Ensemble products per species

README.md

@@ -35,10 +35,64 @@ Another feature is to manipulate the field values by scaling with an arbitrary f
 
 ## Installation
 
-You can install pyflexplot from MCH pypi repository using pip:
+__Prerequisites__: Git, [Miniforge](https://conda-forge.org/download) 
+(or another Conda installation), 
+[Poetry](https://python-poetry.org/docs/#installing-with-the-official-installer)
+
+### Get source code
+
+```bash
+git clone git@github.com:MeteoSwiss-APN/pyflexplot.git
+cd pyflexplot
+```
+
+### Create Conda environment
+
+Create a Conda environment with only the desired Python version and Poetry and activate it
+
+```bash
+conda create -n pyflexplot python=3.10 poetry=1.8
+conda activate pyflexplot
+```
+
+Configure Poetry to not create a new virtual environment. If it detects an already enabled
+virtual environment (eg a Conda environment) it will install dependencies into it:
+
+```bash
+poetry config --local virtualenvs.create false
+```
+
+### Build the project (Poetry)
+Alternative build with mchbuild see further below.
+
+```bash
+poetry install
+```
+
+### Build the project (mchbuild)
+
+_Documentation to be added._
+
+### Run tests and quality tools
+
+```bash
+poetry run pytest
+```
+
+If no errors occur, the tests save plots in their respective folders in the
+
+#### Run quality assurance tools
+
+Run pylint to check code style of Python files (if any):
+
+```bash
+poetry run pylint src
+```
+
+Run mypy to check typing:
 
 ```bash
-pip install pyflexplot -i https://service.meteoswiss.ch/nexus/repository/python-all/simple
+poetry run mypy
 ```
 
 ## Run pyflexplot
@@ -243,58 +297,6 @@ pyflexplot --preset "$preset" --merge-pdfs --dest=s3://<s3-bucket-name>
 
 ## Development
 
-__Prerequisites__: Git, [Miniconda](https://docs.anaconda.com/free/miniconda/) or
-[Miniforge](https://github.com/conda-forge/miniforge)
-(for installation of Conda), or
-[Poetry](https://python-poetry.org/docs/#installing-with-the-official-installer)
-
-### Install dependencies & start the service locally (CSCS)
-
-Clone the repo and enter the project folder:
-
-```bash
-git clone git@github.com:MeteoSwiss-APN/pyflexplot.git && cd pyflexplot
-```
-
-Create a Conda environment with only the desired Python version and Poetry and activate it:
-
-```bash
-conda create --yes --name pyflexplot python=3.10 poetry=1.8
-conda activate pyflexplot
-```
-
-Configure Poetry to not create a new virtual environment. If it detects an already enabled virtual (eg Conda) environment it will install dependencies into it:
-
-```bash
-poetry config --local virtualenvs.create false
-```
-
-Install packages:
-
-```bash
-poetry install
-```
-
-### Run the tests and quality tools
-
-Run tests:
-
-```bash
-poetry run pytest
-```
-
-Run pylint to check code style of Python files (if any):
-
-```bash
-poetry run pylint src
-```
-
-Run mypy to check typing:
-
-```bash
-poetry run mypy
-```
-
 ### Updating the Test References
 
 Pyflexplot includes a set of functionality tests that compare generated output against predefined reference data.

src/pyflexplot/data/presets/opr/icon-ch1-ctrl/all_png.toml

@@ -7,7 +7,7 @@ model = "ICON-CH1-CTRL"
 lang = "de"
 outfile_time_format = "%Y%m%dT%H%M"
 combine_species = false
-outfile = "forecast-iconch1eps-dispersion~{base_time}~{plot_variable}~{domain}~{release_site}~{species_id}~{time_step}.png"
+outfile = "forecast-iconch1eps-dispersion~{base_time}~{plot_variable}~{domain}~{release_site}~{species_name}~{time_step}.png"
 
