update pre-commit hooks and format all files

.github/dependabot.yml

@@ -1,7 +1,7 @@
 version: 2
 updates:
   - package-ecosystem: pip
-    directory: "/"
+    directory: '/'
     schedule:
       interval: daily
   - package-ecosystem: 'github-actions'

.github/workflows/main.yaml

@@ -2,9 +2,15 @@ name: CI
 
 on:
   push:
-    branches: "*"
+    branches:
+      - main
   pull_request:
-    branches: "*"
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   test:
@@ -19,7 +25,7 @@ jobs:
       - uses: conda-incubator/setup-miniconda@v2.1.1
         with:
           python-version: ${{ matrix.python-version }}
-          mamba-version: "*"
+          mamba-version: '*'
           activate-environment: carbonplan
           channels: conda-forge
           channel-priority: true
@@ -73,10 +79,3 @@ jobs:
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.docker_meta.outputs.tags }}
           labels: ${{ steps.docker_meta.outputs.labels }}
-
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2.4.0
-      - uses: actions/setup-python@v2.3.1
-      - uses: pre-commit/action@v2.0.3

.pre-commit-config.yaml

@@ -1,44 +1,45 @@
+ci:
+  autoupdate_schedule: quarterly
+exclude: notebooks/fire/figure_foresttype.ipynb
 repos:
-
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
     hooks:
-    - id: trailing-whitespace
-    - id: end-of-file-fixer
-    - id: check-docstring-first
-    - id: check-json
-    - id: check-yaml
-    - id: pretty-format-json
-      args: ["--autofix", "--indent=2", "--no-sort-keys"]
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: mixed-line-ending
 
--   repo: https://github.com/ambv/black
-    rev: 20.8b1
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.2.2
     hooks:
-    - id: black
-      args: ["--line-length", "100", "--skip-string-normalization"]
+      - id: pyupgrade
+        args:
+          - '--py310-plus'
 
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.0
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
     hooks:
-    - id: flake8
+      - id: black
+      - id: black-jupyter
 
--   repo: https://github.com/asottile/seed-isort-config
-    rev: v2.2.0
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
     hooks:
-    - id: seed-isort-config
--   repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.8.0
+      - id: blackdoc
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 5.0.4
     hooks:
-    - id: isort
+      - id: flake8
 
--   repo: https://github.com/deathbeds/prenotebook
-    rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
     hooks:
-    - id: prenotebook
+      - id: isort
 
-# for R code
-# -   repo: https://github.com/lorenzwalthert/precommit
-#     rev: v0.1.3
-#     hooks:
-#     - id: style-files
-#       args: [--style_pkg=styler, --style_fun=tidyverse_style]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.4
+    hooks:
+      - id: prettier

.prettierrc.toml

@@ -0,0 +1,3 @@
+tabWidth = 2
+semi = false
+singleQuote = true

README.md

@@ -32,12 +32,13 @@ Several notebooks are additionally provided that show the use of these tools for
 ## data products
 
 As part of this project we have created derived data products for five key variables relevant to evaluating forest carbon storage potential and risks.
+
 - `biomass` The potential carbon storage in forests assuming continued growth of existing forests.
 - `fire` The risks associated with forest fires.
 - `drought` The risk to forests from insect-related tree mortality.
 - `insects` The risk to forests from insect-related tree mortality.
 
-Gridded rasters for each of these layers are available for the continental United States at a 4km spatial scale. For biomass and fire, projections are shown through the end of the 21st century in decadal increments. Drought and insect models are still in development so we currently only show historical risks for these disturbance types.  All data are accessible via this [catalog](https://github.com/carbonplan/forest-risks/blob/master/carbonplan_forest_risks/data/catalog.yaml). Additional formats and download options will be provided in the future.
+Gridded rasters for each of these layers are available for the continental United States at a 4km spatial scale. For biomass and fire, projections are shown through the end of the 21st century in decadal increments. Drought and insect models are still in development so we currently only show historical risks for these disturbance types. All data are accessible via this [catalog](https://github.com/carbonplan/forest-risks/blob/master/carbonplan_forest_risks/data/catalog.yaml). Additional formats and download options will be provided in the future.
 
