RDRP-1087 outliers

[AnneONS]

Pull Request submission

The code src.outlier_detection.auto_outliers.py has a large function flag_outliers.

I have created a separate function that indicates the number or rows that should be clipped for outliering, with a unit test.

This unit test illustrates how many rows get outliered depending on the size of valid entries in a cell.

Closes or fixes

• Detail the ticket(s) you are closing with this PR
  Closes #1087

Code

• Code runs The code runs on my machine and/or CDSW
• Conflicts resolved There are no conflicts (I have performed a rebase if necessary)
• Requirements My/our code functions according to the requirements of the ticket
• Dependencies I have updated the environment yaml so it includes any new libraries I have used
• Configuration file updated any high level parameters that the user may interact with have been put into the config file (and imported to the script)
• Clean Code
  • Code is as PEP 8 compliant as I can humanly make it
  • Code passess flake8 linting check
  • Code adheres to DRY
• Type hints All new functions have type hints

Documentation

Any new code includes all the following forms of documentation:

• Function Documentation Docstrings within the function(s')/methods have been created
  • Includes Args and returns for all major functions
  • The docstring details data types
• Updated Documentation: User and/or developer working doc has been updated

Data

• All data needed to run this script is available in Dev/Test
• All data is excluded from this pull request
• Secrets checker pre-commit passes

Testing

• Unit tests Unit tests have been created and are passing or a new ticket to create tests has been created

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Peer Review Section

• All requirements install from (updated) requirements.txt
• Documentation has been created and is clear - check the working document
• Doctrings (Google format) have been created and accurately describe the function's functionality
• Unit tests pass, or if not present a new ticket to create tests has been created
• Code runs The code runs on reviewer's machine and/or CDSW

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction.

• I recommend merging this request.

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Review comments

Insert detailed comments here!

These might include, but not exclusively:

• bugs that need fixing (does it work as expected? and does it work with other code
  that it is likely to interact with?)
• alternative methods (could it be written more efficiently or with more clarity?)
• documentation improvements (does the documentation reflect how the code actually works?)
• additional tests that should be implemented (do the tests effectively assure that it
  works correctly?)
• code style improvements (could the code be written more clearly?)
• Do the changes represent a change in functionality so the version number should increase? Start a discussion if so.
• As a review you can generates the same outputs from running the code

Your suggestions should be tailored to the code that you are reviewing.
Be critical and clear, but not mean. Ask questions and set actions.

[github-actions]

