Renaming to Fluxie

README.md

@@ -7,38 +7,38 @@ Follow the steps below to run the notebook and plot model results.
 ## Installation
 
 #### At your local machine
-Clone the repository and install fluxy:
+Clone the repository and install fluxie:
 ```
-git clone https://github.com/openghg/fluxy.git
-cd fluxy
+git clone https://github.com/openghg/fluxie.git
+cd fluxie
 pip install -e .
 ```
 
 #### At ICOS Jupyter Hub
 Create and activate virtual environment:
 ```
-python -m venv fluxy-env         
-source fluxy-env/bin/activate
+python -m venv fluxie-env         
+source fluxie-env/bin/activate
 ```
 Install IPython kernel package for Jupyter into the current environment and register the current environment as a new kernel:
 ```
 pip install --upgrade pip
 pip install ipykernel
-python -m ipykernel install --user --name fluxy-env --display-name "fluxy-env"
+python -m ipykernel install --user --name fluxie-env --display-name "fluxie-env"
 ```
-And finally install fluxy:
+And finally install fluxie:
 ```
-git clone https://github.com/openghg/fluxy.git
-cd fluxy
+git clone https://github.com/openghg/fluxie.git
+cd fluxie
 pip install -e .
 ```
 
 ## Quick start 
 
-If you want to try fluxy, the easiest way is to run the example notebook `scripts/example_basics.ipynb`.
-It will run with some test data and show you what fluxy can do.
+If you want to try fluxie, the easiest way is to run the example notebook `scripts/example_basics.ipynb`.
+It will run with some test data and show you what fluxie can do.
 
-**Note for ICOS Jupyter Hub:** make sure that your newly created environment (fluxy-env in the example above) is the selected kernel in the drop down list in the upper right corner. If it does not show up, restart your Jupyter instance following these instructions: https://icos-carbon-portal.github.io/jupyter/how_to/#restart-your-jupyter-instance
+**Note for ICOS Jupyter Hub:** make sure that your newly created environment (fluxie-env in the example above) is the selected kernel in the drop down list in the upper right corner. If it does not show up, restart your Jupyter instance following these instructions: https://icos-carbon-portal.github.io/jupyter/how_to/#restart-your-jupyter-instance
 
 ## Prepare input files
 ### 1. Flux and concentration netCDF files with model results

data/templates/PAR-AVE-EYE_cell_area.cdl

@@ -23,7 +23,7 @@ variables:
 		cell_area:domain = "EUROPE" ;
 
 // global attributes:
-		:description = "area per latitude longitude grid cell, used in fluxy to calculate region/country flux annual totals from spatial fluxes" ;
+		:description = "area per latitude longitude grid cell, used in fluxie to calculate region/country flux annual totals from spatial fluxes" ;
 		:creator = "Alice Ramsden, Met Office" ;
 		:creation_date = "2025-07-10" ;
 }

data/templates/README_templates.md

@@ -31,7 +31,7 @@ The most important variables are described below. Please refer to the cdl files
 | percentile_flux_total_prior_inversion_grid     | mol m-2 s-1 | time, percentile, latitude, longitude | Percentile of prior total `<species>` fluxes on the reduced inversion grid
 | percentile_flux_total_posterior_inversion_grid | mol m-2 s-1 | time, percentile, latitude, longitude | Percentile of posterior total `<species>` fluxes on the reduced inversion grid
 
-(1) fluxy accepts any SI unit of the type "amount length-2 time-1" and "mass length-2 time-1". However, please make sure that all grid variables have the same units.
+(1) fluxie accepts any SI unit of the type "amount length-2 time-1" and "mass length-2 time-1". However, please make sure that all grid variables have the same units.
 
 | By-country variables                    | Units (2) | Dimensions    | Description                                      |
 |:----------------------------------------|:----------|:--------------|:-------------------------------------------------|
@@ -45,7 +45,7 @@ The most important variables are described below. Please refer to the cdl files
 | *Optional*
 | covariance_flux_total_posterior_country | kg2 yr-2  | time, country, country    | Covariance of country-total posterior `<species>` fluxes
 
-(2) fluxy accepts any SI unit of the type "mass time-1" for country flux variables and "mass2 time-2" for the covariance variable. However, please make sure that all by-country variables have the same units and that the covariance variable has the respective squared units.
+(2) fluxie accepts any SI unit of the type "mass time-1" for country flux variables and "mass2 time-2" for the covariance variable. However, please make sure that all by-country variables have the same units and that the covariance variable has the respective squared units.
 
