v4.0.0

PreprocessMD v4.0.0

Diff since v3.1.1

Closed issues:

• Generate cohorts from concept sets (#201)
• Add doctests for generate_cohort() (#204)
• Change MLJ.jl from a dependency to a weakdep (#211)

Merged pull requests:

• added generate_cohort function (#202) (@Mounika-Thakkallapally)
• Add doctest (#205) (@AshlinHarris)
• Update CONTRIBUTING.md (#206) (@AshlinHarris)
• Add subset_invalid_date (#209) (@AshlinHarris)
• Include MLJ as a weakdep (#214) (@AshlinHarris)
• Add compat (#215) (@AshlinHarris)

v3.1.1

PreprocessMD v3.1.1

Diff since v3.1.0

Closed issues:

• Add progress meters for long computations (#170)

Merged pull requests:

• Update dependency versions (#194) (@AshlinHarris)
• Update MLJ compatibility (#197) (@AshlinHarris)
• Add description to docstring (#198) (@AshlinHarris)

v3.1.0

PreprocessMD v3.1.0

Diff since v3.0.1

Closed issues:

• Convert any input into OMOP (#49)
• Improve example pipeline (#105)
• Include randomized tests (#126)
• top_n_values() should supply a default number (#141)
• Use const for global type unions (#145)
• add_label_column!() docstring contains a blank item in the argument list (#146)
• Examples should display function inputs (#153)
• Generate new doctest output automatically (#158)
• Package update: PreprocessMD.jl 3.0.1 (#162)
• Need warnings for overly large inputs (#169)
• Change script examples to REPL examples (#176)
• Unable to test warnings with @test_logs (#183)
• Update Project.toml (#186)

Merged pull requests:

• Remove unused functions (#163) (@AshlinHarris)
• Create CONTRIBUTING.md (#164) (@AshlinHarris)
• Improve example pipeline (#165) (@AshlinHarris)
• Update CONTRIBUTING.md (#167) (@AshlinHarris)
• Create README.md (#173) (@AshlinHarris)
• Add doctest output back to documentation (#175) (@AshlinHarris)
• Add default n to top_n_values() (#177) (@AshlinHarris)
• Change docstring script examples to REPL examples (#178) (@AshlinHarris)
• Make global types constant (#179) (@AshlinHarris)
• Add package docstring (#180) (@AshlinHarris)
• Add warnings for large inputs (#182) (@AshlinHarris)
• .gitattributes: set text=auto (#185) (@DilumAluthge)
• Update Project.toml (#187) (@AshlinHarris)
• Add note about doctest=:fix (#188) (@AshlinHarris)
• Enforce LF line endings (#189) (@AshlinHarris)
• Test for warning messages (#190) (@AshlinHarris)

v3.0.1

PreprocessMD v3.0.1

Diff since v3.0.0

Closed issues:

• Output is copied along with code (#140)
• Package update: PreprocessMD.jl 3.0.0 (#150)
• Adjust dependencies (#151)
• Need docstring example for top_n_values() (#156)
• Generate new doctest output automatically (#158)
• Add using statements to docstring examples (#159)

Merged pull requests:

• Correct dependencies (#152) (@AshlinHarris)
• Add verbosity flags for testset levels (#154) (@AshlinHarris)
• Hide function output in documentation (#155) (@AshlinHarris)
• Add docstring example for top_n_values() (#157) (@AshlinHarris)
• Add using statements to docstring examples (#160) (@AshlinHarris)
• Add fix=false to doctest() (#161) (@AshlinHarris)

v3.0.0

PreprocessMD v3.0.0

Diff since v2.0.0

Closed issues:

• Package update: PreprocessMD.jl 2.0.0 (#117)
• Support medical codes (#118)
• Set label column (#119)
• Suppress output in test sets (#123)
• Duplicate tests (#129)
• Reduce dependencies for test/runtests.jl (#132)
• Compatability with Julia v1.6.7 (#133)
• Test support for earlier versions of each dependency (#135)
• Codecov fails (#138)
• Refactor tests (#143)
• Remove MLDemo (#147)

Merged pull requests:

• Add set_label_column!() (#120) (@AshlinHarris)
• Update version (#121) (@AshlinHarris)
• Use medical codes (#122) (@AshlinHarris)
• Suppress output within testsets (#124) (@AshlinHarris)
• Add Suppressor to tests (#125) (@AshlinHarris)
• 105 improve example pipeline (#128) (@AshlinHarris)
• Remove outdated testset (#131) (@AshlinHarris)
• Julia v1.6.7 compatability check (#134) (@AshlinHarris)
• Support dependency downgrades (#136) (@AshlinHarris)
• CompatHelper: bump compat for MLJ to 0.18, (keep existing compat) (#137) (@github-actions[bot])
• Improve code coverage (#139) (@AshlinHarris)
• Reduce dependencies (#142) (@AshlinHarris)
• Remove MLDemo and its dependency (Suppressor) (#148) (@AshlinHarris)
• 143 Refactor testsets (#149) (@AshlinHarris)

v2.0.0

PreprocessMD v2.0.0

Diff since v1.0.0

Closed issues:

