Merge branch 'main-dev' into pydantic-colocationsetup

.github/workflows/CI.yml

@@ -100,4 +100,4 @@ jobs:
     - name: Install pyaerocom
       run: python -m pip install . --no-deps
     - name: Run pytest
-      run: python -m pytest -ra -q --cov --no-cov-on-fail --cov-report xml
+      run: python -m pytest -ra -q --cov --no-cov-on-fail --cov-report xml

pyaerocom/aeroval/experiment_processor.py

@@ -70,7 +70,8 @@ def _run_single_entry(self, model_name, obs_name, var_list):
             if self.cfg.processing_opts.only_json:
                 files_to_convert = col.get_available_coldata_files(var_list)
             else:
-                col.run(var_list)
+                model_read_kwargs = self.cfg.model_cfg[model_name]["kwargs"]
+                col.run(var_list, model_read_kwargs=model_read_kwargs)
                 files_to_convert = col.files_written
 
             if self.cfg.processing_opts.only_colocation:
@@ -122,11 +123,7 @@ def run(self, model_name=None, obs_name=None, var_list=None, update_interface=Tr
         if not self.cfg.model_cfg:
             logger.info("No model found, will make dummy model data")
             self.cfg.webdisp_opts.hide_charts = ["scatterplot"]
-            self.cfg.webdisp_opts.hide_pages = [
-                "maps.php",
-                "intercomp.php",
-                "overall.php",
-            ]
+            self.cfg.webdisp_opts.pages = ["evaluation", "infos"]
             model_id = make_dummy_model(obs_list, self.cfg)
             self.cfg.processing_opts.obs_only = True
             use_dummy_model = True

pyaerocom/aeroval/modelentry.py

@@ -1,3 +1,4 @@
+import inspect
 from copy import deepcopy
 
 from pyaerocom._lowlevel_helpers import BrowseDict, DictStrKeysListVals, DictType, StrType
@@ -55,6 +56,8 @@ def __init__(self, model_id, **kwargs):
         self.model_rename_vars = {}
         self.model_read_aux = {}
 
+        self.kwargs = kwargs
+
         self.update(**kwargs)
 
     @property
@@ -64,6 +67,16 @@ def aux_funs_required(self):
         """
         return True if bool(self.model_read_aux) else False
 
+    def json_repr(self) -> dict:
+        sup_rep = super().json_repr()
+
+        for key in sup_rep["model_read_aux"]:
+            sup_rep["model_read_aux"][key]["fun"] = inspect.getsource(
+                deepcopy(sup_rep["model_read_aux"][key]["fun"])
+            )
+
+        return sup_rep
+
     def get_vars_to_process(self, obs_vars: list) -> tuple:
         """
         Get lists of obs / mod variables to be processed

pyaerocom/aeroval/setupclasses.py

@@ -261,7 +261,7 @@ class WebDisplaySetup(BaseModel):
     hide_charts: tuple[str, ...] = ()
     hide_pages: tuple[str, ...] = ()
     ts_annotations: dict[str, str] = Field(default_factory=dict)
-    add_pages: tuple[str, ...] = ()
+    pages: tuple[str, ...] = ["maps", "evaluation", "intercomp", "overall", "infos"]
 
 
 class EvalRunOptions(BaseModel):

pyaerocom/colocation_auto.py

@@ -38,6 +38,7 @@
 
 
 class Colocator:
+
     """High level class for running co-location
 
     Note
@@ -52,6 +53,7 @@ class Colocator:
     }
 
     STATUS_CODES: dict[int, str] = {
+
         1: "SUCCESS",
         2: "NOT OK: Missing/invalid model variable",
         3: "NOT OK: Missing/invalid obs variable",
@@ -592,7 +594,10 @@ def _instantiate_gridded_reader(self, what):
             data_id = self.colocation_setup.obs_id
             data_dir = self.colocation_setup.obs_data_dir
         reader_class = self._get_gridded_reader_class(what=what)
-        reader = reader_class(data_id=data_id, data_dir=data_dir)
+        if what == "model" and reader_class in self.MODELS_WITH_KWARGS:
+            reader = reader_class(data_id=data_id, data_dir=data_dir, **self.model_read_kwargs)
+        else:
+            reader = reader_class(data_id=data_id, data_dir=data_dir)
         return reader
 
     def _get_gridded_reader_class(self, what):

pyaerocom/config.py

@@ -3,6 +3,7 @@
 import os
 from configparser import ConfigParser
 from pathlib import Path
+from typing import Union
 
 import numpy as np
 
@@ -18,6 +19,7 @@
 from pyaerocom.grid_io import GridIO
 from pyaerocom.region_defs import ALL_REGION_NAME, HTAP_REGIONS, OLD_AEROCOM_REGIONS
 from pyaerocom.varcollection import VarCollection
+from pyaerocom.variable import Variable
 
 logger = logging.getLogger(__name__)
 
@@ -220,6 +222,9 @@ def __init__(self, config_file=None, try_infer_environment=True):
         self._var_param = None
         self._coords = None
 
