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sequence writing tests to excel #1013

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merged 7 commits into from
Oct 16, 2024

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Close #1001

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ready for review

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@check-spelling-bot Report

🔴 Please review

See the 📂 files view, the 📜action log, or 📝 job summary for details.

Unrecognized words (1)

SPSS

Previously acknowledged words that are now absent anomymous datas spss 🫥
To accept these unrecognized words as correct and remove the previously acknowledged and now absent words, you could run the following commands

... in a clone of the [email protected]:Public-Health-Scotland/source-linkage-files.git repository
on the sequence-extracts-tests-writing branch (ℹ️ how do I use this?):

curl -s -S -L 'https://raw.githubusercontent.com/check-spelling/check-spelling/main/apply.pl' |
perl - 'https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/11364344451/attempts/1'

OR

To have the bot accept them for you, reply quoting the following line:
@check-spelling-bot apply updates.

Available 📚 dictionaries could cover words (expected and unrecognized) not in the 📘 dictionary

This includes both expected items (313) from .github/actions/spelling/expect.txt and unrecognized words (1)

Dictionary Entries Covers Uniquely
cspell:fullstack/dict/fullstack.txt 419 3 3
cspell:k8s/dict/k8s.txt 153 4 1
cspell:php/dict/php.txt 1689 4
cspell:node/dict/node.txt 891 3 1
cspell:npm/dict/npm.txt 302 3

Consider adding them (in .github/workflows/spelling.yml) for uses: check-spelling/check-spelling@main in its with:

      with:
        extra_dictionaries:
          cspell:fullstack/dict/fullstack.txt
          cspell:k8s/dict/k8s.txt
          cspell:php/dict/php.txt
          cspell:node/dict/node.txt
          cspell:npm/dict/npm.txt

To stop checking additional dictionaries, add (in .github/workflows/spelling.yml) for uses: check-spelling/check-spelling@main in its with:

check_extra_dictionaries: ''
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You could add these patterns to .github/actions/spelling/patterns.txt:

# Automatically suggested patterns
# hit-count: 3 file-count: 1
# Compiler flags
(?:^|[\t ,"'`=(])-[DPWXYLlf](?=[A-Z]{2,}|[A-Z][a-z]|[a-z]{2,})

Errors (2)

See the 📂 files view, the 📜action log, or 📝 job summary for details.

❌ Errors Count
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❌ ignored-expect-variant 3

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We talked through this one and the code looks good. Ready to merge

@Jennit07 Jennit07 merged commit 74947ce into december-2024 Oct 16, 2024
10 of 11 checks passed
@Jennit07 Jennit07 deleted the sequence-extracts-tests-writing branch October 16, 2024 11:07
github-merge-queue bot pushed a commit that referenced this pull request Dec 10, 2024
* Move `cli` warning messages before `return()` (#1016)

* reorder episode file functions cli messages

* reorder indiv file functions cli messages

* Refine cli messages

* reorder cli messages

* Style code

---------

Co-authored-by: Jennit07 <[email protected]>

* Update check_year_valid.R (#1017)

Co-authored-by: Jennit07 <[email protected]>

* Remove person_id. Matched in later process

* Remove redundant #TODO comments

* remove redundant #TODO comments

* Update news - sep release date

* Write temp data (#1014)

* add_test_to_filename and write_temp_data function

* Update documentation

* remove test_mode default

* Update documentation

* add read_temp_data

* Style code

* Update documentation

* change test_mode to write_temp_to_disk and add clean temp function

* Update documentation

* Style code

* Style code

* Include extra temp file

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>

* sequence writing tests to excel (#1013)

* sequence writing tests to excel

* Style code

* minor changes

* fix bugs in anonymous function

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

* Sc latest quarter (#1012)

* prompt warnings of latest period when reading in sc data

* Style code

* add warning to show latest quarter for sc client

* Style code

* Update R/read_lookup_sc_client.R

Co-authored-by: Jennit07 <[email protected]>

* Update R/read_lookup_sc_demographics.R

Co-authored-by: Jennit07 <[email protected]>

* Update R/read_sc_all_alarms_telecare.R

Co-authored-by: Jennit07 <[email protected]>

* Update R/read_sc_all_care_home.R

Co-authored-by: Jennit07 <[email protected]>

* Update R/read_sc_all_home_care.R

Co-authored-by: Jennit07 <[email protected]>

* Update R/read_sc_all_sds.R

Co-authored-by: Jennit07 <[email protected]>

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

* death join and distinct refined death (#1015)

* distinct death date, keep the earliest one and remove na

* add activity after death 100% accurate joining

* Style code

* remove redundant combine death function

* Update documentation

* fix NA in activity_after_death

* Style code

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

* 1018 moving dd hl1 (#1019)

* moving dd and homelessness to front

* fix typos

* Update documentation

* Style code

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

* Update process_extract_ae.R (#1020)

* Update process_extract_ae.R

* Style code

---------

Co-authored-by: lizihao-anu <[email protected]>

* Organise pre processing scripts (#1023)

* Create a new folder to organise scripts

* Add comments

* Move script to folder

* Style code

---------

Co-authored-by: Jennit07 <[email protected]>

* Clean test folder (#1021)

* Update refs script

* Add check_year_valid to update_refs script

* Update documentation

* Add description to 00_update_refs

* Update wb name and paths for write_xlsx

* Style code

* Clean up github redundant scripts

* Rename script to match function name

* Update documentation

* Update cost test path

* write to disk only if file does not exist

* Remove object

* Update R/00-update_refs.R

Co-authored-by: Zihao Li <[email protected]>

---------

Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Zihao Li <[email protected]>

* Update homelessness completeness code  (#1026)

* Update homelessness completeness

* Style code

---------

Co-authored-by: Jennit07 <[email protected]>

* Update documentation

* update namespace

* Update references

* update process_tests_sc_demographics

* Update - write temp file on `create_episode_file`

* get_chi for data

* Style code

* IT deaths changes

* Style code

* remove get_chi

* Specify year in episode file tests

* specify year in indiv tests

* Update `check_year_valid`

* Fix `ch_provider` new coding guidance

* Add `full.names` parameter to `write_temp_data`

* Revert "Fix `ch_provider` new coding guidance"

This reverts commit d2d584b.

* filter na episodes by filtering period

* Update running scripts indiv file

* Update `check_year_valid`

* update end_date

* Update NEWS.md

* Update create_individual_file.R

* update test-check_year_valid

* fix binding issue and remove redundance

* Style code

* R cmd check over v4.1.2

---------

Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>
Co-authored-by: lizihao-anu <[email protected]>
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2 participants