Merge branch 'main' into ctd-plot

.github/workflows/deploy-docs.yml

@@ -48,7 +48,7 @@ jobs:
 
     - name: Deploy
       if: success() && github.event_name == 'release'
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/build/html

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0
   hooks:
     - id: trailing-whitespace
     - id: check-ast
@@ -14,7 +14,7 @@ repos:
       files: requirements-dev.txt
 
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.8.0
+  rev: v1.10.0
   hooks:
   - id: mypy
     exclude: docs/source/conf.py
@@ -27,14 +27,14 @@ repos:
     - id: blackdoc
 
 - repo: https://github.com/econchick/interrogate
-  rev: 237be78f9c6135fc1a620d211cdfdc5d3885082b
+  rev: 1.7.0
   hooks:
     - id: interrogate
       exclude: ^(docs|tests)
       args: [--config=pyproject.toml]
 
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
     - id: codespell
       exclude: >
@@ -50,14 +50,14 @@ repos:
     - id: add-trailing-comma
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.3.0
+  rev: v0.4.7
   hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.1
+  rev: 1.8.5
   hooks:
     - id: nbqa-check-ast
     - id: nbqa-black
@@ -73,7 +73,7 @@ repos:
     - id: nb-strip-paths
 
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: 1.7.0
+  rev: 2.1.3
   hooks:
     - id: pyproject-fmt
 

gliderpy/__init__.py

@@ -5,13 +5,11 @@
 except ImportError:
     __version__ = "unknown"
 
-from .plotting import plot_track
-from .plotting import plot_transect
 from .fetchers import GliderDataFetcher
-
+from .plotting import plot_track, plot_transect
 
 __all__ = [
     "GliderDataFetcher",
     "plot_track",
     "plot_transect",
-]
+]

gliderpy/fetchers.py

@@ -47,7 +47,10 @@ def standardise_df(glider_df: pd.DataFrame, dataset_url: str) -> pd.DataFrame:
     glider_df.columns = glider_df.columns.str.lower()
     glider_df = glider_df.set_index("time (utc)")
     glider_df = glider_df.rename(columns=server_parameter_rename)
-    glider_df.index = pd.to_datetime(glider_df.index)
+    glider_df.index = pd.to_datetime(
+        glider_df.index,
+        format="%Y-%m-%dT%H:%M:%SZ",
+    )
     # We need to sort b/c of the non-sequential submission of files due to
     # the nature of glider data transmission.
     glider_df = glider_df.sort_index()

gliderpy/plotting.py

@@ -43,6 +43,7 @@ def plot_track(df: pd.DataFrame) -> tuple(plt.Figure, plt.Axes):
     ax.set_extent([x.min() - dx, x.max() + dx, y.min() - dy, y.max() + dy])
     return fig, ax
 
+
 @register_dataframe_method
 def plot_transect(
     df: pd.DataFrame,
@@ -82,6 +83,7 @@ def plot_transect(
     ax.set_ylabel("pressure")
     return fig, ax
 
+
 @register_dataframe_method
 def plot_ctd(
     df: pd.DataFrame,
@@ -118,4 +120,5 @@ def plot_ctd(
         lines2, labels2 = ax2.get_legend_handles_labels()
         ax.legend(lines + lines2, labels + labels2, loc="lower center")
 
-        return fig, ax2
+        return fig, ax2
+

pyproject.toml

@@ -2,19 +2,19 @@
 build-backend = "setuptools.build_meta"
 requires = [
   "setuptools>=42",
-  "setuptools_scm[toml]>=3.4",
+  "setuptools-scm[toml]>=3.4",
   "wheel",
 ]
 
 [project]
 name = "gliderpy"
 description = "Glider Data Fetcher"
 readme = "README.md"
-license = {file = "LICENSE.txt"}
+license = { file = "LICENSE.txt" }
 maintainers = [
-    {name = "Callum Rollo", email = "[email protected]"},
-    {name = "Lindsay Abrams"},
-    {name = "Filipe Fernandes"},
+  { name = "Callum Rollo", email = "[email protected]" },
+  { name = "Lindsay Abrams" },
+  { name = "Filipe Fernandes" },
 ]
 requires-python = ">=3.10"
 classifiers = [
@@ -27,18 +27,21 @@ dynamic = [
   "dependencies",
   "version",
 ]
-[project.urls]
-documentation = "https://ioos.github.io/gliderpy"
-homepage = "https://github.com/ioos/gliderpy"
-repository = "https://github.com/ioos/gliderpy"
+urls.documentation = "https://ioos.github.io/gliderpy"
+urls.homepage = "https://github.com/ioos/gliderpy"
+urls.repository = "https://github.com/ioos/gliderpy"
 
 [tool.setuptools]
-packages = ["gliderpy"]
+packages = [
+  "gliderpy",
+]
 include-package-data = true
 
 [tool.setuptools.dynamic]
-dependencies = {file = ["requirements.txt"]}
-readme = {file = "README.md", content-type = "text/markdown"}
+dependencies = { file = [
+  "requirements.txt",
+] }
+readme = { file = "README.md", content-type = "text/markdown" }
 
 [tool.setuptools_scm]
 write_to = "gliderpy/_version.py"
@@ -60,9 +63,9 @@ ignore = [
 
 [tool.pytest.ini_options]
 filterwarnings = [
-    "error:::gliderpy.*",
-    "ignore::UserWarning",
-    "ignore::RuntimeWarning",
+  "error:::gliderpy.*",
+  "ignore::UserWarning",
+  "ignore::RuntimeWarning",
 ]
 
 [tool.interrogate]
@@ -73,7 +76,11 @@ ignore-semiprivate = false
 ignore-private = false
 ignore-module = false
 fail-under = 95
-exclude = ["setup.py", "docs", "tests"]
+exclude = [
+  "setup.py",
+  "docs",
+  "tests",
+]
 verbose = 1
 quiet = false
 color = true

tests/test_plotting.py

@@ -1,16 +1,18 @@
 """Test transect."""
 
-import pytest
-import matplotlib as mpl
 from pathlib import Path
-from gliderpy.plotting import plot_track
-from gliderpy.plotting import plot_transect
+
+import pytest
+
 from gliderpy.fetchers import GliderDataFetcher
+from gliderpy.plotting import plot_track, plot_transect
 
 root = Path(__file__).parent
 
+
 @pytest.mark.mpl_image_compare(baseline_dir=root.joinpath("baseline/"))
 def test_plot_track():
+    """Image comparison test for plot_track."""
     glider_grab = GliderDataFetcher()
 
     glider_grab.fetcher.dataset_id = "whoi_406-20160902T1700"
@@ -22,15 +24,15 @@ def test_plot_track():
     return fig
 
 
-
 @pytest.mark.mpl_image_compare(baseline_dir=root.joinpath("baseline/"))
 def test_plot_transect():
+    """Image comparison test for plot_transect."""
     glider_grab = GliderDataFetcher()
 
     glider_grab.fetcher.dataset_id = "whoi_406-20160902T1700"
     df = glider_grab.to_pandas()
     # Generate the plot
-    fig, ax = plot_transect(df, 'temperature')
+    fig, ax = plot_transect(df, "temperature")
 
     # Return the figure for pytest-mpl to compare
     return fig