Datasets:

atomology
/

WannierDatasets

Tags:

physics

Wannier functions

License:

Dataset card Files Files and versions

xet

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WannierDatasets / make_artifacts.jl

qiaojunfeng

Only check git committed datasets

2d50f81 8 months ago

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#!/usr/bin/env -S julia --project
# Script to generate `Artifacts.toml` and `artifacts/*.tar.gz`.
#
# For the 1st time running this script, you need to run
#   using Pkg; Pkg.instantiate()
# to install the dependencies.
#
# Artifacts docs:
# https://pkgdocs.julialang.org/v1/artifacts/
#
using Pkg
Pkg.instantiate()

using Tar, Inflate, SHA, TOML
using Dates: unix2datetime

const artifacts_dir = joinpath(@__DIR__, "artifacts")
const datasets_dir = joinpath(@__DIR__, "datasets")
const deploy_branch = "artifacts"

"""
Create a artifact tarball for a folder.
# Arguments
- `folder`: subfolders in `datasets/` folder, e.g. `"Si2"`
- `local_url`: use local file path for the url, for testing only
"""
function create_artifact(folder::AbstractString; local_url::Bool=false)
    fullpath = joinpath(datasets_dir, folder)
    isdir(fullpath) || return

    mkpath(artifacts_dir)

    # exclude the inputs folder which contains the input files for generating the datasets
    tar_excludes = ["inputs", ".gitignore", "README.md"]

    # gzip compression level, highest
    GZIP = "-9"
    # By default, use gzip
    compress_prog = "gzip $GZIP"
    # Try to use pigz for parallel compression.
    # However, it is not available in github workflow (ubuntu-latest)
    try
        run(`which pigz`)
        # -k: keep original files
        global compress_prog = "pigz $GZIP -k"
    catch
        # pigz is not available
    end

    tar_cmd = [
        Sys.isapple() ? "gtar" : "tar",
        "--exclude-vcs",
        "--exclude-vcs-ignores",
        "--use-compress-program=$compress_prog",
    ]
    append!(tar_cmd, ["--exclude=" * f for f in tar_excludes])

    tar_name = "$(folder).tar.gz"
    outpath = joinpath(artifacts_dir, tar_name)
    prev_dir = pwd()
    cd(fullpath) do
        files = readdir()
        # check w90 prefix is the same as the folder name, otherwise
        # `Wannier.Datasets.load_dataset(folder)` won't work
        "$(folder).win" in files || @warn "No $folder.win file in the folder $folder?"

        run(Cmd(vcat(tar_cmd, ["-cvf", outpath], files)))
    end
    cd(prev_dir)

    if local_url
        # if you want to test locally
        url = "file://$(outpath)"
    else
        # use huggingface `artifacts` branch to host the artifacts
        url = "https://huggingface.co/datasets/atomology/WannierDatasets/resolve/artifacts/$(tar_name)"
    end

    artifact_name = folder
    res =
        artifact_name => Dict(
            "git-tree-sha1" => Tar.tree_hash(IOBuffer(inflate_gzip(outpath))),
            "lazy" => true,
            "download" =>
                [Dict("url" => url, "sha256" => bytes2hex(open(sha256, outpath)))],
        )

    # print the result as toml
    buf = IOBuffer()
    TOML.print(buf, Dict(res))
    s = String(take!(buf))
    @info "New artifact:\n$s"

    return res
end

"""
Get the git hash of the latest commit of a file.
"""
function git_hash(path::AbstractString; branch::AbstractString="HEAD")
    return read(`git log -n 1 --pretty=format:"%H" $branch -- "$path"`, String)
end

"""
Get the date of a git commit.
"""
function git_date(githash::AbstractString)
    # get the date of the commit, unix timestamp
    g = strip(read(`git show -s --format=%ct $githash`, String))
    return unix2datetime(parse(Float64, g))
end

"""
Get the list of files in a git tree.
"""
function git_lstree(path::AbstractString; args::AbstractVector{<:AbstractString}=String[], branch::AbstractString="HEAD")
    cmd = `git ls-tree $args --name-only $branch -- "$path"`
    output = chomp(read(cmd, String))
    isempty(output) && return String[]
    return split(output, '\n')
end

"""
Get list of artifact tarballs in the deploy branch.
"""
function list_previous_artifacts()
    # if this command fails with the error
    # `fatal: Not a valid object name artifacts`
    # you need to run at least once
    # `git checkout artifacts`
    # to create the artifacts branch
    files = try
        git_lstree("."; args=["-r"], branch=deploy_branch)
    catch e
        @warn "Failed to list previous artifacts, perhaps you need to run \
            `git checkout artifacts` at least once to create the branch?"
        throw(e)
        String[]
    end
    filter!(f -> endswith(f, ".tar.gz"), files)
    return Dict(f => git_hash(f; branch=deploy_branch) for f in files)
end

