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openproblems [next release]

Breaking changes

Major changes

  • Update Viash to 0.9.0 (PR #911).

Minor changes

  • Add the CELLxGENE immune cell atlas dataset as a common test resource (PR #907).

  • Update dataset_id for tenx_visium, zenodo_spatial, zenodo_spatial_slidetags datasets and use mouse_brain_coronal as a test resource in the spatially_variable_genes task (PR #908).

  • Update get_task_info, get_method_info and get_metrics_info reporting components with more info and extend output (PR #915).

Bug fixes

  • Fix extracting metadata from anndata files in the extract_metadata component (PR #914).

  • Fix path in touch cmd in reporting/process_task_results/run_test.sh (PR #915).

openproblems v2.0.0

A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.

Most relevant parts of the overall structure:

  • src/tasks: Benchmarking tasks:

    • batch_integration: Batch integration
    • denoising: Denoising
    • dimensionality_reduction: Dimensionality reduction
    • match_modalities: Match modalities
    • predict_modality: Predict modality
    • spatial_decomposition: Spatial decomposition
    • spatially_variable_genes: Spatially variable genes

  • src/datasets: Components for creating common datasets. Loaders:

    • cellxgene_census: Query cells from a CellxGene Census
    • openproblems_neurips2021_bmmc: Fetch a dataset from the OpenProblems NeurIPS2021 competition
    • openproblems_neurips2022_pbmc: Fetch a dataset from the OpenProblems NeurIPS2022 competition
    • openproblems_v1: Fetch a legacy OpenProblems v1 dataset
    • openproblems_v1_multimodal: Fetch a legacy OpenProblems v1 multimodal dataset
    • tenx_visium: Fetch a and convert 10x Visium dataset
    • zenodo_spatial: Fetch and process an Anndata file containing DBiT seq, MERFISH, seqFISH, Slide-seq v2, STARmap, and Stereo-seq data from Zenodo.
    • zenodo_spatial_slidetags: Download a compressed file containing gene expression matrix and spatial locations from zenodo.

  • src/common: Common components used by all tasks.

    • check_dataset_schema: Check whether an h5ad dataset adheres to a dataset schema
    • check_yaml_schema: Check whether a YAML adheres to a JSON schema
    • comp_tests: Reusable component unit tests
    • create_component: Create a component Viash component.
    • create_task_readme: Create a README for an OpenProblems task.
    • extract_metadata: Extract the .uns metadata from an h5ad file.
    • helper_functions: Commonly used helper functions in Python or in R,
    • process_task_results: Process the raw tasks results (containing raw logs, unprocessed component configs, and various metrics) into nicely formatted task results.
    • schemas: JSON schemas for YAML files in the repository
    • sync_test_resources: Synchronise the test resources from s3 to resources_test

For more information related to the structure of this repository, see the documentation.

openproblems v1.0.0

Note: This changelog was automatically generated from the git log.

New functionality

  • Added cell2location to the spatial_decomposition task.
  • Added nearest-neighbor ranking matrix computation to _utils.
  • Datasets now store nearest-neighbor ranking matrix in adata.obsm["X_ranking"].
  • Added support for parsing Nextflow output and generating benchmark results for the website.
  • Added max_samples parameter to qlocal, qglobal, qnn_auc, lcmc, qnn, and continuity metrics to allow for subsampling of data for faster computation.
  • Added new scArches based methods: scarches_scanvi_xgb_all_genes and scarches_scanvi_xgb_hvg.
  • Added prediction_method parameter to _scanvi_scarches to specify prediction method.
  • Added _pred_xgb function to perform XGBoost prediction based on latent representations.
  • Added obsm parameter to _xgboost function to allow specifying the embedding space for XGBoost training.

Major changes

  • Updated scvi-tools to version 0.20 in both Python and R environments.
  • Updated datasets to include nearest-neighbor ranking matrix.
  • Modified dimensionality reduction task to include nearest-neighbor ranking matrix computation in dataset generation.
  • The website update workflow was refactored to use a new workflow using json instead of markdown.
  • Updated the website generation process to remove duplicate BibTex entries.
  • Added a new parse_metadata.py script for generating metadata for the website.
  • Added a new function to openproblems.utils.py to get the member ID of a task, dataset, method or metric.
  • Removed the redundant computation and storage of the nearest-neighbor ranking matrix in datasets.

Minor changes

  • Updated method names to be shorter and more consistent across tasks.
  • Improved method summaries for clarity.
  • Updated JAX and JAXlib versions to 0.4.6.
  • Updated dependencies to support new versions of Snakemake and GitPython.
  • Removed code related to "nbt2022-reproducibility" repo and merged it into the main website.
  • Updated the schema for benchmark results to include submission time, code version, and resource usage metrics.
  • Improved error handling and added logging to the parsing script.
  • Removed the "raw.json" file from the results directory and merged all data into a single "results.json" file.
  • Updated the workflow to upload the final results to the website's results directory instead of the data directory.
  • Removed unnecessary code and refactored the parsing script for better readability.
  • Added unit tests for the new parsing script.
  • Updated the run_tests workflow to skip testing on the test_website branch.
  • Updated the run_tests workflow to skip testing on the test_process branch.
  • Updated the create-pull-request step to set the author for the pull request.
  • Updated the run_tests workflow to skip testing on pull request reviews.
  • Updated the update_website_content workflow to update the website on the main branch.
  • Updated the main.bib file to fix a typo.
  • Removed extraneous headings from task README files.
  • Updated generate_test_matrix.py to use the new openproblems.utils.get_member_id function.
  • Updated the website generation process to copy BibTex files to the correct location.
  • Updated the process_requires section in setup.py to include gitpython.
  • Updated git commit hash generation for openproblems functions.
  • Modified _xgboost to allow for specifying tree_method.
  • Modified _scanvi_scarches to consistently use unlabeled_category.
  • Modified _scanvi_scarches to remove unnecessary copying of labels.
  • Removed _scanvi_scarches functions that were redundant with _scanvi_scarches.
  • Removed unused _scanvi functions.
  • Modified _scanvi_scarches to allow for specifying prediction_method and handle unlabeled_category consistently.

