jerlov 0.3.0__tar.gz → 0.3.2__tar.gz

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Files changed (44) hide show
  1. {jerlov-0.3.0/jerlov.egg-info → jerlov-0.3.2}/PKG-INFO +14 -1
  2. {jerlov-0.3.0 → jerlov-0.3.2}/README.md +13 -0
  3. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/__init__.py +1 -1
  4. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/_data.py +37 -7
  5. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/backscattering.py +8 -4
  6. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/colour.py +2 -2
  7. jerlov-0.3.2/jerlov/py.typed +0 -0
  8. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/water.py +13 -5
  9. {jerlov-0.3.0 → jerlov-0.3.2/jerlov.egg-info}/PKG-INFO +14 -1
  10. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov.egg-info/SOURCES.txt +2 -0
  11. {jerlov-0.3.0 → jerlov-0.3.2}/pyproject.toml +2 -1
  12. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_api.py +55 -0
  13. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_backscattering.py +20 -0
  14. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_packaging.py +38 -0
  15. jerlov-0.3.2/tests/test_quoted_figures.py +192 -0
  16. {jerlov-0.3.0 → jerlov-0.3.2}/LICENSE +0 -0
  17. {jerlov-0.3.0 → jerlov-0.3.2}/NOTICE +0 -0
  18. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/__init__.py +0 -0
  19. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/austin1986_kd.csv +0 -0
  20. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/austin1986_model.csv +0 -0
  21. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/boss2001_chi.csv +0 -0
  22. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/cie1931_2deg_cmf.csv +0 -0
  23. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/cie_d65.csv +0 -0
  24. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/jerlov1968_kd.csv +0 -0
  25. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/jerlov1968_total_irradiance.csv +0 -0
  26. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/jerlov1976_kd.csv +0 -0
  27. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/paulson1977_shortwave.csv +0 -0
  28. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/smart2007_b_from_c.csv +0 -0
  29. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/solonenko2015_iop.csv +0 -0
  30. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/williamson2022_iop.csv +0 -0
  31. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/williamson2022_measured.csv +0 -0
  32. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/data/williamson2023_depth.csv +0 -0
  33. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/scene.py +0 -0
  34. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/shortwave.py +0 -0
  35. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov/sources.py +0 -0
  36. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov.egg-info/dependency_links.txt +0 -0
  37. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov.egg-info/requires.txt +0 -0
  38. {jerlov-0.3.0 → jerlov-0.3.2}/jerlov.egg-info/top_level.txt +0 -0
  39. {jerlov-0.3.0 → jerlov-0.3.2}/setup.cfg +0 -0
  40. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_colour.py +0 -0
  41. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_depth.py +0 -0
  42. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_reproduces_papers.py +0 -0
  43. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_scene.py +0 -0
  44. {jerlov-0.3.0 → jerlov-0.3.2}/tests/test_shortwave.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: jerlov
3
- Version: 0.3.0
3
+ Version: 0.3.2
4
4
  Summary: Inherent optical properties of Jerlov water types, with provenance
5
5
  Author: T. Ishibashi
6
6
  License-Expression: Apache-2.0
@@ -298,6 +298,19 @@ questions the first edition of Jerlov settled, and the rest notes.
298
298
  `DECISIONS.md` records why the package is shaped the way it is, including the
299
299
  alternatives that were rejected and why.
300
300
 
301
+ ## Contributing, and reporting a wrong number
302
+
303
+ `CONTRIBUTING.md` sets out what goes in and what it takes: a primary source, a
304
+ script in `tools/` that produces the table, checks inside that script against
305
+ the paper's own equations, an entry in `DATA.md`, and a regression test.
306
+
307
+ **A coefficient that disagrees with a paper you have is the most useful report
308
+ this package can receive.** `DATA.md` exists because several such
309
+ disagreements turned out to be defects in the literature rather than here.
310
+ Issues: <https://github.com/tishibashi-cpu/jerlov/issues>
311
+
312
+ `CHANGELOG.md` covers every release.
313
+
301
314
  ## Licence
302
315
 
303
316
  Apache-2.0. The Williamson & Hollins data are Crown copyright, Dstl, under
@@ -273,6 +273,19 @@ questions the first edition of Jerlov settled, and the rest notes.
273
273
  `DECISIONS.md` records why the package is shaped the way it is, including the
274
274
  alternatives that were rejected and why.
275
275
 
