Make matplotlib dependency optional (#1131)

* Make matplotlib dependency optional

* Add dep for docs

* Improve testing.

* Auto-format.

Author: delucchi-cmu

.github/workflows/smoke-test.yml

@@ -30,14 +30,23 @@ jobs:
     - name: Install dependencies
       run: |
         sudo apt-get update
-        uv pip install --system -e .[dev,full]
+        uv pip install --system -e .[dev]
         if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - name: List dependencies
       run: |
         pip list
     - name: Run unit tests with pytest
       run: |
         python -m pytest
+    - name: Install FULL dependencies
+      run: |
+        uv pip install --system -e .[full]
+    - name: List FULL dependencies
+      run: |
+        pip list
+    - name: Run FULL unit tests with pytest
+      run: |
+        python -m pytest
     - name: Send status to Slack app
       if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
       id: slack

.setup_dev.sh

@@ -41,6 +41,8 @@ python -m pip install -e . > /dev/null
 
 echo "Installing developer dependencies in local environment"
 python -m pip install -e .'[dev]' > /dev/null
+python -m pip install -e .'[full]' > /dev/null
+if [ -f requirements.txt ]; then python -m pip install -r requirements.txt > /dev/null; fi
 if [ -f docs/requirements.txt ]; then python -m pip install -r docs/requirements.txt > /dev/null; fi
 
 echo "Installing pre-commit"

docs/requirements.txt

@@ -4,6 +4,7 @@ ipython
 ipywidgets
 jupytext
 lsst-sphgeom
+matplotlib
 nbconvert
 nbsphinx
 sphinx

pyproject.toml

@@ -52,6 +52,7 @@ full = [
     "ipykernel", # Support for Jupyter notebooks
     "ipywidgets", # useful for tqdm in notebooks.
     "lsst-sphgeom ; sys_platform == 'darwin' or sys_platform == 'linux'", # To handle spherical sky polygons, not available on Windows
+    "matplotlib",
 ]
 
 [build-system]
@@ -65,9 +66,6 @@ build-backend = "setuptools.build_meta"
 write_to = "src/lsdb/_version.py"
 
 [tool.pytest.ini_options]
-markers = [
-    "sphgeom: mark tests as having a runtime dependency on lsst-sphgeom",
-]
 testpaths = [
     "tests",
     "src",

src/lsdb/catalog/dataset/healpix_dataset.py

@@ -5,7 +5,7 @@
 import warnings
 from collections.abc import Sequence
 from pathlib import Path
-from typing import Callable, Iterable, Type
+from typing import TYPE_CHECKING, Callable, Iterable, Type
 
 import astropy
 import dask
@@ -15,15 +15,11 @@
 import pandas as pd
 from astropy.coordinates import SkyCoord
 from astropy.units import Quantity
-from astropy.visualization.wcsaxes import WCSAxes
-from astropy.visualization.wcsaxes.frame import BaseFrame
 from dask.dataframe.core import _repr_data_series
 from deprecated import deprecated  # type: ignore
 from hats.catalog.healpix_dataset.healpix_dataset import HealpixDataset as HCHealpixDataset
-from hats.inspection.visualize_catalog import get_fov_moc_from_wcs, initialize_wcs_axes
 from hats.pixel_math import HealpixPixel
 from hats.pixel_math.healpix_pixel_function import get_pixel_argsort
-from matplotlib.figure import Figure
 from mocpy import MOC
 from pandas._typing import Renamer
 from typing_extensions import Self
@@ -48,6 +44,11 @@
 from lsdb.loaders.hats.hats_loading_config import HatsLoadingConfig
 from lsdb.types import DaskDFPixelMap
 
+if TYPE_CHECKING:
+    from astropy.visualization.wcsaxes import WCSAxes
+    from astropy.visualization.wcsaxes.frame import BaseFrame
+    from matplotlib.figure import Figure
+
 
 # pylint: disable=protected-access,too-many-public-methods,too-many-lines,import-outside-toplevel,cyclic-import
 class HealpixDataset(Dataset):
@@ -1376,7 +1377,16 @@ def plot_points(
         tuple[Figure, WCSAxes]
             The figure and axes used for the plot
         """
-        fig, ax, wcs = initialize_wcs_axes(
+        try:
+            # pylint: disable=import-outside-toplevel
+            from hats.inspection._plotting import _get_fov_moc_from_wcs, _initialize_wcs_axes
+            from matplotlib import pyplot as plt  # pylint: disable=unused-import
+        except ImportError as exc:
+            raise ImportError(
+                "matplotlib is required to use this method. Install with pip or conda."
+            ) from exc
+
+        fig, ax, wcs = _initialize_wcs_axes(
             projection=projection,
             fov=fov,
             center=center,
@@ -1387,7 +1397,7 @@ def plot_points(
             figsize=(9, 5),
         )
 