+        # Custom variables
+        self._custom_var_dict = None
+
         # Attributes that are used to store search directories
         self.OBSLOCS_UNGRIDDED = {}
         self.OBS_UNGRIDDED_POST = {}
@@ -308,6 +313,25 @@ def infer_basedir_and_config(self):
                         return (basedir, self._config_files[cfg_id])
         raise FileNotFoundError("Could not establish access to any registered database")
 
+    def register_custom_variables(
+        self, vars: Union[dict[str, Variable], dict[str, dict[str, str]]]
+    ) -> None:
+        var_dict = {}
+        for key, item in vars.items():
+            if isinstance(item, Variable):
+                var_dict[key] = item
+            elif isinstance(item, dict):
+                if "var_name" in item and "units" in item:
+                    var_dict[key] = Variable(**item)
+                else:
+                    raise ValueError(
+                        f"Dict item {item} must atleast have the keys 'var_name' and 'units'"
+                    )
+            else:
+                raise ValueError(f"Item {item} must be either dict or Variable")
+        self._custom_var_dict = var_dict.copy()
+        self._var_param = None
+
     @property
     def has_access_users_database(self):
         chk_dir = self._check_subdirs_cfg["users-db"]
@@ -482,6 +506,10 @@ def VARS(self):
         """Instance of class VarCollection (for default variable information)"""
         if self._var_param is None:  # has not been accessed before
             self._var_param = VarCollection(self._var_info_file)
+
+            if self._custom_var_dict is not None:
+                for var in self._custom_var_dict:
+                    self._var_param.add_var(self._custom_var_dict[var])
         return self._var_param
 
     @property

pyaerocom/data/emep_variables.ini

@@ -105,4 +105,7 @@ concCocCoarse = "SURF_ugC_PM_OMCOARSE"
 concecFine = "SURF_ug_ECFINE"
 concecCoarse = "SURF_ug_ECCOARSE"
 concoxn = "SURF_ugN_OXN"
-vmrno = "SURF_ppb_NO"
+vmrno = "SURF_ppb_NO"
+
+#Data used for Pollen data
+concspores = "SURF_ug_FUNGAL_SPORES"

pyaerocom/data/variables.ini

@@ -3078,6 +3078,22 @@ unit = ug C m-3
 description=Mass concentration of total carbon
 unit = ug m-3
 
+[conchoa]
+description=Mass concentration hydrocarbon like OA
+unit = ug m-3
+
+[concbcbb]
+description=Mass concentration elemental carbon, biomass burning
+unit = ug m-3
+
+[concspores]
+description=Mass concentration fungal spores
+unit = ug m-3
+
+[concpolyol]
+description=Mass concentration Polyol
+unit = ug m-3
+
 [conco3]
 description=Mass concentration of ozone
 unit = ug m-3

pyaerocom/io/mscw_ctm/additional_variables.py

@@ -385,3 +385,12 @@ def calc_concSso2(concso2):
     concSso2.attrs["units"] = "ug S m-3"
 
     return concSso2
+
+
+def calc_concpolyol(concspores):
+    # polyol is 4.5% of spores. Spores is in ug/cm3 in Gunnars run, eventhough the unit is marked as ugm-3, so a factor of 1000 is needed for unit change
+    factor = 45.0 / 1000.0
+
+    concpolyol = concspores.copy(deep=True) * factor
+    concpolyol.attrs["units"] = "ug m-3"
+    return concpolyol

pyaerocom/io/mscw_ctm/emep_variables.toml

@@ -105,4 +105,5 @@ concCocCoarse = "SURF_ugC_PM_OMCOARSE"
 concecFine = "SURF_ug_ECFINE"
 concecCoarse = "SURF_ug_ECCOARSE"
 concoxn = "SURF_ugN_OXN"
-vmrno = "SURF_ppb_NO"
+vmrno = "SURF_ppb_NO"
+concspores = "SURF_ug_FUNGAL_SPORES"

pyaerocom/io/mscw_ctm/reader.py

@@ -24,6 +24,7 @@
     calc_concno3pm10,
     calc_concno3pm25,
     calc_concNtnh,
+    calc_concpolyol,
     calc_concso4t,
     calc_concSso2,
     calc_concsspm25,
@@ -103,6 +104,8 @@ class ReadMscwCtm:
         "concNno2": ["concno2"],
         "concSso2": ["concso2"],
         "vmro3": ["conco3"],
+        # For Pollen
+        # "concpolyol": ["concspores"],
     }
 
     # Functions that are used to compute additional variables (i.e. one
@@ -145,6 +148,7 @@ class ReadMscwCtm:
         "concNno2": calc_concNno2,
         "concSso2": calc_concSso2,
         "vmro3": calc_vmro3,
+        # "concpolyol": calc_concpolyol,
     }
 
     #: supported filename masks, placeholder is for frequencies
@@ -167,7 +171,7 @@ class ReadMscwCtm:
 
     DEFAULT_FILE_NAME = "Base_day.nc"
 