276
+ ## Contributing, and reporting a wrong number
277
+
278
+ `CONTRIBUTING.md` sets out what goes in and what it takes: a primary source, a
279
+ script in `tools/` that produces the table, checks inside that script against
280
+ the paper's own equations, an entry in `DATA.md`, and a regression test.
281
+
282
+ **A coefficient that disagrees with a paper you have is the most useful report
283
+ this package can receive.** `DATA.md` exists because several such
284
+ disagreements turned out to be defects in the literature rather than here.
285
+ Issues: <https://github.com/tishibashi-cpu/jerlov/issues>
286
+
287
+ `CHANGELOG.md` covers every release.
288
+
276
289
  ## Licence
277
290
 
278
291
  Apache-2.0. The Williamson & Hollins data are Crown copyright, Dstl, under
@@ -78,4 +78,4 @@ __all__ = [
78
78
  "MissingQuantityError",
79
79
  ]
80
80
 
81
- __version__ = "0.3.0"
81
+ __version__ = "0.3.2"
@@ -8,13 +8,13 @@ silently cleaned up on the way in.
8
8
  from __future__ import annotations
9
9
 
10
10
  import csv
11
+ import os
12
+ import sys
11
13
  from functools import lru_cache
12
14
  from importlib import resources
13
15
 
14
16
  import numpy as np
15
17
 
16
- import numpy as np
17
-
18
18
  #: numpy.trapezoid is the name from NumPy 2.0; before that it was numpy.trapz,
19
19
  #: which 2.0 removed. The package claims to work from NumPy 1.22, so neither
20
20
  #: can be assumed. This lives here rather than in a module about colour so
@@ -23,6 +23,36 @@ import numpy as np
23
23
  #: supported NumPy.
24
24
  trapezoid = getattr(np, "trapezoid", None) or np.trapz
25
25
 
26
+ _PACKAGE_DIR = os.path.dirname(os.path.abspath(__file__)) + os.sep
27
+
28
+
29
+ def caller_stacklevel() -> int:
30
+ """The ``stacklevel`` that points a warning at the caller's own code.
31
+
32
+ Call it from the function that calls ``warnings.warn``. A fixed number
33
+ is right only for one call path: ``Water.c`` reaches the flag check one
34
+ frame deeper than ``Water.a`` does, and ``Scene`` deeper still, so a
35
+ constant pointed some warnings at this package instead of at the line
36
+ that asked for the value.
37
+ """
38
+ frame = sys._getframe(1)
39
+ level = 1
40
+ while frame is not None and frame.f_code.co_filename.startswith(_PACKAGE_DIR):
41
+ frame = frame.f_back
42
+ level += 1
43
+ return level
44
+
45
+
46
+ def _frozen(array: np.ndarray) -> np.ndarray:
47
+ """Make a cached array read-only.
48
+
49
+ The loaders below are cached, so every caller gets the same array
50
+ objects. Writing into one would silently change the table for every
51
+ later caller in the process.
52
+ """
53
+ array.setflags(write=False)
54
+ return array
55
+
26
56
  #: Values whose ``status`` is one of these should not be used without the
27
57
  #: caller being told. See README sections 1-6.
28
58
  QUESTIONABLE = frozenset({"suspect", "missing", "extrapolated",
@@ -75,8 +105,8 @@ def spectrum(
75
105
  )
76
106
  order = np.argsort(wl)
77
107
  return (
78
- np.asarray(wl, dtype=float)[order],
79
- np.asarray(values, dtype=float)[order],
108
+ _frozen(np.asarray(wl, dtype=float)[order]),
109
+ _frozen(np.asarray(values, dtype=float)[order]),
80
110
  tuple(statuses[i] for i in order),
81
111
  )
82
112
 
@@ -104,7 +134,7 @@ def austin_model() -> tuple[np.ndarray, np.ndarray, np.ndarray]:
104
134
  m = np.array([float(r["M_slope"]) for r in rows])
105
135
  kw = np.array([float(r["Kw_pure_seawater_per_m"]) for r in rows])
106
136
  order = np.argsort(wl)
107
- return wl[order], m[order], kw[order]
137
+ return _frozen(wl[order]), _frozen(m[order]), _frozen(kw[order])
108
138
 