 | Auxiliary variables | Units  |  Dimensions                  | Description                                |
 |:--------------------|:-------|:-----------------------------|:-------------------------------------------|
@@ -94,7 +94,7 @@ The most important variables are described below. Please refer to the cdl files
 | stdev_mf_observed_variability	  | mol mol-1 | index      | Variability of observed mole fraction within aggregation interval
 | stdev_mf_model                  | mol mol-1 | index      | Model uncertainty of simulated mole fraction
 
-(3) fluxy also accepts ppm, ppb and ppt. However, please make sure that all variables have the same units.
+(3) fluxie also accepts ppm, ppb and ppt. However, please make sure that all variables have the same units.
 
 ## 3. Eddy covariance flux file
 

data/templates/ec_flux.cdl

@@ -82,10 +82,10 @@ variables:
 		:title = "Eddy covariance fluxes from Hardau" ; 
 		:institution = "Empa" ; 
 		:source = "Eddypro V2" ; 
-		:comment = "Data processed with Eddypro V2 for fluxy plots" ; 
+		:comment = "Data processed with Eddypro V2 for fluxie plots" ; 
 		:creation_date = "2025-07-21T16:55:02.806705" ; 
-		:fluxy_substance = "<species>" ; 
-		:fluxy_data_type = "eddy_flux" ; 
-		:fluxy_model = "EDDY_HARDAU" ; 
+		:fluxie_substance = "<species>" ; 
+		:fluxie_data_type = "eddy_flux" ; 
+		:fluxie_model = "EDDY_HARDAU" ; 
 
 }   

fluxy/cli/annex_plot_generator.py → fluxie/cli/annex_plot_generator.py

@@ -6,16 +6,16 @@
 
 from config_annex_plot import AnnexConfig
 
-from fluxy.cli.utils_annex_plot import (
+from fluxie.cli.utils_annex_plot import (
     get_species_specific_settings,
     create_str_dataframe,
     make_table,
 )
-from fluxy.io import read_config_files, read_model_output, read_flux_total_fgases
-from fluxy.operators.select import slice_flux
-from fluxy.config import set_model_colors, set_model_labels
-from fluxy.plots.flux_timeseries import plot_country_flux
-from fluxy.plots.flux_map import plot_flux_map_over_time
+from fluxie.io import read_config_files, read_model_output, read_flux_total_fgases
+from fluxie.operators.select import slice_flux
+from fluxie.config import set_model_colors, set_model_labels
+from fluxie.plots.flux_timeseries import plot_country_flux
+from fluxie.plots.flux_map import plot_flux_map_over_time
 
 logger = logging.getLogger(__name__)
 

fluxy/cli/utils_annex_plot.py → fluxie/cli/utils_annex_plot.py

@@ -45,7 +45,7 @@ def create_str_dataframe(
     The values are string of the form "<mean> \\pm <uncertainty>", made to be usable directly to make the tex output for the annexes tables. Set the units and right number of digits.
     NOTE: Assume that the units in res is Tg CO2-eq yr-1
     Args:
-        res: pandas dataframe containing the results. It should be the output (or concatenation of outputs) of `plot_country_flux` from fluxy/plots/flux_timeseries.py
+        res: pandas dataframe containing the results. It should be the output (or concatenation of outputs) of `plot_country_flux` from fluxie/plots/flux_timeseries.py
             The columns of this dataframe are "type", "model", "sector", "country", "species", "time", "mean_val", "min_unc", "max_unc".
         inventory_year: inventory year to put in the outputted dataframe (has to b present in <res>).
         species: species to put include in the table

fluxy/io.py → fluxie/io.py

@@ -15,11 +15,11 @@
 import pandas as pd
 import xarray as xr
 
-from fluxy import config
-from fluxy.operators.flux_align_dataset import align_time
-from fluxy.operators.regions import extract_region_flux
-from fluxy.operators.select import slice_flux, get_intake_height, get_site_index
-from fluxy.types import DataType, DataTypes, file_pattern
+from fluxie import config
+from fluxie.operators.flux_align_dataset import align_time
+from fluxie.operators.regions import extract_region_flux
+from fluxie.operators.select import slice_flux, get_intake_height, get_site_index
+from fluxie.types import DataType, DataTypes, file_pattern
 
 logger = logging.getLogger(__name__)
 