Documentation

  • Improved the documentation of the auprc metric.
  • Improved the documentation of the cell2location methods.
  • Document sub-stub task behaviour

Bug fixes

  • Fixed an error in neuralee_default where the subsample_genes argument could be too small.
  • Fixed an error in knn_naive where the is_baseline argument was set to False.
  • Fixed calculation of ranking matrix in _utils to include ties.
  • Fixed a bug in load_tenx_5k_pbmc() where a warning about non-unique variable names was being raised.
  • Removed the unused _utils.py file.
  • Removed the X_ranking entry from the obsm attribute of datasets.
  • The _fit() function in nn_ranking.py now subsamples the data if max_samples is specified.
  • The nn_ranking metrics now use subsampling in the _fit() function to improve performance.
  • Fixed the git hash generation for openproblems functions
  • Fixed a warning about pkg_resources being deprecated
  • Removed unnecessary fetch-depth: 1 from workflow
  • Fixed potential issue in _scanvi_scarches where labels_pred could be overwritten
  • Fixed potential issue in _pred_xgb where num_round wasn't being used correctly
  • Fixed an issue where baseline methods were not being filtered correctly from the benchmark results.
  • Fixed an issue where metrics with all NaN values were not being removed from the benchmark results.
  • Fixed an issue where some metrics were not being parsed correctly from the Nextflow output.
  • Fixed an issue where the "mean_score" field was not being calculated correctly for each method.
  • Fixed an issue where the "code_version" field was not being populated correctly for each method.
  • Fixed an issue where the "submission_time" field was not being populated correctly for each method.
  • Fixed an issue where the resource usage metrics were not being parsed correctly from the Nextflow output.
  • Updated the run_tests workflow to skip testing on the test_website branch.
  • Updated the run_tests workflow to skip testing on the test_process branch.
  • Updated the create-pull-request step to set the author for the pull request.
  • Updated the run_tests workflow to skip testing on pull request reviews.
  • Updated the `updatewebsite

openproblems v0.8.0

Note: This changelog was automatically generated from the git log.

New functionality

  • Added the zebrafish_labs dataset to the dimensionality reduction task.
  • Added the diffusion_map method to the dimensionality reduction task.
  • Added the spectral_features method to the dimensionality reduction task, which uses diffusion maps to create embedding features.
  • Added the distance_correlation_spectral metric to the dimensionality reduction task, which evaluates the similarity of the high-dimensional Laplacian eigenmaps on the full data matrix and the dimensionally-reduced matrix.
  • Added baseline methods for batch integration: no integration, random integration, random integration by cell type, random integration by batch.
  • Added alra_sqrt_reversenorm, alra_log_reversenorm methods for ALRA with reversed normalization order.
  • Added celltype_random_embedding_jitter method to randomize embedding with jitter.

Minor changes

  • Improved the density_preservation metric calculation.
  • Updated the distance_correlation metric to use the new diffusion_map method.
  • Increased the default number of components used for distance_correlation_spectral to 1000.
  • Made metrics more robust by copying the AnnData object before passing it to the metric function.
  • Added is_baseline flag to adata.uns in method decorator.
  • Added is_baseline field to adata.uns for all methods.
  • Increased default values for max_epochs_sp and max_epochs_sc in destvi method.
  • Changed default value of early_stopping_monitor to elbo_validation from reconstruction_loss_train in destvi method.
  • Added train_size and validation_size arguments to the sc_model.train call in destvi method.
  • Added batch_size and plan_kwargs arguments to the st_model.train call in destvi method.
  • Refactor ALRA methods for improved clarity and consistency.
  • Added tests for new ALRA methods with reversed normalization order.
  • Added jitter parameter to _random_embedding function.
  • Updated celltype_random_embedding to use jitter=None in _random_embedding.
  • Removed unnecessary parameters from the sample_dataset function.
  • Removed unnecessary checks for PCA and neighbors in the check_dataset function.
  • Updated pytest.ini to ignore deprecation warning related to pkg_resources.
  • Added permission to all workflows to read and write contents
  • Added permission to write pull requests to several workflows
  • Added permission to write packages to the run_tests workflow.

Bug fixes

  • Fixed a bug in density_preservation that caused it to return 0 when there were NaN values in the embedding.
  • Removed unused true_features_log_cp10k and true_features_log_cp10k_hvg methods.
  • Removed unnecessary imports in metrics.
  • Removed unnecessary neighbors calls in metrics.
  • Removed unused _get_split function.
  • Added embedding_to_graph and feature_to_graph functions for graph-based metrics.
  • Added get_split function for metrics that require splitting data into training and testing sets.
  • Added feature_to_embedding function for embedding-based metrics.
  • Fixed issue where baseline methods were not properly documented.
  • Increased default maximum epochs for spatial models to improve performance.
  • Improved training parameters for both spatial and single-cell models to improve stability and performance.
  • Updated validation metric used for early stopping in spatial model to improve training quality.

Documentation

  • Updated documentation to clarify that the AnnData object passed to metric functions is a copy.
  • Updated the documentation for batch integration tasks to reflect the change in the expected format of the dataset objects.

Major changes

  • Moved baseline methods from individual task modules to a common module.
  • Removed redundant baseline methods from individual task modules.
  • Increased default values for max_epochs_sp and max_epochs_sc in destvi method.

openproblems v0.7.4

Note: This changelog was automatically generated from the git log.

New functionality

  • Added metadata for all datasets, methods, and metrics.

Major changes

  • Updated nf-openproblems to v1.10.

Minor changes

  • Added a new docker_pull rule to the Snakemake workflow to pull Docker images.
  • Added a new docker rule to the Snakemake workflow to build Docker images.
  • Changed the pytest command to include coverage for the test directory.
  • Added new environment variables for the TOWER_TEST_ACTION_ID and TOWER_FULL_ACTION_ID to the Snakemake workflow.
  • Updated the scripts/install_renv.R script to increase the number of retry attempts.

openproblems v0.7.3

Note: This changelog was automatically generated from the git log.

