Rdrp 994 clone folders

[zorge69]

Created all input and output folders in /bat/res_dev/

Updated the make_dir to use the config explicitly
Fixed a bug in the usage of tree_to_list.
Uploaded anonymised snapshot to /res_dev/anonymised
Uploaded anonymised backdata to /bat/res_dev/project_data/2021_surveys/BERD/06_imputation/backdata_output
Uploaded all mappers to /bat/res_dev/project_data/2023_surveys/mappers/v1 (ultfoc is anonymised)
Created log folder /bat/res_dev/project_data/logs/run_logs

The program still does not run. We need to merge the singleton class to develop. We need to undo the explicit passage of config argument in rd_make_dirs

Insert detailed bullet points about your changes here!

Insert any instructions to help the reviewer, e.g. "install new requirements from requirements.txt"

*Let the reviewer know what data files are needed (and if applicable, where they are to be found)

Closes or fixes

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

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.

---

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/aggregation
__init__.py	0	0	100%
src/construction
__init__.py	0	0	100%
all_data_construction.py	46	46	0%	1–2, 4–5, 7, 9, 17, 23, 46–47, 50, 55–56, 60–62, 66–67, 70, 77, 80, 83–87, 89, 94–95, 100–101, 104–106, 110, 114–117, 122–123, 125, 130–131, 135, 137
construction_helpers.py	104	14	86%	31–42, 220, 287
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	19	19	0%	1–2, 4–6, 9, 26, 29, 32, 37, 40–41, 44, 47, 49, 53, 57, 60–61
src/estimation
__init__.py	0	0	100%
apply_weights.py	19	2	89%	41–42
calculate_weights.py	52	0	100%
src/freezing
__init__.py	0	0	100%
freezing_apply_changes.py	73	21	71%	36–39, 42–43, 46–48, 51–54, 58, 66–69, 73–74, 76
freezing_compare.py	72	24	66%	111–112, 160–161, 187, 190–192, 195–197, 201–203, 205–207, 209–210, 242, 267, 270, 273, 276
freezing_utils.py	11	0	100%
src/imputation
MoR.py	133	2	98%	294, 444
__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	119	50	57%	39, 52–55, 58–59, 61–62, 64–65, 67–68, 70–71, 73–74, 76–77, 79, 88, 90–91, 93–94, 263, 265, 267–268, 270, 274, 295, 298, 302, 305–306, 308, 393, 395–396, 399, 411–412, 414, 416, 432–433, 436–437, 439
impute_civ_def.py	98	47	52%	164, 167, 197, 199–200, 203–204, 207–209, 214–215, 217, 220, 222–225, 227, 229, 234–235, 237, 240, 242–244, 247, 249–250, 252–253, 255–256, 269, 272–276, 278–279, 282–283, 285–286, 288
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	71	58	18%	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, 217, 221, 223
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	188	122	35%	105, 107, 113–115, 119, 125, 128, 130, 135, 140, 145, 266, 269, 271, 274, 278, 282, 304–305, 308, 311–312, 315, 318–319, 322, 324–325, 327, 329, 332–333, 335, 337, 340, 343–344, 346, 349–351, 353–356, 358, 374, 376, 383, 385–386, 388–389, 391, 393, 395, 397, 400, 403–404, 407, 409, 411, 429–430, 432, 434–435, 437–439, 441–442, 445, 447–448, 451, 453–454, 472, 474, 477–479, 481, 483–484, 486–487, 490, 492–493, 496, 498, 500–501, 521, 525, 528–529, 532–533, 536, 539, 541, 546, 548, 553, 555, 562–563, 566, 569–570, 572, 575, 577, 579, 584, 586–587
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
pg_conversion.py	40	8	80%	52, 55, 58, 122, 125, 128, 162–163
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_staging.py	35	35	0%	3–7, 9, 11, 14, 22, 25, 27–29, 31, 34, 40, 44, 46, 49, 80–81, 84, 89, 93, 96, 99–104, 107–108, 110, 112
src/outlier_detection
__init__.py	0	0	100%
auto_outliers.py	81	0	100%
manual_outliers.py	16	0	100%
src/outputs
