add environment file, local settings, and drop localizesl (#9)

.gitignore

@@ -89,4 +89,4 @@ target/
 .mypy_cache/
 
 # dask
-dask-worker-space
+dask-worker-space

HISTORY.rst

@@ -1,8 +1,14 @@
 History
 =======
 
+v1.1.1
+------
+* Update settings file for local development
+* Add environment.yml
+* Drop no longer used LocalizeSL submodule
+
 v1.1.0
-----------
+------
 * Updates consistent with revisions to Depsky et al. 2023
 
 v1.0.2

README.md

@@ -8,7 +8,16 @@ This repository hosts the code used to create the [SLIIDERS](https://doi.org/10.
 
 ## Installation
 
-Most users will want to just use the datasets directly, accessible at the DOIs linked above. If you wish to recreate and/or modify the datasets, which we encourage, you will need to run the Jupyter notebooks in this repository. A collection of helper functions, organized into a Python package, is necessary to run the notebooks and can be found within the `sliiders` directory. A simple pip install will install this package
+Most users will want to just use the datasets directly, accessible at the DOIs linked above. If you wish to recreate and/or modify the datasets, which we encourage, you will need to run the Jupyter notebooks in this repository.
+
+A first step is to create a conda environment with the necessary packages. First install [mamba](https://mamba.readthedocs.io/en/latest/) and then, from the root directory of this repo, run
+
+```bash
+mamba env create -f environment/environment.yml
+mamba activate sliiders
+```
+
+Next, a collection of helper functions, organized into a Python package, is necessary to run the notebooks and can be found within the `sliiders` directory. A simple pip install will install this package
 
 ```bash
 pip install -e sliiders
@@ -59,6 +68,7 @@ We encourage community contributions. At the moment, we have no contribution tem
 ## Authors
 
 The original authors of this code include:
+
 * Daniel Allen
 * Ian Bolliger
 * Junho Choi
@@ -74,4 +84,4 @@ Please use the following citation when citing the preprint (this will be updated
 
 ```
 Depsky, N., Bolliger, I., Allen, D., Choi, J. H., Delgado, M., Greenstone, M., Hamidi, A., Houser, T., Kopp, R. E., and Hsiang, S.: DSCIM-Coastal v1.0: An Open-Source Modeling Platform for Global Impacts of Sea Level Rise, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2022-198, 2022.
-```
+```

environment/environment.yml

@@ -0,0 +1,35 @@
+name: sliiders
+channels:
+  - conda-forge
+dependencies:
+  - beautifulsoup4
+  - cartopy
+  - contextily
+  - dask-geopandas
+  - distributed
+  - fsspec
+  - jupyterlab
+  - matplotlib
+  - networkx
+  - numba
+  - numpy
+  - numpy_groupies
+  - pandas
+  - pandas-datareader
+  - pint
+  - pygeos
+  - pyinterp
+  - python
+  - pypdf2
+  - pyreadr
+  - regionmask
+  - requests
+  - rioxarray
+  - scikit-learn
+  - scipy
+  - shapely
+  - statsmodels
+  - tqdm
+  - xarray
+  - xesmf
+  - zarr

notebooks/data-cleaning/01-clean-country-socioecon-data.ipynb

@@ -425,7 +425,7 @@
    "outputs": [],
    "source": [
     "df.to_parquet(\n",
-    "    str(sset.PATH_EXPOSURE_POP_INT), storage_options={\"token\": str(sset.CRED_PATH)}\n",
+    "    str(sset.PATH_EXPOSURE_POP_INT), storage_options=sset.STORAGE_OPTIONS\n",
     ")"
    ]
   },

sliiders/io.py

@@ -8,9 +8,7 @@
 import rioxarray as rio
 import xarray as xr
 
-from sliiders.settings import CRED_PATH
-
-CRED_PATH_STR = str(CRED_PATH)
+from sliiders.settings import STORAGE_OPTIONS
 
 
 def read_gdf(fpath):
@@ -50,19 +48,15 @@ def save(obj, path, *args, **kwargs):
         meth = "to_parquet"
     else:
         raise ValueError(type(obj))
-    getattr(obj, meth)(
-        str(path), *args, storage_options={"token": CRED_PATH_STR}, **kwargs
-    )
+    getattr(obj, meth)(str(path), *args, storage_options=STORAGE_OPTIONS, **kwargs)
 
 
 def open_zarr(path, **kwargs):
-    return xr.open_zarr(str(path), storage_options={"token": CRED_PATH_STR}, **kwargs)
+    return xr.open_zarr(str(path), storage_options=STORAGE_OPTIONS, **kwargs)
 
 
 def read_parquet_dask(path, **kwargs):
-    return ddf.read_parquet(
-        str(path), storage_options={"token": CRED_PATH_STR}, **kwargs
-    )
+    return ddf.read_parquet(str(path), storage_options=STORAGE_OPTIONS, **kwargs)
 
 
 def _fuseify(path):