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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
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2024-10-18 08:08:08 +00:00
parent cd0af18851
commit 43cfb251c7
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target/executable/dimred/densmap/.config.vsh.yaml
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@@ -1,435 +0,0 @@
name: "densmap"
namespace: "dimred"
version: "dev"
authors:
- name: "Jakub Majercik"
roles:
- "maintainer"
info:
role: "Contributor"
links:
email: "jakub@data-intuitive.com"
github: "jakubmajercik"
linkedin: "jakubmajercik"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatics Engineer"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
description: "Input h5mu file"
info: null
example:
- "input.h5mu"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--modality"
info: null
default:
- "rna"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--uns_neighbors"
description: "The `.uns` neighbors slot as output by the `find_neighbors` component."
info: null
default:
- "neighbors"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--obsm_pca"
description: "The slot in `.obsm` where the PCA results are stored.\n"
info: null
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--obsm_knn_indices"
description: "The slot in `.obsm` where the kNN indices are stored.\n"
info: null
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--obsm_knn_distances"
description: "The slot in `.obsm` where the kNN distances are stored.\n"
info: null
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output h5mu file."
info: null
example:
- "output.h5mu"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--output_compression"
description: "The compression format to be used on the output h5mu object."
info: null
example:
- "gzip"
required: false
choices:
- "gzip"
- "lzf"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--obsm_output"
description: "The .obsm key to use for storing the densMAP results.."
info: null
default:
- "X_densmap"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Arguments UMAP"
arguments:
- type: "double"
name: "--min_dist"
description: "The effective minimum distance between embedded points. Smaller\
\ values will result \nin a more clustered/clumped embedding where nearby points\
\ on the manifold are drawn \ncloser together, while larger values will result\
\ on a more even dispersal of points. \nThe value should be set relative to\
\ the spread value, which determines the scale at \nwhich embedded points will\
\ be spread out. \n"
info: null
default:
- 0.5
required: false
min: 0.0
max: 10.0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--spread"
description: "The effective scale of embedded points. In combination with `min_dist`\
\ this \ndetermines how clustered/clumped the embedded points are.\n"
info: null
default:
- 1.0
required: false
min: 0.0
max: 10.0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--num_components"
description: "The number of dimensions of the embedding."
info: null
default:
- 2
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--max_iter"
description: "The number of iterations (epochs) of the optimization. Called `n_epochs`\
\ \nin the original UMAP. Default is set to 500 if \nneighbors['connectivities'].shape[0]\
\ <= 10000, else 200.\n"
info: null
default:
- 0
required: false
min: 0
max: 1000
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--alpha"
description: "The initial learning rate for the embedding optimization."
info: null
default:
- 1.0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--gamma"
description: "Weighting applied to negative samples in low dimensional embedding\
\ optimization. \nValues higher than one will result in greater weight being\
\ given to negative samples.\n"
info: null
default:
- 1.0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--negative_sample_rate"
description: "The number of negative samples to select per positive sample\nin\
\ the optimization process. Increasing this value will result\nin greater repulsive\
\ force being applied, greater optimization\ncost, but slightly more accuracy.\n"
info: null
default:
- 5
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--init_pos"
description: "How to initialize the low dimensional embedding. Called `init` in\
\ the original UMAP. Options are:\n \n* Any key from `.obsm`\n* `'paga'`: positions\
\ from `paga()`\n* `'spectral'`: use a spectral embedding of the graph\n* `'random'`:\
\ assign initial embedding positions at random.\n"
info: null
default:
- "spectral"
required: false
choices:
- "paga"
- "spectral"
- "random"
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Arguments densMAP"
arguments:
- type: "double"
name: "--lambda"
description: "Controls the regularization weight of the density correlation term\
\ in densMAP. \nHigher values prioritize density preservation over the UMAP\
\ objective, and vice versa \nfor values closer to zero. Setting this parameter\
\ to zero is equivalent to running \nthe original UMAP algorithm.\n"
info: null
default:
- 2.0
required: false
min: 0.01
max: 10.0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--fraction"
description: "Controls the fraction of epochs (between 0 and 1) where the density-augmented\
\ objective \nis used in densMAP. The first (1 - dens_frac) fraction of epochs\
\ optimize the original \nUMAP objective before introducing the density correlation\
\ term.\n"
info: null
default:
- 0.3
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--var_shift"
description: "A small constant added to the variance of local radii in the embedding\
\ when calculating \nthe density correlation objective to prevent numerical\
\ instability from dividing by a \nsmall number.\n"
info: null
default:
- 0.1
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "setup_logger.py"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "A modification of UMAP that adds an extra cost term in order to preserve\
\ information \nabout the relative local density of the data. It is performed on\
\ the same inputs as UMAP.\n"
test_resources:
- type: "python_script"
path: "test.py"
is_executable: true
- type: "file"
path: "pbmc_1k_protein_v3"
- 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:
- "highcpu"
- "midmem"
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:3.12-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"
- "umap-learn"
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/dimred/densmap/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/dimred/densmap"
executable: "target/executable/dimred/densmap/densmap"
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"