 [_base._concentration]
 plot_variable = "concentration"

src/pyflexplot/data/presets/opr/icon-ch1-ctrl/all_shp.toml

@@ -28,13 +28,13 @@ time = -1
 combine_species = true
 
 [_base._concentration."_shp+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_Konzentration_{species_id}_{time_step}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_Konzentration_{species_name}_{time_step}.shp"
 
 [_base._concentration._integr."_shp+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_integrierte_Luftaktivitaet_{species_id}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_integrierte_Luftaktivitaet_{species_name}.shp"
 
 [_base._tot_deposition."_shp+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_Deposition_{species_id}_{time_step}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_Deposition_{species_name}_{time_step}.shp"
 
 [_base._affected_area."_shp+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_Dispersion_beaufschl_Gebiet.shp"

src/pyflexplot/data/presets/opr/icon-ch2-eps/all_pdf.toml

@@ -7,7 +7,7 @@ ens_member_id = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1
 model = "ICON-CH2-EPS"
 lang = "de"
 outfile_time_format = "%Y%m%dT%H%M"
-combine_species = true
+combine_species = false
 
 [_base._concentration]
 plot_variable = "concentration"
@@ -29,21 +29,25 @@ plot_variable = "affected_area"
 integrate = true
 level = 0
 time = -1
+combine_species = true
 
 [_base._concentration."_probability+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_probability_{domain}.pdf"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._concentration._integr."_probability+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_probability_{domain}.pdf"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._tot_deposition."_probability+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_probability_{domain}.pdf"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._affected_area."_probability+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_probability_{domain}.pdf"
@@ -55,6 +59,7 @@ outfile = "{release_start}_{release_site}_FLEXPART-{model}_probability_{domain}.
 plot_type = "multipanel"
 multipanel_param = "time"
 time = [2, 4, 8, -1]
+combine_species = true
 
 [_base._concentration._integr."_pctl95+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_percentile_{domain}.pdf"
@@ -93,9 +98,11 @@ time = 0
 
 [_base._concentration._cloud."_arrival+"]
 ens_variable = "cloud_arrival_time"
+combine_species = true
 
 [_base._concentration._cloud."_departure+"]
 ens_variable = "cloud_departure_time"
+combine_species = true
 
 [_base._concentration._integr."_min+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_cloud_statistics_{domain}.pdf"
@@ -136,14 +143,17 @@ ens_variable = "mean"
 [_base._concentration._integr."_median+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_cloud_statistics_{domain}.pdf"
 ens_variable = "median"
+
 [_base._tot_deposition."_median+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_cloud_statistics_{domain}.pdf"
 ens_variable = "median"
+
 [_base._affected_area."_median+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_cloud_statistics_{domain}.pdf"
 ens_variable = "median"
 
 ["**".full]
 domain = "full"
+
 ["**".ch]
 domain = "ch"

src/pyflexplot/data/presets/opr/icon-ch2-eps/all_png.toml

@@ -7,8 +7,8 @@ ens_member_id = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1
 model = "ICON-CH2-EPS"
 lang = "de"
 outfile_time_format = "%Y%m%dT%H%M"
-combine_species = true
-outfile = "forecast-iconch2eps-dispersion~{base_time}~{plot_variable}-{ens_variable}~{domain}~{release_site}~1~{time_step}.png"
+combine_species = false
+outfile = "forecast-iconch2eps-dispersion~{base_time}~{plot_variable}-{ens_variable}~{domain}~{release_site}~{species_name}~{time_step}.png"
 
 [_base._concentration]
 plot_variable = "concentration"
@@ -30,18 +30,22 @@ plot_variable = "affected_area"
 integrate = true
 level = 0
 time = -1
+combine_species = true
 
 [_base._concentration."_probability+"]
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._concentration._integr."_probability+"]
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._tot_deposition."_probability+"]
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._affected_area."_probability+"]
 ens_variable = "probability"
@@ -66,9 +70,11 @@ time = 0
 
 [_base._concentration._cloud."_arrival+"]
 ens_variable = "cloud_arrival_time"
+combine_species = true
 
 [_base._concentration._cloud."_departure+"]
 ens_variable = "cloud_departure_time"
+combine_species = true
 
