maint: add pytest and numpy ruff rules

this helps prepare the support of numpy 2.0

.pre-commit-config.yaml

@@ -11,27 +11,12 @@ repos:
         exclude_types:
           - "svg"
         description: "Remove trailing whitespaces"
-  # Run Black on files
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-    - id: black
   # Fast linter to replace flake8
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.5.5'
+    rev: 'v0.6.4'
     hooks:
+     # linter
      - id: ruff
        fail_fast: true
-  # Same tools but for Jupyter notebooks
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.8.5
-    hooks:
-      - id: nbqa-black
-        name: nbqa-black
-        description: "Run 'black' on a Jupyter Notebook"
-        language: python
-        require_serial: true
-      - id: nbqa-ruff
-        name: nbqa-ruff
-        description: "Run ruff on a Jupyter notebook"
-        fail_fast: true
+     # formatter
+     - id: ruff-format

notebooks/from_astropy_table.ipynb

@@ -139,7 +139,7 @@
     ")\n",
     "moc.border(ax=ax, wcs=galactic_wcs, color=\"k\")\n",
     "\n",
-    "ax.grid(True)"
+    "ax.grid(visible=True)"
    ]
   }
  ],

notebooks/tmoc.ipynb

@@ -15,9 +15,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from mocpy import TimeMOC\n",
     "from astropy.time import Time, TimeDelta\n",
-    "from astroquery.vizier import Vizier"
+    "from astroquery.vizier import Vizier\n",
+    "from mocpy import TimeMOC"
    ]
   },
   {

pyproject.toml

@@ -82,9 +82,6 @@ frozen = false
 # Require Cargo.lock is up to date
 locked = false
 
-[tool.nbqa.addopts]
-ruff = ["--ignore=B018,FBT003,T201"]
-
 [tool.ruff]
 fix = true
 show-fixes = true
@@ -94,14 +91,13 @@ extend-include = ["*.ipynb"]
 target-version = "py38"
 
 [tool.ruff.lint]
-ignore-init-module-imports = true
 extend-select = ["SIM", "FBT", "D", "UP", "N", "S", "B", "A",
                  "C4", "ICN", "RET", "ARG", "PD", "PGH",
                  "RUF", "YTT", "BLE", "COM", "DTZ", "EXE",
-                 "ISC", "ICN001", "PIE", "PTH", "W", "I", "T20"
+                 "ISC", "ICN001", "PIE", "PTH", "W", "I", "T20",
+                 "PYI", "PT", "SIM", "NPY"
                 ]
-extend-ignore = ["E501", "D203", "D213", "D100", "N816", "D105", "N806", "N803", "FBT002", "N802"]
-# E501: line length (done by black in our case)
+extend-ignore = ["D203", "D213", "D100", "N816", "D105", "N806", "N803", "FBT002", "N802"]
 # N806, N816: variables names should be lowercase (would require to change all API)
 # D203: 1 blank line required before class docstring (not compatible with numpy docstyle)
 # FBT002: Boolean default in function definition (would require to change all API)

python/mocpy/tests/test_abstract_moc.py

@@ -29,7 +29,7 @@ def moc():
     return MOC.from_str("0/0-11")
 
 
-@pytest.fixture()
+@pytest.fixture
 def path(tmp_path):
     return tmp_path / "path"
 
@@ -50,10 +50,10 @@ def test_failing_instantiation():
 
 def test_failing_save(moc, path):
     """All the pitfalls in the save method."""
+    moc.save(path)
+    assert path.is_file()
     with pytest.raises(OSError, match=r"File *"):
         moc.save(path)
-        assert path.is_file()
-        moc.save(path)
     with pytest.raises(ValueError, match=r"The ``fold`` argument*"):
         moc.save(path, format="fits", overwrite=True, fold=80)
     with pytest.raises(ValueError, match=r"The ``fits_keyword`` argument*"):

python/mocpy/tests/test_moc.py

@@ -14,8 +14,10 @@
 
 from ..moc import MOC, WCS
 
+rng = np.random.default_rng()
 