Minor changes

  • Updated scib version to 1.1.3 in docker/openproblems-r-extras/requirements.txt and docker/openproblems-r-pytorch/requirements.txt.

Bug fixes

  • Added pytest-timestamper to test dependencies for better debugging.

openproblems v0.7.2

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed an issue where pymde did not work on sparse data.

openproblems v0.7.1

Note: This changelog was automatically generated from the git log.

Minor changes

  • Added hvg_unint and n_genes_pre to the lung batch.

openproblems v0.7.0

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a bibtex file main.bib for storing all references cited in the repository.
  • Added a section on adding paper references to CONTRIBUTING.md explaining how to add entries to main.bib and link to them in markdown documents.
  • Added new baseline methods for dimensionality reduction: "True Features (logCPM)", "True Features (logCPM, 1kHVG)".
  • Added alra_log method, which implements ALRA with log normalization.
  • Added alra_sqrt method, which implements ALRA with square root normalization.
  • Added PyMDE dimensionality reduction methods
  • Added citations for Chen et al. (2009) "Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis", Kraemer et al. (2018) "dimRed and coRanking - Unifying Dimensionality Reduction in R", Lee et al. (2009) "Quality assessment of dimensionality reduction: Rank-based criteria", Lueks et al. (2011) "How to Evaluate Dimensionality Reduction? - Improving the Co-ranking Matrix", Szubert et al. (2019) "Structure-preserving visualisation of high dimensional single-cell datasets", and Venna et al. (2006) "Local multidimensional scaling".
  • Added install_renv.R script to install R packages using renv with retries
  • Added a new metric to evaluate the conservation of highly variable genes (HVGs) after batch integration.
  • Added support for lung data from Vieira Braga et al.
  • Added magic_reverse_norm and magic_approx_reverse_norm methods which reverse the order of normalization and transformation in the MAGIC algorithm.
  • Added a new workflow to comment on pull request status.

Major changes

  • Updated the openproblems repository to cite papers using bibtex references.
  • Renamed alra method to alra_sqrt.
  • Updated spacexr to latest version.
  • Added fc_cutoff and fc_cutoff_reg parameters to rctd method to control minimum log-fold-change for genes in the normalization and RCTD steps.
  • Renamed the "multimodal_data_integration" task to "matching_modalities".
  • Bumped version to 0.7.0.

Minor changes

  • Added BibTex references to all data loaders in openproblems/data.
  • Added BibTex references to all methods in openproblems/tasks.
  • Added BibTex references to all metrics in openproblems/tasks.
  • Updated update_website_content.yml to copy main.bib to the Open Problems website.
  • Added a BibTeX Tidy hook to .pre-commit-config.yaml.
  • Updated scvi-tools version to ~0.19 in both openproblems-python-pytorch and openproblems-r-pytorch dockerfiles.
  • Updated cell2location version to 47c8d6dc90dd3f1ab639861e8617c6ef0b62bb89 in the openproblems-python-pytorch dockerfile.
  • Updated bslib to version 0.4.2.
  • Updated htmltools to version 0.5.4.
  • Updated the alra_sqrt method to use square root normalization.
  • Updated the alra_log method to use log normalization.
  • Updated the method names to reflect the normalization used.
  • Updated dependencies for gtfparse and polars.
  • Added PyMDE dependency to requirements.txt
  • Updated the API to specify that datasets should provide log CPM-normalized counts in `adata.X

openproblems v0.6.1

Note: This changelog was automatically generated from the git log.

New functionality

  • Added cell2location_detection_alpha_1 method, which uses detection_alpha=1 and a hard-coded reference.
  • Added a new parameter hard_coded_reference to cell2location_detection_alpha_1 method.
  • Added a new baseline method for dimensionality reduction using high-dimensional Laplacian Eigenmaps.
  • Added organism metadata to datasets.
  • Added a new image, openproblems-python-bedtools, to contain packages required for running pybedtools and pyensembl Python packages.
  • Added support for TensorFlow 2.9.0.
  • Added a new schema for storing results in JSON format.
  • Added a new function to parse Nextflow trace files to this JSON schema.
  • Added rmse_spectral metric, which calculates the root mean squared error (RMSE) between high-dimensional Laplacian eigenmaps on the full (or processed) data matrix and the dimensionally-reduced matrix.
  • Added new methods to LIANA: magnitude_max, magnitude_sum, specificity_max, and specificity_sum.
  • Added aggregate_how parameter to liana R function to allow aggregation by "magnitude" or "specificity".
  • Added top_prop parameter to odds_ratio metric to allow specifying the proportion of interactions to consider for calculating the odds ratio.

Major changes

  • Removed unused openproblems-python-batch-integration docker image.
  • Moved scanorama, bbknn, scVI, mnnpy and scib from openproblems-python-batch-integration to openproblems-r-pytorch.
  • Moved cell2location, molecular-cross-validation, neuralee, tangram and phate from openproblems-python-extras to openproblems-python-pytorch.
  • Moved pybedtools, pyensembl and scalex from openproblems-python-extras to openproblems-python-pytorch.
  • Moved dca and keras from openproblems-python-tf2.4 to openproblems-python-tensorflow.
  • Added openproblems-python-bedtools docker image.
  • Added openproblems-python-tensorflow docker image.
  • Added openproblems-python-pytorch docker image.
  • Moved harmony-pytorch from openproblems-r-extras to openproblems-r-pytorch.
  • Added openproblems-r-pytorch docker image.
  • Updated anndata2ri version in openproblems-r-base.
  • Updated kBET version in openproblems-r-extras.
  • Updated scib version in openproblems-r-extras.
  • Updated scvi-tools version in openproblems-r-pytorch.
  • Updated torch version in openproblems-r-pytorch.
  • Moved the codecov action to run only on success
  • Updated the workflow to upload coverage reports to GitHub Actions as an artifact
  • Renamed the run_benchmark job to setup_benchmark.
  • Added a new run_benchmark job that runs after setup_benchmark.
  • Moved the benchmark running logic from the run_benchmark job to the new run_benchmark job.
  • Added a setup-environment step to setup_benchmark job.
  • Added outputs to the setup_benchmark job.
  • Renamed the nbt2022-reproducibility to website-experimental