"""
Get folder names in `datasets/` that are newer than the corresponding
tarball.
"""
function list_new_folders()
    prev_artifacts = list_previous_artifacts()

    new_folders = String[]
    # This include all the folders in `datasets/`
    # dirs = readdir(datasets_dir)
    # This only include the folders that have been git committed to the main branch
    # Note it needs exactly the `datasets/` as path: not abosulute path, with
    # trailing slash to list subfolders.
    dirs = map(basename, git_lstree(basename(datasets_dir) * "/"; branch="main"))
    for data in dirs
        startswith(data, "_") && continue
        startswith(data, ".") && continue
        isdir(joinpath(datasets_dir, data)) || continue

        dir_hash = git_hash(joinpath(basename(datasets_dir), data))
        artifact_hash = get(prev_artifacts, "$(data).tar.gz", nothing)
        # @info "dir_hash: $dir_hash, artifact_hash: $artifact_hash"
        if !isnothing(artifact_hash)
            # if date of dir_hash is older than artifact_hash
            # then we do not need to update the artifact
            (git_date(dir_hash) <= git_date(artifact_hash)) && continue
        end
        push!(new_folders, data)
    end
    return new_folders
end

"""
Remove the `artifacts_dir` folder and create a new one.
"""
function clean_artifacts_dir()
    print("I will clean the `$(artifacts_dir)` folder [y/N]: ")
    n = readline()
    if lowercase(n) != "y"
        println("Aborting...")
        return false
    end
    rm(artifacts_dir; force=true, recursive=true)
    mkpath(artifacts_dir)
    println("Cleaned `$(artifacts_dir)` folder.")
    return true
end

"""
Get previous Artifacts.toml from deploy branch.
"""
function read_artifact_toml()
    return try
        content = read(`git show $deploy_branch:Artifacts.toml`)
        return TOML.parse(String(content))
    catch e
        return Dict{String,Any}()
    end
end

function (@main)(args)
    artifacts = read_artifact_toml()

    new_folders = list_new_folders()
    if isempty(new_folders)
        println("No new folders to process.")
        return
    end

    if "dryrun" in args
        println("New folders to process:")
        for folder in new_folders
            println("- $folder")
        end
    else
        clean_artifacts_dir() || return

        for folder in new_folders
            artifact = create_artifact(folder)
            # existing entries will be replaced
            push!(artifacts, artifact)
            # break
        end

        open("Artifacts.toml", "w") do io
            TOML.print(io, artifacts)
        end
    end
end

	#!/usr/bin/env -S julia --project
	# Script to generate `Artifacts.toml` and `artifacts/*.tar.gz`.
	#
	# For the 1st time running this script, you need to run
	# using Pkg; Pkg.instantiate()
	# to install the dependencies.
	#
	# Artifacts docs:
	# https://pkgdocs.julialang.org/v1/artifacts/
	#
	using Pkg
	Pkg.instantiate()

	using Tar, Inflate, SHA, TOML
	using Dates: unix2datetime

	const artifacts_dir = joinpath(@__DIR__, "artifacts")
	const datasets_dir = joinpath(@__DIR__, "datasets")
	const deploy_branch = "artifacts"

	"""
	Create a artifact tarball for a folder.

	# Arguments
	- `folder`: subfolders in `datasets/` folder, e.g. `"Si2"`
	- `local_url`: use local file path for the url, for testing only
	"""
	function create_artifact(folder::AbstractString; local_url::Bool=false)
	fullpath = joinpath(datasets_dir, folder)
	isdir(fullpath) \|\| return

	mkpath(artifacts_dir)

	# exclude the inputs folder which contains the input files for generating the datasets
	tar_excludes = ["inputs", ".gitignore", "README.md"]

	# gzip compression level, highest
	GZIP = "-9"
	# By default, use gzip
	compress_prog = "gzip $GZIP"
	# Try to use pigz for parallel compression.
	# However, it is not available in github workflow (ubuntu-latest)
	try
	run(`which pigz`)
	# -k: keep original files
	global compress_prog = "pigz $GZIP -k"
	catch
	# pigz is not available
	end

	tar_cmd = [
	Sys.isapple() ? "gtar" : "tar",
	"--exclude-vcs",
	"--exclude-vcs-ignores",
	"--use-compress-program=$compress_prog",
	]
	append!(tar_cmd, ["--exclude=" * f for f in tar_excludes])

	tar_name = "$(folder).tar.gz"
	outpath = joinpath(artifacts_dir, tar_name)
	prev_dir = pwd()
	cd(fullpath) do
	files = readdir()
	# check w90 prefix is the same as the folder name, otherwise
	# `Wannier.Datasets.load_dataset(folder)` won't work
	"$(folder).win" in files \|\| @warn "No $folder.win file in the folder $folder?"

