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openproblems-v2 0.1.0

general

NEW FUNCTIONALITY

  • Updated all current tasks in v2 to latest changes in OP v1 (PR #214)

MAJOR CHANGES

  • Relocate task directories to new src/tasks/ location (PR #142).

  • Update Docker images to our base images; ghcr.io/openproblems-bio/base-python and ghcr.io/openproblems-bio/base-r (PR #168).

  • Update batch integration docker images to OpenProblems base images (PR #171).

  • Changed default normalization CPM to CP10k (PR #214)

MINOR CHANGES

  • Update test scripts (PR #143).

  • Update "baseline" to "control" (PR #146).

  • Add task image thumbnails to api (PR #231).

BUG FIXES

  • dimensionality_reduction/methods/tsne: Use GitHub version of MulticoreTSNE.

  • label_projection/methods/seurat_transferdata: Temporarily disable component as it appears to not be working (PR #206).

  • Remove the ns-list action for workflows in integration test (PR #208)

common

NEW FUNCTIONALITY

  • extract_scores: Summarise a metrics output tsv.

  • Created test data resources_test/pancreas with src/common/resources_test_scripts/pancreas.sh.

  • get_api_info: Extract api info from tasks.

  • get_method_info: Extract method info from config yaml.

  • get_metric_info: Extract metric info from config yaml.

  • get_results: Extract benchmark scores.

  • get_task_info: Extract task info.

  • comp_tests: Common unit tests that can be used by all tasks.

  • check_dataset_schema: Check if the dataset used has the required fields defined in the api file_*.yaml files.

  • Create_component: Creates a template folder with a viash config and script file depending on the task api.

MINOR CHANGES

  • Refactor and standardize metric and method info fields (PR #99).

  • Add url check to method and metric unit test (PR #160).

  • Add library.bib file check to component unit test (PR #167)

  • Lower bound scvi-tools to 1.1.0 for all methods using the package (PR #416).

BUG FIXES

  • fix typos in metric and common defenition schemas (PR #212)

migration

NEW FUNCTIONALITY

  • list_git_shas: create list of latest commit hashes of all files in repo.

  • check_migration_status: compare git shas from methods with v1

datasets

NEW FUNCTIONALITY

  • workflows/process_openproblems_v1: Fetch and process legacy OpenProblems v1 datasets, whilst adding extra information to the .uns.

  • normalization/log_cpm: A log CPM normalization method.

  • normalization/log_scran_pooling: A log scran pooling normalization method.

  • normalization/sqrt_cpm: A sqrt CPM normalization method.

  • normalization/l1_sqrt: A scaled L1 sqrt normalization. extracted from Alra method in the denoising task from v1

  • subsample: Subsample an h5ad file. Allows keeping observations from specific batches and celltypes, also allows keeping certain features.

  • resources_test_scripts: Scripts to create test_resources for local development with "pancreas", "pancreas_tasks" and "multimodal".

V1 MIGRATION

  • loaders/openproblems_v1: Fetch a dataset from OpenProblems v1, whilst adding extra information to the .uns.

  • loaders/openproblems_v1_multimodal: Fetch a multimodal dataset from OpenProblems v1, whilst adding extra information to the .uns.

batch_integration

MINOR CHANGES

  • Updated methods/scanvi to use counts as preferred_normalization

  • Updated methods/scvi to use counts as preferred_normalization

NEW FUNCTIONALITY

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the process, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • resources_test/label_projection/pancreas with src/tasks/label_projection/resources_test_scripts/pancreas.sh.

  • workflows/run: Added nf-tower test script (PR #205).

  • metrics/lisi: Added a component for cLISI and iLISI graph metrics from scib (PR #213).

V1 MIGRATION

  • Removed the separate subtask specific subfolders. The "subtask" is added to the config.

  • control_methods/no_integration: Migrated from v1.

  • control_methods/perfect_integration: Migrated from v1, renaming "random embedding" to "perfect integration".

  • control_methods/random_integration: Migrated from v1.

  • methods/bbknn: Migrated from v1 graph.

  • methods/combat: Migrated from v1 feature.

  • methods/scanorama_embed: Migrated from v1 embedding.

  • methods/scanorama_feature: Migrated from v1 feature.

  • methods/scvi: Migrated from v1 embedding.

  • metrics/asw_batch: Migrated from v1 embedding.

  • metrics/asw_label: Migrated from v1 embedding.

  • metrics/cell_cycle_conservation: Migrated from v1 embedding.

  • metrics/clustering_overlap: Migrated from v1 graph NMI & ARI.

  • metrics/graph_connectivity: Migrated from v1 graph.

  • metrics/hvg_overlap: Migrated from v1 feature.

  • metrics/isolated_label_asw: Migrated from v1 embedding.

  • metrics/isolated_label_f1: Migrated from v1 graph.

  • metrics/kbet: Migrated from v1 embedding.

  • metrics/pcr: Migrated from v1 embedding.

MINOR CHANGES

  • Removed the .uns["output_type"] field from output anndata in methods and control methods. (PR #205)

label_projection

MINOR CHANGES

  • Updated methods/scanvi to use counts as preferred_normalization

NEW FUNCTIONALITY

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the process, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • resources_test/label_projection/pancreas with src/tasks/label_projection/resources_test_scripts/pancreas.sh.

    • workflows/run: Added nf-tower test script. (PR #205)

V1 MIGRATION

  • methods/knn: Migrated from v1.

  • methods/logistic_regression: Migrated from v1.

  • methods/mlp: Migrated from v1.

  • methods/scanvi: Migrated and adapted from v1.