109
139
 
110
140
  @lru_cache(maxsize=None)
@@ -119,5 +149,5 @@ def b_from_c_ratio() -> tuple[np.ndarray, dict[str, np.ndarray]]:
119
149
  for r in rows
120
150
  if r["statistic"] == stat
121
151
  }
122
- out[stat] = np.array([by_wl[w] for w in wl])
123
- return np.array(wl), out
152
+ out[stat] = _frozen(np.array([by_wl[w] for w in wl]))
153
+ return _frozen(np.array(wl)), out
@@ -70,11 +70,15 @@ def pure_water_vsf(angle_deg, wavelength_nm, salinity_psu: float = 37.0):
70
70
  The amplitude carries about 15 percent uncertainty, which the authors give
71
71
  as the agreement between measurement and theory.
72
72
  """
73
- angle = np.atleast_1d(np.asarray(angle_deg, dtype=float))
73
+ angle = np.asarray(angle_deg, dtype=float)
74
74
  amplitude = (1.38 * (np.asarray(wavelength_nm, dtype=float) / 500.0) ** -4.32
75
75
  * (1 + 0.3 * salinity_psu / 37.0) * 1e-4)
76
76
  out = amplitude * (1 + _ratio() * np.cos(np.radians(angle)) ** 2)
77
- return _like_input(np.atleast_1d(out), angle_deg)
77
+ # Angle and wavelength broadcast against each other; the answer is a
78
+ # float only when neither of them was an array.
79
+ if np.ndim(out) == 0:
80
+ return float(out)
81
+ return out
78
82
 
79
83
 
80
84
  def pure_water_backscattering(wavelength_nm, salinity_psu: float = 37.0):
@@ -181,7 +185,7 @@ def bb_from_vsf(beta, angle_deg: float, wavelength_nm, *,
181
185
  "scattering function varies steeply here and a single-angle "
182
186
  "measurement pins bb poorly.",
183
187
  AngleWarning,
184
- stacklevel=2,
188
+ stacklevel=_data.caller_stacklevel(),
185
189
  )
186
190
 
187
191
  scalar = np.ndim(beta) == 0 and np.ndim(wavelength_nm) == 0
@@ -198,7 +202,7 @@ def bb_from_vsf(beta, angle_deg: float, wavelength_nm, *,
198
202
  "so the particle contribution came out negative. Check the "
199
203
  "calibration, the wavelength and the salinity.",
200
204
  AngleWarning,
201
- stacklevel=2,
205
+ stacklevel=_data.caller_stacklevel(),
202
206
  )
203
207
 
204
208
  def shape(values):
@@ -163,7 +163,7 @@ def integrate_response(spectrum, wavelengths, response, response_wavelengths,
163
163
  "The integral is over the overlap and is biased by what was left "
164
164
  "out",
165
165
  CoverageWarning,
166
- stacklevel=2,
166
+ stacklevel=_data.caller_stacklevel(),
167
167
  )
168
168
 
169
169
  resampled = np.stack(
@@ -202,7 +202,7 @@ def xyz_to_srgb(xyz, *, clip: bool = True) -> np.ndarray:
202
202
  "the colour lies outside the sRGB gamut"
203
203
  + (" and has been clipped" if clip else ""),
204
204
  GamutWarning,
205
- stacklevel=2,
205
+ stacklevel=_data.caller_stacklevel(),
206
206
  )
207
207
  if clip:
208
208
  linear = np.clip(linear, 0.0, 1.0)
File without changes
@@ -75,7 +75,9 @@ class Water:
75
75
  source: Source | None = None,
76
76
  flags: dict[str, tuple[str, ...]] | None = None,
77
77
  ) -> None:
78
- self.wavelengths = np.asarray(wavelengths, dtype=float)
78
+ # Copied, so that neither the caller's arrays nor the packaged tables
79
+ # can change underneath this object, and it cannot change them.
80
+ self.wavelengths = np.array(wavelengths, dtype=float)
79
81
  if self.wavelengths.ndim != 1 or self.wavelengths.size == 0:
80
82
  raise ValueError("wavelengths must be a non-empty 1-D array")
81
83
  if np.any(np.diff(self.wavelengths) <= 0):
@@ -85,7 +87,7 @@ class Water:
85
87
  for key, value in (("a", a), ("b", b), ("Kd", kd)):
86
88
  if value is None:
87
89
  continue
88
- arr = np.asarray(value, dtype=float)
90
+ arr = np.array(value, dtype=float)
89
91
  if arr.shape != self.wavelengths.shape:
90
92
  raise ValueError(f"{key} must have the same shape as wavelengths")
91
93
  self._series[key] = arr
@@ -163,7 +165,7 @@ class Water:
163
165
  + "; ".join(sorted(hit))
164
166
  + ". See the package README for what is known about them.",
165
167
  ProvenanceWarning,
166
- stacklevel=3,
168
+ stacklevel=_data.caller_stacklevel(),
167
169
  )
168
170
 
