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Merge pull request #13 from PharmCat/dev
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find methods, docs
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@PharmCat
PharmCat authored Jan 13, 2025
2 parents 3cdfafa + 3f4a98b commit 2de7726
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Showing 6 changed files with 143 additions and 19 deletions.
47 changes: 36 additions & 11 deletions .github/workflows/Tier1.yml
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Expand Up @@ -16,22 +16,47 @@ on:
paths-ignore:
- 'LICENSE.md'
- 'README.md'
concurrency:
# Skip intermediate builds: always.
# Cancel intermediate builds: only if it is a pull request build.
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
jobs:
ci:
test:
name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
julia-version: [1.6, 1.7, 1.8]
julia-arch: [x64]
os: [ubuntu-latest, macOS-latest, windows-2019]
version:
- '1.8'
- '1'
os:
- ubuntu-latest
- macOS-latest
- windows-latest
arch:
- x64
steps:
- uses: actions/checkout@v3
- uses: julia-actions/setup-julia@v1
- uses: actions/checkout@v4
- uses: julia-actions/setup-julia@v2
with:
version: ${{ matrix.julia-version }}
version: ${{ matrix.version }}
arch: ${{ matrix.arch }}
- uses: actions/cache@v4
env:
cache-name: cache-artifacts
with:
path: ~/.julia/artifacts
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
restore-keys: |
${{ runner.os }}-test-${{ env.cache-name }}-
${{ runner.os }}-test-
${{ runner.os }}-
- uses: julia-actions/julia-buildpkg@v1
- uses: julia-actions/julia-runtest@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: julia-actions/julia-uploadcodecov@latest
if: ${{ startsWith(matrix.os, 'Ubuntu') && startsWith(matrix.julia-version, '1.6') }}
- uses: julia-actions/julia-processcoverage@v1
- uses: codecov/codecov-action@v4
if: ${{ matrix.os == 'ubuntu-latest' && matrix.version == '1' && matrix.arch == 'x64' }}
with:
file: lcov.info
token: ${{ secrets.CODECOV_TOKEN }}
2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "MetidaBase"
uuid = "075456b7-4006-432f-9324-2f8453996c49"
authors = ["PharmCat <[email protected]> and contributors"]
version = "0.12.0"
version = "0.13.0"

[deps]
CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
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4 changes: 3 additions & 1 deletion src/MetidaBase.jl
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Expand Up @@ -9,7 +9,9 @@ module MetidaBase
import Tables: istable, columnaccess, columns, getcolumn, columnnames, schema, rowaccess, rows
import CPUSummary: num_cores

import Base: getindex, length, ht_keyindex, show, pushfirst!, iterate, size, findfirst, push!, append!
import Base: getindex, length, ht_keyindex, show, pushfirst!, iterate, size, findfirst, findlast, findall, findnext, findprev, push!, append!

export DataSet, MetidaTable, getdata, getid

include("abstracttype.jl")
include("m_tables.jl")
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102 changes: 98 additions & 4 deletions src/dataset.jl
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Expand Up @@ -25,7 +25,7 @@ function Base.getindex(d::DataSet, ind::Int)
d.ds[ind]
end

Base.getindex(d::DataSet, inds::UnitRange{Int64}) = subset(d, inds)
Base.getindex(d::DataSet, inds) = subset(d, inds)


@inline function getresultindex_safe(rd::T, ind::Symbol) where T <: AbstractResultData
Expand All @@ -34,6 +34,8 @@ end
@inline function getresultindex_unsafe(rd::T, ind::Symbol) where T <: AbstractResultData
rd.result[ind]
end
getresultindex_safe(rd, ind::AbstractString) = getresultindex_safe(rd, Symbol(ind))
getresultindex_unsafe(rd, ind::AbstractString) = getresultindex_unsafe(rd, Symbol(ind))

function Base.getindex(d::DataSet{T}, col::Int, ind) where T <: AbstractResultData
getresultindex_safe(d[col], ind)
Expand Down Expand Up @@ -106,15 +108,30 @@ end
# filter!
################################################################################
function Base.filter(f::Function, d::DataSet)
ds = getdata(d)
inds = findall(f, ds)
DataSet(ds[inds])
DataSet(filter(f, getdata(d)))
end
function Base.filter!(f::Function, d::DataSet)
filter!(f, getdata(d))
d
end

function Base.filter(f::Dict{:Symbol, Function}, d::DataSet)
k = keys(f)
a = filter(x -> f[first(k)](getid(x, first(k))), getdata(d))
if length(k) > 1
for kn = 2:length(k)
filter!(x -> f[k[kn]](getid(x, k[kn])), a)
end
end
DataSet(a)
end
function Base.filter!(f::Dict{:Symbol, Function}, d::DataSet)
for k in keys(f)
filter!(x -> f[k](getid(x, k)), getdata(d))
end
d
end