Detailed Coverage Report

File	Stmts	Miss	Cover	Missing
src
__init__.py	0	0	100%
src/construction
__init__.py	0	0	100%
all_data_construction.py	47	47	0%	1, 3–4, 6, 8, 16, 22, 45–46, 49, 54–55, 59–61, 65–66, 69, 76–78, 83, 86–90, 92, 97–98, 103–104, 107–109, 113, 117–120, 125–126, 128, 133–134, 138, 140
construction_helpers.py	104	14	86%	31–42, 239, 306
construction_main.py	27	27	0%	2–3, 5, 7, 11–12, 15, 18, 54–57, 64, 68–71, 74, 78–81, 84, 89–91, 93
construction_read_validate.py	34	34	0%	2–3, 5, 8, 11, 16, 18, 21, 46–49, 51–52, 55–56, 59, 66–68, 72–73, 79, 82, 101–103, 105–106, 109, 116–117, 122, 129
construction_validation.py	102	9	91%	83, 86, 113, 121–122, 127, 138, 168, 218
postcode_construction.py	21	21	0%	1–2, 4–6, 9, 26, 29, 32, 37, 40–41, 44, 47–49, 51, 55, 59, 62–63
src/estimation
__init__.py	0	0	100%
apply_weights.py	18	2	88%	46–47
calculate_weights.py	52	0	100%
estimation_main.py	22	22	0%	2–4, 6–8, 10, 13, 29, 35, 38, 41–42, 44–51, 53
src/freezing
__init__.py	0	0	100%
freezing_apply_changes.py	70	21	70%	31–34, 37–38, 41–43, 46–49, 53, 61–64, 68–69, 71
freezing_compare.py	68	22	67%	107–108, 156–157, 181, 184, 187–189, 193–195, 197–199, 201–202, 234, 257, 260, 263, 266
freezing_main.py	46	46	0%	1–3, 5, 7–12, 15, 18, 42–43, 46–47, 49–53, 55, 63, 66–68, 71–72, 76–78, 83–84, 86–87, 90–91, 95, 98, 109–112, 114–116
freezing_utils.py	11	0	100%
src/imputation
MoR.py	150	7	95%	57–58, 73, 293, 445, 489–490
__init__.py	0	0	100%
apportionment.py	36	10	72%	124, 126, 141, 143, 145, 157–159, 162, 164
expansion_imputation.py	37	30	18%	23–24, 26–27, 30, 33–35, 39, 42, 44, 47–48, 50, 53, 56, 76–78, 82, 85, 88, 91, 97, 102, 105, 107, 113, 116, 120
imputation_helpers.py	138	56	59%	67, 69, 78, 85, 98–101, 104–105, 107–108, 110–111, 113–114, 116–117, 119–120, 122–123, 125, 134, 136–137, 139–140, 309, 311–312, 316–317, 319, 323, 344, 347, 351, 354–355, 357, 445, 447–448, 451, 463–464, 467–468, 470, 472, 488–489, 492–493, 495
imputation_main.py	75	75	0%	3–6, 8–18, 21, 24, 55, 58, 61, 64–65, 68–69, 72, 74, 79, 82–83, 86, 89–90, 93, 95, 99–100, 104–106, 109, 113–114, 117–118, 121–124, 126, 130, 133–134, 136–140, 142, 144–146, 148–150, 152–153, 156, 159, 162–167, 169
impute_civ_def.py	99	47	52%	165, 168, 198, 200–201, 204–205, 208–210, 215–216, 218, 221, 223–226, 228, 230, 235–236, 238, 241, 243–245, 248, 250–251, 253–254, 256–257, 270, 273–277, 279–280, 283–284, 286–287, 289
manual_imputation.py	19	19	0%	1–2, 4, 6, 9–10, 28–29, 33, 35, 37, 44, 59, 61–62, 64–65, 67–68
sf_expansion.py	74	61	17%	24, 27, 30–31, 34–35, 38, 41, 44–45, 48, 50, 57–58, 61, 66–67, 70, 72, 75–76, 78, 80, 83, 87, 89, 100, 103, 107, 109–110, 112, 114, 117, 120, 129, 132, 135, 144, 147, 149, 155, 161, 173, 176, 181–182, 184, 192–193, 196, 200, 204, 207, 215, 222–223, 226, 228, 232, 234
short_to_long.py	21	21	0%	1, 3–4, 7, 20, 23, 25, 32–33, 35, 37–38, 40–41, 43–45, 47, 49, 53, 55
tmi_imputation.py	181	127	29%	28–29, 57, 59, 65–67, 71, 77, 80, 82, 87, 92, 97, 218, 221, 223, 226, 230, 234, 256–257, 260, 263–264, 267, 270–271, 274, 276–277, 279, 281, 284–285, 287, 289, 292, 295–296, 298, 301–303, 305–308, 310, 326, 328, 335, 337–338, 340–341, 343, 345, 347, 349, 352, 355–356, 359, 361, 363, 381–382, 384, 386–387, 389–391, 393–394, 397, 399–400, 403, 405–406, 424, 426, 429–431, 433, 435–436, 438–439, 442, 444–445, 448, 450, 452–453, 473, 477, 480–481, 484–485, 488, 491, 493, 498, 500, 505, 507, 514–515, 520, 527–528, 530, 533–534, 536, 539, 541, 543, 548, 550–551
