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Use absolute path for config.default.yaml in _helpers.py #1137

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Use absolute path for config.default.yaml in _helpers.py #1137

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b82e402
add absolute path to config.default.yaml
yerbol-akhmetov Oct 9, 2024
271c78a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 10, 2024
c1ffc88
add release notes
yerbol-akhmetov Oct 10, 2024
8b17ca6
Merge branch 'absolute_path_fixes' of https://github.com/yerbol-akhme…
yerbol-akhmetov Oct 10, 2024
7513a04
download files using absolute path, not based on os.getcwd()
yerbol-akhmetov Oct 11, 2024
6fabdcc
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 11, 2024
61a1821
add prefix to outputs of retrieve_databundle_light if exists
yerbol-akhmetov Oct 13, 2024
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2 changes: 2 additions & 0 deletions doc/release_notes.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@ E.g. if a new rule becomes available describe how to use it `make test` and in o

* Include a dedicated cutout for Europe in bundle_config.yaml `PR #1125 <https://github.com/pypsa-meets-earth/pypsa-earth/pull/1125>`_

* Use absolute path for `config.default.yaml` in `_helpers.py` for facilitate smooth module import `PR #1137 <https://github.com/pypsa-meets-earth/pypsa-earth/pull/1137>`_

PyPSA-Earth 0.4.1
=================

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8 changes: 7 additions & 1 deletion scripts/_helpers.py
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Expand Up @@ -36,8 +36,14 @@
# filename of the regions definition config file
REGIONS_CONFIG = "regions_definition_config.yaml"

# absolute path to base directory (pypsa-earth)
BASE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))

def check_config_version(config, fp_config="config.default.yaml"):
# absolute path to config.default.yaml
CONFIG_DEFAULT_PATH = os.path.join(BASE_DIR, "config.default.yaml")


def check_config_version(config, fp_config=CONFIG_DEFAULT_PATH):
"""
Check that a version of the local config.yaml matches to the actual config
version as defined in config.default.yaml.
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17 changes: 7 additions & 10 deletions scripts/build_shapes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import requests
import xarray as xr
from _helpers import (
BASE_DIR,
configure_logging,
create_logger,
three_2_two_digits_country,
Expand Down Expand Up @@ -85,7 +86,7 @@ def download_GADM(country_code, update=False, out_logging=False):
GADM_url = f"https://geodata.ucdavis.edu/gadm/gadm4.1/gpkg/{GADM_filename}.gpkg"

GADM_inputfile_gpkg = os.path.join(
os.getcwd(),
BASE_DIR,
"data",
"gadm",
GADM_filename,
Expand Down Expand Up @@ -489,7 +490,7 @@ def download_WorldPop_standard(
]

WorldPop_inputfile = os.path.join(
os.getcwd(), "data", "WorldPop", WorldPop_filename
BASE_DIR, "data", "WorldPop", WorldPop_filename
) # Input filepath tif

if not os.path.exists(WorldPop_inputfile) or update is True:
Expand Down Expand Up @@ -543,7 +544,7 @@ def download_WorldPop_API(
WorldPop_filename = f"{two_2_three_digits_country(country_code).lower()}_ppp_{year}_UNadj_constrained.tif"
# Request to get the file
WorldPop_inputfile = os.path.join(
os.getcwd(), "data", "WorldPop", WorldPop_filename
BASE_DIR, "data", "WorldPop", WorldPop_filename
) # Input filepath tif
os.makedirs(os.path.dirname(WorldPop_inputfile), exist_ok=True)
year_api = int(str(year)[2:])
Expand Down Expand Up @@ -580,12 +581,10 @@ def convert_GDP(name_file_nc, year=2015, out_logging=False):
name_file_tif = name_file_nc[:-2] + "tif"

# path of the nc file
GDP_nc = os.path.join(os.getcwd(), "data", "GDP", name_file_nc) # Input filepath nc
GDP_nc = os.path.join(BASE_DIR, "data", "GDP", name_file_nc) # Input filepath nc

# path of the tif file
GDP_tif = os.path.join(
os.getcwd(), "data", "GDP", name_file_tif
) # Input filepath nc
GDP_tif = os.path.join(BASE_DIR, "data", "GDP", name_file_tif) # Input filepath nc

# Check if file exists, otherwise throw exception
if not os.path.exists(GDP_nc):
Expand Down Expand Up @@ -628,9 +627,7 @@ def load_GDP(