	run(Cmd(vcat(tar_cmd, ["-cvf", outpath], files)))
	end
	cd(prev_dir)

	if local_url
	# if you want to test locally
	url = "file://$(outpath)"
	else
	# use huggingface `artifacts` branch to host the artifacts
	url = "https://huggingface.co/datasets/atomology/WannierDatasets/resolve/artifacts/$(tar_name)"
	end

	artifact_name = folder
	res =
	artifact_name => Dict(
	"git-tree-sha1" => Tar.tree_hash(IOBuffer(inflate_gzip(outpath))),
	"lazy" => true,
	"download" =>
	[Dict("url" => url, "sha256" => bytes2hex(open(sha256, outpath)))],
	)

	# print the result as toml
	buf = IOBuffer()
	TOML.print(buf, Dict(res))
	s = String(take!(buf))
	@info "New artifact:\n$s"

	return res
	end

	"""
	Get the git hash of the latest commit of a file.
	"""
	function git_hash(path::AbstractString; branch::AbstractString="HEAD")
	return read(`git log -n 1 --pretty=format:"%H" $branch -- "$path"`, String)
	end

	"""
	Get the date of a git commit.
	"""
	function git_date(githash::AbstractString)
	# get the date of the commit, unix timestamp
	g = strip(read(`git show -s --format=%ct $githash`, String))
	return unix2datetime(parse(Float64, g))
	end

	"""
	Get the list of files in a git tree.
	"""
	function git_lstree(path::AbstractString; args::AbstractVector{<:AbstractString}=String[], branch::AbstractString="HEAD")
	cmd = `git ls-tree $args --name-only $branch -- "$path"`
	output = chomp(read(cmd, String))
	isempty(output) && return String[]
	return split(output, '\n')
	end

	"""
	Get list of artifact tarballs in the deploy branch.
	"""
	function list_previous_artifacts()
	# if this command fails with the error
	# `fatal: Not a valid object name artifacts`
	# you need to run at least once
	# `git checkout artifacts`
	# to create the artifacts branch
	files = try
	git_lstree("."; args=["-r"], branch=deploy_branch)
	catch e
	@warn "Failed to list previous artifacts, perhaps you need to run \
	`git checkout artifacts` at least once to create the branch?"
	throw(e)
	String[]
	end
	filter!(f -> endswith(f, ".tar.gz"), files)
	return Dict(f => git_hash(f; branch=deploy_branch) for f in files)
	end

	"""
	Get folder names in `datasets/` that are newer than the corresponding
	tarball.
	"""
	function list_new_folders()
	prev_artifacts = list_previous_artifacts()

	new_folders = String[]
	# This include all the folders in `datasets/`
	# dirs = readdir(datasets_dir)
	# This only include the folders that have been git committed to the main branch
	# Note it needs exactly the `datasets/` as path: not abosulute path, with
	# trailing slash to list subfolders.
	dirs = map(basename, git_lstree(basename(datasets_dir) * "/"; branch="main"))
	for data in dirs
	startswith(data, "_") && continue
	startswith(data, ".") && continue
	isdir(joinpath(datasets_dir, data)) \|\| continue

	dir_hash = git_hash(joinpath(basename(datasets_dir), data))
	artifact_hash = get(prev_artifacts, "$(data).tar.gz", nothing)
	# @info "dir_hash: $dir_hash, artifact_hash: $artifact_hash"
	if !isnothing(artifact_hash)
	# if date of dir_hash is older than artifact_hash
	# then we do not need to update the artifact
	(git_date(dir_hash) <= git_date(artifact_hash)) && continue
	end
	push!(new_folders, data)
	end
	return new_folders
	end

	"""
	Remove the `artifacts_dir` folder and create a new one.
	"""
	function clean_artifacts_dir()
	print("I will clean the `$(artifacts_dir)` folder [y/N]: ")
	n = readline()
	if lowercase(n) != "y"
	println("Aborting...")
	return false
	end
	rm(artifacts_dir; force=true, recursive=true)
	mkpath(artifacts_dir)
	println("Cleaned `$(artifacts_dir)` folder.")
	return true
	end

	"""
	Get previous Artifacts.toml from deploy branch.
	"""
	function read_artifact_toml()
	return try
	content = read(`git show $deploy_branch:Artifacts.toml`)
	return TOML.parse(String(content))
	catch e
	return Dict{String,Any}()
	end
	end

	function (@main)(args)
	artifacts = read_artifact_toml()

	new_folders = list_new_folders()
	if isempty(new_folders)
	println("No new folders to process.")
	return
	end

	if "dryrun" in args
	println("New folders to process:")
	for folder in new_folders
	println("- $folder")
	end
	else
	clean_artifacts_dir() \|\| return

	for folder in new_folders
	artifact = create_artifact(folder)
	# existing entries will be replaced
	push!(artifacts, artifact)
	# break
	end

	open("Artifacts.toml", "w") do io
	TOML.print(io, artifacts)
	end
	end
	end