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Merge release v2.1.0 into stable branch #60

Merged
merged 51 commits into from
Mar 14, 2024
Merged

Merge release v2.1.0 into stable branch #60

merged 51 commits into from
Mar 14, 2024

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yavyx
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@yavyx yavyx commented Mar 14, 2024

Updating the stable branch with release v2.1.0

Changelog

  • Added support for date intervals
  • Repo can be used as a stand-alone module
  • Added index and minify command line arguments with respective docs
  • Bug fixes and misc improvements

Refer to the v2.1.0 release to see a detailed changelog.

daisieh and others added 30 commits December 18, 2023 21:22
@daisieh
update packages
0af78af
@daisieh
applymap is deprecated
7c84690
@daisieh
build files
0208763
@daisieh
Update test.yml
01c9541
@daisieh
Merge pull request #47 from CanDIG/daisieh/updates
f23bd22
@daisieh
compile result for load_manifest
5ade787
@daisieh
add some prints
e7153f4
@daisieh
stub for validation
9193cf4
@daisieh
don't hard-code main result key
1f7aaf6
@daisieh
another key to not hard-code
808715c
@daisieh
programatically use schema class based on manifest
d29cf0e
@daisieh
use a default dateparser
54f33ba
@daisieh
add reference date and date interval calculations
daba925
@daisieh
if date_intervals are used for birth and death, use month_intervals
5f25983
@daisieh
update templates to use date_interval
ec8db08
@daisieh
temporarily don't count interval errors
e35f769
@daisieh
check to see if the identifier exists on the sheet
7c535b3
@mshadbolt
add new manifest param to README
bebb169
@mshadbolt
added reference_date to manifest docs
665a810
@daisieh
Merge pull request #48 from CanDIG/daisieh/genomic
c898c2e
@mshadbolt
Merge branch 'develop' into daisieh/date-intervals
897799f
@daisieh
pass date_resolution into earliest_date mapping
65ae481
@daisieh
add date_resolution to the templates
1661036
@daisieh
add date_resolution to required_fields for Donor
c001f36
@daisieh
add test values for Donor.date_resolution
1a75e3f
@daisieh
sheet should be consistently the first param's sheet
da05b60
@mshadbolt
add docstrings
c9ff51b
@mshadbolt
update mapping docs
ac20357
@daisieh
raise an exception if there's no reference_date
e76c1a1
@daisieh
docstrings
5889ecf
daisieh and others added 21 commits January 26, 2024 15:42
@daisieh
Merge pull request #49 from CanDIG/daisieh/date-intervals
5b74358 
DIG-1245: dates as date intervals
@DavidBrownlee
Module path changes to allow running standalone (not as an included m…
c4a1624 
…odule.)
@DavidBrownlee
module import path fixed for validate_coverage.py as well.
96d6249
@DavidBrownlee
Updte sample_inputs to work as standalone (not imported library).
c90eca0
@DavidBrownlee
Added documentation clarity for writing and using custom functions.
e25e0cf
@daisieh
Merge pull request #50 from CanDIG/david/runStandAlone
eb23190 
Module path changes to allow running standalone (not as an included m…
@daisieh
merge
f247ef7
@DavidBrownlee @daisieh
Validate that date intervals are integers.
7637349
@DavidBrownlee @daisieh
month_interval is now always calculated. day_interval is optional.
bdb3ccf
@daisieh
merge
07e4960
@DavidBrownlee @daisieh
Minor correction to sample_inputs/moh_template.csv.
189c36f
@daisieh
Merge pull request #51 from CanDIG/david/acceptDateIntervals
c0aaeac 
DIG-1473: Accept date intervals (rather than absolute dates).
@lilyyangyi301
change float() to floating() in mapping functions
bc91757
@lilyyangyi301
revert
0870368
@lilyyangyi301
change float() to floating() in mapping functions
f02fa8c
@lilyyangyi301
Merge pull request #54 from CanDIG/lilyyang/fix_floating_mapping_func…
a9ba7c7 
…tion

change float() to floating() in mapping functions
@mshadbolt
DIG-1150: Template update and documentation for DateIntervals (#53)
815cbfc 
* update template script

* add build to gitignore

* update templates to intervals

* update moh_diffs

* update mapping functions doc
@mshadbolt @daisieh
Add index and minify command line arguments (#55)
8a01ff9 
* add minification option

* add index arg

* check before opening file

* fix args

* Update src/clinical_etl/CSVConvert.py

Co-authored-by: Daisie Huang <[email protected]>

---------

Co-authored-by: Daisie Huang <[email protected]>
@mshadbolt
update docs for new args (#56)
cb4269e
@mshadbolt
add main and have CSVConvert as CLI script (#57)
1513b0d
@mshadbolt
fix int method, more details in warning (#58)
b3b4816
@yavyx yavyx requested review from daisieh and mshadbolt March 14, 2024 20:32
mshadbolt
mshadbolt approved these changes Mar 14, 2024
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LGTM

@yavyx yavyx merged commit 188f1e9 into stable Mar 14, 2024
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@mshadbolt mshadbolt mshadbolt approved these changes

@daisieh daisieh Awaiting requested review from daisieh

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5 participants
@yavyx @mshadbolt @daisieh @DavidBrownlee @lilyyangyi301