ENH: Logistic completeness function #521

philipp128 · 2022-02-22T07:24:27Z

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This PR adds a feature to calculate the logistic completeness function. Closes #519.

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Lucia-Fonseca

Comments on readability, naming convention and potentially extra unit tests.

skypy/utils/completeness_function.py

Lucia-Fonseca · 2022-02-22T11:53:56Z

skypy/utils/completeness_function.py

+def logistic_completeness_function(m, m95, m50):
+    r'''Compute logistic completeness function.
+
+    This function calculates the logistic completeness function


Can you provide a reference?

skypy/utils/completeness_function.py

skypy/utils/tests/test_completeness_function.py

philipp128 · 2022-02-25T13:40:15Z

Edit: It works now and the docs should be fine.

~~Docs are failing. I am waiting to resolve this right now cause I have a problem with the docs anyway.~~

~~The docs for completeness function is not rendered properly. It is included but not linked or specified -> see attached~~ ~~image. I do not know where the problem is.~~

~~@rrjbca do you know whether I forgot sth?~~

rrjbca · 2022-03-11T15:36:41Z

I would also suggest making this part of skypy.utils.photometry. In effect the completeness is an extrinsic photometric property of the sources. This would again save creating a new submodule.

skypy/utils/completeness_function.py

…pleteness_function

…eness_function module.

Lucia-Fonseca

Just a comment on docstrings, but looks good.

skypy/utils/photometry.py

rrjbca

You shouldn't need six tests for different combinations of array shapes; one slightly more complex broadcasting test should be sufficient e.g:

m = np.full((2, 1, 1), 21)
m95 = np.full((3, 1), 22)
m50 = np.full(5, 23)
p = logistic_completeness_function(m, m95, m50)
assert p.shape = np.broadcast(m, m95, m50).shape

In your final test check more magnitudes that have analytic values:

m95 = 24
m50 = 25
m = [np.finfo(np.float64).min, m95, m50, 2*m50-m95, np.finfo(np.float64).max]
p = logistic_completeness_function(m, m95, m50)
assert np.allclose(p, [1, 0.95, 0.5, 0.05, 0])

The reference to López-Sanjuan 2017 is not linked anywhere in the docstring. Also note the correct spelling of the name with the accent.

