Add noxfile for routine project maintenance (landlab#1469)

* add a nox config file

* add nox as a dev requirement

* use nox for docs and lint workflows

* remove old make_changelog.py script

* remove lint from previously unlinted files

* add news fragment

* update black to 22.6.0 for pre-commit

* remove .so files when cleaning

* add towncrier folder for building docs

* add sphinx-jinja as a doc requirement

* style notebooks for black

* disable towncrier for linting; it's done elsewhere

.github/workflows/docs.yml

@@ -30,10 +30,9 @@ jobs:
           - name: Show conda installation info
             run: |
               conda info
-              conda list
     
           - name: Install dependencies
-            run: pip install -e ".[docs]"
+            run: pip install nox
 
           - name: Build documentation
-            run: make -C docs clean html
+            run: nox -s docs

.github/workflows/flake8.yml

@@ -23,5 +23,5 @@ jobs:
 
       - name: Lint
         run: |
-          pip install flake8
-          flake8 landlab tests
+          pip install nox
+          nox -s lint

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.1.0
+  rev: 22.6.0
   hooks:
   - id: black
     name: black

docs/build_func_lists.py

@@ -19,7 +19,6 @@
 
 '''
 """
-import re
 from copy import copy
 
 import numpy as np

docs/build_grid_func_docs.py

@@ -19,7 +19,6 @@
 Any changes made directly to the above files will be lost whenever this script
 is run.
 """
-import re
 from copy import copy
 
 import numpy as np

docs/fix_redirects.py

@@ -8,7 +8,7 @@
 with open("build/linkcheck/output.txt", "r") as f:
     link_out = f.readlines()
 
-#%%
+
 for link in link_out:
     if "redirected" in link:
         file_name = os.path.join(_SRC, link.split(":")[0])

docs/landlab_ext.py

@@ -27,7 +27,6 @@ class LandlabLexer(RegexLexer):
 
 
 def doctree_read(app, doctree):
-    env = app.builder.env
     for node in doctree.traverse(addnodes.productionlist):
         for production in node:
             if not isinstance(production, addnodes.production):

docs/source/conf.py

@@ -13,21 +13,12 @@
 
 import os
 import pathlib
-import sys
 from datetime import date
 
 import landlab
 
 docs_dir = os.path.dirname(__file__)
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__),
-#                                                 os.pardir)))
-sys.path.insert(0, os.path.abspath("../.."))
-sys.path.insert(0, os.path.abspath(".."))
-sys.path.insert(0, ".")
 
 # -- General configuration -----------------------------------------------------
 
@@ -44,6 +35,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.autosummary",
     "sphinxcontrib.towncrier",
+    "sphinx_jinja",
 ]
 
 if os.getenv("READTHEDOCS"):
@@ -370,4 +362,5 @@
 
 towncrier_draft_autoversion_mode = "draft"  # or: 'sphinx-release', 'sphinx-version'
 towncrier_draft_include_empty = True
-towncrier_draft_working_directory = pathlib.Path(docs_dir).parent.parent
+# towncrier_draft_working_directory = pathlib.Path(docs_dir).parent.parent
+towncrier_draft_working_directory = pathlib.Path(docs_dir).parent / "towncrier"

docs/towncrier/news

@@ -0,0 +1 @@
+../../news

docs/towncrier/pyproject.toml

@@ -0,0 +1 @@
+../../pyproject.toml

news/1469.misc

@@ -0,0 +1,3 @@
+Added a *nox* file to help with routine project maintenance tasks like, for
+example, running the tests, and checking for coding style.
+

notebooks/conftest.py

@@ -1,4 +1,3 @@
-import os
 import pathlib
 
 import pytest

notebooks/teaching/geomorphology_exercises/channels_streampower_notebooks/stream_power_channels_class_notebook.ipynb

@@ -333,7 +333,7 @@
     "    mg1,\n",
     "    number_of_watersheds=3,\n",
     "    main_channel_only=True,\n",
-    "    minimum_channel_threshold=dxy ** 2,\n",
+    "    minimum_channel_threshold=dxy**2,\n",
     ")\n",
     "prf.run_one_step()\n",
     "\n",
@@ -702,7 +702,7 @@
     "    mg2,\n",
     "    number_of_watersheds=3,\n",
     "    main_channel_only=True,\n",
-    "    minimum_channel_threshold=dxy ** 2,\n",
+    "    minimum_channel_threshold=dxy**2,\n",
     ")\n",
     "prf2.run_one_step()\n",
     "\n",

notebooks/teaching/surface_water_hydrology_exercises/overland_flow_notebooks/hydrograph_class_notebook.ipynb