src/mapping
__init__.py	0	0	100%
cellno_mapping.py	17	4	76%	49–51, 53
itl_mapping.py	10	0	100%
mapping_helpers.py	55	5	90%	24–27, 69
mapping_main.py	49	49	0%	3–5, 7–15, 17, 20, 45, 50, 59, 68, 75, 78, 85, 88–90, 97, 99, 102–104, 107, 109–111, 114, 117, 122–123, 126, 128–132, 134–136, 139, 142, 145
pg_conversion.py	40	8	80%	52, 55, 58, 122, 125, 128, 162–163
pnp_mapping.py	24	24	0%	1–2, 5, 8, 17–19, 21, 24, 27, 38–40, 42, 46, 49, 57, 73, 75, 78, 89–91, 93
ultfoc_mapping.py	34	4	88%	49–51, 95
src/northern_ireland
__init__.py	0	0	100%
ni_headcount_fte.py	29	29	0%	2–4, 6, 8, 11, 25, 27, 29, 31, 33, 35, 37, 40, 55, 57–59, 61, 63–64, 66–67, 69, 72, 81, 83–84, 86
ni_main.py	21	21	0%	3–9, 11, 14, 34, 37–39, 45, 52–54, 62, 64–65, 67
ni_staging.py	33	33	0%	3–6, 8–9, 11, 14, 22, 25, 27–29, 31, 34, 40, 44, 46, 49, 78–79, 82, 87, 91, 94, 97–102, 104, 106
src/outlier_detection
__init__.py	0	0	100%
auto_outliers.py	90	0	100%
manual_outliers.py	16	0	100%
outlier_main.py	39	39	0%	2–4, 6–8, 10, 13, 42, 44–46, 48–49, 52, 55, 58–63, 65, 70–71, 74, 79–82, 85–89, 91, 94, 96, 98
src/outputs
__init__.py	0	0	100%
export_files.py	92	92	0%	5–11, 13–14, 18, 24, 42, 44, 51–54, 61, 68, 73, 76, 103, 109, 112, 119, 121, 124, 130, 132–133, 136–140, 143–144, 147, 158–160, 162, 165, 178, 180–181, 183, 186, 206, 209, 212–213, 220, 224, 227–229, 232, 234, 236, 238–239, 241, 244–248, 250–251, 253, 256–258, 261, 264, 267, 282, 285–286, 294, 297, 299, 301, 311, 313–315, 324, 326, 329–330
form_output_prep.py	18	13	27%	25–27, 29–30, 34, 36–37, 39, 41, 43, 47, 49
frozen_group.py	43	43	0%	3–4, 6, 8–11, 13, 16, 45, 47–50, 53, 71, 123, 134, 161, 164–168, 170, 172, 175, 178–179, 181, 184, 187, 192–193, 196–197, 200, 203–205, 208–209, 211
gb_sas.py	23	23	0%	2–4, 6–9, 11, 14, 30, 33, 38, 41, 44, 47, 52, 55, 58–60, 63–64, 66
intram_by_civil_defence.py	21	0	100%
intram_by_itl.py	54	15	72%	44–47, 51, 141, 144, 147–149, 152–153, 157–158, 167
intram_by_pg.py	35	0	100%
intram_by_sic.py	33	33	0%	2–5, 7, 10, 30–31, 34–35, 38–39, 41, 44–46, 51, 67–71, 73, 76, 79, 82, 85, 88–89, 92–93, 96, 98
intram_totals.py	14	14	0%	3–4, 6–7, 9, 12, 29–30, 33, 36, 39–40, 42–43
long_form.py	17	17	0%	2–4, 6–9, 11, 14, 29, 32, 35, 38–40, 42–43
manifest_output.py	82	82	0%	1–5, 9, 12–13, 16, 34, 50–53, 56–57, 61–62, 67–68, 76, 79–83, 86–92, 94, 112–113, 118, 120–121, 126, 129, 131, 133, 135, 139, 149, 154–155, 161, 164–165, 167–168, 174–177, 183–185, 187, 194, 196, 201, 203–205, 207–208, 210–211, 213–216, 218, 221, 223, 229–230, 233–234
map_output_cols.py	38	7	81%	150–151, 153, 155, 158, 161, 163
ni_sas.py	19	19	0%	2–8, 10, 13, 26, 29, 32, 35, 40, 43–45, 48–49
outputs_helpers.py	17	0	100%
outputs_main.py	83	83	0%	3–4, 7, 10–22, 24, 27, 49, 54–56, 61, 64, 67–69, 74, 77–78, 81–83, 89, 92–94, 100, 103–105, 107–108, 113, 116–118, 127, 130–132, 136–137, 146, 149–151, 158, 161–163, 167–168, 176, 179–181, 188, 191–193, 198, 201–203, 210, 213–215, 217–219, 221
short_form.py	34	13	61%	78, 85, 87, 104, 107, 110, 113, 116, 119–121, 123–124
tau.py	25	25	0%	2–8, 10, 13, 30, 34, 37, 40, 43, 46, 51, 54, 56–57, 60–62, 65–66, 68
total_fte.py	12	12	0%	2–5, 8, 11, 26, 28–29, 35, 40–41
src/site_apportionment