 ## license
 

carbonplan_forest_risks/load/cmip.py

@@ -50,7 +50,6 @@ def cmip(
         if member is None:
             member = members[model]
 
-
         path = setup.loading(store)
 
         prefix = f'cmip6/{method}/conus/4000m/{sampling}/{model}.{scenario}.{member}.zarr'

carbonplan_forest_risks/load/fia.py

@@ -444,7 +444,7 @@ def fia_state_grouped(store, state, clean):
         key = f'year_{year}'
         if key in df.columns:
             if clean:
-                df = df[(df[key] < 9999) | np.isnan((df[key]))]
+                df = df[(df[key] < 9999) | np.isnan(df[key])]
             if sum(np.isnan(df[key])) == len(df):
                 del df[key]
 

carbonplan_forest_risks/plot/fire.py

@@ -321,7 +321,7 @@ def full_eval(
     }
 
     for metric, performance in eval_metrics.items():
-        print('performance at {} scale is: {}'.format(metric, performance))
+        print(f'performance at {metric} scale is: {performance}')
 
     return eval_metrics, evaluation(
         data,

carbonplan_forest_risks/prepare.py

@@ -39,7 +39,7 @@ def annualize(
     elif variable == 'cwd':
         aggregated = aggregated.max()
     else:
-        print('{} not implemented'.format(variable))
+        print(f'{variable} not implemented')
 
     # drop your first year if you were rolling
     if climate_prepend is not None:

carbonplan_forest_risks/utils.py

@@ -128,7 +128,7 @@ def weighted_mean(ds, *args, **kwargs):
 
 
 def get_store(bucket, prefix, account_key=None):
-    ''' helper function to create a zarr store'''
+    '''helper function to create a zarr store'''
 
     if account_key is None:
         account_key = os.environ.get('BLOB_ACCOUNT_KEY', None)

envs/python-notebook/environment.yml

@@ -2,7 +2,7 @@ name: carbonplan
 channels:
   - conda-forge
 dependencies:
-  - pangeo-notebook=2020.10.08  # don't bump until we bump the dask-gateway chart
+  - pangeo-notebook=2020.10.08 # don't bump until we bump the dask-gateway chart
   - adlfs
   - altair
   - altair_data_server
@@ -83,7 +83,7 @@ dependencies:
       - numbagg
       - showit
       - git+https://github.com/jhamman/scikit-downscale.git@a502557f322cf6a8cd2e34008b31f1b89b7e8190
-      - git+https://github.com/jhamman/zarr.git@fix/absstore  # for current version of azure api
-      - git+https://github.com/jhamman/climate_indices.git@39bbf038c77922f8f0a46bb69704d6aace4179f9  # for no-nco deps, expanded range of pdsi
-      - git+https://github.com/altair-viz/altair_data_server.git  # for remote hosting
+      - git+https://github.com/jhamman/zarr.git@fix/absstore # for current version of azure api
+      - git+https://github.com/jhamman/climate_indices.git@39bbf038c77922f8f0a46bb69704d6aace4179f9 # for no-nco deps, expanded range of pdsi
+      - git+https://github.com/altair-viz/altair_data_server.git # for remote hosting
       - git+https://github.com/carbonplan/cmip6-downscaling.git@e8cc4ad89ed3da47a1e46ccc441cdda8eebbc152