-        fov_moc = get_fov_moc_from_wcs(wcs)
+        fov_moc = _get_fov_moc_from_wcs(wcs)
 
         computed_catalog = (
             self.search(MOCSearch(fov_moc)).compute() if fov_moc is not None else self.compute()

src/lsdb/core/plotting/plot_points.py

@@ -1,17 +1,16 @@
 from __future__ import annotations
 
-from typing import Type
+from typing import TYPE_CHECKING, Type
 
 import astropy
-import matplotlib.pyplot as plt
 import pandas as pd
 from astropy.coordinates import SkyCoord
 from astropy.units import Quantity
-from astropy.visualization.wcsaxes import WCSAxes
-from astropy.visualization.wcsaxes.frame import BaseFrame
-from hats.inspection.visualize_catalog import initialize_wcs_axes
-from matplotlib.figure import Figure
-from mocpy.moc.plot.utils import _set_wcs
+
+if TYPE_CHECKING:
+    from astropy.visualization.wcsaxes import WCSAxes
+    from astropy.visualization.wcsaxes.frame import BaseFrame
+    from matplotlib.figure import Figure
 
 
 def plot_points(
@@ -81,7 +80,16 @@ def plot_points(
     tuple[Figure, WCSAxes]
         The figure and axes used for the plot
     """
-    fig, ax, wcs = initialize_wcs_axes(
+
+    try:
+        # pylint: disable=import-outside-toplevel
+        from hats.inspection.visualize_catalog import _initialize_wcs_axes
+        from matplotlib import pyplot as plt
+        from mocpy.moc.plot.utils import _set_wcs
+    except ImportError as exc:
+        raise ImportError("matplotlib is required to use this method. Install with pip or conda.") from exc
+
+    fig, ax, wcs = _initialize_wcs_axes(
         projection=projection,
         fov=fov,
         center=center,

src/lsdb/core/search/abstract_search.py

@@ -7,14 +7,13 @@
 import nested_pandas as npd
 from astropy.coordinates import SkyCoord
 from astropy.units import Quantity
-from astropy.visualization.wcsaxes import WCSAxes
-from astropy.visualization.wcsaxes.frame import BaseFrame
 from hats.catalog import TableProperties
-from hats.inspection.visualize_catalog import initialize_wcs_axes
-from matplotlib import pyplot as plt
-from matplotlib.figure import Figure
 
 if TYPE_CHECKING:
+    from astropy.visualization.wcsaxes import WCSAxes
+    from astropy.visualization.wcsaxes.frame import BaseFrame
+    from matplotlib.figure import Figure
+
     from lsdb.types import HCCatalogTypeVar
 
 
@@ -135,7 +134,16 @@ def plot(
         tuple[Figure, WCSAxes]
             The figure and axes used for the plot
         """
-        fig, ax, wcs = initialize_wcs_axes(
+        try:
+            # pylint: disable=import-outside-toplevel
+            from hats.inspection._plotting import _initialize_wcs_axes
+            from matplotlib import pyplot as plt
+        except ImportError as exc:
+            raise ImportError(
+                "matplotlib is required to use this method. Install with pip or conda."
+            ) from exc
+
+        fig, ax, wcs = _initialize_wcs_axes(
             projection=projection,
             fov=fov,
             center=center,

src/lsdb/core/search/region_search.py

@@ -1,9 +1,10 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import astropy.units as u
 import nested_pandas as npd
 import pandas as pd
-from astropy.visualization.wcsaxes import SphericalCircle, WCSAxes
 from hats.catalog import TableProperties
 from hats.pixel_math import HealpixPixel, get_healpix_pixel, spatial_index
 from hats.pixel_math.region_to_moc import wrap_ra_angles
@@ -24,6 +25,9 @@
 from lsdb.core.search.abstract_search import AbstractSearch
 from lsdb.types import HCCatalogTypeVar
 
+if TYPE_CHECKING:
+    from astropy.visualization.wcsaxes import WCSAxes
+
 
 class BoxSearch(AbstractSearch):
     """Perform a box search to filter the catalog. This type of search is used for a
@@ -73,6 +77,14 @@ def search_points(self, frame: npd.NestedFrame, metadata: TableProperties) -> np
         return cone_filter(frame, self.ra, self.dec, self.radius_arcsec, metadata)
 
     def _perform_plot(self, ax: WCSAxes, **kwargs):
+        try:
+            # pylint: disable=import-outside-toplevel
+            from astropy.visualization.wcsaxes import SphericalCircle
+        except ImportError as exc:
+            raise ImportError(
+                "matplotlib is required to use this method. Install with pip or conda."
+            ) from exc
+
         kwargs_to_use = {"ec": "tab:red", "fc": "none"}
         kwargs_to_use.update(kwargs)
 
@@ -194,6 +206,13 @@ class PolygonSearch(AbstractSearch):
     """
 
     def __init__(self, vertices: list[tuple[float, float]], fine: bool = True):
+        try:
+            # pylint: disable=unused-import,import-outside-toplevel
+            from lsst.sphgeom import ConvexPolygon
+        except ImportError as exc:
+            raise ImportError(
+                "lsst-sphgeom is required to use this method. Install with pip or conda."
+            ) from exc
         super().__init__(fine)
         validate_polygon(vertices)
         self.vertices = vertices

tests/conftest.py

@@ -396,27 +396,6 @@ def cone_search_margin_expected(cone_search_expected_dir):
     return pd.read_csv(cone_search_expected_dir / "margin.csv", index_col=SPATIAL_INDEX_COLUMN)
 