-@pytest.fixture()
+
+@pytest.fixture
 def isets():
     a = MOC.from_depth29_ranges(
         29,
@@ -106,6 +108,10 @@ def test_n_cells():
         match=f"The depth should be comprised between 0 and {MOC.MAX_ORDER}*",
     ):
         MOC.n_cells(-2)
+    with pytest.raises(
+        ValueError,
+        match=f"The depth should be comprised between 0 and {MOC.MAX_ORDER}*",
+    ):
         MOC.n_cells(MOC.MAX_ORDER + 1)
     assert MOC.n_cells(6) == 4 * MOC.n_cells(5)
 
@@ -207,31 +213,28 @@ def test_new_empty_serialization():
 
 def get_random_skycoords(size):
     return SkyCoord(
-        ra=np.random.uniform(0, 360, size),
-        dec=np.random.uniform(-90, 90, size),
+        ra=rng.random(size) * 360,
+        dec=rng.random(size) * 180 - 90,
         unit="deg",
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def skycoords_gen_f():
     def gen_f(size):
         return SkyCoord(
-            np.random.uniform(0, 360, size),
-            np.random.uniform(-90, 90, size),
+            ra=rng.random(size) * 360,
+            dec=rng.random(size) * 180 - 90,
             unit="deg",
         )
 
     return gen_f
 
 
-@pytest.fixture()
+@pytest.fixture
 def lonlat_gen_f():
     def gen_f(size):
-        return (
-            np.random.uniform(0, 360, size) * u.deg,
-            np.random.uniform(-90, 90, size) * u.deg,
-        )
+        return ((rng.random(size) * 360) * u.deg, (rng.random(size) * 180 - 90) * u.deg)
 
     return gen_f
 
@@ -356,15 +359,15 @@ def test_from_fits_image_without_cdelt():
     MOC.from_fits_images(["resources/horsehead.fits"], max_norder=15)
 
 
-@pytest.fixture()
+@pytest.fixture
 def moc_from_fits_image():
     image_path = "resources/image_with_mask.fits.gz"
 
     with fits.open(image_path) as hdulist:
         return MOC.from_fits_image(hdu=hdulist[0], max_norder=7, mask=hdulist[0].data)
 
 
-@pytest.fixture()
+@pytest.fixture
 def moc_from_json():
     return MOC.from_json({"8": [45, 78], "4": [42, 57]})
 
@@ -380,7 +383,7 @@ def test_moc_serialize_and_from_json(moc_from_json):
 
 
 @pytest.mark.parametrize(
-    "expected, moc_str",
+    ("expected", "moc_str"),
     [
         (
             MOC.from_json(
@@ -406,7 +409,7 @@ def test_from_str(expected, moc_str):
 
 
 @pytest.mark.parametrize(
-    "expected, moc_str",
+    ("expected", "moc_str"),
     [
         (
             MOC.from_json(
@@ -458,7 +461,7 @@ def test_moc_serialize_to_json(moc_from_fits_image):
 
 
 @pytest.mark.parametrize(
-    "moc, expected",
+    ("moc", "expected"),
     [
         (
             MOC.from_json(
@@ -526,7 +529,7 @@ def test_mpl_border():
 def test_moc_contains(order):
     # defines 20 random healpix cells of the required order
     size = 20
-    healpix_arr = np.random.randint(0, 12 * 4**order, size, dtype="uint64")
+    healpix_arr = rng.integers(0, 12 * 4**order, size, dtype="uint64", endpoint=True)
     # defines a moc containing the 20 points
     moc = MOC.from_json(json_moc={str(order): np.unique(healpix_arr).tolist()})
     # the complementary should not contain them
@@ -773,7 +776,7 @@ def test_from_cones():
         MOC.from_cones(lon, lat, radius=radii, max_depth=14, union_strategy="big_cones")
 