# path of the nc file
name_file_tif = name_file_nc[:-2] + "tif"
GDP_tif = os.path.join(
os.getcwd(), "data", "GDP", name_file_tif
) # Input filepath tif
GDP_tif = os.path.join(BASE_DIR, "data", "GDP", name_file_tif) # Input filepath tif

if update | (not os.path.exists(GDP_tif)):
if out_logging:
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19 changes: 11 additions & 8 deletions scripts/retrieve_databundle_light.py
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Expand Up @@ -143,7 +143,7 @@ def download_and_unzip_zenodo(config, rootpath, hot_run=True, disable_progress=F
"""
resource = config["category"]
file_path = os.path.join(rootpath, "tempfile.zip")
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])
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Why do you propose PREFIX here instead of BASE_DIR as in the other cases?

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Thanks, @davide-f. That is the valid point. I have used BASE_DIR as the first try. And it worked fine as standalone for rule execution. But to make sure rules see each other and trigger, outputs and inputs needs to match. So submodules/pypsa-earth/data/eez/eez_v11.gpkg is not equal to absolute path /home/yerbol/efuels/.../submodules/pypsa-earth/data/eez/eez_v11.gpkg when it comes to input outputs of snakemake.

With BASE_DIR instead build_shapes were not triggering retrieve_databundle_light. But retrieve_databundle_light worked just fine separately when calling it. CI test actually helped me to figure that out (https://github.com/pypsa-meets-earth/pypsa-earth/actions/runs/11314101704/job/31463655978)

BASE_DIR is good for handling files inside of the script, that are not tight to input/outputs of snakemake. If it is input/output, only PREFIX makes the full workflow intact and preserve rule connections.

url = config["urls"]["zenodo"]

if hot_run:
Expand Down Expand Up @@ -188,7 +188,7 @@ def download_and_unzip_gdrive(config, rootpath, hot_run=True, disable_progress=F
"""
resource = config["category"]
file_path = os.path.join(rootpath, "tempfile.zip")
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])
url = config["urls"]["gdrive"]

# retrieve file_id from path
Expand Down Expand Up @@ -266,7 +266,7 @@ def download_and_unzip_protectedplanet(
"""
resource = config["category"]
file_path = os.path.join(rootpath, "tempfile_wpda.zip")
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])
url = config["urls"]["protectedplanet"]

def get_first_day_of_month(date):
Expand Down Expand Up @@ -438,7 +438,7 @@ def download_and_unzip_direct(config, rootpath, hot_run=True, disable_progress=F
True when download is successful, False otherwise
"""
resource = config["category"]
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])
url = config["urls"]["direct"]

file_path = os.path.join(destination, os.path.basename(url))
Expand Down Expand Up @@ -492,7 +492,7 @@ def download_and_unzip_hydrobasins(
True when download is successful, False otherwise
"""
resource = config["category"]
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])
url_templ = config["urls"]["hydrobasins"]["base_url"]
suffix_list = config["urls"]["hydrobasins"]["suffixes"]

Expand Down Expand Up @@ -543,7 +543,7 @@ def download_and_unzip_post(config, rootpath, hot_run=True, disable_progress=Fal
True when download is successful, False otherwise
"""
resource = config["category"]
destination = os.path.relpath(config["destination"])
destination = os.path.join(PREFIX, config["destination"])

# load data for post method
postdata = config["urls"]["post"]
Expand Down Expand Up @@ -792,8 +792,8 @@ def datafiles_retrivedatabundle(config):


def merge_hydrobasins_shape(config_hydrobasin, hydrobasins_level):
basins_path = config_hydrobasin["destination"]
output_fl = config_hydrobasin["output"][0]
basins_path = os.path.join(PREFIX, config_hydrobasin["destination"])
output_fl = os.path.join(PREFIX, config_hydrobasin["output"][0])

files_to_merge = [
"hybas_{0:s}_lev{1:02d}_v1c.shp".format(suffix, hydrobasins_level)
Expand Down Expand Up @@ -824,6 +824,9 @@ def merge_hydrobasins_shape(config_hydrobasin, hydrobasins_level):
countries = snakemake.params.countries
logger.info(f"Retrieving data for {len(countries)} countries.")

# get prefix (exists only if importing rule as import, else empty string)
PREFIX = snakemake.log[0].split("log")[0]

# load enable configuration
config_enable = snakemake.config["enable"]
# load databundle configuration
Expand Down
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