Minor changes

  • Updated numpy and scipy dependencies in setup.py.
  • Updated scikit-learn, louvain, python-igraph, decorator and colorama dependencies in setup.py.
  • Improved Docker image caching.
  • Removed the counts layer from the immune_cells, pancreas datasets, and the batch_integration_feature task.
  • Removed the counts layer from generate_synthetic_dataset functions in spatial decomposition datasets.
  • Updated the normalize functions to not modify the data in place.
  • Updated the log_cpm_hvg function to annotate HVGs instead of subsetting the data.
  • Updated the _high_dim function in the nn_ranking metric to subset to HVGs.
  • Updated the dimensionality_reduction task README to clarify the role of the highly_variable key.
  • Reduced the random noise added to the one-hot embedding in the _random_embedding function from (-0.1, 0.1) to (-0.01, 0.01).
  • Removed high_dim_pca and high_dim_spectral methods.
  • Updated the random_features method to use the check_version function.
  • Moved raw output files from website to the NBT 2022 reproducibility repository.
  • Updated the process_results.yml workflow to include the NBT 2022 reproducibility repository.
  • Updated the run_tests.yml workflow to skip tests when pushing to specific branches.
  • Removed # ci skip from commit message in CI workflow.
  • Removed redundant file deletion from process_results.yml workflow.
  • Added update_website_content.yml workflow to update benchmark content on the website repository.
  • Modified the process_results.yml workflow to update website content based on results.
  • Changed the update_website_content.yml workflow to trigger on both the main and test_website branches.
  • Updated workflow to push changes to the website only if there are changes to the website content.
  • Added environment variable to track changes.
  • Removed unused git command.
  • Decreased number of samples for testing.
  • Updated igraph to 0.10.* in setup.py.
  • Updated anndata2ri to 1.1.* in openproblems-r-base/README.md.
  • Updated kBET to a10ffea in openproblems-r-extras/r_requirements.txt.
  • Updated scib to f0be826 in openproblems-r-extras/requirements.txt.
  • Updated harmony-pytorch to 0.1.* in openproblems-r-pytorch/requirements.txt.
  • Updated torch to 1.13.* in openproblems-r-pytorch/requirements.txt.
  • Updated scanorama to 1.7.0 in openproblems-r-pytorch/requirements.txt.
  • Updated scvi-tools to 0.16.* in openproblems-r-pytorch/requirements.txt.
  • Updated the regulatory_effect_prediction task to use

openproblems v0.6.0

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a new dataset: "Pancreas (inDrop)"
  • Added a new function: "pancreas"
  • Added a new utility function: "utils.split_data"
  • Added tabula_muris_senis_lung_random dataset.
  • Added celltype_random_embedding baseline method for batch integration embedding.
  • Added celltype_random_graph baseline method for batch integration graph.
  • Added a new argument sctransform_n_cells to the seuratv3 function to allow users to specify the number of cells used to build the negative binomial regression in the SCTransform function.
  • Added a new sample dataset that is smaller and more efficient than the previous one.
  • Added a "mean score" metric to the results table.
  • Added support for loading the sample dataset in load_sample_data.
  • Added support for running benchmarks on pull requests.
  • Added a new workflow for creating a test matrix.
  • Added a new script to generate a test matrix for the run_tester workflow.
  • Added a new script for cleaning up runner diskspace.
  • Added support for uploading docker images to ECR.

Minor changes

  • Added tabula_muris_senis dataset to openproblems/tasks/denoising/datasets/__init__.py.
  • Updated styler to version 1.8.1.
  • Updated the method for normalizing scores to correctly account for baseline method scores.
  • Improved the way NaN and infinite values are handled in the ranking calculation.
  • Removed redundant code that was previously used to upload results and markdown artifacts to test.
  • Removed the raw output files from the website data directory.
  • Updated the list of reviewers for the pull request to include more relevant team members.
  • Changed the reference to "Code" to "Library" in the JSON output to better reflect the data presented.
  • Added a check to ensure that the task has a minimum number of non-baseline methods before processing results.
  • Removed the check to ensure that the task has a minimum number of methods before processing results.
  • Removed redundant code that was previously used to handle incomplete tasks.
  • Updated the workflow to use a consistent version of Python across all jobs.
  • Updated flake8 dependency to https://github.com/pycqa/flake8.
  • Improved random embedding for celltype_random_embedding and celltype_random_graph.
  • Removed pip check from Dockerfile.
  • Updated code to use a more consistent random number generator.
  • Updated liana code to inverse the distribution of the aggregate rank.
  • Improved the logic in odds_ratio to ensure that the numerator/denominator is not zero.
  • Removed unnecessary NXF_DEFAULT_DSL from run_tester workflow.
  • Increased the number of cells used to build the negative binomial regression in the SCTransform function from 3000 to 5000.
  • Adjusted the default values for n_pca and sctransform_n_cells in the seuratv3 function for test and non-test cases.
  • Updated the seuratv3_wrapper.R script to pass the sctransform_n_cells argument to the SCTransform function.
  • Moved the sample dataset from the multimodal folder to the sample folder.
  • Refactored the sample data generation to be more efficient.
  • Modified the compute_ranking function to calculate and add the "mean score" to the dataset_results dictionary.
  • Updated the dataset_results_to_json function to include the "mean score" in the results table.
  • Updated the pull request template to reflect recent changes and improvements in the workflow.
  • Updated the workflow to include a new test_full_benchmark branch.
  • Removed redundant code from the workflow.

openproblems v0.5.21

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a new metric, AUPRC, for evaluating cell-cell communication predictions.
  • Added support for aggregating method scores using "max" and "sum" operations.
  • Implemented a new method, true events, which predicts all possible interactions.
  • Added a new method, random events, which randomly predicts interactions.
  • Implemented LIANA, CellPhoneDB, Connectome, Log2FC, NATMI, and SingleCellSignalR methods with the option to aggregate scores using "max" or "sum."
  • Added LIANA, CellPhoneDB, Connectome, Log2FC, NATMI, and SingleCellSignalR methods to the cell-cell communication ligand-target task.
  • Added LIANA, CellPhoneDB, Connectome, Log2FC, NATMI, and SingleCellSignalR methods to the cell-cell communication source-target task.

