vortex-nwp 2.0.0b1__py3-none-any.whl → 2.0.0b2__py3-none-any.whl

vortex/nwp/__init__.py

@@ -3,9 +3,12 @@ The NWP VORTEX extension package.
 """
 
 # Recursive inclusion of packages with potential FootprintBase classes
-from . import algo, data, tools, syntax
+from . import algo as algo
+from . import data as data
+from . import tools as tools
+from . import syntax as syntax
 
 #: No automatic export
 __all__ = []
 
-__tocinfoline__ = 'The NWP VORTEX extension'
+__tocinfoline__ = "The NWP VORTEX extension"

vortex/nwp/algo/__init__.py

@@ -3,10 +3,19 @@ AlgoComponents for NWP
 """
 
 # Recursive inclusion of packages with potential FootprintBase classes
-from . import forecasts, fpserver, coupling, mpitools, odbtools, stdpost, assim, \
-    eps, eda, request, monitoring, clim
-from . import oopsroot, oopstests
+from . import forecasts as forecasts
+from . import fpserver as fpserver
+from . import coupling as coupling
+from . import mpitools as mpitools
+from . import odbtools as odbtools
+from . import stdpost as stdpost
+from . import assim as assim
+from . import eps as eps
+from . import eda as eda
+from . import request as request
+from . import monitoring as monitoring
+from . import clim as clim
+from . import oopsroot as oopsroot
+from . import oopstests as oopstests
 
-
-#: No automatic export
 __all__ = []

vortex/nwp/algo/assim.py

@@ -24,13 +24,13 @@ class MergeVarBC(Parallel):
     """
 
     _footprint = dict(
-        attr = dict(
-            kind = dict(
-                values = ['mergevarbc'],
+        attr=dict(
+            kind=dict(
+                values=["mergevarbc"],
             ),
-            varbcout = dict(
-                optional = True,
-                default  = 'VARBC.cycle_out',
+            varbcout=dict(
+                optional=True,
+                default="VARBC.cycle_out",
             ),
         )
     )
@@ -50,21 +50,21 @@ class Anamix(IFSParallel):
     """Merge the surface and atmospheric analyses into a single file"""
 
     _footprint = dict(
-        info='Merge surface and atmospheric analyses',
+        info="Merge surface and atmospheric analyses",
         attr=dict(
             kind=dict(
-                values=['anamix'],
+                values=["anamix"],
             ),
             conf=dict(
                 default=701,
             ),
             xpname=dict(
-                default='CANS',
+                default="CANS",
             ),
             timestep=dict(
                 default=1,
-            )
-        )
+            ),
+        ),
     )
 
 
@@ -72,19 +72,19 @@ class SstAnalysis(IFSParallel):
     """SST (Sea Surface Temperature) Analysis"""
 
     _footprint = dict(
-        attr = dict(
-            kind = dict(
-                values  = ['sstana', 'sst_ana', 'sst_analysis', 'c931'],
-                remap   = dict(autoremap = 'first'),
+        attr=dict(
+            kind=dict(
+                values=["sstana", "sst_ana", "sst_analysis", "c931"],
+                remap=dict(autoremap="first"),
             ),
-            conf = dict(
-                default = 931,
+            conf=dict(
+                default=931,
             ),
-            xpname = dict(
-                default = 'ANAL',
+            xpname=dict(
+                default="ANAL",
             ),
-            timestep = dict(
-                default  = '1.',
+            timestep=dict(
+                default="1.",
             ),
         )
     )
@@ -94,36 +94,36 @@ class SeaIceAnalysis(IFSParallel):
     """Sea Ice Analysis"""
 
     _footprint = dict(
-        attr = dict(
-            kind = dict(
-                values  = ['seaiceana', 'seaice_ana', 'seaice_analysis', 'c932'],
-                remap   = dict(autoremap = 'first'),
+        attr=dict(
+            kind=dict(
+                values=["seaiceana", "seaice_ana", "seaice_analysis", "c932"],
+                remap=dict(autoremap="first"),
+            ),
+            conf=dict(
+                default=932,
             ),
-            conf = dict(
-                default = 932,
+            xpname=dict(
+                default="ANAL",
             ),
-            xpname = dict(
-                default = 'ANAL',
+            timestep=dict(
+                default="1.",
             ),
-            timestep = dict(
-                default  = '1.',
+            date=dict(
+                type=Date,
             ),
-            date = dict(
-                type     = Date,
-            )
         )
     )
 