  • methods/scanvi_scarches: Migrated and adapted from v1.

  • methods/seurat_transferdata: Migrated and adapted from v1.

  • methods/xgboost: Migrated from v1.

  • control_methods/majority_vote: Migrated from v1.

  • control_methods/random_labels: Migrated from v1.

  • control_methods/true_labels: Migrated from v1.

  • metric/accuracy: Migrated from v1.

  • metric/f1: Migrated from v1.

denoising

NEW FUNCTIONALITY

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the split, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • resources_test/denoising/pancreas with src/tasks/denoising/resources_test_scripts/pancreas.sh.

  • workflows/run: Added nf-tower test script. (PR #205)

V1 MIGRATION

  • control_methods/no_denoising: Migrated from v1. Extracted from baseline method

  • control_methods/perfect_denoising: Migrated from v1.Extracted from baseline method

  • methods/alra: Migrated from v1. Changed from python to R and uses lg_cpm normalised data instead of L1 sqrt

  • methods/dca: Migrated and adapted from v1.

  • methods/knn_smoothing: Migrated and adapted from v1.

  • methods/magic: Migrated from v1.

  • metrics/mse: Migrated from v1.

  • metrics/poisson: Migrated from v1.

Changes from V1

  • Anndata layers are used to store data instead of obsm

  • extended the use of sparse data in methods unless it was not possible

  • process_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics.

Dimensionality reduction

New functionality

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the split, control method, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • control_methods: Added a component for baseline methods specifically.

  • resources_test/dimensionality_reduction/pancreas with src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh.

  • Added variant key to config files to store variants (different input parameters) of every component.

  • workflows/run: Added nf-tower test script. (PR #205)

V1 migration

  • control_methods/true_features: Migrated from v1. Extracted from baseline method True Features.

  • control_methods/random_features: Migrated from v1. Extracted from baseline method Random Features.

  • methods/umap: Migrated from v1.

  • methods/ivis: Migrated from v1.

  • methods/tsne: Migrated and adapted from v1.

  • methods/densmap: Migrated and adapted from v1.

  • methods/phate: Migrated from v1.

  • methods/pca: Migrated from v1.

  • methods/neuralee: Migrated from v1.

  • metrics/distance_correlation: Migrated from v1, but will likely be removed.

  • metrics/trustworthiness: Migrated from v1, but will likely be removed.

  • metrics/density_preservation: Migrated from v1.

  • metrics/coranking: Migrated from v1. This script originally called nn_ranking.py and written in Python.

Changes from V1

  • Raw counts and normalized expression data is stored in .layers["counts"] and .layers["normalized"], respectively, instead of in .X.

  • A process_dataset has been implemented to make a distinction between the data a method is allowed to see (here called the train data) and what a metric is allowed to see (here called the test data).

  • methods/ivis had originally been removed from the v1 (temporarily) but has been added back to the v2.

  • The metrics as defined in the nn_ranking.py script have been documented and refactored into an R component metrics/coranking.

  • metrics/rmse should be removed because RMSE metrics don't really make sense here.

  • metrics/trustworthiness should be removed because it is already included in metrics/coranking.

  • methods/simlr: Added new SIMLR method.

  • metrics/clustering_performance: Added new metric to assess clustering on the reduced dimensional embeddings using NMI and ARI.

match_modalities (PR #201)

New functionality

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the split, control method, method and metric components.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • control_methods: Added a component for baseline methods specifically.

  • resources_test/dimensionality_reduction/pancreas with src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh.

  • Added variant key to config files to store variants (different input parameters) of every component.

  • workflows/run: Added nf-tower test script.

V1 migration

  • control_methods/true_features: Migrated from v1. Extracted from baseline method True Features.

  • control_methods/random_features: Migrated from v1. Extracted from baseline method Random Features.

  • methods/harmonic_alignment: Migrated from v1.

  • methods/mnn: Migrated from v1.

  • methods/procrustes: Migrated from v1.

  • metrics/knn_auc: Migrated from v1.

  • metrics/mse: Migrated from v1.

Changes from V1

  • methods/scot: Add new scot method.

  • Raw counts and normalized expression data is stored in .layers["counts"] and .layers["normalized"], respectively, instead of in .X.

  • The methods and metrics now take 2 modal datasets as input instead of 1.

spatial_decomposition (PR #365)

NEW FUNCTIONALITY

  • api/file_*: Created a file format specifications for the h5ad files throughout the pipeline.

  • api/comp_*: Created an api definition for the process, method and metric components.

  • dataset_simulator: Added a component to simulate spatial datasets with the required ground-truth.

  • process_dataset: Added a component for processing common datasets into task-ready dataset objects.

  • resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas with src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh.

  • Added variant key to config files to store the different input parameter sets for components.

  • workflows/run: Added nf-tower test script.

V1 MIGRATION

  • methods/cell2location: Migrated from v1.

  • methods/destvi: Migrated from v1.

  • methods/nmfreg: Migrated from v1.

  • methods/nnls: Migrated and adapted from v1.

  • methods/rctd: Migrated and adapted from v1.

  • methods/seurat: Migrated and adapted from v1.

  • methods/stereoscope: Migrated from v1.

  • methods/tangram: Migrated from v1.

  • methods/vanillanmf: Migrated from v1.

  • control_methods/random_proportions: Migrated from v1.

  • control_methods/true_proportions: Migrated from v1.

  • metric/r2: Migrated from v1.

Changes from V1

  • Raw counts and normalized expression data is stored in .layers["counts"] and .layers["normalized"], respectively, instead of in .X.

  • A process_dataset has been implemented to make a distinction between the data that a method or metric is allowed to see.