@@ -546,7 +546,7 @@ def read_flux_total_fgases(
     if all_species is None:
         raise ValueError(
             f"No list of species was found in the config_data for {species}. "
-            + f"If config_data was created with read_config_files from fluxy/io.py, update configs/species_info.json."
+            + f"If config_data was created with read_config_files from fluxie/io.py, update configs/species_info.json."
         )
     if "CO2-eq" not in unit:
         raise ValueError("Unit should be in CO2-eq.")
@@ -661,7 +661,7 @@ def create_flux_total_fgases(ds_all, species, regions, models, only_overlapping)
             If True, only includes time periods where all models have data. Otherwise, uses all available data.
     Returns:
         ds_output (dictionary of datasets):
-            dictionnary of xarray datasets ready to be used with fluxy plot methods.
+            dictionnary of xarray datasets ready to be used with fluxie plot methods.
     """
     ds_output = {}
     for model in models:
@@ -768,7 +768,7 @@ def edit_vars_and_attributes(
             Options for "monthly" and "yearly".
         file_type (str):
             Output file type.
-            See :py:class:`fluxy.types.DataType` for options.
+            See :py:class:`fluxie.types.DataType` for options.
         regions_info (dict of str):
             Dictionary with country and region names (read from config file).
         species (str, optional):

fluxy/operators/convert.py → fluxie/operators/convert.py

@@ -3,7 +3,7 @@
 import re
 from collections import Counter
 from typing import Literal
-from fluxy import config
+from fluxie import config
 
 logger = logging.getLogger(__name__)
 

fluxy/operators/ecflux.py → fluxie/operators/ecflux.py

@@ -1,6 +1,6 @@
 import logging
-from fluxy.types import DsAll
-from fluxy.operators.utils import apply_to_dict_or_single
+from fluxie.types import DsAll
+from fluxie.operators.utils import apply_to_dict_or_single
 import xarray as xr
 
 

fluxy/operators/flux_combine.py → fluxie/operators/flux_combine.py

@@ -1,7 +1,7 @@
 import xarray as xr
 import logging
 
-from fluxy.operators.flux_align_dataset import align_time
+from fluxie.operators.flux_align_dataset import align_time
 
 logger = logging.getLogger(__name__)
 

fluxy/operators/flux_map_resample.py → fluxie/operators/flux_map_resample.py

@@ -6,7 +6,7 @@
 import warnings
 
 from typing import List, Tuple, Literal
-from fluxy.plots.utils import print_period, get_frequency
+from fluxie.plots.utils import print_period, get_frequency
 
 
 def get_flux_mean(

fluxy/operators/flux_prepare_inventory.py → fluxie/operators/flux_prepare_inventory.py

@@ -3,7 +3,7 @@
 
 from matplotlib.cm import get_cmap
 
-from fluxy.operators.regions import extract_region_inventory_flux
+from fluxie.operators.regions import extract_region_inventory_flux
 
 
 def retrieve_inventories(

fluxy/operators/flux_scale_by_sector_proportions.py → fluxie/operators/flux_scale_by_sector_proportions.py

@@ -3,8 +3,8 @@
 import numpy as np
 import xarray as xr
 from pathlib import Path
-from fluxy.operators.convert import get_units_conversion_factor
-from fluxy.operators.flux_align_dataset import align_lat_lon
+from fluxie.operators.convert import get_units_conversion_factor
+from fluxie.operators.flux_align_dataset import align_lat_lon
 
 logger = logging.getLogger(__name__)
 

fluxy/operators/mf.py → fluxie/operators/mf.py

@@ -2,10 +2,10 @@
 import xarray as xr
 import pandas as pd
 import logging
-from fluxy.operators.convert import get_variables
+from fluxie.operators.convert import get_variables
 from typing import Literal
 
-from fluxy.operators.stats import stats_observed_vs_simulated
+from fluxie.operators.stats import stats_observed_vs_simulated
 
 logger = logging.getLogger(__name__)
 
@@ -133,7 +133,7 @@ def stats_mf(
     Calculates multiple statistical measures of the fit between the posterior
     mean mf and the observed mole fraction.
 