     def find_namelists(self, opts=None):
         namrh_list = super().find_namelists(opts)
         if not namrh_list:
-            logger.critical('No namelist was found.')
-            raise ValueError('No namelist was found for seaice analysis')
+            logger.critical("No namelist was found.")
+            raise ValueError("No namelist was found for seaice analysis")
         return namrh_list
 
     def prepare_namelist_delta(self, rh, namcontents, namlocal):
         super().prepare_namelist_delta(rh, namcontents, namlocal)
-        self._set_nam_macro(namcontents, namlocal, 'IDAT', int(self.date.ymd))
+        self._set_nam_macro(namcontents, namlocal, "IDAT", int(self.date.ymd))
         return True
 
 
@@ -131,21 +131,21 @@ class Canari(IFSParallel, odb.OdbComponentDecoMixin):
     """Surface analysis."""
 
     _footprint = dict(
-        info = 'Surface assimilation based on optimal interpolation',
-        attr = dict(
-            kind = dict(
-                values  = ['canari'],
+        info="Surface assimilation based on optimal interpolation",
+        attr=dict(
+            kind=dict(
+                values=["canari"],
             ),
-            binarysingle = dict(
-                default = 'basicnwpobsort',
+            binarysingle=dict(
+                default="basicnwpobsort",
             ),
-            conf = dict(
-                default = 701,
+            conf=dict(
+                default=701,
             ),
-            xpname = dict(
-                default = 'CANS',
+            xpname=dict(
+                default="CANS",
             ),
-        )
+        ),
     )
 
     def prepare(self, rh, opts):
@@ -153,18 +153,30 @@ class Canari(IFSParallel, odb.OdbComponentDecoMixin):
         super().prepare(rh, opts)
 
         # Looking for input observations
-        obsodb = [x for x in self.lookupodb() if x.rh.resource.part.startswith('surf')]
+        obsodb = [
+            x
+            for x in self.lookupodb()
+            if x.rh.resource.part.startswith("surf")
+        ]
         if not obsodb:
-            raise ValueError('No surface obsdata for canari')
+            raise ValueError("No surface obsdata for canari")
         self.odb_date_and_layout_from_sections(obsodb)
 
         # Find the unique input ODb database
         ssurf = obsodb.pop()
         if obsodb:
-            logger.error('More than one surface obsdata provided')
-            logger.error('Using : %s / %s', ssurf.rh.resource.layout, ssurf.rh.resource.part)
+            logger.error("More than one surface obsdata provided")
+            logger.error(
+                "Using : %s / %s",
+                ssurf.rh.resource.layout,
+                ssurf.rh.resource.part,
+            )
             for sobs in obsodb:
-                logger.error('Skip : %s / %s', sobs.rh.resource.layout, sobs.rh.resource.part)
+                logger.error(
+                    "Skip : %s / %s",
+                    sobs.rh.resource.layout,
+                    sobs.rh.resource.part,
+                )
 
         # Fix paths + generate a global IOASSING file
         cma_path = self.system.path.abspath(ssurf.rh.container.localpath())
@@ -188,25 +200,25 @@ class Screening(IFSParallel, odb.OdbComponentDecoMixin):
     """Observation screening."""
 
     _footprint = dict(
-        info = 'Observations screening.',
-        attr = dict(
-            kind = dict(
-                values  = ['screening', 'screen', 'thinning'],
-                remap   = dict(autoremap = 'first'),
+        info="Observations screening.",
+        attr=dict(
+            kind=dict(
+                values=["screening", "screen", "thinning"],
+                remap=dict(autoremap="first"),
             ),
-            binarysingle = dict(
-                default = 'basicnwpobsort',
+            binarysingle=dict(
+                default="basicnwpobsort",
             ),
-            ioassign = dict(
-                optional = False,
+            ioassign=dict(
+                optional=False,
             ),
-            conf = dict(
-                default = 2,
+            conf=dict(
+                default=2,
             ),
-            xpname = dict(
-                default = 'SCRE',
+            xpname=dict(
+                default="SCRE",
             ),
-        )
+        ),
     )
 
     def prepare(self, rh, opts):
@@ -220,11 +232,11 @@ class Screening(IFSParallel, odb.OdbComponentDecoMixin):
         # Perform the pre-merging stuff (this will create the ECMA virtual DB)
         virtualdb_path = self.odb_merge_if_needed(allodb)
         # Prepare the CCMA DB
-        ccma_path = self.odb_create_db(layout='CCMA')
+        ccma_path = self.odb_create_db(layout="CCMA")
 