169
171
  def a(self, wl):
@@ -368,7 +370,7 @@ def kd_spectrum(kd, wavelength_nm: float, at):
368
370
  "Austin & Petzold (1986) reported exactly this problem in "
369
371
  "Jerlov's own type I values.",
370
372
  ProvenanceWarning,
371
- stacklevel=2,
373
+ stacklevel=_data.caller_stacklevel(),
372
374
  )
373
375
  result = np.interp(query, wl, m) / m1 * (kd - kw1) + np.interp(query, wl, kw)
374
376
  return _like_input(result, at)
@@ -395,5 +397,11 @@ def b_from_c(c, wavelength_nm, *, bw, cw, bound: str = "average"):
395
397
  f"wavelength outside the measured range ({wl[0]:g}-{wl[-1]:g} nm)"
396
398
  )
397
399
  ratio = np.interp(query, wl, ratios[bound])
400
+ if np.ndim(wavelength_nm) == 0:
401
+ ratio = ratio[0]
398
402
  result = (np.asarray(c, dtype=float) - cw) * ratio + bw
399
- return _like_input(np.atleast_1d(result), wavelength_nm)
403
+ # c and the wavelength broadcast against each other; the answer is a
404
+ # float only when neither of them was an array.
405
+ if np.ndim(result) == 0:
406
+ return float(result)
407
+ return result
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: jerlov
3
- Version: 0.3.0
3
+ Version: 0.3.2
4
4
  Summary: Inherent optical properties of Jerlov water types, with provenance
5
5
  Author: T. Ishibashi
6
6
  License-Expression: Apache-2.0
@@ -298,6 +298,19 @@ questions the first edition of Jerlov settled, and the rest notes.
298
298
  `DECISIONS.md` records why the package is shaped the way it is, including the
299
299
  alternatives that were rejected and why.
300
300
 
301
+ ## Contributing, and reporting a wrong number
302
+
303
+ `CONTRIBUTING.md` sets out what goes in and what it takes: a primary source, a
304
+ script in `tools/` that produces the table, checks inside that script against
305
+ the paper's own equations, an entry in `DATA.md`, and a regression test.
306
+
307
+ **A coefficient that disagrees with a paper you have is the most useful report
308
+ this package can receive.** `DATA.md` exists because several such
309
+ disagreements turned out to be defects in the literature rather than here.
310
+ Issues: <https://github.com/tishibashi-cpu/jerlov/issues>
311
+
312
+ `CHANGELOG.md` covers every release.
313
+
301
314
  ## Licence
302
315
 
303
316
  Apache-2.0. The Williamson & Hollins data are Crown copyright, Dstl, under
@@ -6,6 +6,7 @@ jerlov/__init__.py
6
6
  jerlov/_data.py
7
7
  jerlov/backscattering.py
8
8
  jerlov/colour.py
9
+ jerlov/py.typed
9
10
  jerlov/scene.py
10
11
  jerlov/shortwave.py
11
12
  jerlov/sources.py
@@ -35,6 +36,7 @@ tests/test_backscattering.py
35
36
  tests/test_colour.py
36
37
  tests/test_depth.py
37
38
  tests/test_packaging.py
39
+ tests/test_quoted_figures.py
38
40
  tests/test_reproduces_papers.py
39
41
  tests/test_scene.py
40
42
  tests/test_shortwave.py
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
4
4
 