notebooks/biomass/biomass_model.ipynb

@@ -78,9 +78,7 @@
     "f = [df[inds][\"tmean_mean\"], df[inds][\"ppt_mean\"]]\n",
     "(\n",
     "    plot.xy(x=x, y=y, color=f[0], cmap=\"magma\", xlim=[0, 250], ylim=[0, 600])\n",
-    "    | plot.xy(\n",
-    "        x=x, y=y, color=f[1], cmap=\"viridis\", xlim=[0, 250], ylim=[0, 600]\n",
-    "    )\n",
+    "    | plot.xy(x=x, y=y, color=f[1], cmap=\"viridis\", xlim=[0, 250], ylim=[0, 600])\n",
     ").resolve_scale(color=\"independent\")"
    ]
   },
@@ -182,10 +180,7 @@
     "xlim = [0, 250]\n",
     "ylim = [-200, 700]\n",
     "(\n",
-    "    (\n",
-    "        plot.xy(x=x, y=y, xlim=xlim, ylim=ylim)\n",
-    "        + plot.line(x=x, y=model.predict(x, f, [50, 50]))\n",
-    "    )\n",
+    "    (plot.xy(x=x, y=y, xlim=xlim, ylim=ylim) + plot.line(x=x, y=model.predict(x, f, [50, 50])))\n",
     "    | (\n",
     "        plot.xy(x=x, y=model.sample(x, f), xlim=xlim, ylim=ylim)\n",
     "        + plot.line(x=x, y=model.predict(x, f, [50, 50]))\n",
@@ -222,10 +217,7 @@
     "xlim = [0, 250]\n",
     "ylim = [-200, 700]\n",
     "(\n",
-    "    (\n",
-    "        plot.xy(x=x, y=y, xlim=xlim, ylim=ylim)\n",
-    "        + plot.line(x=x, y=model.predict(x, f, [50, 50]))\n",
-    "    )\n",
+    "    (plot.xy(x=x, y=y, xlim=xlim, ylim=ylim) + plot.line(x=x, y=model.predict(x, f, [50, 50])))\n",
     "    | (\n",
     "        plot.xy(x=x, y=model.sample(x, f), xlim=xlim, ylim=ylim)\n",
     "        + plot.line(x=x, y=model.predict(x, f, [50, 50]))\n",

notebooks/drought/drought_results.ipynb

@@ -46,9 +46,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pf = pd.read_parquet(\n",
-    "    \"/Users/freeman/github/carbonplan/forests/scripts/data/drought.parquet\"\n",
-    ")"
+    "pf = pd.read_parquet(\"/Users/freeman/github/carbonplan/forests/scripts/data/drought.parquet\")"
    ]
   },
   {

notebooks/fire/fire_model.ipynb

@@ -81,9 +81,7 @@
    "outputs": [],
    "source": [
     "mask = load.nlcd(store=\"local\", classes=\"all\", year=2001)\n",
-    "groups = load.nftd(\n",
-    "    store=\"local\", groups=\"all\", coarsen=coarsen, mask=mask, area_threshold=1500\n",
-    ")"
+    "groups = load.nftd(store=\"local\", groups=\"all\", coarsen=coarsen, mask=mask, area_threshold=1500)"
    ]
   },
   {
@@ -101,9 +99,7 @@
    },
    "outputs": [],
    "source": [
-    "climate = load.terraclim(\n",
-    "    store=\"local\", tlim=tlim, coarsen=coarsen, data_vars=data_vars, mask=mask\n",
-    ")"
+    "climate = load.terraclim(store=\"local\", tlim=tlim, coarsen=coarsen, data_vars=data_vars, mask=mask)"
    ]
   },
   {
@@ -188,9 +184,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "r = rasterio.open(\n",
-    "    \"/Users/freeman/workdir/carbonplan-data/processed/mtbs/conus/30m/2006.tif\"\n",
-    ")"
+    "r = rasterio.open(\"/Users/freeman/workdir/carbonplan-data/processed/mtbs/conus/30m/2006.tif\")"
    ]
   },
   {
@@ -303,9 +297,7 @@
     "x = mtbs[\"time\"]\n",
     "y = mtbs[\"vlf\"].mean([\"x\", \"y\"])\n",
     "\n",
-    "plot.line(\n",
-    "    x=x, y=y, width=900, height=200, color=\"rgb(175,91,92)\", strokeWidth=2\n",
-    ")"
+    "plot.line(x=x, y=y, width=900, height=200, color=\"rgb(175,91,92)\", strokeWidth=2)"
    ]
   },
   {
@@ -468,9 +460,7 @@
     "        color=\"rgb(175,91,92)\",\n",
     "        strokeWidth=2,\n",
     "    )\n",
-    "    + plot.line(\n",
-    "        x=x, y=y2, width=900, height=200, color=\"rgb(175,91,92)\", strokeWidth=2\n",
-    "    )\n",
+    "    + plot.line(x=x, y=y2, width=900, height=200, color=\"rgb(175,91,92)\", strokeWidth=2)\n",
     ")"
    ]
   },