         # Fix paths + generate a global IOASSING file
         self.odb.fix_db_path(self.virtualdb, virtualdb_path)
-        self.odb.fix_db_path('CCMA', ccma_path)
+        self.odb.fix_db_path("CCMA", ccma_path)
         self.odb.ioassign_gather(virtualdb_path, ccma_path)
 
         # Some extra settings
@@ -235,7 +247,7 @@ class Screening(IFSParallel, odb.OdbComponentDecoMixin):
         self.odb_handle_raw_dbs()
 
         # Fix the input databases intent
-        self.odb_rw_or_overwrite_method(* allodb)
+        self.odb_rw_or_overwrite_method(*allodb)
 
         # Look for channels namelists and set appropriate links
         self.setchannels()
@@ -246,12 +258,12 @@ class IFSODBCCMA(IFSParallel, odb.OdbComponentDecoMixin):
 
     _abstract = True
     _footprint = dict(
-        attr = dict(
-            virtualdb = dict(
-                default = 'ccma',
+        attr=dict(
+            virtualdb=dict(
+                default="ccma",
             ),
-            binarysingle = dict(
-                default = 'basicnwpobsort',
+            binarysingle=dict(
+                default="basicnwpobsort",
             ),
         )
     )
@@ -264,17 +276,23 @@ class IFSODBCCMA(IFSParallel, odb.OdbComponentDecoMixin):
 
         # Looking for input observations
         allodb = self.lookupodb()
-        allccma = [x for x in allodb if x.rh.resource.layout.lower() == 'ccma']
+        allccma = [x for x in allodb if x.rh.resource.layout.lower() == "ccma"]
         if allccma:
             if len(allccma) > 1:
-                logger.error('Multiple CCMA databases detected: only the first one is taken into account')
+                logger.error(
+                    "Multiple CCMA databases detected: only the first one is taken into account"
+                )
         else:
-            raise ValueError('Missing CCMA input data for ' + self.kind)
+            raise ValueError("Missing CCMA input data for " + self.kind)
 
         # Set env and IOASSIGN
         ccma = allccma.pop()
         ccma_path = sh.path.abspath(ccma.rh.container.localpath())
-        self.odb_date_and_layout_from_sections([ccma, ])
+        self.odb_date_and_layout_from_sections(
+            [
+                ccma,
+            ]
+        )
         self.odb.fix_db_path(ccma.rh.resource.layout, ccma_path)
         self.odb.ioassign_gather(ccma_path)
 
@@ -289,19 +307,19 @@ class Minim(IFSODBCCMA):
     """Observation minimisation."""
 
     _footprint = dict(
-        info='Minimisation in the assimilation process.',
+        info="Minimisation in the assimilation process.",
         attr=dict(
             kind=dict(
-                values=['minim', 'min', 'minimisation'],
-                remap=dict(autoremap='first'),
+                values=["minim", "min", "minimisation"],
+                remap=dict(autoremap="first"),
             ),
             conf=dict(
                 default=131,
             ),
             xpname=dict(
-                default='MINI',
+                default="MINI",
             ),
-        )
+        ),
     )
 
     def prepare(self, rh, opts):
@@ -309,28 +327,44 @@ class Minim(IFSODBCCMA):
         super().prepare(rh, opts)
 
