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clean configs.ipynb docs and type annotation
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@franckalbinet
franckalbinet committed Oct 3, 2024
1 parent 1c32153 commit 0bebf35
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82 changes: 52 additions & 30 deletions marisco/configs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
import os
import re
from functools import partial
from typing import Union
from typing import List, Dict, Callable, Tuple, Any, Optional

from .inout import read_toml, write_toml
import pandas as pd
Expand All @@ -27,7 +27,9 @@
MARISCO_CFG_DIRNAME = '.marisco'

# %% ../nbs/api/configs.ipynb 5
def base_path(): return Path.home() / MARISCO_CFG_DIRNAME
def base_path():
"Return the path to the `.marisco` folder under your home directory."
return Path.home() / MARISCO_CFG_DIRNAME

# %% ../nbs/api/configs.ipynb 8
CONFIGS = {
Expand Down Expand Up @@ -56,16 +58,24 @@ def base_path(): return Path.home() / MARISCO_CFG_DIRNAME
}

# %% ../nbs/api/configs.ipynb 12
def cfg(): return read_toml(base_path() / CFG_FNAME)
def cfg():
"Return the configuration as a dictionary."
return read_toml(base_path() / CFG_FNAME)

# %% ../nbs/api/configs.ipynb 13
def nuc_lut_path(): return Path(cfg()['dirs']['lut']) / NUCLIDE_LOOKUP_FNAME
def nuc_lut_path():
"Return the path to the nuclide lookup table."
return Path(cfg()['dirs']['lut']) / NUCLIDE_LOOKUP_FNAME

# %% ../nbs/api/configs.ipynb 14
def lut_path(): return Path(cfg()['dirs']['lut'])
def lut_path():
"Return the path to the lookup tables directory."
return Path(cfg()['dirs']['lut'])

# %% ../nbs/api/configs.ipynb 15
def cache_path(): return Path(cfg()['dirs']['cache'])
def cache_path():
"Return the path to the cache directory."
return Path(cfg()['dirs']['cache'])

# %% ../nbs/api/configs.ipynb 16
CONFIGS_CDL = {
Expand Down Expand Up @@ -411,61 +421,69 @@ def cache_path(): return Path(cfg()['dirs']['cache'])

# %% ../nbs/api/configs.ipynb 19
def cdl_cfg():
"Return the CDL configuration as a dictionary."
"Return the CDL (Common Data Language) configuration as a dictionary."
try:
return read_toml(base_path() / CDL_FNAME)
except FileNotFoundError:
return CONFIGS_CDL

# %% ../nbs/api/configs.ipynb 20
def grp_names():
"Return the group names as defined in `cdl.toml`"
"Return the group names as defined in `cdl.toml`."
return [v['name'] for v in cdl_cfg()['grps'].values()]

# %% ../nbs/api/configs.ipynb 21
def species_lut_path():
"Return the path to the species lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'species_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 22
def bodyparts_lut_path():
"Return the path to the body parts lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'body_part_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 23
def biogroup_lut_path():
"Return the path to the biota group lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'bio_group_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 24
def sediments_lut_path():
"Return the path to the sediment type lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'sed_type_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 25
def unit_lut_path():
"Return the path to the unit lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'unit_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 26
def detection_limit_lut_path():
"Return the path to the detection limit lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'dl_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 27
def filtered_lut_path():
"Return the path to the filtered lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'filt_t'][0]['fname']
return src_dir / fname

# %% ../nbs/api/configs.ipynb 28
def area_lut_path():
"Return the path to the area lookup table."
src_dir = lut_path()
fname = [enum for enum in cdl_cfg()['enums'] if enum['name'] == 'area_t'][0]['fname']
return src_dir / fname
Expand All @@ -478,31 +496,34 @@ def area_lut_path():

# %% ../nbs/api/configs.ipynb 31
def name2grp(
name:str, # Name of the group
cdl:dict, # CDL configuration
name: str, # Group name
cdl: dict, # CDL configuration
):
# Reverse `cdl.toml` config group dict so that group config key can be retrieve based on its name
return {v['name']:k for k, v in cdl['grps'].items()}[name]

# %% ../nbs/api/configs.ipynb 34
def nc_tpl_name():
"Return the name of the MARIS NetCDF template as defined in `configs.toml`"
p = base_path()
return read_toml(p / 'configs.toml')['names']['nc_template']

# %% ../nbs/api/configs.ipynb 35
def nc_tpl_path():
"Return the name of the MARIS NetCDF template as defined in `configs.toml`"
"Return the path of the MARIS NetCDF template as defined in `configs.toml`"
p = base_path()
return p / read_toml(p / 'configs.toml')['names']['nc_template']

# %% ../nbs/api/configs.ipynb 37
def sanitize(s:Union[str, float] # String to sanitize
) -> str: # Sanitized string
def sanitize(
s: str|float # String or float to sanitize
) -> str|float: # Sanitized string or original float
"""
Sanitize dictionary key to comply with NetCDF enumeration type:
Sanitize dictionary key to comply with NetCDF enumeration type:
- remove `(`, `)`, `.`, `/`, `-`
- strip the string
- Remove `(`, `)`, `.`, `/`, `-`
- Strip the string
- Return original value if it's not a string (e.g., NaN)
"""
if isinstance(s, str):
s = re.sub(r'[().]', '', s)
Expand All @@ -521,13 +542,14 @@ def try_int(x):
return x

# %% ../nbs/api/configs.ipynb 42
def get_lut(src_dir: str, # Directory containing lookup tables
fname: str, # Excel file lookup table name
key: str, # Excel file column name to be used as dict keys
value: str, # Excel file column name to be used as dict values
do_sanitize: bool=True, # Sanitization required?
reverse: bool=False # Reverse lookup table (value, key)
) -> dict: # MARIS lookup table (key, value)
def get_lut(
src_dir: str, # Directory containing lookup tables
fname: str, # Excel file lookup table name
key: str, # Excel file column name to be used as dict keys
value: str, # Excel file column name to be used as dict values
do_sanitize: bool=True, # Sanitization required?
reverse: bool=False # Reverse lookup table (value, key)
) -> dict: # MARIS lookup table (key, value)
"Convert MARIS db lookup table excel file to dictionary `{'name': id, ...}` or `{id: name, ...}` if `reverse` is True."
fname = Path(src_dir) / fname
df = pd.read_excel(fname, usecols=[key, value]).dropna(subset=value)
Expand All @@ -543,10 +565,10 @@ def get_lut(src_dir: str, # Directory containing lookup tables

# %% ../nbs/api/configs.ipynb 45
class Enums():
"Return dictionaries of MARIS NetCDF's enumeration types"
"Return dictionaries of MARIS NetCDF's enumeration types."
def __init__(self,
lut_src_dir:str,
cdl_enums:dict
lut_src_dir:str, # Directory containing lookup tables
cdl_enums:dict # CDL configuration enumeration types
):
fc.store_attr()
self.types = self.lookup()
Expand All @@ -564,11 +586,11 @@ def lookup(self):

# %% ../nbs/api/configs.ipynb 49
def get_enum_dicts(
lut_src_dir:str,
cdl_enums:dict,
**kwargs
lut_src_dir:str, # Directory containing lookup tables
cdl_enums:dict, # CDL configuration enumeration types
**kwargs # Additional arguments
):
"Return a dict of NetCDF enumeration types"
"Return a dict of NetCDF enumeration types."
enum_types = {}
for enum in cdl_enums:
name, fname, key, value = enum.values()
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