Merge pull request #73 from ocefpaf/modernize

Modernize
ioos · Oct 22, 2024 · d1f1e36 · d1f1e36
2 parents dcbf42a + 1840f1f
commit d1f1e36
Show file tree

Hide file tree

Showing 16 changed files with 249 additions and 210 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -10,8 +10,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        os: [windows-latest, ubuntu-latest, macos-latest]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
       fail-fast: false
 
     steps:
@@ -23,7 +23,7 @@ jobs:
         environment-name: TEST
         init-shell: bash
         create-args: >-
-          python=3 pip
+          python=${{ matrix.python-version }} pip
           --file requirements.txt
           --file requirements-dev.txt
           --channel conda-forge

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,26 +13,6 @@ repos:
     - id: file-contents-sorter
       files: requirements-dev.txt
 
-- repo: https://github.com/PyCQA/flake8
-  rev: 7.1.1
-  hooks:
-    - id: flake8
-      exclude: docs/source/conf.py
-      args: [--max-line-length=105]
-
-- repo: https://github.com/pycqa/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-      additional_dependencies: [toml]
-      args: ["--profile", "black", "--filter-files"]
-
-- repo: https://github.com/psf/black
-  rev: 24.10.0
-  hooks:
-  - id: black
-    language_version: python3
-
 - repo: https://github.com/keewis/blackdoc
   rev: v0.3.9
   hooks:
@@ -56,23 +36,39 @@ repos:
       args:
         - --quiet-level=2
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.17.0
-  hooks:
-    - id: pyupgrade
-      args:
-        - --py36-plus
-
 - repo: https://github.com/asottile/add-trailing-comma
   rev: v3.1.0
   hooks:
     - id: add-trailing-comma
 
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.3.0
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.7.0
+  hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 1.8.7
+  hooks:
+    - id: nbqa-check-ast
+    - id: nbqa-black
+    - id: nbqa-ruff
+      args: [
+        --fix,
+        --config=ruff.toml,
+        ]
+
+- repo: https://github.com/bdice/nb-strip-paths
+  rev: v0.1.0
+  hooks:
+    - id: nb-strip-paths
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: 2.4.3
   hooks:
-    - id: pydocstyle
-      exclude: ^(docs|setup.py)
+    - id: pyproject-fmt
 