Bug fixes

  • Fixed a bug where the odds ratio metric was not handling cases where the numerator or denominator was zero.

Minor changes

  • Updated the IRkernel package version in the R base docker image to 1.3.1.
  • Updated the saezlab/liana package version in the R extras docker image to 0.1.7.
  • Updated the boto3 package version in the main docker image to 1.26.*.
  • Added a check to the cell-cell communication dataset validation to ensure that there are no duplicate entries in the target data.
  • Updated the documentation for the cell-cell communication ligand-target task.
  • Updated the documentation for the cell-cell communication source-target task.

openproblems v0.5.20

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed an issue where a sparse matrix was not being converted to CSR format.
  • Fixed a bug in docker_run.sh where pip check was not being executed.

Minor changes

  • Updated pkgload to version 1.3.1.

openproblems v0.5.19

Note: This changelog was automatically generated from the git log.

Minor changes

  • Converted sparse matrix to csr format.

openproblems v0.5.18

Note: This changelog was automatically generated from the git log.

Minor changes

  • Converted sparse matrices to CSR format.

openproblems v0.5.17

Note: This changelog was automatically generated from the git log.

openproblems v0.5.16

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed a bug where the bioconductor version was incorrect.
  • Fixed a bug where the matrix in obs was incorrect.

Minor changes

  • Updated the scran package to version 1.24.1.
  • Updated the batchelor and scuttle packages.

openproblems v0.5.15

Note: This changelog was automatically generated from the git log.

openproblems v0.5.14

Note: This changelog was automatically generated from the git log.

Major changes

  • Updated workflow to run tests against prod branch.

openproblems v0.5.13

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Skip benchmark if tester fails.

openproblems v0.5.12

Note: This changelog was automatically generated from the git log.

New functionality

  • Explicitly push prod images on tag

Documentation

  • Added short metric descriptions to README

Minor changes

  • Added labels tests

openproblems v0.5.11

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Reverted bump of louvain to 0.8, which caused issues.

Minor changes

  • Updated torch requirement to 1.13 in the openproblems-r-pytorch docker.

openproblems v0.5.10

Note: This changelog was automatically generated from the git log.

New functionality

  • Added support for SCALEX version 1.0.2.

Minor changes

  • Updated RcppAnnoy to version 0.0.20.
  • Updated SageMaker requirement to version 2.116.*.

Bug fixes

  • Fixed a bug in the docker_hash function, which now returns a string instead of an integer.
  • Fixed a bug in the scalex method, which now correctly handles the outdir parameter.

openproblems v0.5.9

Note: This changelog was automatically generated from the git log.

Minor changes

  • Update rpy2 requirement from <3.5.5 to <3.5.6
  • Update ragg to 1.2.4

Bug fixes

  • Don't fail job if hash fails

openproblems v0.5.8

Note: This changelog was automatically generated from the git log.

Minor changes

  • Updated scIB to 77ab015.

openproblems v0.5.7

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a new batch integration subtask for corrected feature matrices.
  • Added a new sub-task for batch integration, "batch integration embed", which includes all methods that output a joint embedding of cells across batches.
  • Added a new sub-task for batch integration, "batch integration graph", which includes all methods that output a cell-cell similarity graph (e.g., a kNN graph).

openproblems v0.5.6

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed an issue where the :: in branch names would cause problems.
  • Fixed an issue where the check_r_dependencies.yml workflow was not properly handling branch names with ::.

Minor changes

  • Updated the caret package to version 6.0-93.
  • Updated the README to include information about the Open Problems team and task leaders.
  • Replaced the NuSVR method with a faster alternative, improving performance.

New functionality

  • Added a new method for running Seuratv3 from a fork, allowing for more efficient use of resources.
  • Added a new requirement to the r_requirements.txt file for the bslib package.
  • Added a new requirement to the r_requirements.txt file for the caret package.

Documentation

  • Added a new section to the README to document the process of running Seuratv3 from a fork.
  • Updated the README to include a list of all contributors to the Open Problems project.

openproblems v0.5.5

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fix sampling and reindexing
  • Fix docker unavailable error to include image name

New functionality

  • Require minimum celltype count for spatial_decomposition

Minor changes

  • Update Rcpp to 1.0.9
  • Update to nf-openproblems v1.7

openproblems v0.5.4

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed an issue where some cell types were missing from the output.

openproblems v0.5.3

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Fixed a bug in the rctd method where cell types with fewer than 25 cells were not being used.

openproblems v0.5.2

Note: This changelog was automatically generated from the git log.

Bug fixes

  • Handle missing function error by catching FileNotFoundError and NoSuchFunctionError instead of just RuntimeError.

openproblems v0.5.1

Note: This changelog was automatically generated from the git log.

Major changes

  • Updated scipy requirement from ==1.8.* to >=1.8,<1.10.
  • Updated igraph to version 1.3.4.

Minor changes

  • Changed the mnnpy dependency to use a patch version instead of a specific commit hash.

Bug fixes

  • Changed docker_hash to use the Docker API if docker is not available.
  • Use curl to retrieve the Docker hash if docker fails.
  • Fixed an issue with using git+https for mnnpy.

openproblems v0.5.0

Note: This changelog was automatically generated from the git log.