-    def __init__(self, data_id=None, data_dir=None):
+    def __init__(self, data_id=None, data_dir=None, **kwargs):
         self._data_dir = None
         # opened dataset (for performance boost), will be reset if data_dir is
         # changed
@@ -180,6 +184,12 @@ def __init__(self, data_id=None, data_dir=None):
         self._files = None
 
         self.var_map = emep_variables()
+        if "emep_vars" in kwargs:
+            new_map = kwargs["emep_vars"]
+            if isinstance(new_map, dict):
+                self.var_map.update(new_map)
+            else:
+                logger.warn(f"New map {new_map} is not a dict. Skipping")
 
         if data_dir is not None:
             if not isinstance(data_dir, str) or not os.path.exists(data_dir):
@@ -765,6 +775,30 @@ def preprocess_units(units, prefix):
             return "m-1"
         return units
 
+    def add_aux_compute(self, var_name, vars_required, fun):
+        """Register new variable to be computed
+
+        Parameters
+        ----------
+        var_name : str
+            variable name to be computed
+        vars_required : list
+            list of variables to read, that are required to compute `var_name`
+        fun : callable
+            function that takes a list of `GriddedData` objects as input and
+            that are read using variable names specified by `vars_required`.
+        """
+        if isinstance(vars_required, str):
+            vars_required = [vars_required]
+        if not isinstance(vars_required, list):
+            raise ValueError(
+                f"Invalid input for vars_required. Need str or list. Got: {vars_required}"
+            )
+        elif not callable(fun):
+            raise ValueError("Invalid input for fun. Input is not a callable object")
+        self.AUX_REQUIRES[var_name] = vars_required
+        self.AUX_FUNS[var_name] = fun
+
 
 class ReadEMEP(ReadMscwCtm):
     """Old name of :class:`ReadMscwCtm`."""

pyaerocom/io/pyaro/read_pyaro.py

@@ -99,6 +99,17 @@ class PyaroToUngriddedData:
     _STOPTIMEINDEX = 10  # can be used to store stop time of acq.
     _TRASHINDEX = 11  # index where invalid data can be moved to (e.g. when outliers are removed)
 
+    # List of keys needed by every station from Pyaro. Used to find extra metadata
+    STATION_KEYS = (
+        "station",
+        "latitude",
+        "longitude",
+        "altitude",
+        "long_name",
+        "country",
+        "url",
+    )
+
     def __init__(self, config: PyaroConfig) -> None:
         self.data: UngriddedData = UngriddedData()
         self.config = config
@@ -218,6 +229,9 @@ def _get_metadata_from_pyaro(self, station: Station) -> list[dict[str, str]]:
 
         return metadata
 
+    def _get_additional_metadata(self, station: Station) -> list[dict[str, str]]:
+        return station.metadata
+
     def _make_single_ungridded_metadata(
         self, station: Station, name: str, ts_type: Optional[TsType], units: dict[str, str]
     ) -> MetadataEntry:
@@ -233,34 +247,11 @@ def _make_single_ungridded_metadata(
             country=station["country"],
             ts_type=str(ts_type) if ts_type is not None else "undefined",
         )
-        entry.update(self._get_metadata_from_pyaro(station))
+        entry.update(self._get_metadata_from_pyaro(station=station))
+        entry.update(self._get_additional_metadata(station=station))
 
         return MetadataEntry(entry)
 
-    def _make_ungridded_metadata(
-        self, stations: dict[str, Station], var_idx: dict[str, int], units: dict[str, str]
-    ) -> Metadata:
-        idx = 0
-        metadata = {}
-        for name, station in stations.items():
-            metadata[idx] = dict(
-                data_id=self.config.name,
-                variables=list(self.get_variables()),
-                var_info=units,
-                latitude=station["latitude"],
-                longitude=station["longitude"],
-                altitude=station["altitude"],
-                station_name=station["long_name"],
-                station_id=name,
-                country=station["country"],
-                ts_type="undefined",  # TEMP: Changes dynamically below
-            )
-
-            metadata[idx].update(self._get_metadata_from_pyaro(station))
-            idx += 1
-
-        return Metadata(metadata)
-
     def _pyaro_dataline_to_ungriddeddata_dataline(
         self, data: np.void, idx: int, var_idx: int
     ) -> np.ndarray:

pyaerocom/scripts/cams2_83/evaluation.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import time
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from datetime import date, timedelta
 from enum import Enum
@@ -179,7 +178,7 @@ def runnermos(
 
     logger.info("Running Statistics (MOS)")
     ExperimentProcessor(stp).run()
-    print("Done Running Statistics (MOS)")
+    logger.info("Done Running Statistics (MOS)")
 
 
 def runnermedianscores(
@@ -198,8 +197,6 @@ def runnermedianscores(
 
     stp = EvalSetup(**cfg)
 
-    start = time.time()
-
     logger.info(
         "Running CAMS2_83 Specific Statistics, cache is not cleared, colocated data is assumed in place, regular statistics are assumed to have been run"
     )
@@ -216,4 +213,4 @@ def runnermedianscores(
         logger.info(f"Making median scores plot with pool {pool} and analysis {analysis}")
         CAMS2_83_Processer(stp).run(analysis=analysis)
 
-    print(f"Long run: {time.time() - start} sec")
+    logger.info("Median scores run finished")