-    This calls :py:func:`fluxy.operators.stats.stats_observed_vs_simulated`
+    This calls :py:func:`fluxie.operators.stats.stats_observed_vs_simulated`
 
     Args:
         ds_all (dictionary of datasets):

fluxy/operators/regions.py → fluxie/operators/regions.py

@@ -6,7 +6,7 @@
 import numpy as np
 import xarray as xr
 
-from fluxy.operators.convert import get_units_conversion_factor
+from fluxie.operators.convert import get_units_conversion_factor
 
 logger = logging.getLogger(__name__)
 

fluxy/operators/sectors.py → fluxie/operators/sectors.py

@@ -1,7 +1,7 @@
 import numpy as np
 import xarray as xr
 
-from fluxy.operators.utils import apply_to_dict_or_single
+from fluxie.operators.utils import apply_to_dict_or_single
 
 
 def sectors_group_from_config_or_dict(

fluxy/operators/select.py → fluxie/operators/select.py

@@ -7,7 +7,7 @@
 import pandas as pd
 import xarray as xr
 
-from fluxy.operators.convert import scale_variables
+from fluxie.operators.convert import scale_variables
 
 logger = logging.getLogger(__name__)
 

fluxy/operators/stats.py → fluxie/operators/stats.py

@@ -2,7 +2,7 @@
 import numpy as np
 import pandas as pd
 import xarray as xr
-from fluxy.operators.select import get_unique_sites, slice_site
+from fluxie.operators.select import get_unique_sites, slice_site
 
 
 def stats_observed_vs_simulated(

fluxy/operators/utils.py → fluxie/operators/utils.py

@@ -2,7 +2,7 @@
 
 import xarray as xr
 
-from fluxy.types import DsAll
+from fluxie.types import DsAll
 
 
 def apply_to_dict_or_single(func):

fluxy/plots/correlation.py → fluxie/plots/correlation.py

@@ -5,9 +5,9 @@
 import xarray as xr
 import numpy as np
 
-from fluxy import config
-from fluxy.operators.select import slice_site
-from fluxy.types import VariableType
+from fluxie import config
+from fluxie.operators.select import slice_site
+from fluxie.types import VariableType
 import matplotlib.pyplot as plt
 
 logger = logging.getLogger(__name__)

fluxy/plots/ec_flux/sectorial_stack.py → fluxie/plots/ec_flux/sectorial_stack.py

@@ -3,7 +3,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from fluxy.plots.utils import stack_plot
+from fluxie.plots.utils import stack_plot
 
 WIND_LABELS = {
     4: ["N", "E", "S", "W"],

fluxy/plots/flux_map.py → fluxie/plots/flux_map.py

@@ -5,11 +5,11 @@
 import numpy as np
 import logging
 
-from fluxy.operators.flux_align_dataset import align_map_data
-from fluxy.operators.flux_combine import combine_map_dataset
-from fluxy.operators.flux_map_diff import define_var_plot, make_model_diff_ds
-from fluxy.operators.flux_map_resample import resample_over_period
-from fluxy.plots.utils import (
+from fluxie.operators.flux_align_dataset import align_map_data
+from fluxie.operators.flux_combine import combine_map_dataset
+from fluxie.operators.flux_map_diff import define_var_plot, make_model_diff_ds
+from fluxie.operators.flux_map_resample import resample_over_period
+from fluxie.plots.utils import (
     Region,
     add_colorbar,
     add_custom_markers,
@@ -66,7 +66,7 @@ def plot_flux_map(
         config_data (dict of dict):
             Dictionary of models and species information (read from json file).
         model_labels (list):
-            List of model_labels from fluxy.config.
+            List of model_labels from fluxie.config.
         cmap (str, optional):
             Colour map for flux plots.
         cmap_diff (str, optional):
@@ -330,7 +330,7 @@ def plot_flux_map_model_comparison(
         config_data (dict of dict):
             Dictionary of models and species information (read from json file).
         model_labels (list):
-            List of model_labels from fluxy.config.
+            List of model_labels from fluxie.config.
         cmap (str, optional):
             Colour map for flux plots.
         cmap_diff (str, optional):
@@ -562,7 +562,7 @@ def plot_flux_map_over_time(
         config_data (dict of dict):
             Dictionary of models and species information (read from json file).
         model_labels (list):
-            List of model_labels from fluxy.config.
+            List of model_labels from fluxie.config.
         chop_by (str or list):
             Time units to perform the average, options for 'year', 'month' and 'season'.
             Alternatively, a list of starting dates or months number can be provided.
@@ -1090,7 +1090,7 @@ def plot_flux_map_period_comparison(
         config_data (dict of dict):
             Dictionary of models and species information (read from json file).
         model_labels (list):
-            List of model_labels from fluxy.config.
+            List of model_labels from fluxie.config.
         chop_by (str or list):
             Time units to perform the average, options for 'year', 'month' and 'season'.
             Alternatively, a list of starting dates or months number can be provided.