Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merge Dec-update-23 branch into master #890

Merged
merged 212 commits into from
Jan 9, 2024
Merged

Merge Dec-update-23 branch into master #890

merged 212 commits into from
Jan 9, 2024

Conversation

Jennit07
Copy link
Collaborator

@Jennit07 Jennit07 commented Jan 9, 2024

December update has been completed and now we want to bring all the branches back up to date and merge this into master

Moohan and others added 30 commits July 28, 2023 11:44
The new version is needed to read the SLFs now. We use this in `get_existing_data_for_tests()`
* remove unnecessary code from `get_anon_chi`

`get_anon_chi` was updated in slfhelper v0.10

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5669528966/attempts/1
Accepted in #759 (comment)

Signed-off-by: check-spelling-bot <[email protected]>

---------

Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: Megan McNicol <[email protected]>
These take a very long time to run, so were skipped at the last update. They need to be revisited.
* Correct some documentation

This resolves a build warning.

* Style code

---------

Co-authored-by: Moohan <[email protected]>
Lots of layout changes, as well as lots of implicit to explicit integer / double changes.
* Format postcode into `pc7` format

* Style code

* Style code

* Update documentation

* Update comment in R/process_extract_ae.R

* Implement catch-all for PC7 format

---------

Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
* Remove some obsolete code

Renaming and removing some functions.

* Style code

---------

Co-authored-by: Moohan <[email protected]>
Co-authored-by: Zihao Li <[email protected]>
* Simplify `create_hscp_test_flags`

* Update documentation

* Style code

* simplify `create_hb_test_flags`

* implement hscp test flags into tests

* Simplify `create_demog_test_flags`

---------

Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Moohan <[email protected]>
* updated code from case_when to case_match as it's a bit easier to read

* Style code

* changed some more `case_when` to `case_match`

* Style code

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5752014211/attempts/1
Accepted in #780 (comment)

Signed-off-by: check-spelling-bot <[email protected]>

* Add tests for `convert_sending_location_to_lca`

---------

Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: marjom02 <[email protected]>
Co-authored-by: SwiftySalmon <[email protected]>
Co-authored-by: James McMahon <[email protected]>
In processed extract variable is called hscp, and in final SLF it's called hscp2018.

Fixed with nested if statement

Co-authored-by: marjom02 <[email protected]>
Tiny error and a simple fix.

Co-authored-by: Jennit07 <[email protected]>
* fix duplicated matches in chi in sc data.

* Update R/create_individual_file.R

* update on join_sc_client

* Create a test checking if individual files have duplicated chi

* add duplicated chi number to the tests in process_tests_individual_file

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: James McMahon <[email protected]>
Update `check_year_valid` for NSUs
…785)

* Update `get_boxi_extract_path` for DN/CMH data

* Remove extra function

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5856792420/attempts/1
Accepted in #785 (comment)

Signed-off-by: check-spelling-bot <[email protected]>

---------

Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
Co-authored-by: James McMahon <[email protected]>
* further obsolete code change

* fix the preventable_beddays

Co-authored-by: James McMahon <[email protected]>

---------

Co-authored-by: James McMahon <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* fix warning on `:=`

* Update R/aggregate_by_chi.R

Co-authored-by: James McMahon <[email protected]>

* Style code

---------

Co-authored-by: James McMahon <[email protected]>
Co-authored-by: lizihao-anu <[email protected]>
This was already set up, just not used for some reason. Note that this will switch from using a `.rds` to `.parquet` (unless you do `get_source_extract_path(year, "Homelessness", ext = "rds")`).