5
5
  [project]
6
6
  name = "jerlov"
7
- version = "0.3.0"
7
+ version = "0.3.2"
8
8
  description = "Inherent optical properties of Jerlov water types, with provenance"
9
9
  readme = "README.md"
10
10
  requires-python = ">=3.10"
@@ -30,3 +30,4 @@ include = ["jerlov*"]
30
30
 
31
31
  [tool.setuptools.package-data]
32
32
  "jerlov.data" = ["*.csv"]
33
+ "jerlov" = ["py.typed"]
@@ -213,3 +213,58 @@ def test_interpolating_across_a_gap_still_gives_nan():
213
213
  assert np.isnan(w.a(650)) # a published value that is wrong
214
214
  assert np.isnan(w.a(660)) # and interpolation across it
215
215
  assert np.isnan(w.a(675))
216
+
217
+
218
+ def test_b_from_c_keeps_every_c_at_a_single_wavelength():
219
+ """An array of c at one wavelength used to come back as its first value."""
220
+ c = np.array([0.5, 1.0, 2.0])
221
+ out = jerlov.b_from_c(c, 488.0, bw=0.003, cw=0.02)
222
+ assert out.shape == (3,)
223
+ for value, single in zip(out, c):
224
+ assert value == pytest.approx(
225
+ jerlov.b_from_c(float(single), 488.0, bw=0.003, cw=0.02)
226
+ )
227
+ assert isinstance(jerlov.b_from_c(0.5, 488.0, bw=0.003, cw=0.02), float)
228
+
229
+
230
+ def test_a_returned_water_cannot_corrupt_the_packaged_table():
231
+ """The loaders are cached; a caller's in-place edit must stay local."""
232
+ w = jerlov.water("III")
233
+ before = jerlov.water("III").wavelengths.copy()
234
+ w.wavelengths *= 2.0
235
+ assert np.array_equal(jerlov.water("III").wavelengths, before)
236
+
237
+
238
+ def test_the_cached_tables_are_read_only():
239
+ from jerlov import _data
240
+
241
+ wl, m, kw = _data.austin_model()
242
+ with pytest.raises(ValueError):
243
+ wl[0] = 0.0
244
+ wl, values, _ = _data.spectrum(
245
+ "williamson2022_iop.csv", "III", "a", "value_per_m"
246
+ )
247
+ with pytest.raises(ValueError):
248
+ values[0] = 0.0
249
+
250
+
251
+ def test_measurements_are_copied_not_shared():
252
+ wl = np.array([400.0, 500.0, 600.0])
253
+ a = np.array([0.1, 0.2, 0.3])
254
+ mine = Water.from_measurements(wl, a=a)
255
+ a[1] = 99.0
256
+ assert mine.a(500.0) == pytest.approx(0.2)
257
+
258
+
259
+ @pytest.mark.parametrize("method", ["kd", "c"])
260
+ def test_a_provenance_warning_points_at_the_callers_line(method):
261
+ """Not at water.py: `c` reaches the check one frame deeper than `kd`."""
262
+ source = "jerlov1976" if method == "kd" else "williamson2022"
263
+ w = jerlov.water("9C" if method == "kd" else "III", source=source)
264
+ query = 349.5 if method == "kd" else 305.0
265
+ with warnings.catch_warnings(record=True) as caught:
266
+ warnings.simplefilter("always")
267
+ getattr(w, method)(query)
268
+ flagged = [c for c in caught if issubclass(c.category, ProvenanceWarning)]
269
+ assert flagged
270
+ assert all(c.filename == __file__ for c in flagged)
@@ -165,3 +165,23 @@ def test_it_says_nothing_about_a_jerlov_type():
165
165
  """The point of DATA.md section 10 has not quietly gone away."""
166
166
  with pytest.raises(jerlov.MissingQuantityError):
167
167
  jerlov.water("III").bb(532)
168
+
169
+
170
+ def test_one_angle_many_wavelengths_gives_one_value_per_wavelength():
171
+ """A scalar angle used to return the first wavelength's value alone."""
172
+ nms = [450.0, 532.0, 700.0]
173
+ vsf = jerlov.pure_water_vsf(124.0, nms)
174
+ assert np.shape(vsf) == (3,)
175
+ for value, nm in zip(vsf, nms):
176
+ assert value == pytest.approx(jerlov.pure_water_vsf(124.0, nm))
177
+
178
+
179