Minor changes

  • Updated several R package dependencies.
  • Updated several Python package dependencies.
  • Added several new methods for spatial decomposition: RCTD, DestVI, Stereoscope.
  • Added a new dataset for dimensionality reduction: Mouse hematopoietic stem cell differentiation.
  • Improved documentation for tasks and datasets.

Bug fixes

  • Fixed a bug where the lintr package was not being installed correctly.
  • Fixed a bug where the BRANCH_PARSED variable was not being properly sanitized in the run_tests.yml workflow.
  • Fixed a bug in _scanvi and _scvi functions where the max_epochs parameter was not being passed to the scanvi and scvi functions.
  • Fixed a bug in install_renv.R causing incorrect installation of packages from R repositories.
  • Fixed an issue where the dependency upgrade script would fail to capture the output of the upgrade process.
  • Fixed an issue where the dependency upgrade script would not correctly write updates to the requirements file.
  • Fixed an issue where the git_hash function was not being called for external modules.
  • Fixed a bug in openproblems/tasks/denoising/methods/__init__.py that prevented DCA from being used.
  • Fixed a bug in neuralee_default where it could fail due to sparseness of data.
  • Fixed a bug in scanvi_all_genes where the code version was not being set correctly.
  • Fixed a bug in scanvi_hvg where the code version was not being set correctly.
  • Fixed a bug in scarches_scanvi_all_genes where the code version was not being set correctly.
  • Fixed a bug in scarches_scanvi_hvg where the code version was not being set correctly.

New functionality

  • Added a new denoising method called "DCA" based on a deep count autoencoder.
  • Added xgboost_log_cpm and xgboost_scran methods to openproblems.tasks.label_projection.
  • Added a new command-line interface for testing datasets, methods, and metrics.
  • Added a new install_renv.R script to simplify the installation of the renv package.
  • Added automated CI check to find and suggest available updates to R packages in docker images.
  • Added a hash to the docker image that is based on the age of the code.
  • Added data_reference to dataset metadata.
  • Added docker_hash function to retrieve the docker image hash associated with an image.
  • Added support for retrieving the docker image hash for R functions that have a defined __r_file__.

Documentation

  • Updated contributing guide to reflect the main branch as the default branch.
  • Updated issue templates to reflect the main branch as the default branch.
  • Updated pull request template to reflect the main branch as the default branch.

openproblems v0.4.4

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a new docker image openproblems-r-pytorch for running Harmony in Python

Major changes

  • Moved harmony to Python-based harmony-pytorch

Bug fixes

  • Fixed an issue where adata.var was not being correctly handled in _utils.py
  • Updated the documentation for the openproblems-r-extras docker image

openproblems v0.4.3

Note: This changelog was automatically generated from the git log.

New functionality

  • Added PHATE with sqrt potential

Bug fixes

  • Fixed path to R_HOME
  • Fixed Dockerfile to use R 4.2
  • Minor CI fixes

openproblems v0.4.2

Note: This changelog was automatically generated from the git log.

Minor changes

  • Run scran pooling in series, not in parallel.

openproblems v0.4.1

Note: This changelog was automatically generated from the git log.

New functionality

  • Added FastMNN, Harmony, and Liger methods for batch integration.
  • Added bbknn_full_unscaled method.
  • Added Dependabot configuration for pip and GitHub Actions dependencies.

Minor changes

  • Updated dependencies: scib, bbknn, scanorama, annoy, and mnnpy.
  • Improved the performance of several methods by pre-processing the data before running them.

Bug fixes

  • Fixed bugs in fastMNN, harmony, liger, scanorama, scanvi, scvi, mnn, and combat that caused incorrect embedding.

openproblems v0.4.0

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a new file workflow/generate_website_markdown.py to generate website markdown files for all tasks and datasets.
  • Updated Nextflow version to v1.5.
  • Updated Nextflow version to v1.6.

Major changes

  • Added code version to the output of each method.
  • Updated nextflow version to v1.3.
  • Updated nextflow version to v1.4.
  • Updated docker version to 20.10.15.
  • Removed Docker setup from CI workflow.
  • Updated Python version to 3.8.13.

Minor changes

  • Updated dependencies for the Docker images.
  • Updated pre-commit hooks to include requirements-txt-fixer.
  • Updated Nextflow workflow to version 1.4.
  • Updated the location of method versions in the results directory.
  • Updated the Tower action ID.

Bug fixes

  • Fixed a bug where Docker images were not properly pushed to Docker Hub.
  • Updated requirements.txt files to fix dependency conflicts.
  • Removed unnecessary dependencies from CI workflows to reduce disk space usage on GitHub runners.

openproblems v0.3.5

Note: This changelog was automatically generated from the git log.

New functionality

  • Added new integration methods: BBKNN, Combat, FastMNN feature, FastMNN embed, Harmony, Liger, MNN, Scanorama feature, Scanorama embed, Scanvi, Scvi
  • Added new metrics: graph_connectivity, iso_label_f1, nmi
  • Added _utils.py with functions: hvg_batch, scale_batch
  • Added run_bbknn function.
  • Added a test for the trustworthiness metric, which now passes for sparse matrices.
  • Added a test for the density preservation metric, which now passes against densmap for a reasonable degree of similarity.
  • Added tests for all methods and metrics.
  • Added a new workflow to automatically delete untagged images from the OpenProblems ECR repository.
  • Added a new workflow to process results and create a PR to update the OpenProblems benchmark.
  • Added support for running tests with the process extra in setup.py.
  • Added densmap dimensionality reduction method.
  • Added neuralee dimensionality reduction method.
  • Added alra denoising method.
  • Added scarches_scanvi label projection method.
  • Added bbknn batch integration graph method.
  • Added beta regulatory effect prediction method.
  • Added a new invite-contributors.yml file to the repository.

Major changes

  • The test_methods.py file has been simplified by removing unused arguments.
  • The test_metrics.py file has been simplified by removing unused arguments.
  • The test_utils/docker.py file has been modified to allow specifying the docker image as a decorator argument.
  • Updated Nextflow version to 22.04.0.
  • Modified the processing of Nextflow results to save them in a temporary directory.
  • Modified workflow/parse_nextflow.py to parse results from Nextflow runs.
  • Modified .github/workflows/run_tests.yml to cancel previous runs when a new commit is pushed.