 
-@pytest.fixture()
+@pytest.fixture
 def mocs():
     moc1 = {"1": [0]}
     moc1_increased = {"0": [0], "1": [17, 19, 22, 23, 35]}
@@ -812,7 +815,7 @@ def test_neighbours(mocs):
 
 
 # --- TESTING MOC operations ---#
-@pytest.fixture()
+@pytest.fixture
 def mocs_op():
     moc1 = MOC.from_json({"0": [0, 2, 3, 4, 5]})
     moc2 = MOC.from_json({"0": [0, 1, 7, 4, 3]})
@@ -862,7 +865,7 @@ def test_from_fits_old():
 
 
 @pytest.mark.parametrize(
-    "input_MOC, expected",
+    ("input_MOC", "expected"),
     [
         (
             MOC.from_json({"0": [1, 3]}),
@@ -931,7 +934,7 @@ def test_from_valued_healpix_cells():
 
 
 @pytest.mark.parametrize(
-    "cumul_from, cumul_to",
+    ("cumul_from", "cumul_to"),
     [(-5.0, 1.0), (np.nan, np.inf), (np.nan, np.nan), (np.inf, np.nan), (-10.0, -5.0)],
 )
 def test_from_valued_healpix_cells_weird_values(cumul_from, cumul_to):

python/mocpy/tests/test_stmoc.py

@@ -10,7 +10,7 @@
 from ..tmoc import TimeMOC
 
 
-@pytest.fixture()
+@pytest.fixture
 def stmoc_2mass():
     two_mass_data = Table.read(
         "resources/STMOC/2MASS-list-images.fits.gz",
@@ -33,7 +33,7 @@ def stmoc_2mass():
     )
 
 
-@pytest.fixture()
+@pytest.fixture
 def stmoc_xmm_dr8():
     xmm_dr8_data = Table.read("resources/STMOC/vizier_votable.b64")
     times_xmm = Time(xmm_dr8_data["MJD0"].data, format="mjd", scale="tdb")

python/mocpy/tests/test_tmoc.py

@@ -58,6 +58,10 @@ def test_n_cells():
         match=f"The depth should be comprised between 0 and {TimeMOC.MAX_ORDER}*",
     ):
         TimeMOC.n_cells(-1)
+    with pytest.raises(
+        ValueError,
+        match=f"The depth should be comprised between 0 and {TimeMOC.MAX_ORDER}*",
+    ):
         TimeMOC.n_cells(TimeMOC.MAX_ORDER + 1)
     assert TimeMOC.n_cells(10) == 2 * TimeMOC.n_cells(9)
 
@@ -134,7 +138,10 @@ def test_tmoc_from_time_ranges():
     assert tmoc.max_time == tmoc2.max_time
     assert tmoc == tmoc2
 
-    with pytest.raises(ValueError):
+    with pytest.raises(
+        ValueError,
+        match=r"Mismatch between min\_times and max\_times of shapes \(0,\) and \(1,\)",
+    ):
         TimeMOC.from_time_ranges(
             Time([], format="jd", scale="tdb"),
             Time([3], format="jd", scale="tdb"),
@@ -234,7 +241,7 @@ def test_contains():
 
 
 @pytest.mark.parametrize(
-    "a, b, expect",
+    ("a", "b", "expect"),
     [
         (
             TimeMOC.from_times(Time(np.array([0, 2]), format="jd", scale="tdb")),
@@ -260,7 +267,7 @@ def test_union(a, b, expect):
 
 
 @pytest.mark.parametrize(
-    "a, b, expect",
+    ("a", "b", "expect"),
     [
         (
             TimeMOC.from_times(Time(np.array([0, 2]), format="jd", scale="tdb")),
@@ -286,7 +293,7 @@ def test_difference(a, b, expect):
 
 
 @pytest.mark.parametrize(
-    "a, b, expect",
+    ("a", "b", "expect"),
     [
         (
             TimeMOC.from_times(Time(np.array([0, 1, 2]), format="jd", scale="tdb")),