@@ -179,15 +179,15 @@
     "## Assign storm conditions based on flag in Code Block 2\n",
     "if storm_flag == \"Base\":\n",
     "    starting_precip_mmhr = 5.0\n",
-    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10 ** -7)\n",
+    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10**-7)\n",
     "    storm_duration = 7200.0\n",
     "elif storm_flag == \"HigherIntensity\":\n",
     "    starting_precip_mmhr = 10.0\n",
-    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10 ** -7)\n",
+    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10**-7)\n",
     "    storm_duration = 3600.0\n",
     "elif storm_flag == \"LongerDuration\":\n",
     "    starting_precip_mmhr = 2.5\n",
-    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10 ** -7)\n",
+    "    starting_precip_ms = starting_precip_mmhr * (2.77778 * 10**-7)\n",
     "    storm_duration = 14400.0"
    ]
   },

notebooks/tutorials/agent_based_modeling/wolf_sheep/wolf_sheep_with_soil_creep.ipynb

@@ -216,7 +216,7 @@
     "\n",
     "            # Death\n",
     "            if self.energy < 0:\n",
-    "                #self.model.grid._remove_agent(self.pos, self)\n",
+    "                # self.model.grid._remove_agent(self.pos, self)\n",
     "                self.model.grid.remove_agent(self)\n",
     "                self.model.schedule.remove(self)\n",
     "                living = False\n",
@@ -256,13 +256,13 @@
     "            self.energy += self.model.wolf_gain_from_food\n",
     "\n",
     "            # Kill the sheep\n",
-    "            #self.model.grid._remove_agent(self.pos, sheep_to_eat)\n",
+    "            # self.model.grid._remove_agent(self.pos, sheep_to_eat)\n",
     "            self.model.grid.remove_agent(sheep_to_eat)\n",
     "            self.model.schedule.remove(sheep_to_eat)\n",
     "\n",
     "        # Death or reproduction\n",
     "        if self.energy < 0:\n",
-    "            #self.model.grid._remove_agent(self.pos, self)\n",
+    "            # self.model.grid._remove_agent(self.pos, self)\n",
     "            self.model.grid.remove_agent(self)\n",
     "            self.model.schedule.remove(self)\n",
     "        else:\n",

notebooks/tutorials/data_record/DataRecord_tutorial.ipynb

@@ -531,11 +531,11 @@
     "    for i in range(0, dr_3.number_of_items):\n",
     "        # value of block erodibility:\n",
     "        if dr_3.dataset[\"boulder_litho\"].values[i] == \"limestone\":\n",
-    "            k_b = 10 ** -5\n",
+    "            k_b = 10**-5\n",
     "        elif dr_3.dataset[\"boulder_litho\"].values[i] == \"sandstone\":\n",
-    "            k_b = 3 * 10 ** -6\n",
+    "            k_b = 3 * 10**-6\n",
     "        elif dr_3.dataset[\"boulder_litho\"].values[i] == \"granite\":\n",
-    "            k_b = 3 * 10 ** -7\n",
+    "            k_b = 3 * 10**-7\n",
     "        else:\n",
     "            print(\"Unknown boulder lithology\")\n",
     "\n",