__init__.py	0	0	100%
output_status_filtered.py	26	15	42%	25, 27, 31–32, 34–35, 37, 44–45, 72, 75, 77, 79–80, 82
site_apportionment.py	126	3	97%	467, 469–470
site_apportionment_main.py	25	25	0%	3–5, 7–8, 12, 14, 17, 39–40, 43, 45, 48–49, 57–58, 60–61, 64, 69–72, 74–75
src/staging
__init__.py	0	0	100%
postcode_validation.py	56	3	94%	131–132, 220
spp_parser.py	14	0	100%
spp_snapshot_processing.py	34	0	100%
staging_helpers.py	86	15	82%	173, 176, 178, 181–182, 185–186, 188–189, 192, 196–197, 199, 203, 209
staging_main.py	98	98	0%	3–5, 7, 9–11, 15, 18, 64–66, 69, 71, 75–77, 79–80, 84, 86–87, 90, 93, 96–97, 99–100, 105–107, 111–114, 116–117, 123, 128–130, 132–133, 136, 148–150, 155, 158, 162, 164, 166–168, 171, 175, 177, 179–183, 186, 189, 191–192, 195, 197, 200–204, 207, 211–212, 215–219, 221, 224, 232, 241–242, 244–249, 251, 253–254, 256, 259, 270
validation.py	143	49	65%	34–36, 39, 42, 88–89, 100, 122, 135–136, 141, 145, 153–154, 160–161, 200–201, 207, 209, 212, 214, 221–222, 301, 303–304, 307–308, 311–312, 315, 318–319, 322, 324, 326–327, 341, 343–349, 352, 355
src/utils
__init__.py	0	0	100%
breakdown_validation.py	130	45	65%	29, 186–188, 190–194, 196, 198, 201–202, 208–209, 212, 215, 217, 220, 222, 234–237, 240–243, 259–260, 265, 308–309, 311, 317–318, 360–363, 365–368, 371
config.py	149	2	98%	152–153
defence.py	20	0	100%
helpers.py	73	18	75%	19–20, 24–25, 27, 134–137, 139–140, 143–145, 154, 156–157, 215
local_file_mods.py	120	47	60%	47–53, 98, 148–150, 199–203, 214–215, 226, 237, 248–249, 251, 262–263, 274–275, 284, 292, 303, 305–306, 308–309, 313–315, 319, 333–334, 336–337, 340–341, 343, 360, 365
path_helpers.py	142	8	94%	96, 311, 313, 315–316, 318–319, 321
postcode_reduction_helper.py	38	38	0%	11, 13–14, 16, 19, 21, 24, 26–27, 29–30, 33–34, 37, 39–40, 42–43, 46, 59, 61, 64, 67, 70–71, 73–74, 76, 79, 94, 96, 99–100, 103–104, 106, 108–109
s3_mods.py	127	127	0%	19–20, 22–23, 25, 33, 38–40, 44, 58, 60–61, 64–67, 69–70, 73, 84, 87, 92, 95–96, 99, 110–111, 113, 116, 130, 132–133, 135, 138, 148, 155, 158, 160, 163, 165, 168, 179–180, 182, 185, 193–194, 197, 206–211, 214, 225–226, 229–230, 233, 236, 239, 250–251, 253–256, 258–259, 262, 268, 271, 284, 287, 290, 292, 295, 301, 304, 307–308, 311, 319–321, 323, 326, 330–331, 333, 336, 365, 369, 371, 378, 381, 386–388, 395, 398, 413, 415–416, 418–419, 423, 425, 427, 430, 432–434, 436, 439, 449, 452–453, 456, 459, 461–462, 464–466
singleton_boto.py	20	20	0%	4–5, 8–10, 12–13, 15–22, 24–28
TOTAL	3996	1938	51%

Summary of tests

Tests	Skipped	Failures	Errors	Time
265	2 💤	0 ❌	0 🔥	3.409s ⏱️

[adriano-lopresti]

When running the pipeline I get the following error:

FileExistsError: File: R:/BERD Results System Development 2023/DAP_emulation/2021_surveys/PNP/06_imputation/backdata_output/PNP_2021_backdata_thousands.csv does not exist

To make it run you need to remove the postfix _thousand from the filename in dev_configs.

[adriano-lopresti]

the case where function "get_clip_bands" has a non-zero lower_clip has not been tested. I'm wondering if this is worth doing.
Also, has "flag_outliers" been unit-tested for the case where lower_clip is not zero?

[AnneONS]

Yes, the flag_outliers has been unit tested where the lower_clip is non zero. I think you're right, I'll add in a unit test for get_clip_bands for non-zero lower clip as well, and for when both are non-zero.