Fix broken code quality checks in CI

.github/workflows/pythonpackage.yaml

@@ -35,9 +35,9 @@ jobs:
       - name: Format check with black
         run: |
           black --check .
-      - name: Format check with flake8
+      - name: Format ruff check
         run: |
-          flake8
+          ruff check .
 
   test:
     runs-on: ubuntu-latest

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 
 # Translations
 *.mo

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Fix bad release header links in CHANGELOG.md. ([PR #105](https://github.com/ClimateImpactLab/dscim/pull/105), [@brews](https://github.com/brews))
+- Fixed broken code quality checks in CI. Now using `ruff` instead of `flake8`. ([PR #107](https://github.com/ClimateImpactLab/dscim/pull/107), [@brews](https://github.com/brews))
 
 ## [0.4.0] - 2023-07-06
 

pyproject.toml

@@ -28,3 +28,24 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 fallback_version = "999"
+
+[tool.ruff]
+exclude = [
+    ".eggs",
+    "docs",
+]
+# E402: module level import not at top of file
+# E501: line too long - let black worry about that
+ignore = [
+    "E402",
+    "E501",
+]
+select = [
+    # Pyflakes
+    "F",
+    # Pycodestyle
+    "E",
+    "W",
+    # Pyupgrade
+    "UP",
+]

requirements.txt

@@ -14,7 +14,7 @@ dask-jobqueue==0.8.2
 seaborn==0.12.2
 geopandas==0.13.2
 black==23.7.0
-flake8==6.0.0
+ruff==0.0.278
 netcdf4==1.6.4
 h5netcdf==1.2.0
 impactlab-tools==0.4.0

src/dscim/__init__.py

@@ -1,7 +1,6 @@
 import logging
 import sys
 import os
-import imp
 import yaml
 import xarray
 import pathlib

src/dscim/descriptors.py

@@ -1,7 +1,7 @@
 # from https://github.com/dssg/dickens/blob/master/src/descriptors.py
 
 
-class cachedproperty(object):
+class cachedproperty:
     """Non-data descriptor decorator implementing a read-only property
     which overrides itself on the instance with an entry in the
     instance's data dictionary, caching the result of the decorated

src/dscim/menu/baseline.py

@@ -1,6 +1,3 @@
-import pandas as pd
-import numpy as np
-import xarray as xr
 from dscim.menu.main_recipe import MainRecipe
 
 

src/dscim/menu/main_recipe.py

@@ -1,5 +1,4 @@
 import os
-import dask
 import logging
 import subprocess
 from subprocess import CalledProcessError
@@ -10,7 +9,7 @@
 from dscim.descriptors import cachedproperty
 from itertools import product
 from dscim.menu.decorators import save
-from dscim.menu.simple_storage import StackedDamages, EconVars
+from dscim.menu.simple_storage import StackedDamages
 from dscim.utils.utils import (
     model_outputs,
     compute_damages,
@@ -400,8 +399,6 @@ def output_attrs(self):
             A dict Class metadata
         """
 
-        import dscim
-
         # find machine name
         machine_name = os.getenv("HOSTNAME")
         if machine_name is None:
@@ -894,7 +891,7 @@ def weitzman_min(self, no_cc_consumption, cc_consumption, parameter):
         if self.eta == 1:
             w_utility = np.log(parameter)
             bottom_utility = np.power(parameter, -1) * (parameter - cc_consumption)
-            bottom_coded_cons = np.exp((w_utility - bottom_utility))
+            bottom_coded_cons = np.exp(w_utility - bottom_utility)
 
             clipped_cons = xr.where(
                 cc_consumption > parameter, cc_consumption, bottom_coded_cons
@@ -1048,10 +1045,8 @@ def marginal_damages(self):
                 md = self.median_params_marginal_damages
             else:
                 raise NotImplementedError(
-                    (
-                        f"{agg} is not available. Enter list including"
-                        '["ce", "fair", "median", "median_params"]'
-                    )
+                    f"{agg} is not available. Enter list including"
+                    '["ce", "fair", "median", "median_params"]'
                 )
 
             md = md.assign_coords({"fair_aggregation": agg}).expand_dims(

src/dscim/menu/risk_aversion.py

@@ -1,4 +1,3 @@
-import numpy as np
 import pandas as pd
 import xarray as xr
 from dscim.menu.main_recipe import MainRecipe

src/dscim/menu/simple_storage.py

@@ -1,6 +1,5 @@
 import logging
 import os
-import sys
 import xarray as xr
 import numpy as np
 import pandas as pd

src/dscim/preprocessing/climate/all_masks_rff.py

@@ -1,9 +1,6 @@
 import xarray as xr
-import pandas as pd
-import numpy as np
 from dscim.menu.simple_storage import Climate
 import os
-import sys
 import yaml
 from p_tqdm import p_map
 

src/dscim/preprocessing/climate/ssp_clipped_rff.py

@@ -1,6 +1,4 @@
 import xarray as xr
-import numpy as np
-import pandas as pd
 from p_tqdm import p_map
 from itertools import product
 

src/dscim/preprocessing/climate/stack_iterations.py

@@ -1,8 +1,5 @@
 import xarray as xr
-import pandas as pd
-import numpy as np
 import os
-import sys
 
