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Remove two Pytest warnings due to numpy and pytest mocker in test_dump function #112

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Merged
merged 14 commits into from
Oct 25, 2024
Merged

Remove two Pytest warnings due to numpy and pytest mocker in test_dump function #112

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c0ffe30
Empty build.txt file which is used for C++/C
bobleesj Sep 18, 2024
3e8dd23
Fix arb value to fix warning
bobleesj Sep 18, 2024
b62fddb
Remove patch warning
bobleesj Sep 18, 2024
6e2ed38
Add news
bobleesj Sep 18, 2024
889fac3
Capture the warning behavior
bobleesj Sep 19, 2024
de82a77
Clean up tests for catching error
bobleesj Sep 19, 2024
d65aa57
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Sep 19, 2024
b9b05a5
Shorten comments for test_diffraction_objects
bobleesj Sep 19, 2024
31f3c03
Setup requirements
bobleesj Oct 25, 2024
e69255a
Set valid q range for test dump function
bobleesj Oct 25, 2024
7b12baf
[pre-commit.ci] auto fixes from pre-commit hooks
pre-commit-ci[bot] Oct 25, 2024
0cb34e2
Pre-commit
bobleesj Oct 25, 2024
859755e
Apply pre-commit
bobleesj Oct 25, 2024
a3c5ea7
Merge branch 'codecov' of https://github.com/bobleesj/diffpy.utils in…
bobleesj Oct 25, 2024
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23 changes: 23 additions & 0 deletions news/warning.rst
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@@ -0,0 +1,23 @@
**Added:**

* <news item>

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* Two Pytest warnings due to numpy and pytest mocker in test_dump function

**Security:**

* <news item>
2 changes: 0 additions & 2 deletions requirements/build.txt
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python
setuptools
0 requirements/run.txt → requirements/conda.txt
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1 change: 1 addition & 0 deletions requirements/pip.txt
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numpy
17 changes: 9 additions & 8 deletions tests/test_diffraction_objects.py
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@@ -1,3 +1,4 @@
import warnings
from pathlib import Path

import numpy as np
Expand Down Expand Up @@ -232,18 +233,22 @@ def test_diffraction_objects_equality(inputs1, inputs2, expected):


def test_dump(tmp_path, mocker):
x, y = np.linspace(0, 10, 11), np.linspace(0, 10, 11)
x, y = np.linspace(0, 5, 6), np.linspace(0, 5, 6)
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To recollect our memory: we had this invalid value warning:

RuntimeWarning: invalid value encountered in arcsin
    print(np.rad2deg(2.0 * np.arcsin(q * pre_factor)))

Problem:

In our dummy test_dump function:

The code sets arbitrary q values as:

# x, y = np.linspace(0, 10, 11), np.linspace(0, 10, 11) sets q
# q = np.asarray(q)
# print(q)
[ 0.  1.  2.  3.  4.  5.  6.  7.  8.  9. 10.]

Hence, when we try to convert q to two-theta, using test.wavelength = 1.54:

print(np.rad2deg(2.0 * np.arcsin(q * pre_factor)))
[  0.          14.07850645  28.37532297  43.14126254  58.70709081
  75.57672216  94.66443973 118.15097974 157.27157928          nan
          nan]

We have nan values.

Solution:

Just simply use the valid q range from 0 to 6, etc.

directory = Path(tmp_path)
file = directory / "testfile"
test = Diffraction_object()
test.wavelength = 1.54
test.name = "test"
test.scat_quantity = "x-ray"
test.insert_scattering_quantity(
x, y, "q", metadata={"thing1": 1, "thing2": "thing2", "package_info": {"package2": "3.4.5"}}
x, y, "q", metadata={"thing1": 1, "thing2": "thing2", "package_info": {"package2": "3.4.5"}}
)
with mocker.patch("importlib.metadata.version", return_value="3.3.0"), freeze_time("2012-01-14"):

mocker.patch("importlib.metadata.version", return_value="3.3.0")

with freeze_time("2012-01-14"):
test.dump(file, "q")

with open(file, "r") as f:
actual = f.read()
expected = (
Expand All @@ -256,10 +261,6 @@ def test_dump(tmp_path, mocker):
"3.000000000000000000e+00 3.000000000000000000e+00\n"
"4.000000000000000000e+00 4.000000000000000000e+00\n"
"5.000000000000000000e+00 5.000000000000000000e+00\n"
"6.000000000000000000e+00 6.000000000000000000e+00\n"
"7.000000000000000000e+00 7.000000000000000000e+00\n"
"8.000000000000000000e+00 8.000000000000000000e+00\n"
"9.000000000000000000e+00 9.000000000000000000e+00\n"
"1.000000000000000000e+01 1.000000000000000000e+01\n"
)

assert actual == expected