         # Check if a preconditioning EV map is here
-        evmaprh = self.context.sequence.effective_inputs(role=('PreconEVMap',
-                                                               'PreconditionningEVMap'),
-                                                         kind='precevmap')
+        evmaprh = self.context.sequence.effective_inputs(
+            role=("PreconEVMap", "PreconditionningEVMap"), kind="precevmap"
+        )
         if evmaprh:
             if len(evmaprh) > 1:
-                logger.warning("Several preconditioning EV maps provided. Using the first one.")
-            nprec_ev = evmaprh[0].rh.contents.data['evlen']
+                logger.warning(
+                    "Several preconditioning EV maps provided. Using the first one."
+                )
+            nprec_ev = evmaprh[0].rh.contents.data["evlen"]
             # If there are preconditioning EV: update the namelist
             if nprec_ev > 0:
-                for namrh in [x.rh for x in self.context.sequence.effective_inputs(role='Namelist',
-                                                                                   kind='namelist',)]:
+                for namrh in [
+                    x.rh
+                    for x in self.context.sequence.effective_inputs(
+                        role="Namelist",
+                        kind="namelist",
+                    )
+                ]:
                     namc = namrh.contents
                     try:
-                        namc['NAMVAR'].NPCVECS = nprec_ev
+                        namc["NAMVAR"].NPCVECS = nprec_ev
                         namc.rewrite(namrh.container)
                     except Exception:
-                        logger.critical('Could not fix NAMVAR in %s', namrh.container.actualpath())
+                        logger.critical(
+                            "Could not fix NAMVAR in %s",
+                            namrh.container.actualpath(),
+                        )
                         raise
-                logger.info("%d preconditioning EV will by used (NPCVECS=%d).", nprec_ev, nprec_ev)
+                logger.info(
+                    "%d preconditioning EV will by used (NPCVECS=%d).",
+                    nprec_ev,
+                    nprec_ev,
+                )
             else:
-                logger.warning("A preconditioning EV map was found, " +
-                               "but no preconditioning EV are available.")
+                logger.warning(
+                    "A preconditioning EV map was found, "
+                    + "but no preconditioning EV are available."
+                )
         else:
             logger.info("No preconditioning EV were found.")
 
@@ -339,11 +373,11 @@ class Minim(IFSODBCCMA):
         sh = self.system
 
         # Look up for PREConditionning Eigen Vectors
-        prec = sh.ls('MEMINI*')
+        prec = sh.ls("MEMINI*")
         if prec:
             prec_info = dict(evlen=len(prec))
-            prec_info['evnum'] = [int(x[6:]) for x in prec]
-            sh.json_dump(prec_info, 'precev_map.out', indent=4)
+            prec_info["evnum"] = [int(x[6:]) for x in prec]
+            sh.json_dump(prec_info, "precev_map.out", indent=4)
 
         super().postfix(rh, opts)
 
@@ -352,29 +386,30 @@ class Trajectory(IFSODBCCMA):
     """Observation trajectory."""
 
     _footprint = dict(
-        info='Trajectory in the assimilation process.',
+        info="Trajectory in the assimilation process.",
         attr=dict(
             kind=dict(
-                values=['traj', 'trajectory'],
-                remap=dict(autoremap='first'),
+                values=["traj", "trajectory"],
+                remap=dict(autoremap="first"),
             ),
             conf=dict(
                 default=2,
             ),
             xpname=dict(
-                default='TRAJ',
+                default="TRAJ",
             ),
-        )
+        ),
     )
 
 
 class PseudoTrajectory(BlindRun, drhook.DrHookDecoMixin):
     """Copy a few fields from the Guess file into the Analysis file"""
+
     _footprint = dict(
-        attr = dict(
-            kind = dict(
-                values = ['pseudotraj', 'traj', 'trajectory'],
-                remap   = dict(autoremap = 'first'),
+        attr=dict(
+            kind=dict(
+                values=["pseudotraj", "traj", "trajectory"],
+                remap=dict(autoremap="first"),
             ),
         )
     )
@@ -382,35 +417,43 @@ class PseudoTrajectory(BlindRun, drhook.DrHookDecoMixin):
 
 class SstGrb2Ascii(BlindRun):
     """Transform sst grib files from the BDAP into ascii files"""
+
     _footprint = dict(
-        info = 'Binary to change the format of sst BDAP files.',
-        attr = dict(
-            kind = dict(
-                values = ['lect_bdap'],
+        info="Binary to change the format of sst BDAP files.",
+        attr=dict(
+            kind=dict(
+                values=["lect_bdap"],
             ),
-            date = a_date,
-            nlat = dict(
-                default = 0,
+            date=a_date,
+            nlat=dict(
+                default=0,
             ),
-            nlon = dict(
-                default = 0,
-            )
-        )
+            nlon=dict(
+                default=0,
+            ),
+        ),
     )
 