Minor changes

  • Removed .nextflow, scratch/, openproblems/results/ and openproblems/work/ from .gitignore.
  • Updated CONTRIBUTING.md
  • Methods should not edit adata.obsm["train"] or adata.obsm["test"].
  • Redirects stdout to stderr when running subcommands to ensure that output is printed correctly.
  • Updated CI workflow to skip running tests on push if they failed on the run_tester job, unless the branch name starts with test_benchmark.
  • Refactored the Neuralee method to use a separate function for embedding.
  • Improved performance by using a default value for maxit in fine_tune_kwargs.
  • Removed unnecessary code for storing raw counts in the neuralee_default method.

openproblems v0.3.4

Note: This changelog was automatically generated from the git log.

New functionality

  • Added CeNGEN, Tabula Muris Senis, and Pancreas datasets to the label_projection task.
  • Added scANVI and scArches+scANVI methods to the label_projection task.
  • Added majority_vote and random_labels baseline methods to the label_projection task.
  • Added new methods: densMAP, NeuralEE, scvis
  • Added new metrics: NN Ranking (continuity, co-KNN size, co-KNN AUC, Local continuity meta criterion, Local property metric, Global property metric)
  • Added pre-processing function: log_cpm_hvg()
  • Added support for custom pre-processing functions
  • Added support for variants of methods
  • Added a new batch integration task.
  • Added a batch integration graph subtask.
  • Added a batch integration embedding subtask.
  • Added a batch integration corrected feature matrix subtask.
  • Added ivis method for dimensionality reduction to openproblems.
  • Added self-hosted runner support for run_benchmark workflow using Cirun.io
  • Added a --test flag to the run subcommand, allowing for running a test version of a method.
  • Added test_load_dataset to test/test__load_data.py to test loading and caching of datasets.
  • Added test_method to test/test_methods.py to test application of methods.
  • Added test_trustworthiness_sparse to test/test_metrics.py to test trustworthiness metric on sparse data.
  • Added test_density_preservation_matches_densmap to test/test_metrics.py to test density preservation metric against densmap.
  • Updated test/utils/docker.py to allow specifying the docker image as the last argument.
  • Added --test flag to run subcommand to run the test version of a method.
  • Added Docker image building to run_tests.yml.
  • Added a new workflow to process Nextflow results
  • Added a new workflow to run tests and benchmarks
  • Added support for running benchmarks from tags
  • Added support for running benchmarks from forks
  • Added openproblems-cli command to run test-hash

openproblems v0.3.3

Note: This changelog was automatically generated from the git log.

New functionality

  • Added support for balanced SCOT alignment.

Minor changes

  • Updated the workflow to store benchmark results in /tmp.

Bug fixes

  • Fixed the parsing and committing of benchmark results on tag.
  • Fixed the Github Actions badge link.
  • Fixed the coverage badge.
  • Fixed the benchmark commit.
  • Ignored AWS warning and cleaned up S3 properly.
  • Updated the workflow to continue on error for forks.

openproblems v0.3.2

Note: This changelog was automatically generated from the git log.

New functionality

  • Added trustworthiness metric to the dimensionality reduction task.
  • Added density preservation metric.
  • Added several metrics based on nearest neighbor ranking: continuity, co-KNN size, co-KNN AUC, local continuity meta criterion, local property, global property.
  • Added mouse blood data from Olsson et al. (2016) Nature to the openproblems dataset collection.
  • Added a test mode to the load_olsson_2016_mouse_blood function.
  • Added a dataset function for the mouse_blood_olssen_labelled dataset in the openproblems.tasks.dimensionality_reduction.datasets module.
  • Added ALRA denoising method.
  • Added support for the Single Cell Optimal Transport (SCOT) method for multimodal data integration.
  • SCOT implements Gromov-Wasserstein optimal transport to align single-cell multi-omics data.
  • Added four variations of SCOT:
    • sqrt CPM unbalanced
    • sqrt CPM balanced
    • log scran unbalanced
    • log scran balanced
  • Each variation implements different normalization strategies for the input data.
  • Added scot method to openproblems.tasks.multimodal_data_integration.methods.
  • Added pre-processing to the dimensionality_reduction task.
  • Added pre-processing to all dimensionality_reduction methods.
  • Added Wagner_2018_zebrafish_embryo_CRISPR dataset loader
  • Added PR review checklist to the pull request template.
  • Added cmake==3.18.4 to the docker/openproblems-python-extras/requirements.txt file.
  • Added --version flag to print the version.
  • Added --test-hash flag to print the current hash.
  • Added basic help message.
  • Added install_renv.R script for installing R packages in Docker images.
  • Added docker/.version file to track Docker image version.
  • Added a new docker image for running GitHub Actions.
  • Added a new utils.git module to determine which tasks have changed relative to base/main.
  • Added support for running benchmark tests on tags.
  • Added a test directory for use in the workflow.

openproblems v0.3.1

Note: This changelog was automatically generated from the git log.