• Package registration (#99)
• Replace CSV.File with CSV.read (#106)
• Move all test code to test/runtests.jl (#109)
• Use joinpath() for assembling directories (#110)
• Add other operating systems to ci.yml (#111)
• Consistent scheme for multiple dispatch (#115)

Merged pull requests:

• Replace CSV.File with CSV.read (#107) (@AshlinHarris)
• Replace CSV.File with CSV.read (#108) (@AshlinHarris)
• Add macos-latest and windows-latest to ci.yml (#112) (@AshlinHarris)
• Consolidate test code (#114) (@AshlinHarris)
• Define supported column names (#116) (@AshlinHarris)

v1.0.0

PreprocessMD v1.0.0

Closed issues:

• Develop tests on MIMIC IV OMOP data using Downloads.jl (#1)
• Complete biomedical pipeline (#3)
• Add feasibility checks (#5)
• We should accept any Tables-compatible table as input, instead of only accepting DataFrames (#24)
• Implement machine learning model in example (#42)
• Compatibility issues with MLJ (#45)
• v0.1: Workflows and first function (#48)
• Documentation action fails (#60)
• Clean up and format (#63)
• Don't import entire packages (#64)
• Update all docstrings (#68)
• Change add_label_column!() argument list (#70)
• Add user-centric documentation (#71)
• Add script for local doctests (#74)
• Update test sets (#76)
• Automate documentation with autodocs (#83)

Merged pull requests:

• Improve code cov (#7) (@AshlinHarris)
• Use the BlueStyle code style, and automatically format the source code (#9) (@DilumAluthge)
• Project.toml: add a [compat] entry for julia; also, [compat] entries should not have the v in them (#10) (@DilumAluthge)
• Packages usually should not check the Manifest.toml file into source control (#11) (@DilumAluthge)
• Run CI on both 1.6 and the latest stable Julia; only run CI on Linux; various other tweaks to the CI workflow file (#12) (@DilumAluthge)
• CI: set strict = true when building the documentation (#13) (@DilumAluthge)
• 🤖 Automatically format the source code files (#15) (@github-actions[bot])
• Project.toml: further simplify some [compat] entries (#16) (@DilumAluthge)
• Never use using Foo; instead, either use import Foo, or use using Foo: f, g, h (#17) (@DilumAluthge)
• The package's Project.toml file should only include the dependencies actually used in the source code of the package itself (#18) (@DilumAluthge)
• More fixes for the docs/make.jl file (#22) (@DilumAluthge)
• Remove test/Manifest.toml from source control (#23) (@DilumAluthge)
• CI: rename Code Formatting to just Formatter (#26) (@DilumAluthge)
• 🤖 Automatically format the source code files (#28) (@github-actions[bot])
• Add Aqua.jl to the test suite (#29) (@DilumAluthge)
• Whenever possible, avoid doing try/catch in the test suite (#30) (@DilumAluthge)
• 🤖 Automatically format the source code files (#32) (@github-actions[bot])
• Update dependencies (#33) (@AshlinHarris)
• Ah development (#35) (@AshlinHarris)
• 🤖 Automatically format the source code files (#36) (@github-actions[bot])
• Download OMOP MIMIC files only once each (#37) (@AshlinHarris)
• Support tables (#40) (@AshlinHarris)
• Clean up tests (#46) (@AshlinHarris)
• Full pipeline (#61) (@AshlinHarris)
• Add ML demonstration to docs (#62) (@AshlinHarris)
• Adjust imports (#65) (@AshlinHarris)
• Update readme (#66) (@AshlinHarris)
• Update README.md (#67) (@AshlinHarris)
• Try doctest (#69) (@AshlinHarris)
• Add jldoctest (#72) (@AshlinHarris)
• Change arguments for add_target_column!() (#73) (@AshlinHarris)
• Local doctests (#75) (@AshlinHarris)
• Update test sets (#77) (@AshlinHarris)
• Update docstrings (#79) (@AshlinHarris)
• Add subsetMD() (#84) (@AshlinHarris)
• Use autodocs (#86) (@AshlinHarris)
• Update docs/make.jl (#87) (@AshlinHarris)
• Rewrite README.md (#88) (@AshlinHarris)
• CI: disable the Codecov comment (#89) (@DilumAluthge)
• Update version (#90) (@AshlinHarris)
• Update the TagBot workflow file (#91) (@DilumAluthge)
• Update to v1.0.0 (#93) (@AshlinHarris)
• Set up CompatHelper on this repository (#94) (@DilumAluthge)
• Add .DS_Store to the .gitignore file (#95) (@DilumAluthge)
• Set 'verbose = false' for all testsets (#96) (@AshlinHarris)
• Format function statements for autodocs (#98) (@AshlinHarris)