…d reference in docs

skypy/utils/tests/test_photometry.py

* Update name of default branch to main (#434) * update mailmap (#432) * Write all tables to a single FITS/HDF5 file (#425) * ADR 3: Position sampling and patches of the sky (#422) * BUG: Raise ImportError if optional dependency speclite is not installed (#437) * MAINT: Set NumPy latest supported version to 1.20 #440 * Update status badges (#441) * MAINT: Update Lucia affiliation (#451) * MAINT: add SIT's information (#450) * DOC: Fix contributor guidelines link (#449) Co-authored-by: Richard R <58728519+rrjbca@users.noreply.github.com> Co-authored-by: Nicolas Tessore <n.tessore@ucl.ac.uk> * ENH: Logging for skypy command line script and Pipeline class (#453) * DOC: Describe speclite filters in documentation (#457) * ENH: Config syntax for importing objects (#463) * DOC: List of Features (#456) * DOC: How to construct config files (#454) * DOC: Remove docstring examples (#429) * MAINT: Update Zenodo entry for RPR (#468) * DOC: Readme updates (#460) * DOC: Expanded landing page documentation (#228) * DOC: Inverse transform sampling accuracy warning (#472) * MAINT: Set astropy latest supported version to 4.2 (#483) * DOC: zenodo json members update (#481) * DOC: Ryden04 ellipticity doc missing section (#477) * MAINT: Update numpy and scipy latest supported versions (#488) * BUG: Change invalid ecsv datatype from int to uint16 (#485) * DEV: setuptools==58.0.0 (#493) Co-authored-by: Nicolas Tessore <n.tessore@ucl.ac.uk> * Add compatibility workflow badge (#487) * DEV: Enable pip to install pre-releases in the tox dev environments (#491) * TST: Use tmp_path fixture for temporary files in unit tests (#489) * BUG: Move handling of context arguments after handling of .depends keyword (#465) * BLD: Set astropy latest supported version to 4.3 and speclite minversion to 0.14 (#486) * REV: restore setuptools to latest version on readthedocs (#494) * DEV: pyparsing<3.0.0 (#500) * Check new astropy file overwrite error message in logging test (#498) * REV: restore pyparsing to latest version for doc builds (#501) * DOC: Update citation file with JOSS paper reference (#496) * BLD: Set astropy latest supported version to 5.0 (#504) * BLD: Set python latest supported version to 3.10 (#505) * BLD: Set numpy latest supported version to 1.22 (#506) * BLD: Set python oldest supported version to 3.7 (#507) * DOC: Fix code of conduct link (#508) * Changed y-label in luminosity function example. (#512) * BLD: Set scipy latest supported version to 1.8 (#510) * ENH: Rykoff model of the magnitude uncertainty (#526) * TST: assert photometric error is numerically close to the analytic value (#545) * TST: Drop deprecated astropy.tests.helper.raises (#546) * ENH: compute kcorrect remaining stellar mass (#476) * compute kcorrect remaining stellar mass * added test for stellar mass remain Co-authored-by: Ian Harrison <itrharrison@gmail.com> Co-authored-by: Lucia F. de la Bella <55983939+Lucia-Fonseca@users.noreply.github.com> * ENH: Logistic completeness function (#521) * BLD: Set astropy latest supported version to 5.1 (#547) * BUG: `schechter_smf` callable input and docs (#525) * DOC: Typo in Rykoff error (#550) * add Fox's details (#551) Co-authored-by: Richard R <58728519+rrjbca@users.noreply.github.com> * BLD: Set numpy latest supported version to 1.23 (#552) * codestyle fixes * add six requirement for colossus * tried to fix docs builds * update passenv * rtd configuration Co-authored-by: Richard R <58728519+rrjbca@users.noreply.github.com> Co-authored-by: Nicolas Tessore <n.tessore@ucl.ac.uk> Co-authored-by: Lucia F. de la Bella <55983939+Lucia-Fonseca@users.noreply.github.com> Co-authored-by: Sut-Ieng Tam <30295725+sutieng@users.noreply.github.com> Co-authored-by: philipp128 <48715661+philipp128@users.noreply.github.com> Co-authored-by: Fox Davidson <93545862+Fox-Davidson@users.noreply.github.com>

Adding method to calculate the logistic completeness function.

caf37d7

philipp128 added enhancement Improvement of existing feature module: utils labels Feb 22, 2022

philipp128 requested a review from a team as a code owner February 22, 2022 07:24

philipp128 requested a review from Lucia-Fonseca February 22, 2022 07:25

philipp128 added 2 commits February 22, 2022 08:29

Fixing style issues.

28bc52a

Fixing style in init file.

596379a

Lucia-Fonseca requested changes Feb 22, 2022

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Renaming parameters, improving docs, adding tests

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philipp128 added 2 commits March 1, 2022 08:14

Different way to include in doc.

c66e44b

Fixing docs.

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rrjbca reviewed Mar 11, 2022

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skypy/utils/completeness_function.py Outdated Show resolved Hide resolved

philipp128 added 2 commits May 6, 2022 14:51

Merge branch 'main' of https://github.com/skypyproject/skypy into com…

112f265

…pleteness_function

Shift logistic function in utils.photometry module and delete complet…

6e8d016

…eness_function module.

Lucia-Fonseca previously approved these changes May 9, 2022

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skypy/utils/photometry.py Outdated Show resolved Hide resolved

Implement Docstring suggestion.

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philipp128 dismissed Lucia-Fonseca’s stale review via dd0b4cd May 16, 2022 10:23

rrjbca requested changes May 24, 2022

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Improved test for shapes, improved test for magntiude values, improve…

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…d reference in docs

rrjbca reviewed May 25, 2022

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skypy/utils/tests/test_photometry.py Outdated Show resolved Hide resolved

rrjbca added 2 commits May 25, 2022 12:40

Update skypy/utils/tests/test_photometry.py

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Merge branch 'main' into completeness_function

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rrjbca approved these changes May 25, 2022

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rrjbca merged commit 22ebe38 into skypyproject:main May 25, 2022

ENH: Logistic completeness function #521

ENH: Logistic completeness function #521

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philipp128 commented Feb 25, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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rrjbca commented Mar 11, 2022

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philipp128 commented Feb 22, 2022 •

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philipp128 commented Feb 25, 2022 •

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