+ def test_an_array_of_wavelengths_matches_one_call_per_wavelength():
180
+ """The water term must be subtracted at each wavelength, not the first."""
181
+ nms = [450.0, 532.0, 700.0]
182
+ together = jerlov.bb_from_vsf([0.001] * 3, 124.0, nms)
183
+ for k, nm in enumerate(nms):
184
+ alone = jerlov.bb_from_vsf(0.001, 124.0, nm)
185
+ assert together.bb[k] == pytest.approx(alone.bb)
186
+ assert together.particulate[k] == pytest.approx(alone.particulate)
187
+ assert together.water[k] == pytest.approx(alone.water)
@@ -235,3 +235,41 @@ def test_nothing_reaches_for_a_numpy_2_only_name():
235
235
  "use jerlov._data.trapezoid instead, which resolves whichever name "
236
236
  f"the installed NumPy has: {offenders}"
237
237
  )
238
+
239
+
240
+ @source_tree
241
+ def test_the_files_a_reviewer_looks_for_are_present():
242
+ """JOSS checks for community guidelines; the rest are cheap to keep."""
243
+ for name in ("README.md", "LICENSE", "NOTICE", "CITATION.cff",
244
+ "CONTRIBUTING.md", "CODE_OF_CONDUCT.md", "CHANGELOG.md",
245
+ "DATA.md", "DECISIONS.md", ".zenodo.json"):
246
+ assert (ROOT / name).exists(), f"{name} is missing"
247
+
248
+
249
+ @source_tree
250
+ def test_contributing_says_how_to_report_and_how_to_contribute():
251
+ """The three things JOSS asks a contributing guide to cover."""
252
+ text = (ROOT / "CONTRIBUTING.md").read_text().lower()
253
+ assert "issues" in text, "no way to report a problem is given"
254
+ assert "pip install -e" in text, "no way to set the package up is given"
255
+ assert "pull request" in text, "no way to contribute a change is given"
256
+
257
+
258
+ @source_tree
259
+ def test_the_changelog_covers_the_current_version():
260
+ """A release whose changes are only in a GitHub Release is invisible to
261
+ anyone who installed from PyPI."""
262
+ changelog = (ROOT / "CHANGELOG.md").read_text()
263
+ assert f"## {jerlov.__version__}" in changelog, (
264
+ f"CHANGELOG.md has no entry for {jerlov.__version__}"
265
+ )
266
+
267
+
268
+ @source_tree
269
+ def test_type_hints_reach_the_caller():
270
+ """Annotations are useless to a user without the marker file."""
271
+ assert (ROOT / "jerlov" / "py.typed").exists()
272
+ assert '"jerlov" = ["py.typed"]' in (ROOT / "pyproject.toml").read_text(), (
273
+ "py.typed exists but is not listed as package data, so it will not "
274
+ "be installed"
275
+ )
@@ -0,0 +1,192 @@
1
+ """The numbers the prose quotes must still be the numbers the code gives.
2
+
3
+ README.md, DATA.md and the examples all state figures: a factor of 3.8 here, 46
4
+ percent there. Those were computed once. Nothing has been stopping them from
5
+ drifting away from what the package now returns, and a reader has no way to
6
+ tell when they have.
7
+
8
+ Each test below recomputes one quoted figure. When one fails, the prose is
9
+ what needs fixing, not the test — unless the change to the code was a mistake,
10
+ in which case it is the other way round and the test has done its job.
11
+ """
12
+
13
+ from __future__ import annotations
14
+
15
+ import math
16
+ import pathlib
17
+ import re
18
+ import warnings
19
+
20
+ import numpy as np
21
+ import pytest
22
+
23
+ import jerlov
24
+ from jerlov import _data
25
+
26
+ ROOT = pathlib.Path(__file__).resolve().parent.parent
27
+ source_tree = pytest.mark.skipif(
28
+ not (ROOT / "README.md").exists(),
29
+ reason="not running from a source tree",
30
+ )
31
+
32
+
33
+ def quiet():
34
+ return warnings.catch_warnings()
35
+
36