__init__.py	0	0	100%
export_files.py	88	88	0%	5–11, 13–14, 18, 24, 42, 44, 51, 56, 63, 68, 71, 98, 104, 107, 114, 116, 119, 125, 127–128, 131–135, 138–139, 142, 153–155, 157, 160, 173, 175–176, 178, 181, 201, 204, 207–208, 215, 219, 222–224, 227, 229–230, 233–234, 237–241, 243–244, 246, 249–251, 254, 257, 260, 274, 277–278, 286, 289, 291, 293, 303, 305–307, 316, 318, 321–322
form_output_prep.py	18	13	27%	25–27, 29–30, 34, 36–37, 39, 41, 43, 47, 49
frozen_group.py	45	45	0%	3–4, 6–7, 9–11, 13, 16, 47, 49–52, 55, 73, 125, 136, 163, 166–170, 172, 174, 177, 180–181, 183, 186, 189, 194–195, 198–199, 202, 205–207, 210–213, 215
gb_sas.py	25	25	0%	2–5, 7–9, 11, 14, 32, 35, 40, 43, 46, 49, 54, 57, 60–62, 65–68, 70
intram_by_civil_defence.py	23	23	0%	2–6, 8, 11, 30, 32–33, 36–37, 39, 42, 47, 50, 53–55, 58–61
intram_by_itl.py	55	16	70%	46–50, 54, 146, 149, 152–154, 157–158, 161–162, 172
intram_by_pg.py	31	0	100%
intram_by_sic.py	35	35	0%	2–5, 7, 10, 32–33, 36–37, 40–41, 43, 46–48, 53, 69–73, 75, 78, 81, 84, 87, 90–91, 94–97, 100, 102
intram_totals.py	16	16	0%	3–4, 6–7, 9, 12, 31–32, 35, 38, 41–42, 44–47
long_form.py	19	19	0%	2–5, 7–9, 11, 14, 31, 34, 37, 40–42, 44–47
manifest_output.py	78	78	0%	1–4, 8, 11–12, 15, 33, 48–51, 54–55, 59–60, 65–66, 68, 71–75, 78–84, 86, 104–105, 110, 112–113, 118, 121, 123, 125, 127, 131, 141, 146–147, 153, 156–157, 159–160, 166–169, 174, 181, 183, 188, 190–192, 194–195, 197–198, 200–203, 205, 208, 210, 216–217, 220–221
map_output_cols.py	38	7	81%	150–151, 153, 155, 158, 161, 163
ni_sas.py	21	21	0%	2–8, 10, 13, 28, 31, 34, 37, 42, 45–47, 50–53
outputs_helpers.py	17	0	100%
short_form.py	36	15	58%	78, 85, 87, 105, 108, 111, 114, 117, 120–122, 124–127
tau.py	27	27	0%	2–8, 10, 13, 33, 37, 40, 43, 46, 49, 54, 57, 59–60, 63–65, 68–71, 73
total_fte.py	14	14	0%	2–5, 8, 11, 24, 26–27, 33, 38–41
src/site_apportionment
__init__.py	0	0	100%
output_status_filtered.py	28	17	39%	24, 26, 30–31, 33–34, 36, 43–44, 72, 75, 77, 79–82, 84
site_apportionment.py	124	27	78%	97, 99–105, 458, 460–461, 504, 508, 510, 513, 516, 519, 522, 534, 537, 540, 543, 546, 549, 552, 555, 557
src/staging
__init__.py	0	0	100%
postcode_validation.py	80	3	96%	195–196, 334
spp_parser.py	14	0	100%
spp_snapshot_processing.py	34	0	100%
staging_helpers.py	86	25	70%	113, 116, 119, 122, 125, 128–129, 132, 135, 138, 171, 174, 176, 179–180, 183, 186, 188–189, 192, 196–197, 199, 203, 209
validation.py	135	44	67%	33, 36, 85–86, 97, 119, 132–133, 138, 142, 150–151, 157–158, 197–198, 204, 206, 209, 211, 292, 294–295, 298–299, 302–303, 306, 309–310, 313, 315, 317–318, 332, 334–340, 343, 346
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	148	2	98%	157–158
defence.py	20	0	100%
helpers.py	63	18	71%	19–20, 24–25, 27, 133–136, 138–139, 142–144, 153, 155–156, 214
local_file_mods.py	116	45	61%	48–54, 99, 149–151, 200–204, 215–216, 227, 238, 249–250, 252, 263–264, 275–276, 285, 293, 304, 306–307, 309–310, 314–316, 320, 334–335, 338–339, 341, 358, 363
path_helpers.py	127	8	93%	56, 269, 271, 273–274, 276–277, 279
postcode_reduction_helper.py	38	38	0%	11, 13–14, 16, 19, 22, 25, 27–28, 30–31, 34–35, 38, 40–41, 43–44, 47, 60, 62, 65, 68, 71–72, 74–75, 77, 80, 95, 97, 100–101, 104–105, 107, 109–110
s3_mods.py	42	42	0%	25–26, 30–31, 38–39, 42, 44, 47–48, 52, 66, 68–69, 72–75, 77–78, 81, 92, 95, 100, 103, 106, 109, 120–121, 123, 126, 140, 144–145, 147, 150, 160, 167, 170, 172, 175, 177
singleton_boto.py	12	12	0%	4–5, 8–9, 12–13, 16, 18–20, 24, 26
TOTAL	3354	1381	58%

Summary of tests

Tests	Skipped	Failures	Errors	Time
249	2 💤	0 ❌	0 🔥	4.580s ⏱️

[AnneONS]

This needs to go in 2022_surveys so we can run the 2023 pipeline.

[AnneONS]

I have corrected this one.

[AnneONS]

I have removed config from mk_dirs, and I have also corrected the tree, as it was a bit off. I've checked by creating folders in my own area- it does run and does what it's meant to.