Co-authored-by: Jennit07 <[email protected]>
* Update News for March and June updates

* Update release date

* WIP - update news for Sep update

* Update NEWS.md

Fix some typos / grammar

---------

Co-authored-by: James McMahon <[email protected]>
rchlv and others added 15 commits December 11, 2023 11:54
We had a call to discuss the filter for deaths at the mid point of
calendar year. This includes the changes we discussed. There was also
the issue of the function `rbinom` not working correctly and selecting
out whole groups rather than random samples from each group. This now
works. I will run the code tomorrow to produce some of the tables but
Rachel and I checked the keep population flag counts for 1819 and it
seems a lot more reasonable with the figures. Great work everyone!
Thanks
I have been having an issue when trying to run the episode file. I get
an error with the `vctrs` package as R doesnt like when you try to do a
`bind_rows()` on a list of data which has some empty data. The work
around is to remove this before processing the episode file
* remove duplicate sc_send_lca

* Style code

* remove sc_send_lca to avoid crash in create_episode_file

* undo the changes for select sc_send_lca

---------

Co-authored-by: lizihao-anu <[email protected]>
Co-authored-by: Jennit07 <[email protected]>
* revert back to September update

* revert to september update

* Style code

* revert to september code

* Style code

* Revert to september update code

---------

Co-authored-by: marjom02 <[email protected]>
Co-authored-by: SwiftySalmon <[email protected]>
Co-authored-by: Jennifer Thom <[email protected]>

This comment has been minimized.

rchlv
rchlv previously approved these changes Jan 9, 2024
Copy link
Collaborator

@rchlv rchlv left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We have both looked over this during a call and are happy to merge into master.

This comment has been minimized.

This comment has been minimized.

Requires more investigation as to why they are failing. Exlcuding for now
Copy link

github-actions bot commented Jan 9, 2024

@check-spelling-bot Report

🔴 Please review

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

Unrecognized words (13)
consulations
Exlcuding
gpooh
hri
MONTHFLAG
popluation
RDD
RStudio
sourcedev
SPSS
varible
vctrs
yyyyqx
To accept these unrecognized words as correct, you could run the following commands

... in a clone of the [email protected]:Public-Health-Scotland/source-linkage-files.git repository
on the dec-update-23 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/7460784350/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 (232) from .github/actions/spelling/expect.txt and unrecognized words (13)

Dictionary Entries Covers Uniquely
cspell:k8s/dict/k8s.txt 153 2 1
cspell:filetypes/filetypes.txt 264 2 1
cspell:swift/src/swift.txt 53 2
cspell:npm/dict/npm.txt 302 2
cspell:fullstack/dict/fullstack.txt 419 1 1

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

      with:
        extra_dictionaries:
          cspell:k8s/dict/k8s.txt
          cspell:filetypes/filetypes.txt
          cspell:swift/src/swift.txt
          cspell:npm/dict/npm.txt
          cspell:fullstack/dict/fullstack.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: ''
Pattern suggestions ✂️ (1)

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

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

Errors (5)

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

❌ Errors Count
ℹ️ candidate-pattern 1
❌ check-file-path 1
❌ forbidden-pattern 2
❌ ignored-expect-variant 13
ℹ️ no-newline-at-eof 1

See ❌ Event descriptions for more information.

If the flagged items are 🤯 false positives

If items relate to a ...

  • binary file (or some other file you wouldn't want to check at all).

    Please add a file path to the excludes.txt file matching the containing file.

    File paths are Perl 5 Regular Expressions - you can test yours before committing to verify it will match your files.

    ^ refers to the file's path from the root of the repository, so ^README\.md$ would exclude README.md (on whichever branch you're using).

  • well-formed pattern.

    If you can write a pattern that would match it,
    try adding it to the patterns.txt file.

    Patterns are Perl 5 Regular Expressions - you can test yours before committing to verify it will match your lines.

    Note that patterns can't match multiline strings.

Copy link
Collaborator

@rchlv rchlv left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This looks good to merge into master at this stage, thank you for addressing the checks.

@rchlv rchlv merged commit 7ab162d into master Jan 9, 2024
8 of 17 checks passed
@Jennit07 Jennit07 deleted the dec-update-23 branch March 26, 2024 14:40
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

5 participants