notebooks/tutorials/flow_direction_and_accumulation/compare_FlowDirectors.ipynb

@@ -147,7 +147,7 @@
     "mg3 = RasterModelGrid((10, 10))\n",
     "_ = mg3.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3.x_of_node ** 2 + mg3.y_of_node ** 2 + mg3.y_of_node,\n",
+    "    mg3.x_of_node**2 + mg3.y_of_node**2 + mg3.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "surf_plot(mg3, title=\"Grid 3: A more complicated surface\")"
@@ -448,7 +448,7 @@
     "mg3a = RasterModelGrid((10, 10))\n",
     "_ = mg3a.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3a.x_of_node ** 2 + mg3a.y_of_node ** 2 + mg3a.y_of_node,\n",
+    "    mg3a.x_of_node**2 + mg3a.y_of_node**2 + mg3a.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -476,7 +476,7 @@
     "mg3b = RasterModelGrid((10, 10))\n",
     "_ = mg3b.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3b.x_of_node ** 2 + mg3b.y_of_node ** 2 + mg3b.y_of_node,\n",
+    "    mg3b.x_of_node**2 + mg3b.y_of_node**2 + mg3b.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -504,7 +504,7 @@
     "mg3c = RasterModelGrid((10, 10))\n",
     "_ = mg3c.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3c.x_of_node ** 2 + mg3c.y_of_node ** 2 + mg3c.y_of_node,\n",
+    "    mg3c.x_of_node**2 + mg3c.y_of_node**2 + mg3c.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -530,7 +530,7 @@
     "mg3d = RasterModelGrid((10, 10))\n",
     "_ = mg3d.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3d.x_of_node ** 2 + mg3d.y_of_node ** 2 + mg3d.y_of_node,\n",
+    "    mg3d.x_of_node**2 + mg3d.y_of_node**2 + mg3d.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -556,7 +556,7 @@
     "mg3e = RasterModelGrid((10, 10))\n",
     "_ = mg3e.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3e.x_of_node ** 2 + mg3e.y_of_node ** 2 + mg3e.y_of_node,\n",
+    "    mg3e.x_of_node**2 + mg3e.y_of_node**2 + mg3e.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -592,7 +592,7 @@
     "mg3 = RasterModelGrid((10, 10))\n",
     "_ = mg3.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3.x_of_node ** 2 + mg3.y_of_node ** 2 + mg3.y_of_node,\n",
+    "    mg3.x_of_node**2 + mg3.y_of_node**2 + mg3.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -639,7 +639,7 @@
     "mg3 = RasterModelGrid((10, 10))\n",
     "_ = mg3.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3.x_of_node ** 2 + mg3.y_of_node ** 2 + mg3.y_of_node,\n",
+    "    mg3.x_of_node**2 + mg3.y_of_node**2 + mg3.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -669,7 +669,7 @@
     "mg3 = RasterModelGrid((10, 10))\n",
     "_ = mg3.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3.x_of_node ** 2 + mg3.y_of_node ** 2 + mg3.y_of_node,\n",
+    "    mg3.x_of_node**2 + mg3.y_of_node**2 + mg3.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",
@@ -697,7 +697,7 @@
     "mg3 = RasterModelGrid((10, 10))\n",
     "_ = mg3.add_field(\n",
     "    \"topographic__elevation\",\n",
-    "    mg3.x_of_node ** 2 + mg3.y_of_node ** 2 + mg3.y_of_node,\n",
+    "    mg3.x_of_node**2 + mg3.y_of_node**2 + mg3.y_of_node,\n",
     "    at=\"node\",\n",
     ")\n",
     "\n",

notebooks/tutorials/flow_direction_and_accumulation/the_FlowAccumulator.ipynb

@@ -110,7 +110,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "surf_plot(mg, title=\"Grid 1\")"
    ]

notebooks/tutorials/flow_direction_and_accumulation/the_Flow_Director_Accumulator_PriorityFlood.ipynb

@@ -91,7 +91,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "surf_plot(mg, title=\"Grid 1\")"
    ]
@@ -305,7 +305,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"D4\")\n",
     "fa.run_one_step()\n",
@@ -328,7 +328,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Rho8\")\n",
     "fa.run_one_step()\n",
@@ -351,7 +351,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Rho4\")\n",
     "fa.run_one_step()\n",
@@ -374,7 +374,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Quinn\")\n",
     "fa.run_one_step()\n",
@@ -397,9 +397,11 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
+    ")\n",
+    "fa = PriorityFloodFlowRouter(\n",
+    "    mg, surface=\"topographic__elevation\", flow_metric=\"Freeman\"\n",
     ")\n",
-    "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Freeman\")\n",
     "fa.run_one_step()\n",
     "plt.figure()\n",
     "drainage_plot(mg, \"surface_water__discharge\", title=\"Discharge\")"
@@ -420,9 +422,11 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
+    ")\n",
+    "fa = PriorityFloodFlowRouter(\n",
+    "    mg, surface=\"topographic__elevation\", flow_metric=\"Holmgren\"\n",
     ")\n",
-    "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Holmgren\")\n",
     "fa.run_one_step()\n",
     "plt.figure()\n",
     "drainage_plot(mg, \"surface_water__discharge\", title=\"Discharge\")"
@@ -443,7 +447,7 @@
    "source": [
     "mg = RasterModelGrid((10, 10))\n",
     "_ = mg.add_field(\n",
-    "    \"topographic__elevation\", 3.0 * mg.x_of_node ** 2 + mg.y_of_node ** 2, at=\"node\"\n",
+    "    \"topographic__elevation\", 3.0 * mg.x_of_node**2 + mg.y_of_node**2, at=\"node\"\n",
     ")\n",
     "fa = PriorityFloodFlowRouter(mg, surface=\"topographic__elevation\", flow_metric=\"Dinf\")\n",
     "fa.run_one_step()\n",