 ci:
     autofix_commit_msg: |

diff --git a/notebooks/ocean_s_coordinate.ipynb b/notebooks/ocean_s_coordinate.ipynb
@@ -21,6 +21,7 @@
    "outputs": [],
    "source": [
     "from netCDF4 import Dataset\n",
+    "\n",
     "from odvc.parse_formula_terms import get_formula_terms_variables\n",
     "\n",
     "nc = Dataset(url)\n",
@@ -117,8 +118,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "salt = nc.get_variables_by_attributes(long_name=\"averaged salinity\")[0]\n",
-    "temp = nc.get_variables_by_attributes(long_name=\"averaged potential temperature\")[0]\n",
+    "salt = nc.get_variables_by_attributes(\n",
+    "    long_name=\"averaged salinity\",\n",
+    ")[0]\n",
+    "temp = nc.get_variables_by_attributes(\n",
+    "    long_name=\"averaged potential temperature\",\n",
+    ")[0]\n",
     "\n",
     "s = salt[-1, :, 45, 137]\n",
     "t = temp[-1, :, 45, 137]\n",
@@ -134,7 +139,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "import mpl_toolkits.axisartist as AA\n",
+    "from mpl_toolkits import axisartist\n",
     "from mpl_toolkits.axes_grid1 import host_subplot\n",
     "\n",
     "\n",
@@ -145,7 +150,7 @@
     "\n",
     "fig = plt.figure(figsize=(6, 9))\n",
     "fig.subplots_adjust(bottom=0.1, top=0.85)\n",
-    "ax0 = host_subplot(111, axes_class=AA.Axes)\n",
+    "ax0 = host_subplot(111, axes_class=axisartist.Axes)\n",
     "\n",
     "ax0.invert_yaxis()\n",
     "ax1 = ax0.twiny()\n",
@@ -163,7 +168,7 @@
     "ax0.set_xlabel(\"Temperature (\\xb0C)\")\n",
     "ax1.set_xlabel(r\"Salinity (g kg$^{-1}$)\")\n",
     "\n",
-    "kw = dict(linewidth=2.5)\n",
+    "kw = {\"linewidth\": 2.5}\n",
     "(l0,) = ax0.plot(t, -p, **kw)\n",
     "(l1,) = ax1.plot(s, -p, **kw)\n",
     "\n",
@@ -191,7 +196,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/ocean_s_coordinate_g1.ipynb b/notebooks/ocean_s_coordinate_g1.ipynb
@@ -23,6 +23,7 @@
    "outputs": [],
    "source": [
     "from netCDF4 import Dataset\n",
+    "\n",
     "from odvc.parse_formula_terms import get_formula_terms_variables\n",
     "\n",
     "nc = Dataset(url)\n",
@@ -102,7 +103,11 @@
     "from odvc import ocean_s_coordinate_g1\n",
     "\n",
     "z = ocean_s_coordinate_g1(\n",
-    "    arrays[\"s\"], arrays[\"C\"], arrays[\"eta\"], arrays[\"depth\"], arrays[\"depth_c\"]\n",
+    "    arrays[\"s\"],\n",
+    "    arrays[\"C\"],\n",
+    "    arrays[\"eta\"],\n",
+    "    arrays[\"depth\"],\n",
+    "    arrays[\"depth_c\"],\n",
     ")\n",
     "\n",
     "print(z.shape)"
@@ -114,10 +119,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "salt = nc.get_variables_by_attributes(standard_name=\"sea_water_salinity\")[0]\n",
-    "temp = nc.get_variables_by_attributes(standard_name=\"sea_water_potential_temperature\")[\n",
-    "    0\n",
-    "]\n",
+    "salt = nc.get_variables_by_attributes(\n",
+    "    standard_name=\"sea_water_salinity\",\n",
+    ")[0]\n",
+    "temp = nc.get_variables_by_attributes(\n",
+    "    standard_name=\"sea_water_potential_temperature\",\n",
+    ")[0]\n",
     "\n",
     "s = salt[-1, :, 5, 364]\n",
     "t = temp[-1, :, 5, 364]\n",
@@ -133,12 +140,9 @@
     "%matplotlib inline\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
-    "import mpl_toolkits.axisartist as AA\n",
-    "import seaborn\n",
+    "from mpl_toolkits import axisartist\n",
     "from mpl_toolkits.axes_grid1 import host_subplot\n",
     "\n",
-    "seaborn.set(style=\"ticks\")\n",
-    "\n",
     "\n",
     "def adjust_xlim(ax, offset):\n",
     "    x1, x2 = ax.get_xlim()\n",
@@ -147,7 +151,7 @@
     "\n",
     "fig = plt.figure(figsize=(6, 9))\n",
     "fig.subplots_adjust(bottom=0.1, top=0.85)\n",
-    "ax0 = host_subplot(111, axes_class=AA.Axes)\n",
+    "ax0 = host_subplot(111, axes_class=axisartist.Axes)\n",
     "\n",
     "ax0.invert_yaxis()\n",
     "ax1 = ax0.twiny()\n",