+
37
+ # -- the sources disagree, and by how much --------------------------------
38
+
39
+
40
+ def test_scattering_at_510nm_differs_by_the_stated_factor():
41
+ """README and sources_disagree.py both say 3.8 for Jerlov III."""
42
+ with quiet():
43
+ warnings.simplefilter("ignore")
44
+ measured = float(jerlov.water("III").b(510))
45
+ inverted = float(jerlov.water("III", source="solonenko2015").b(510))
46
+ assert inverted / measured == pytest.approx(3.8, abs=0.05)
47
+
48
+
49
+ def test_the_disagreement_does_not_run_one_way():
50
+ """sources_disagree.py claims Jerlov IB goes the other direction."""
51
+ with quiet():
52
+ warnings.simplefilter("ignore")
53
+ measured = float(jerlov.water("IB").b(510))
54
+ inverted = float(jerlov.water("IB", source="solonenko2015").b(510))
55
+ assert inverted / measured < 0.5
56
+
57
+
58
+ def test_the_three_routes_span_the_stated_factor_at_532nm():
59
+ """DATA.md section 17 says 5.1 for Jerlov III."""
60
+ chlorophyll_model = 1.8998 # Abd El-Mottaleb et al. (2024)
61
+ with quiet():
62
+ warnings.simplefilter("ignore")
63
+ measured = float(jerlov.water("III").c(532))
64
+ inverted = float(jerlov.water("III", source="solonenko2015").c(532))
65
+ assert measured == pytest.approx(0.371, abs=0.001)
66
+ assert inverted == pytest.approx(1.092, abs=0.001)
67
+ assert chlorophyll_model / measured == pytest.approx(5.1, abs=0.05)
68
+
69
+
70
+ # -- the scattering model constants ---------------------------------------
71
+
72
+
73
+ def test_the_small_particle_coefficients_differ_by_the_stated_amount():
74
+ """DATA.md section 6: 1.513 is 31 percent larger than 1.151302."""
75
+ haltrin = jerlov.get_source("williamson2022").scattering.small_coeff
76
+ solonenko = jerlov.get_source("solonenko2015").scattering.small_coeff
77
+ assert haltrin == pytest.approx(1.151302)
78
+ assert solonenko == pytest.approx(1.513)
79
+ assert solonenko / haltrin - 1 == pytest.approx(0.31, abs=0.005)
80
+
81
+
82
+ # -- shortwave penetration ------------------------------------------------
83
+
84
+
85
+ def test_the_shortwave_fit_misses_its_source_by_the_stated_amount():
86
+ """README, DATA.md section 14 and solar_heating.py all say 46 percent."""
87
+ rows = _data._rows("jerlov1968_total_irradiance.csv")
88
+ worst = 0.0
89
+ for row in rows:
90
+ if row["water_type"] not in ("I", "IA", "IB", "II", "III"):
91
+ continue
92
+ if not row["percent_of_surface"]:
93
+ continue
94
+ depth = float(row["depth_m"])
95
+ if depth == 0 or depth > 100:
96
+ continue
97
+ want = float(row["percent_of_surface"]) / 100
98
+ got = jerlov.solar_fraction(row["water_type"], depth)
99
+ worst = max(worst, abs(got - want) / want)
100
+ assert worst == pytest.approx(0.46, abs=0.01)
101
+
102
+
103
+ def test_the_published_R_values_are_what_the_docs_print():
104
+ published = {"I": 0.58, "IA": 0.62, "IB": 0.67, "II": 0.77, "III": 0.78}
105
+ for water_type, value in published.items():
106
+ assert jerlov.shortwave_parameters(water_type).R == pytest.approx(value)
107
+
108
+
109
+ # -- backscattering -------------------------------------------------------
110
+
111
+
112
+ def test_the_worst_chi_p_spread_is_the_stated_figure():
113
+ """README and DATA.md section 18 both say 34.8 percent at 170 degrees."""
114
+ with pytest.warns(jerlov.AngleWarning, match="34.8"):
115
+ result = jerlov.bb_from_vsf(0.002, 170.0, 532.0)
116
+ assert result.quoted_error_percent == pytest.approx(34.8)
117