 [_base._concentration._integr."_min+"]
 ens_variable = "minimum"

src/pyflexplot/data/presets/opr/icon-ch2-eps/all_shp.toml

@@ -7,7 +7,7 @@ ens_member_id = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 1
 model = "ICON-CH2-EPS"
 lang = "de"
 outfile_time_format = "%Y%m%dT%H%M"
-combine_species = true
+combine_species = false
 
 [_base._concentration]
 plot_variable = "concentration"
@@ -29,39 +29,43 @@ plot_variable = "affected_area"
 integrate = true
 level = 0
 time = -1
+combine_species = true
 
 [_base._concentration."_probability+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit-Konzentration_{species_id}_{time_step}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit_Konzentration_{species_name}_{time_step}.shp"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._concentration._integr."_probability+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit-integrierte-Luftaktivitaet_{species_id}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._tot_deposition."_probability+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit-Deposition_{species_id}.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit_Deposition_{species_name}.shp"
 ens_variable = "probability"
 ens_param_thr = 0
+combine_species = true
 
 [_base._affected_area."_probability+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit-beaufschl_Gebiet.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wahrscheinlichkeit_beaufschl_Gebiet.shp"
 ens_variable = "probability"
 ens_param_thr = 0
 
 [_base._concentration._integr."_pctl95+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "percentile"
 ens_param_pctl = 95
 
 [_base._tot_deposition."_pctl95+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil_Deposition_{species_name}.shp"
 ens_variable = "percentile"
 ens_param_pctl = 95
 
 [_base._affected_area."_pctl95+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_95-Perzentil_beaufschl_Gebiet.shp"
 ens_variable = "percentile"
 ens_param_pctl = 95
 
@@ -73,53 +77,55 @@ time = 0
 [_base._concentration._cloud."_arrival+"]
 ens_variable = "cloud_arrival_time"
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wolkenankunftszeit.shp"
+combine_species = true
 
 [_base._concentration._cloud."_departure+"]
 ens_variable = "cloud_departure_time"
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_Wolkenabzugszeit.shp"
+combine_species = true
 
 [_base._concentration._integr."_min+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Minimum_integrierte-Luftaktivitaet.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Minimum_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "minimum"
 
 [_base._tot_deposition."_min+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Minimum_Deposition.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Minimum_Deposition_{species_name}.shp"
 ens_variable = "minimum"
 
 [_base._affected_area."_min+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_Minimum_beaufschl_Gebiet.shp"
 ens_variable = "minimum"
 
 [_base._concentration._integr."_max+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Maximum_integrierte-Luftaktivitaet.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Maximum_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "maximum"
 
 [_base._tot_deposition."_max+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Maximum_Deposition.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Maximum_Deposition_{species_name}.shp"
 ens_variable = "maximum"
 
 [_base._affected_area."_max+"]
 outfile = "{release_start}_{release_site}_FLEXPART-{model}_Maximum_beaufschl_Gebiet.shp"
 ens_variable = "maximum"
 
 [_base._concentration._integr."_mean+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Mittel_integrierte-Luftaktivitaet.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Mittel_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "mean"
 
 [_base._tot_deposition."_mean+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Mittel_Deposition.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Mittel_Deposition_{species_name}.shp"
 ens_variable = "mean"
 
 # [_base._affected_area."_mean+"] # for affected area, mean is same area as max -> skip mean
 # outfile = "{release_start}_{release_site}_FLEXPART-{model}_Mittel_beaufschl_Gebiet.shp"
 # ens_variable = "mean"
 
 [_base._concentration._integr."_median+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Median_integrierte-Luftaktivitaet.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Median_integrierte-Luftaktivitaet_{species_name}.shp"
 ens_variable = "median"
 
 [_base._tot_deposition."_median+"]
-outfile = "{release_start}_{release_site}_FLEXPART-{model}_Median_Deposition.shp"
+outfile = "{release_start}_{release_site}_FLEXPART-{model}_Median_Deposition_{species_name}.shp"
 ens_variable = "median"
 
 [_base._affected_area."_median+"]