@@ -165,7 +169,7 @@
     "ax0.set_xlabel(\"Temperature (\\xb0C)\")\n",
     "ax1.set_xlabel(r\"Salinity (g kg$^{-1}$)\")\n",
     "\n",
-    "kw = dict(linewidth=2.5)\n",
+    "kw = {\"linewidth\": 2.5}\n",
     "(l0,) = ax0.plot(t, -p, **kw)\n",
     "(l1,) = ax1.plot(s, -p, **kw)\n",
     "\n",
@@ -193,7 +197,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/ocean_s_coordinate_g2.ipynb b/notebooks/ocean_s_coordinate_g2.ipynb
@@ -24,6 +24,7 @@
    "outputs": [],
    "source": [
     "from netCDF4 import Dataset\n",
+    "\n",
     "from odvc.parse_formula_terms import get_formula_terms_variables\n",
     "\n",
     "nc = Dataset(url)\n",
@@ -103,7 +104,11 @@
     "from odvc import ocean_s_coordinate_g1\n",
     "\n",
     "z = ocean_s_coordinate_g1(\n",
-    "    arrays[\"s\"], arrays[\"C\"], arrays[\"eta\"], arrays[\"depth\"], arrays[\"depth_c\"]\n",
+    "    arrays[\"s\"],\n",
+    "    arrays[\"C\"],\n",
+    "    arrays[\"eta\"],\n",
+    "    arrays[\"depth\"],\n",
+    "    arrays[\"depth_c\"],\n",
     ")\n",
     "\n",
     "print(z.shape)"
@@ -130,7 +135,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "import mpl_toolkits.axisartist as AA\n",
+    "from mpl_toolkits import axisartist\n",
     "from mpl_toolkits.axes_grid1 import host_subplot\n",
     "\n",
     "\n",
@@ -141,7 +146,7 @@
     "\n",
     "fig = plt.figure(figsize=(6, 9))\n",
     "fig.subplots_adjust(bottom=0.1, top=0.85)\n",
-    "ax0 = host_subplot(111, axes_class=AA.Axes)\n",
+    "ax0 = host_subplot(111, axes_class=axisartist.Axes)\n",
     "\n",
     "ax0.invert_yaxis()\n",
     "ax1 = ax0.twiny()\n",
@@ -159,7 +164,7 @@
     "ax0.set_xlabel(\"Temperature (\\xb0C)\")\n",
     "ax1.set_xlabel(r\"Salinity (g kg$^{-1}$)\")\n",
     "\n",
-    "kw = dict(linewidth=2.5)\n",
+    "kw = {\"linewidth\": 2.5}\n",
     "(l0,) = ax0.plot(t, -p, **kw)\n",
     "(l1,) = ax1.plot(s, -p, **kw)\n",
     "\n",
@@ -187,7 +192,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/ocean_sigma_coordinate-FVCOM.ipynb b/notebooks/ocean_sigma_coordinate-FVCOM.ipynb
@@ -24,6 +24,7 @@
    "outputs": [],
    "source": [
     "from netCDF4 import Dataset\n",
+    "\n",
     "from odvc.parse_formula_terms import get_formula_terms_variables\n",
     "\n",
     "nc = Dataset(url)\n",
@@ -103,10 +104,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "salt = nc.get_variables_by_attributes(standard_name=\"sea_water_salinity\")[0]\n",
-    "temp = nc.get_variables_by_attributes(standard_name=\"sea_water_potential_temperature\")[\n",
-    "    0\n",
-    "]\n",
+    "salt = nc.get_variables_by_attributes(\n",
+    "    standard_name=\"sea_water_salinity\",\n",
+    ")[0]\n",
+    "temp = nc.get_variables_by_attributes(\n",
+    "    standard_name=\"sea_water_potential_temperature\",\n",
+    ")[0]\n",
     "\n",
     "s = salt[-1, :, 175]\n",
     "t = temp[-1, :, 175]\n",
@@ -120,7 +123,7 @@
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
-    "import mpl_toolkits.axisartist as AA\n",
+    "from mpl_toolkits import axisartist\n",
     "from mpl_toolkits.axes_grid1 import host_subplot\n",
     "\n",
     "\n",
@@ -131,7 +134,7 @@
     "\n",
     "fig = plt.figure(figsize=(6, 9))\n",
     "fig.subplots_adjust(bottom=0.1, top=0.85)\n",
-    "ax0 = host_subplot(111, axes_class=AA.Axes)\n",
+    "ax0 = host_subplot(111, axes_class=axisartist.Axes)\n",
     "\n",
     "ax0.invert_yaxis()\n",
     "ax1 = ax0.twiny()\n",
@@ -149,7 +152,7 @@
     "ax0.set_xlabel(\"Temperature (\\xb0C)\")\n",
     "ax1.set_xlabel(r\"Salinity (g kg$^{-1}$)\")\n",
     "\n",
-    "kw = dict(linewidth=2.5)\n",
+    "kw = {\"linewidth\": 2.5}\n",
     "(l0,) = ax0.plot(t, -p, **kw)\n",
     "(l1,) = ax1.plot(s, -p, **kw)\n",
     "\n",
@@ -177,7 +180,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.7"
   }
  },
  "nbformat": 4,