update CI, read specific vars in npzread

.github/workflows/TagBot.yml

@@ -1,9 +1,12 @@
 name: TagBot
 on:
-  schedule:
-    - cron: 0 0 * * *
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '0.7'
+          - '1.0'
+          - '1'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        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
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/docs.yml

@@ -0,0 +1,24 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.4'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.gitignore

@@ -0,0 +1,3 @@
+docs/build
+Manifest.toml
+docs/Manifest.toml

docs/Project.toml

@@ -0,0 +1,6 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
+
+[compat]
+Documenter = "0.25"

docs/make.jl

@@ -0,0 +1,22 @@
+using NPZ
+using Documenter
+
+DocMeta.setdocmeta!(NPZ, :DocTestSetup, :(using NPZ); recursive=true)
+
+makedocs(;
+    modules=[NPZ],
+    repo="https://github.com/fhs/NPZ.jl/blob/{commit}{path}#L{line}",
+    sitename="NPZ",
+    format=Documenter.HTML(;
+        prettyurls=get(ENV, "CI", "false") == "true",
+        canonical="https://fhs.github.io/NPZ.jl",
+        assets=String[],
+    ),
+    pages=[
+        "Reference" => "index.md",
+    ],
+)
+
+deploydocs(;
+    repo="github.com/fhs/NPZ.jl",
+)

docs/src/index.md

@@ -0,0 +1,9 @@
+```@meta
+CurrentModule = NPZ
+```
+
+# NPZ.jl
+
+```@autodocs
+Modules = [NPZ]
+```

src/NPZ.jl

@@ -235,36 +235,64 @@ function samestart(a::AbstractVector, b::AbstractVector)
     length(a) >= nb && view(a, 1:nb) == b
 end
 
-function npzread(filename::AbstractString)
+function _maybetrimext(name::AbstractString)
+    fname, ext = splitext(name)
+    if ext == ".npy"
+        name = fname
+    end
+    name
+end
+
+"""
+    npzread(filename::AbstractString, [vars])
+
+Read an variable or a collection of variables from `filename`. 
+The input needs to be either an `npy` or an `npz` file.
+The optional argument `vars` is used only for `npz` files.
+If it is specified, only the matching variables are read in from the file.
+
+# Example
+
+```julia
+julia> npzwrite("temp.npz", Dict("x" => ones(3), "y" => 3))
+
+julia> npzread("temp.npz") # Reads all variables
+Dict{String,Any} with 2 entries:
+  "x" => [1.0, 1.0, 1.0]
+  "y" => 3
+
+julia> npzread("temp.npz", ["x"]) # Reads only "x"
+Dict{String,Array{Float64,1}} with 1 entry:
+  "x" => [1.0, 1.0, 1.0]
+```
+"""
+function npzread(filename::AbstractString, vars...)
     # Detect if the file is a numpy npy array file or a npz/zip file.
     f = open(filename)
     @compat b = read!(f, Vector{UInt8}(undef, MaxMagicLen))
+
     if samestart(b, ZIPMagic)
-        close(f)
-        f = ZipFile.Reader(filename)
-        data = npzread(f)
-        close(f)
-        return data
-    end
-    if samestart(b, NPYMagic)
+        fz = ZipFile.Reader(filename)
+        data = npzread(fz, vars...)
+        close(fz)
+    elseif samestart(b, NPYMagic)
         seekstart(f)
         data = npzreadarray(f)
+    else
         close(f)
-        return data
+        error("not a NPY or NPZ/Zip file: $filename")
     end
-    error("not a NPY or NPZ/Zip file: $filename")
+
+    close(f)
+    return data
 end
 
-function npzread(dir::ZipFile.Reader)
-    vars = Dict{String,Any}()
-    for f in dir.files
-        name = f.name
-        if endswith(name, ".npy")
-            name = name[1:end-4]
-        end
-        vars[name] = npzreadarray(f)
-    end
-    vars
+function npzread(dir::ZipFile.Reader, 
+    vars = map(f -> _maybetrimext(f.name), dir.files))
+
+    Dict(_maybetrimext(f.name) => npzreadarray(f)
+        for f in dir.files 
+            if f.name in vars || _maybetrimext(f.name) in vars)
 end
 
 function npzwritearray(
@@ -301,12 +329,51 @@ end
 function npzwritearray(f::IO, x::T) where T<:Number
     npzwritearray(f, reinterpret(UInt8, [x]), T, Int[])
 end
+
+"""
+    npzwrite(filename::AbstractString, x)
+
+Write the variable `x` to the `npy` file `filename`. 
+Unlike `numpy`, the extension `.npy` is not appened to `filename`.
+
+!!! warn "Warning"
+    Any existing file with the same name will be overwritten.
+
+# Examples
+```julia
+julia> npzwrite("abc.npy", zeros(3))
+
+julia> npzread("abc.npy")
+3-element Array{Float64,1}:
+ 0.0
+ 0.0
+ 0.0
+```
+"""
 function npzwrite(filename::AbstractString, x)
-    f = open(filename, "w")
-    npzwritearray(f, x)
-    close(f)
+    open(filename, "w") do f
+        npzwritearray(f, x)
+    end
 end
 
+"""
+    npzwrite(filename::AbstractString, vars::Dict{<:AbstractString})
+
+Write the variables in `vars` to an `npz` file named `filename`.
+Unlike `numpy`, the extension `.npz` is not appened to `filename`.
+
+!!! warn "Warning"
+    Any existing file with the same name will be overwritten.
+
+```julia
+julia> npzwrite("temp.npz", Dict("x" => ones(3), "y" => 3))
+
+julia> npzread("temp.npz")
+Dict{String,Any} with 2 entries:
+  "x" => [1.0, 1.0, 1.0]
+  "y" => 3
+```
+"""
 function npzwrite(filename::AbstractString, vars::Dict{<:AbstractString}) 
     dir = ZipFile.Writer(filename)
     for (k, v) in vars

test/runtests.jl

@@ -68,6 +68,11 @@ npzwrite(dictfilename, testdict)
 dictoutput = npzread(dictfilename)
 for (k, v) in testdict
     @test v == dictoutput[k]
+    d = npzread(dictfilename, [k])
+    @test typeof(d) == Dict{String,typeof(v)}
+    val_read = d[k]
+    @test typeof(val_read) == typeof(v)
+    @test val_read == v
 end
 # Write and then read NPY files for each array
 for x in TestArrays