New functionality

  • Added chromatin potential task
  • Added PHATE to the dimensional_reduction task.
  • Added support for testing docker builds on a separate branch.
  • Added support for building images and pushing them to docker hub.
  • Added support for writing methods in R using scprep's RFunction class.
  • Added a CLI interface to openproblems.
  • Added f1_micro metric.
  • Added mlp_log_cpm and mlp_scran methods for label projection.
  • Added pancreas_batch and pancreas_random datasets for label projection.
  • Added f1 metric for label projection.
  • Added metadata to methods and metrics.
  • Added openproblems.tools.decorators for decorating methods and metrics.
  • Added openproblems.tools.normalize for common normalization functions.
  • Added methods for logistic_regression, mlp, harmonic_alignment, mnn, and procrustes.
  • Added metrics for accuracy, f1, knn_auc, and mse.
  • Added openproblems.version to provide package version.
  • Added dataset decorator for registering datasets.
  • Added tools.decorators.profile decorator to measure memory usage and runtime of methods.
  • Added tools.normalize module to provide normalization functions.
  • Added tools.decorators.normalizer decorator to normalize data prior to applying methods.
  • Added a new "data loader" component that loads data in a way that's formatted correctly for a given task.
  • Added CITE-seq Cord Blood Mononuclear Cells dataset.
  • Added snakemake support for automatic evaluation.
  • Added zebrafish data to label projection task.
  • Added a new task, "Link gene expression with chromatin accessibility"
  • Added a new dataset, "sciCAR Mouse Kidney with cell clusters"
  • Added a new method, "BETA"
  • Added a new metric, "Correlation between RNA and ATAC"
  • Added a new task, "Dimensional reduction"
  • Added human blood dataset from Nestorowa et al. Blood. 2016
  • Added 10x PBMC dataset
  • Added load_10x_5k_pbmc function to load the 10x 5k PBMC dataset.

openproblems v0.2.1

Note: This changelog was automatically generated from the git log.

New functionality

  • Added MLP method for label projection task.
  • Added pancreas data loading to label projection task.

Minor changes

  • Updated black.
  • Updated test version of pancreas_batch to have test data.
  • Added random pancreas train data.

Bug fixes

  • Fixed zebrafish code duplication.
  • Fixed pancreas import location.
  • Fixed bug in zebrafish data.
  • Fixed bug in pancreas import.
  • Removed normalization from loader.
  • Removed dummy and cheat metrics/datasets.
  • Removed excess covariates from pancreas dataset.

openproblems v0.2

Note: This changelog was automatically generated from the git log.

New functionality

  • Added zebrafish label projection task

Major changes

  • Moved scIB, rpy2, harmonicalignment, and mnnpy to optional dependencies

Minor changes

  • Improved n_components fix
  • Moved URL into function for neater namespace

Bug fixes

  • Fixed n_svd for truncatedSVD
  • Fixed data loader
  • Fixed n_pca problem
  • Scaled without mean if sparse
  • Scaled data for regression
  • Added check to ensure that data has nonzero size

openproblems v0.1

Note: This changelog was automatically generated from the git log.

New functionality

  • Added a results page to the website.
  • Added a new zebrafish dataset to the openproblems library.
  • Added netlify.toml to deploy website.

Documentation

  • Updated documentation to reflect new features and datasets.

Major changes

  • Bumped version to 0.1.

Minor changes

  • Improved the website's home menu link.
  • Improved website links.
  • Updated website's hero and social links.
  • Updated website's task cards.
  • Updated the website's demo.
  • Improved website's frontmatter.
  • Separated frontmatter from content in website's Markdown files.
  • Fixed black syntax.
  • Excluded website from black.
  • Updated website content to display results.
  • Updated the Travis CI configuration to exclude website from black.

Bug fixes

  • Fixed zebrafish data loader.

openproblems v0.0.3

Note: This changelog was automatically generated from the git log.

New functionality

  • Added harmonic alignment method.
  • Added scicar datasets.
  • Added logistic regression methods.
  • Added ability to normalize obsm.
  • Added test suite.
  • Added normalization tools.

Documentation

  • Updated documentation to reflect normalization changes.

Major changes

  • Migrated normalizations to openproblems.tools.normalize.
  • Updated dataset specification to require normalization in methods.
  • Removed zebrafish dataset.
  • Moved dataset test spec.
  • Removed "mode2_raw" and "raw" from datasets.
  • Added test dataset spec.
  • Consolidated scicar datasets.
  • Migrated references to github repo.

Minor changes

  • Improved sparse array equality test.
  • Improved sparse inequality check.
  • Increased test data size.
  • Normalized mode2.
  • Fixed decorator.
  • Used uns.
  • Used functools.wraps.
  • Updated name of log_scran_pooling function.
  • Fixed storing normalization results.
  • Fixed zebrafish load caching.
  • Fixed zebrafish test.
  • Added normalization functions.
  • Updated logistic regression function to work with anndata properly.
  • Fixed cheat method.
  • Fixed git upload.
  • Fixed Travis CI.
  • Fixed harmonic alignment import.
  • Increased test coverage.

Bug fixes

  • Bugfix harmonic_alignment, closes #4.
  • Bugfix harmonic alignment import.
  • Normalized data inside methods, closes #19.
  • Fix storing normalization results.
  • Fixed zebrafish test.
  • Fix zebrafish load caching.
  • Fix decorator.
  • Fix cheat method.
  • Don't check for raw data -- we are no longer normalizing.

openproblems v0.0.2

Note: This changelog was automatically generated from the git log.

New functionality

  • Added dummy dataset to openproblems/data
  • Added load_dummy function to openproblems/data
  • Added loader decorator to openproblems/data
  • Added loading functions for sciCAR datasets to openproblems/data/scicar
  • Added scicar_cell_lines dataset to openproblems/tasks/multimodal_data_integration/datasets
  • Added scicar_mouse_kidney dataset to openproblems/tasks/multimodal_data_integration/datasets
  • Added dummy dataset to openproblems/tasks/label_projection/datasets

Major changes

  • Changed data structure for multimodal data integration tasks in openproblems/tasks/multimodal_data_integration
  • Bumped version to 0.0.2 in openproblems/version.py
  • Modified the way to run evaluate.sh in .travis.yml
  • Added chmod +x evaluate.sh to .travis.yml

Documentation

  • Added documentation for adding a dataset to a task in README.md
  • Added documentation for dataset loading in README.md
  • Added documentation for adding a new dataset in README.md
  • Updated documentation in openproblems/tasks/multimodal_data_integration/README.md
  • Updated documentation in openproblems/version.py

openproblems v0.0.1

First release of OpenProblems.

methods, 1 metric)

  • Multimodal data integration (2 datasets, 2 methods, 2 metrics)