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Build branch fix-integration-tests with version fix-integration-tests (c1fe2a62)

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Build pipeline: vsh-ci-dev-rdkgl

Source commit: c1fe2a629d

Source message: Update CHANGELOG
This commit is contained in:
CI
2024-10-18 08:08:08 +00:00
parent cd0af18851
commit 43cfb251c7
1457 changed files with 222 additions and 905786 deletions
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226
target/executable/compression/compress_h5mu/.config.vsh.yaml
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@@ -1,226 +0,0 @@
name: "compress_h5mu"
namespace: "compression"
version: "dev"
authors:
- name: "Dries Schaumont"
roles:
- "maintainer"
info:
role: "Core Team Member"
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Arguments"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Path to the input .h5mu."
info: null
example:
- "sample_path"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output"
description: "location of output file."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--compression"
description: "Compression type."
info: null
default:
- "gzip"
required: false
choices:
- "lzf"
- "gzip"
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "compress_h5mu.py"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Compress a MuData file. \n"
test_resources:
- type: "python_script"
path: "run_test.py"
is_executable: true
- type: "file"
path: "e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"
- type: "file"
path: "openpipelinetestutils"
dest: "openpipelinetestutils"
info: null
status: "enabled"
links:
repository: "https://github.com/openpipelines-bio/openpipeline"
docker_registry: "ghcr.io"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
label:
- "singlecpu"
- "lowmem"
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "python:3.10-slim"
target_registry: "images.viash-hub.com"
target_tag: "dev"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
interactive: false
- type: "python"
user: false
packages:
- "anndata==0.10.8"
- "mudata~=0.2.4"
- "pandas!=2.1.2"
- "numpy<2.0.0"
upgrade: true
test_setup:
- type: "docker"
copy:
- "openpipelinetestutils /opt/openpipelinetestutils"
- type: "python"
user: false
packages:
- "/opt/openpipelinetestutils"
upgrade: true
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/compression/compress_h5mu/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/compression/compress_h5mu"
executable: "target/executable/compression/compress_h5mu/compress_h5mu"
viash_version: "0.9.0"
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
git_tag: "0.2.0-1926-g2dbe3b72"
package_config:
name: "openpipeline"
version: "dev"
info:
test_resources:
- type: "s3"
path: "s3://openpipelines-data"
dest: "resources_test"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'dev'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline"
docker_registry: "ghcr.io"
homepage: "https://openpipelines.bio"
documentation: "https://openpipelines.bio/fundamentals"
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"

1188
target/executable/compression/compress_h5mu/compress_h5mu
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49
target/executable/compression/compress_h5mu/compress_h5mu.py
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from h5py import File as H5File
from h5py import Group, Dataset
from pathlib import Path
from typing import Union, Literal
from functools import partial
def compress_h5mu(input_path: Union[str, Path],
output_path: Union[str, Path],
compression: Union[Literal['gzip'], Literal['lzf']]):
input_path, output_path = str(input_path), str(output_path)
def copy_attributes(in_object, out_object):
for key, value in in_object.attrs.items():
out_object.attrs[key] = value
def visit_path(output_h5: H5File,
compression: Union[Literal['gzip'], Literal['lzf']],
name: str, object: Union[Group, Dataset]):
if isinstance(object, Group):
new_group = output_h5.create_group(name)
copy_attributes(object, new_group)
elif isinstance(object, Dataset):
# Compression only works for non-scalar Dataset objects
# Scalar objects dont have a shape defined
if not object.compression and object.shape not in [None, ()]:
new_dataset = output_h5.create_dataset(name, data=object, compression=compression)
copy_attributes(object, new_dataset)
else:
output_h5.copy(object, name)
else:
raise NotImplementedError(f"Could not copy element {name}, "
f"type has not been implemented yet: {type(object)}")
with H5File(input_path, 'r') as input_h5, H5File(output_path, 'w', userblock_size=512) as output_h5:
copy_attributes(input_h5, output_h5)
input_h5.visititems(partial(visit_path, output_h5, compression))
with open(input_path, "rb") as input_bytes:
# Mudata puts metadata like this in the first 512 bytes:
# MuData (format-version=0.1.0;creator=muon;creator-version=0.2.0)
# See mudata/_core/io.py, read_h5mu() function
starting_metadata = input_bytes.read(100)
# The metadata is padded with extra null bytes up until 512 bytes
truncate_location = starting_metadata.find(b"\x00")
starting_metadata = starting_metadata[:truncate_location]
with open(output_path, "br+") as f:
nbytes = f.write(starting_metadata)
f.write(b"\0" * (512 - nbytes))

42
target/executable/compression/compress_h5mu/nextflow_labels.config
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process {
// Default resources for components that hardly do any processing
memory = { 2.GB * task.attempt }
cpus = 1
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null
// Resource labels
withLabel: singlecpu { cpus = 1 }
withLabel: lowcpu { cpus = 4 }
withLabel: midcpu { cpus = 10 }
withLabel: highcpu { cpus = 20 }
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}

200
target/executable/compression/tar_extract/.config.vsh.yaml
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@@ -1,200 +0,0 @@
name: "tar_extract"
namespace: "compression"
version: "dev"
argument_groups:
- name: "Arguments"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Input file"
info: null
example:
- "input.tar.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Folder to restore file(s) to."
info: null
example:
- "output_folder"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--strip_components"
alternatives:
- "-s"
description: "Strip this amount of leading components from file names on extraction.\
\ For example, to extract only 'myfile.txt' from an archive containing the structure\
\ `this/goes/deep/myfile.txt', use 3 to strip 'this/goes/deep/'."
info: null
example:
- 1
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--exclude"
alternatives:
- "-e"
description: "Prevents any file or member whose name matches the shell wildcard\
\ (pattern) from being extracted."
info: null
example:
- "docs/figures"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Extract files from a tar archive"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "LICENSE"
- type: "file"
path: "openpipelinetestutils"
dest: "openpipelinetestutils"
info: null
status: "enabled"
links:
repository: "https://github.com/openpipelines-bio/openpipeline"
docker_registry: "ghcr.io"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
label:
- "singlecpu"
- "lowmem"
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "ubuntu:latest"
target_registry: "images.viash-hub.com"
target_tag: "dev"
namespace_separator: "/"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/compression/tar_extract/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/compression/tar_extract"
executable: "target/executable/compression/tar_extract/tar_extract"
viash_version: "0.9.0"
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
git_tag: "0.2.0-1926-g2dbe3b72"
package_config:
name: "openpipeline"
version: "dev"
info:
test_resources:
- type: "s3"
path: "s3://openpipelines-data"
dest: "resources_test"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
\ := 'includeConfig(\"nextflow_labels.config\")'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'dev'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline"
docker_registry: "ghcr.io"
homepage: "https://openpipelines.bio"
documentation: "https://openpipelines.bio/fundamentals"
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"

42
target/executable/compression/tar_extract/nextflow_labels.config
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@@ -1,42 +0,0 @@
process {
// Default resources for components that hardly do any processing
memory = { 2.GB * task.attempt }
cpus = 1
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null
// Resource labels
withLabel: singlecpu { cpus = 1 }
withLabel: lowcpu { cpus = 4 }
withLabel: midcpu { cpus = 10 }
withLabel: highcpu { cpus = 20 }
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}

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target/executable/compression/tar_extract/tar_extract
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