 
-# pylint: disable=import-outside-toplevel
-def pytest_collection_modifyitems(items):
-    """Modify tests that use the `lsst-sphgeom` package to only run when that
-    package has been installed in the development environment.
-
-    If we detect that we can import `lsst-sphgeom`, this method exits early
-    and does not modify any test items.
-    """
-    try:
-        # pylint: disable=unused-import
-        from lsst.sphgeom import ConvexPolygon
-
-        return
-    except ImportError:
-        pass
-
-    for item in items:
-        if any(item.iter_markers(name="sphgeom")):
-            item.add_marker(pytest.mark.skip(reason="lsst-sphgeom is not installed"))
-
-
 class Helpers:
     @staticmethod
     def assert_divisions_are_correct(catalog):

tests/lsdb/catalog/test_catalog.py

@@ -5,16 +5,14 @@
 import dask.dataframe as dd
 import hats as hc
 import hats.pixel_math.healpix_shim as hp
-import matplotlib as mpl
-import matplotlib.pyplot as plt
 import nested_pandas as npd
 import numpy as np
 import numpy.testing as npt
 import pandas as pd
 import pytest
 from astropy.coordinates import SkyCoord
 from astropy.visualization.wcsaxes import WCSAxes
-from hats.inspection.visualize_catalog import get_fov_moc_from_wcs
+from hats.inspection._plotting import _get_fov_moc_from_wcs
 from hats.pixel_math import HealpixPixel
 from mocpy import WCS
 from nested_pandas.datasets import generate_data
@@ -24,12 +22,14 @@
 from lsdb import Catalog, MarginCatalog
 from lsdb.core.search.region_search import MOCSearch
 
-mpl.use("Agg")
-
 
 @pytest.fixture(autouse=True)
 def reset_matplotlib():
     yield
+    mpl = pytest.importorskip("matplotlib")
+    plt = pytest.importorskip("matplotlib.pyplot")
+
+    mpl.use("Agg")
     plt.close("all")
 
 
@@ -667,9 +667,9 @@ def test_filtered_catalog_has_undetermined_len(small_sky_order1_catalog, small_s
         len(small_sky_order1_catalog.pixel_search([(0, 11)]))
 
 
-@pytest.mark.sphgeom
 def test_filtered_catalog_has_undetermined_len_polygon(small_sky_order1_catalog):
     """Tests that filtered catalogs have an undetermined number of rows"""
+    pytest.importorskip("lsst.sphgeom")
     with pytest.raises(ValueError, match="undetermined"):
         vertices = [(300, -50), (300, -55), (272, -55), (272, -50)]
         len(small_sky_order1_catalog.polygon_search(vertices))
@@ -736,12 +736,13 @@ def test_plot_points(small_sky_order1_catalog, mocker):
 
 
 def test_plot_points_fov(small_sky_order1_catalog, mocker):
+    plt = pytest.importorskip("matplotlib.pyplot")
     mocker.patch("astropy.visualization.wcsaxes.WCSAxes.scatter")
     fig = plt.figure(figsize=(10, 6))
     center = SkyCoord(350, -80, unit="deg")
     fov = 10 * u.deg
     wcs = WCS(fig=fig, fov=fov, center=center, projection="MOL").w
-    wcs_moc = get_fov_moc_from_wcs(wcs)
+    wcs_moc = _get_fov_moc_from_wcs(wcs)
     _, ax = small_sky_order1_catalog.plot_points(fov=fov, center=center)
     comp_cat = small_sky_order1_catalog.search(MOCSearch(wcs_moc)).compute()
     WCSAxes.scatter.assert_called_once()
@@ -751,12 +752,13 @@ def test_plot_points_fov(small_sky_order1_catalog, mocker):
 
 
 def test_plot_points_wcs(small_sky_order1_catalog, mocker):
+    plt = pytest.importorskip("matplotlib.pyplot")
     mocker.patch("astropy.visualization.wcsaxes.WCSAxes.scatter")
     fig = plt.figure(figsize=(10, 6))
     center = SkyCoord(350, -80, unit="deg")
     fov = 10 * u.deg
     wcs = WCS(fig=fig, fov=fov, center=center).w
-    wcs_moc = get_fov_moc_from_wcs(wcs)
+    wcs_moc = _get_fov_moc_from_wcs(wcs)
     _, ax = small_sky_order1_catalog.plot_points(wcs=wcs)
     comp_cat = small_sky_order1_catalog.search(MOCSearch(wcs_moc)).compute()
     WCSAxes.scatter.assert_called_once()
@@ -766,6 +768,7 @@ def test_plot_points_wcs(small_sky_order1_catalog, mocker):
 
 
 def test_plot_points_colorcol(small_sky_order1_catalog, mocker):
+    plt = pytest.importorskip("matplotlib.pyplot")
     mocker.patch("astropy.visualization.wcsaxes.WCSAxes.scatter")
     mocker.patch("matplotlib.pyplot.colorbar")
     _, ax = small_sky_order1_catalog.plot_points(color_col="id")