################################################################################
# Base.findfirst
################################################################################
Expand All @@ -123,6 +140,83 @@ function Base.findfirst(d::DataSet{<: AbstractIdData}, sort::Dict)
findfirst(x-> sort ⊆ getid(x), getdata(d))
end

################################################################################
# Base.findlast
################################################################################

function Base.findlast(d::DataSet{<: AbstractIdData}, sort::Dict)
findlast(x-> sort ⊆ getid(x), getdata(d))
end

################################################################################
# Base.findnext
################################################################################

function Base.findnext(d::DataSet{<: AbstractIdData}, sort::Dict, i::Int)
findnext(x-> sort ⊆ getid(x), getdata(d), i)
end


################################################################################
# Base.findprev
################################################################################

function Base.findprev(d::DataSet{<: AbstractIdData}, sort::Dict, i::Int)
findprev(x-> sort ⊆ getid(x), getdata(d), i)
end

################################################################################
# Base.findall
################################################################################

function Base.findall(d::DataSet{<: AbstractIdData}, sort::Dict)
findall(x-> sort ⊆ getid(x), getdata(d))
end

################################################################################
# find*el
################################################################################

function findfirstel(d::DataSet{<: AbstractIdData}, sort::Dict)
ind = findfirst(x-> sort ⊆ getid(x), getdata(d))
if isnothing(ind)
return nothing
else
return d[ind]
end
end
function findlastel(d::DataSet{<: AbstractIdData}, sort::Dict)
ind = findlast(x-> sort ⊆ getid(x), getdata(d))
if isnothing(ind)
return nothing
else
return d[ind]
end
end
function findnextel(d::DataSet{<: AbstractIdData}, sort::Dict, i::Int)
ind = findnext(x-> sort ⊆ getid(x), getdata(d), i)
if isnothing(ind)
return nothing
else
return d[ind]
end
end
function findprevel(d::DataSet{<: AbstractIdData}, sort::Dict, i::Int)
ind = findprev(x-> sort ⊆ getid(x), getdata(d), i)
if isnothing(ind)
return nothing
else
return d[ind]
end
end
function findallel(d::DataSet{<: AbstractIdData}, sort::Dict)
ind = findall(x-> sort ⊆ getid(x), getdata(d))
if isnothing(ind)
return nothing
else
return d[ind]
end
end
################################################################################
# SELF
################################################################################
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2 changes: 1 addition & 1 deletion src/utils.jl
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Expand Up @@ -101,7 +101,7 @@ end
"""
cvfromsd(σ::Real)::AbstractFloat
CV from variance.
CV from LnSD.
"""
function cvfromsd(σ)
return sqrt(exp(σ^2) - 1)
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5 changes: 4 additions & 1 deletion test/runtests.jl
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Expand Up @@ -149,7 +149,10 @@ using Test, Tables, TypedTables, DataFrames, CSV
########################################################################

@test MetidaBase.findfirst(exidds, Dict(:a => 1, :b => 1)) == 1

@test MetidaBase.findlast(exidds, Dict(:a => 1, :b => 1)) == 1
@test MetidaBase.findall(exidds, Dict(:a => 1, :b => 1)) == [1]
@test MetidaBase.findnext(exidds, Dict(:a => 2, :b => 3), 1) ==2
@test MetidaBase.findprev(exidds, Dict(:a => 2, :b => 3), 3) == 2
#######################################################################


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4 comments on commit 2de7726

@PharmCat
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Registration pull request created: JuliaRegistries/General/123080

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.13.0 -m "<description of version>" 2de772656f1200adb302361fe1079cb0cd5ed984
git push origin v0.13.0

@PharmCat
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Release notes:

Breaking Changes

  • Changed getindex
  • Changed filter
  • Add findlast , findnext , findprev , findallel
  • Add find*el

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Registration pull request updated: JuliaRegistries/General/123080

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.13.0 -m "<description of version>" 2de772656f1200adb302361fe1079cb0cd5ed984
git push origin v0.13.0

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