+ middle = [jerlov.bb_from_vsf(0.002, a, 532.0).quoted_error_percent
118
+ for a in (100.0, 120.0, 140.0, 160.0)]
119
+ assert max(middle) <= 6.5, "the 3-6 percent claim no longer holds"
120
+
121
+
122
+ def test_chi_w_and_chi_p_cross_where_the_docs_say():
123
+ """DATA.md section 18 quotes 116.9 degrees against the paper's ~118."""
124
+ r = (1 - jerlov.backscattering.DEPOLARISATION_RATIO) / (
125
+ 1 + jerlov.backscattering.DEPOLARISATION_RATIO)
126
+ angles = np.linspace(90.0, 170.0, 80001)
127
+ gap = [(1 + r / 3) / (1 + r * math.cos(math.radians(a)) ** 2)
128
+ - jerlov.particulate_chi(a) for a in angles]
129
+ crossing = float(angles[int(np.argmin(np.abs(gap)))])
130
+ assert crossing == pytest.approx(116.9, abs=0.1)
131
+
132
+
133
+ # -- the example that argues against defaults -----------------------------
134
+
135
+
136
+ def test_the_guess_overstates_contrast_by_the_stated_amount():
137
+ """from_one_measurement.py computes 65 percent and the prose repeats it.
138
+
139
+ The example computes this rather than hard-coding it, so this test is
140
+ what stops the *prose* around it from going stale.
141
+ """
142
+ wl = np.arange(420.0, 681.0, 20.0)
143
+ a = 0.02 + 0.35 * np.exp(-(wl - 420.0) / 90.0) + 0.30 * (wl > 600)
144
+ b = 0.45 * (550.0 / wl) ** 0.8
145
+ water = jerlov.Water.from_measurements(wl, a=a, b=b)
146
+
147
+ measured = jerlov.bb_from_vsf(0.0021, 140.0, 532.0, salinity_psu=35.0)
148
+ ratio = measured.bb / water.b(532.0)
149
+ assert ratio == pytest.approx(0.033, abs=0.001)
150
+
151
+ surface = np.interp(wl, *jerlov.d65(), left=0.0, right=0.0)
152
+ with quiet():
153
+ warnings.simplefilter("ignore")
154
+ scene = jerlov.Scene.at_depth(
155
+ water, 8.0, surface, wl,
156
+ kd=jerlov.water("II", source="austin1986"))
157
+ white = scene.downwelling / np.pi
158
+ contrasts = {}
159
+ for label, value in (("guess", 0.015), ("measured", ratio)):
160
+ b_inf = jerlov.veiling_radiance_estimate(
161
+ water, scene.downwelling, wl, backscatter_ratio=value)
162
+ observed = scene.observe(np.full_like(wl, 0.5), 5.0,
163
+ veiling_radiance=b_inf)
164
+ contrasts[label] = float(
165
+ np.mean(np.abs(observed.contrast(0.1 * white))))
166
+ overstatement = contrasts["guess"] / contrasts["measured"] - 1
167
+ assert overstatement == pytest.approx(0.65, abs=0.03)
168
+
169
+
170
+ # -- the prose and the code are checked against each other ----------------
171
+
172
+
173
+ @source_tree
174
+ def test_the_readme_quotes_a_transmittance_the_package_produces():
175
+ """`solar_fraction("IB", 10.0)` appears in the README with its answer."""
176
+ readme = (ROOT / "README.md").read_text()
177
+ match = re.search(
178
+ r'solar_fraction\("IB", 10\.0\).*?#\s*([\d.]+)', readme)
179
+ assert match, "the README no longer shows that call with its result"
180
+ assert jerlov.solar_fraction("IB", 10.0) == pytest.approx(
181
+ float(match.group(1)), abs=0.0005)
182
+
183
+
184
+ @source_tree
185
+ def test_the_readme_quotes_a_chi_p_the_package_produces():
186
+ readme = (ROOT / "README.md").read_text()
187
+ match = re.search(r"r\.chi_p, r\.quoted_error_percent\s*#\s*([\d.]+),\s*([\d.]+)",
188
+ readme)
189
+ assert match, "the README no longer shows chi_p with its value"
190
+ result = jerlov.bb_from_vsf(0.0021, 140.0, 532.0)
191
+ assert result.chi_p == pytest.approx(float(match.group(1)))
192
+ assert result.quoted_error_percent == pytest.approx(float(match.group(2)))
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