new inversion plugin

aiida_flexpart/calculations/inversion.py

@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+from aiida import orm, common, engine
+from aiida.plugins import DataFactory
+import yaml
+
+NetCDF = DataFactory('netcdf.data')
+
+
+class Inversion(engine.CalcJob):
+    @classmethod
+    def define(cls, spec):
+        """Define inputs and outputs of the calculation."""
+        # yapf: disable
+        super().define(spec)
+
+        #INPUTS metadata
+        spec.inputs['metadata']['options']['resources'].default = {
+            'num_machines': 1,
+            'num_mpiprocs_per_machine': 1,
+        }
+        spec.input('metadata.options.custom_scheduler_commands', valid_type=str, default='')
+        spec.input('metadata.options.withmpi', valid_type=bool, default=False)
+        spec.input('metadata.options.output_filename', valid_type=str, default='aiida.out', required=True)
+        #spec.input('metadata.options.parser_name', valid_type=str, default='collect.sens')
+
+        #Inputs
+        spec.input_namespace('remotes', valid_type = NetCDF, required=True)
+        spec.input_namespace('observations', valid_type = NetCDF, required=True)
+
+        spec.input('inv_params',valid_type = orm.Dict, required = True,
+                   help = 'File containing inversion settings, either as R source file or yaml')
+        spec.input('start_date',valid_type = orm.Str, required = True,
+                   help = 'Start date (yyyy-mm-dd)')
+        spec.input('end_date',valid_type = orm.Str, required = True,
+                   help = 'End date (yyyy-mm-dd)')
+        spec.input('chunk',valid_type = orm.Str, required = True,
+                   help = "Options are 'year' and 'month'. Default is 'year'")
+        spec.input('chunk_w',valid_type = orm.Str, required = True,
+                   help = """Width of the individual inversion chunk. These can be wider than
+			                 the chunking itself to allow for running average fluxes.,
+                             Possible values are 'year' and '3year' for 'chunk.by=year' and,
+                             'month' and '3month' for 'chunk.by=month'. Default is 'year'
+                         """)
+
+        #exit codes
+        spec.outputs.dynamic = True
+
+    def prepare_for_submission(self, folder):
+
+        codeinfo = common.CodeInfo()
+        codeinfo.cmdline_params = [
+            '-f',
+            'inversion_settings.yaml',
+            '-s',
+            self.inputs.start_date.value,
+            '-e',
+            self.inputs.end_date.value,
+            '-c',
+            self.inputs.chunk.value,
+            '-w',
+            self.inputs.chunk_w.value,
+        ]
+        codeinfo.code_uuid = self.inputs.code.uuid
+        codeinfo.stdout_name = self.metadata.options.output_filename
+        codeinfo.withmpi = self.inputs.metadata.options.withmpi
+
+        with folder.open('inversion_settings.yaml', 'w') as f:
+                _ = yaml.dump(self.inputs.inv_params.get_dict(), f)
+
+        # Prepare a `CalcInfo` to be returned to the engine
+        calcinfo = common.CalcInfo()
+        calcinfo.codes_info = [codeinfo]
+        calcinfo.retrieve_list = ['aiida.out']
+
+        return calcinfo

pyproject.toml

@@ -7,7 +7,7 @@ name = "aiida_flexpart"
 
 [project]
 name = "aiida-flexpart"
-version = "0.1.3"
+version = "0.1.4"
 readme = "README.md"
 license = {file = 'LICENSE'}
 description = "AiiDA plugin for the FLEXPART code (simulation of atmospheric transport processes)."
@@ -21,13 +21,14 @@ classifiers = [
     "Programming Language :: Python :: 3",
 
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 dependencies = [
     "aiida-core>=1.6.5,<3.0.0",
     "six",
     "psycopg2-binary<2.9",
     "voluptuous",
     "jinja2",
+    "netCDF4"
 ]
 
 [[project.authors]]
@@ -51,25 +52,27 @@ docs = [
     "sphinx-rtd-theme",
 ]
 
+[project.entry-points."aiida.data"]
+"netcdf.data" = "aiida_flexpart.data.nc_data:NetCdfData"
+
 [project.entry-points."aiida.calculations"]
 "flexpart.cosmo" = "aiida_flexpart.calculations.flexpart_cosmo:FlexpartCosmoCalculation"
 "flexpart.ifs" = "aiida_flexpart.calculations.flexpart_ifs:FlexpartIfsCalculation"
 "flexpart.post" = "aiida_flexpart.calculations.flexpart_post:PostProcessingCalculation"
-"collect.sensitivities" = "aiida_flexpart.calculations.collect_sens:CollectSensitivitiesCalculation"
+"collect.sensitivities" = "aiida_flexpart.calculations.collect_sens:CollectSensCalculation"
+"inversion.calc" = "aiida_flexpart.calculations.inversion:Inversion"
 
 [project.entry-points."aiida.parsers"]
 "flexpart.cosmo" = "aiida_flexpart.parsers.flexpart_cosmo:FlexpartCosmoParser"
 "flexpart.ifs" = "aiida_flexpart.parsers.flexpart_ifs:FlexpartIfsParser"
 "flexpart.post" = "aiida_flexpart.parsers.flexpart_post:FlexpartPostParser"
+"collect.sens" = "aiida_flexpart.parsers.collect_sens:CollectSensParser"
 
 [project.entry-points."aiida.workflows"]
 "flexpart.multi_dates" = "aiida_flexpart.workflows.multi_dates_workflow:FlexpartMultipleDatesWorkflow"
 "flexpart.multi_workflow" = "aiida_flexpart.workflows.parent_workflow:ParentWorkflow"
 "inspect.workflow" = "aiida_flexpart.workflows.inspect:InspectWorkflow"
 
-[project.entry-points."aiida.data"]
-"netcdf.data" = "aiida_flexpart.data.nc_data:NetCdfData"
-
 
 [tool.pylint.format]
 max-line-length = 125