 USER = os.getenv("USER")
 from p_tqdm import p_map

src/dscim/preprocessing/climate/stack_masks.py

@@ -1,11 +1,6 @@
 import xarray as xr
-import pandas as pd
-import numpy as np
 import os
-import sys
-import yaml
 from p_tqdm import p_map
-from itertools import product
 
 USER = os.getenv("USER")
 

src/dscim/preprocessing/input_damages.py

@@ -5,7 +5,6 @@
 import os
 import re
 import logging
-import warnings
 import multiprocessing
 import numpy as np
 import pandas as pd

src/dscim/preprocessing/midprocessing.py

@@ -1,5 +1,4 @@
 import os
-import sys
 import shutil
 
 USER = os.getenv("USER")

src/dscim/preprocessing/misc/check_nans.py

@@ -1,11 +1,8 @@
 # Pass a directory, output log files detailing number of nans each file has
 
-import os
-import numpy as np
 import pandas as pd
 import xarray as xr
 import glob
-import shutil
 import csv
 from p_tqdm import p_uimap
 

src/dscim/preprocessing/misc/convert_float32.py

@@ -1,6 +1,5 @@
 import os
 import numpy as np
-import pandas as pd
 import xarray as xr
 import glob
 import shutil

src/dscim/preprocessing/preprocessing.py

@@ -1,19 +1,12 @@
-from math import ceil
 from pathlib import Path
 import os
-import sys
 
 USER = os.getenv("USER")
-import dask
 import dask.array as da
-import dask.config
 import numpy as np
 import xarray as xr
-from dask.distributed import Client, progress
 from dscim.utils.functions import ce_func, mean_func
 import yaml
-import time
-import argparse
 
 
 def ce_from_chunk(
@@ -87,7 +80,7 @@ def reduce_damages(
         ), "Adding up does not take an eta argument. Please set to None."
     # client = Client(n_workers=35, memory_limit="9G", threads_per_worker=1)
 
-    with open(config, "r") as stream:
+    with open(config) as stream:
         c = yaml.safe_load(stream)
         params = c["sectors"][sector]
 
@@ -209,7 +202,7 @@ def sum_AMEL(
     AMEL,
 ):
     # load config
-    with open(config, "r") as stream:
+    with open(config) as stream:
         loaded_config = yaml.safe_load(stream)
         params = loaded_config["sectors"]
 
@@ -385,7 +378,7 @@ def clip_damages(
     """
 
     # load config
-    with open(config, "r") as stream:
+    with open(config) as stream:
         loaded_config = yaml.safe_load(stream)
         params = loaded_config["sectors"][sector]
 

src/dscim/utils/generate_yaml.py

@@ -1,5 +1,4 @@
 import os
-import sys
 import yaml
 import dscim
 from dscim import Waiter

src/dscim/utils/menu_runs.py

@@ -5,18 +5,12 @@
 from pathlib import Path
 
 import os
-import gc
-import time
 import yaml
 
 USER = os.getenv("USER")
-import numpy as np
-import pandas as pd
-import xarray as xr
 import dask
 
 dask.config.set(**{"array.slicing.split_large_chunks": False})
-from dscim import ProWaiter
 from itertools import product
 
 MENU_OPTIONS = {
@@ -44,7 +38,7 @@ def run_ssps(
     if fair_dims_list is None:
         fair_dims_list = [["simulation"]]
 
-    with open(config, "r") as stream:
+    with open(config) as stream:
         conf = yaml.safe_load(stream)
 
     for sector, pulse_year, menu_disc, eta_rho, mask, fair_dims in product(
@@ -132,7 +126,7 @@ def run_rff(
     order="scc",
     regenerate_sccs=True,
 ):
-    with open(config, "r") as stream:
+    with open(config) as stream:
         conf = yaml.safe_load(stream)
 
     for sector, pulse_year, menu_disc, eta_rho in product(

src/dscim/utils/plotting_utils.py

@@ -1,4 +1,4 @@
-from matplotlib.ticker import SymmetricalLogLocator, FuncFormatter
+from matplotlib.ticker import SymmetricalLogLocator
 import numpy as np
 
 

src/dscim/utils/rff.py

@@ -5,13 +5,10 @@
 from itertools import product
 from functools import partial
 import os
-import sys
 from numpy.testing import assert_allclose
 from datetime import datetime
 import fsspec
-import pyarrow
 import gurobipy as gp
-import time
 from scipy.sparse import coo_matrix
 from gurobipy import GRB
 

src/dscim/utils/utils.py

@@ -1,14 +1,10 @@
-import os
 import warnings
-import dask
 import logging
 import xarray as xr
 import pandas as pd
 import numpy as np
-from pathlib import Path
 import statsmodels.formula.api as smf
 import impactlab_tools.utils.weighting
-import dask.dataframe as dd
 from itertools import product
 
 logger = logging.getLogger(__name__)

tests/__init__.py

@@ -1,7 +1,6 @@
 import os
 import dask
 import zipfile
-import pytest
 import pandas as pd
 import xarray as xr
 

tests/test_preprocessing.py

@@ -1,18 +1,13 @@
 import xarray as xr
 import numpy as np
-import math
 import pytest
-import copy
-import dscim.utils.utils as estimations
-from dscim.menu.risk_aversion import RiskAversionRecipe
 from dscim.preprocessing.preprocessing import (
     subset_USA_ssp_econ,
     subset_USA_reduced_damages,
     sum_AMEL,
     reduce_damages,
     ce_from_chunk,
 )
-from pathlib import Path
 import yaml