     def prepare(self, rh, opts):
         """Add namelist delta, prepare the environment and build the arguments needed."""
         super().prepare(rh, opts)
-        for namrh in [x.rh for x in self.context.sequence.effective_inputs(role='Namelist',
-                                                                           kind='namelist', )]:
+        for namrh in [
+            x.rh
+            for x in self.context.sequence.effective_inputs(
+                role="Namelist",
+                kind="namelist",
+            )
+        ]:
             namc = namrh.contents
             try:
-                namc.newblock('NAMFILE')
-                namc['NAMFILE'].NBFICH = 1
-                namc['NAMFILE']['CCNFICH(1)'] = 'GRIB_SST'
+                namc.newblock("NAMFILE")
+                namc["NAMFILE"].NBFICH = 1
+                namc["NAMFILE"]["CCNFICH(1)"] = "GRIB_SST"
                 namc.rewrite(namrh.container)
             except Exception:
-                logger.critical('Could not fix NAMFILE in %s', namrh.container.actualpath())
+                logger.critical(
+                    "Could not fix NAMFILE in %s", namrh.container.actualpath()
+                )
                 raise
 
     def spawn_command_options(self):
@@ -427,49 +470,60 @@ class SstGrb2Ascii(BlindRun):
 
 class IceNetCDF2Ascii(BlindRun):
     """Transform ice NetCDF files from the BDPE into ascii files"""
+
     _footprint = dict(
-        info = 'Binary to change the format of ice BDPE files.',
-        attr = dict(
-            kind = dict(
-                values = ['ice_nc2ascii'],
-            ),
-            output_file = dict(
-                optional = True,
-                default = "ice_concent"
+        info="Binary to change the format of ice BDPE files.",
+        attr=dict(
+            kind=dict(
+                values=["ice_nc2ascii"],
             ),
-            param = dict(
-                optional = True,
-                default = "ice_conc",
+            output_file=dict(optional=True, default="ice_concent"),
+            param=dict(
+                optional=True,
+                default="ice_conc",
             ),
-        )
+        ),
     )
 
     def prepare(self, rh, opts):
         super().prepare(rh, opts)
         # Look for the input files
-        list_netcdf = self.context.sequence.effective_inputs(role='NetCDFfiles',
-                                                             kind='observations')
-        hn_file = ''
-        hs_file = ''
+        list_netcdf = self.context.sequence.effective_inputs(
+            role="NetCDFfiles", kind="observations"
+        )
+        hn_file = ""
+        hs_file = ""
         for sect in list_netcdf:
             part = sect.rh.resource.part
             filename = sect.rh.container.filename
             if part == "ice_hn":
-                if hn_file == '':
+                if hn_file == "":
                     hn_file = filename
-                    logger.info('The input file for the North hemisphere is: %s.', hn_file)
+                    logger.info(
+                        "The input file for the North hemisphere is: %s.",
+                        hn_file,
+                    )
                 else:
-                    logger.warning('There was already one file for the North hemisphere. '
-                                   'The following one, %s, is not used.', filename)
+                    logger.warning(
+                        "There was already one file for the North hemisphere. "
+                        "The following one, %s, is not used.",
+                        filename,
+                    )
             elif part == "ice_hs":
-                if hs_file == '':
+                if hs_file == "":
                     hs_file = filename
-                    logger.info('The input file for the South hemisphere is: %s.', hs_file)
+                    logger.info(
+                        "The input file for the South hemisphere is: %s.",
+                        hs_file,
+                    )
                 else:
-                    logger.warning('There was already one file for the South hemisphere. '
-                                   'The following one, %s, is not used.', filename)
+                    logger.warning(
+                        "There was already one file for the South hemisphere. "
+                        "The following one, %s, is not used.",
+                        filename,
+                    )
             else:
-                logger.warning('The following file is not used: %s.', filename)
+                logger.warning("The following file is not used: %s.", filename)
         self.input_file_hn = hn_file
         self.input_file_hs = hs_file
 
@@ -479,5 +533,5 @@ class IceNetCDF2Ascii(BlindRun):
             file_in_hn=self.input_file_hn,
             file_in_hs=self.input_file_hs,
             param=self.param,
-            file_out=self.output_file
+            file_out=self.output_file,
         )