Tracking issues/notes installation and setting up

[jkikstra]

1. after running pip install -e .[tests] in a new conda environment, pytest tests yields:`

ERROR: usage: pytest [options] [file_or_dir] [file_or_dir] [...]
pytest: error: unrecognized arguments: --cov --cov-report term-missing tests
  inifile: C:\Users\kikstra\Documents\GitHub\concordia\pyproject.toml
  rootdir: C:\Users\kikstra\Documents\GitHub\concordia

2. Change README to not suggest pip install (but go through conda/mamba route)
3. what worked: mamba env create -f environment.yml/mamba env create -f environment.yml
4. do cd notebooks, then run jupytext --sync workflow.py (NB delete comment) --> works
5. workflow.ipynb runs until config.yaml (copy from example_config.yaml)
6. sync the RESCUE sharepoint, and change data_path in config.yaml to that path
7. "region_mapping" -> "regionmapping" & change path of regionmappings to config.yaml to "$scenario_path/regionmappingH12.csv" & change MyModelName to "REMIND-MAgPIE 3.2.0-4.7.0"
8. everything (alternative 2: downscaled = workflow.harmonize_and_downscale()) works (may take a bit due to downloading and loading the first time - 13 mins on jarmo's laptop and IIASA wifi)
9. not working: writing out - AttributeError: 'DataFrame' object has no attribute 'include_in_total' - because we expect "variabledefs-region" instead of "variabledefs-rescue"
10. changing to "variabledefs-region" however leads to KeyError: 'global' in when running workflow.harmonize_and_downscale()

-- new commits came in on the main branch --
after updating the environment using mamba env update -f environment.yml we continue

11. in build-harmonization-report, we run into an issue with plotting, (most likely) caused by a downgrading of pandas, which is forced by geoutils 0.1.1 which forced pandas to be <2.2

-- now start changing things for pretend_REMIND_is_MESSAGE.csv --

12. (not message related) when running ur = set_openscm_registry_as_default(), we get No module named 'openscm_units', so quick-fix is mamba install -c conda-forge openscm-units+restart kernel --> real fix is by adding openscm-units to the environment.yml later
13. note to self: user needs to be careful to have the correct index column, e.g. if a column reads "unit" instead of the currently expected "Unit", there will be an error
14. error: when trying to create indexraster_region, we get the error Mapping undefined for some countrys: bes, cuw, ggy, jey, sxm --> so it is crucial to list somewhere all the countries that need to be defined
15. now I added bes, cuw, ggy, jey, sxm to region_definitions_message.csv
16. all the rest that I tried seems to work for now!
17. Let's add back the CO2 global overrides for CDR Aff and Agg Ag LUC
    
    changes to
    
    with comparison plots:
    

[jkikstra]

Things done for MESSAGE-pretending-REMIND file:

• create a copy of the entire "RESCUE - WP 1\data_2024_03_14\rescue" folder
• delete in the scenarios folder: REMIND-MAgPIE-CEDS-RESCUE-Tier1-2024-04-25.csv, REMIND-MAgPIE-CEDS-RESCUE-Tier1-2023-12-13.csv (input emissions scenario files), regionmappingH12.csv (model region mapping)
• change in the scenarios folder: harmonization_overrides.xlsx (to only column names, empty rows
• add in the scenarios folder: pretend_REMIND_is_MESSAGE.csv (input emissions scenario file) and region_definitions_message.csv (model region mapping)
• change config.yml fields:
  • data_path
  • regionmappings