / 'infrastructure/build/tools/GenerateLoader'
-    gen_feigns_tool = lfric_source / 'infrastructure/build/tools/GenerateFeigns'
+
+    tools_path = lfric_source / 'infrastructure' / 'build' / 'tools'
+    gen_namelist_tool = tools_path / 'GenerateNamelist'
+    gen_loader_tool = tools_path / 'GenerateLoader'
+    gen_feigns_tool = tools_path / 'GenerateFeigns'
 
     config_dir = config_dir or config.source_root / 'configuration'
 
@@ -37,7 +42,8 @@ def configurator(config, lfric_source: Path, gpl_utils_source: Path, rose_meta_c
     env['PYTHONPATH'] += f':{rose_lfric_path}'
 
     # "rose picker"
-    # creates rose-meta.json and config_namelists.txt in gungho/source/configuration
+    # creates rose-meta.json and config_namelists.txt in
+    # gungho/source/configuration
     logger.info('rose_picker')
     rose_picker = Script(rose_picker_tool)
     rose_picker.run(additional_parameters=[str(rose_meta_conf),
@@ -56,7 +62,8 @@ def configurator(config, lfric_source: Path, gpl_utils_source: Path, rose_meta_c
     # create configuration_mod.f90 in source root
     logger.info('GenerateLoader')
     gen_loader = Script(gen_loader_tool)
-    names = [name.strip() for name in open(config_dir / 'config_namelists.txt').readlines()]
+    names = [name.strip()
+             for name in open(config_dir / 'config_namelists.txt').readlines()]
     configuration_mod_fpath = config.source_root / 'configuration_mod.f90'
     gen_loader.run(additional_parameters=[configuration_mod_fpath,
                                           *names])
@@ -70,7 +77,8 @@ def configurator(config, lfric_source: Path, gpl_utils_source: Path, rose_meta_c
 
     # put the generated source into an artefact
     # todo: we shouldn't need to do this, should we?
-    #       it's just going to be found in the source folder with everything else.
+    #       it's just going to be found in the source folder with everything
+    #       else.
     config._artefact_store['configurator_output'] = [
         configuration_mod_fpath,
         feign_config_mod_fpath
@@ -80,7 +88,8 @@ def configurator(config, lfric_source: Path, gpl_utils_source: Path, rose_meta_c
 @step
 def fparser_workaround_stop_concatenation(config):
     """
-    fparser can't handle string concat in a stop statement. This step is a workaround.
+    fparser can't handle string concat in a stop statement. This step is a
+    workaround.
 
     https://github.com/stfc/fparser/issues/330
 

run_configs/lfric/mesh_tools.py

@@ -21,24 +21,35 @@
     lfric_source = lfric_source_config.source_root / 'lfric'
     gpl_utils_source = gpl_utils_source_config.source_root / 'gpl_utils'
 
-    # this folder just contains previous output, for testing the overrides mechanism.
+    # this folder just contains previous output, for testing the overrides
+    # mechanism.
     psyclone_overrides = Path(__file__).parent / 'mesh_tools_overrides'
 
     with BuildConfig(project_label='mesh tools $compiler $two_stage',
                      tool_box=ToolBox()) as state:
-        grab_folder(state, src=lfric_source / 'infrastructure/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'mesh_tools/source/', dst_label='')
-        grab_folder(state, src=lfric_source / 'components/science/source/', dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'infrastructure/source/',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'mesh_tools/source/',
+                    dst_label='')
+        grab_folder(state,
+                    src=lfric_source / 'components/science/source/',
+                    dst_label='')
 
         # grab the psyclone overrides folder into the source folder
-        grab_folder(state, src=psyclone_overrides, dst_label='mesh_tools_overrides')
+        grab_folder(state,
+                    src=psyclone_overrides,
+                    dst_label='mesh_tools_overrides')
 
         # generate more source files in source and source/configuration
+        rose_meta_path = lfric_source / 'mesh_tools' / 'rose-meta' \
+            / 'lfric-mesh_tools' / 'HEAD' / 'rose-meta.conf'
         configurator(
             state,
             lfric_source=lfric_source,
             gpl_utils_source=gpl_utils_source,
-            rose_meta_conf=lfric_source / 'mesh_tools/rose-meta/lfric-mesh_tools/HEAD/rose-meta.conf',
+            rose_meta_conf=rose_meta_path,
         )
 
         find_source_files(
@@ -50,7 +61,9 @@
 
         preprocess_fortran(state)
 
-        preprocess_x90(state, common_flags=['-DRDEF_PRECISION=64', '-DUSE_XIOS', '-DCOUPLED'])
+        preprocess_x90(state, common_flags=['-DRDEF_PRECISION=64',
+                                            '-DUSE_XIOS',
+                                            '-DCOUPLED'])
 
         psyclone(
             state,
@@ -63,8 +76,11 @@
 
         analyse(
             state,
-            root_symbol=['cubedsphere_mesh_generator', 'planar_mesh_generator', 'summarise_ugrid'],
-            # ignore_mod_deps=['netcdf', 'MPI', 'yaxt', 'pfunit_mod', 'xios', 'mod_wait'],
+            root_symbol=['cubedsphere_mesh_generator',
+                         'planar_mesh_generator',
+                         'summarise_ugrid'],
+            # ignore_mod_deps=['netcdf', 'MPI', 'yaxt', 'pfunit_mod', 'xios',
+            #                  'mod_wait'],
         )
 
         compile_fortran(state, common_flags=['-c'])
@@ -75,8 +91,12 @@
         link_exe(
             state,
             flags=[
-                '-lyaxt', '-lyaxt_c', '-lnetcdff', '-lnetcdf', '-lhdf5',  # EXTERNAL_DYNAMIC_LIBRARIES
-                '-lxios',  # EXTERNAL_STATIC_LIBRARIES
+                # EXTERNAL_DYNAMIC_LIBRARIES
+                '-lyaxt', '-lyaxt_c',
+                '-lnetcdff', '-lnetcdf',
+                '-lhdf5',
+                # EXTERNAL_STATIC_LIBRARIES
+                '-lxios',
                 '-lstdc++',
             ],
         )