update

DeplanckeLab · Aug 13, 2024 · e7d73f4 · e7d73f4
1 parent a458556
commit e7d73f4
Show file tree

Hide file tree

Showing 256 changed files with 6 additions and 0 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.gitignore b/.gitignore
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
diff --git a/LICENSE.md b/LICENSE.md
diff --git a/README.md b/README.md
diff --git a/docs/override/main.html b/docs/override/main.html
diff --git a/docs/source/.pages b/docs/source/.pages
diff --git a/docs/source/CNAME b/docs/source/CNAME
diff --git a/docs/source/benchmark/diff/models.py b/docs/source/benchmark/diff/models.py
diff --git a/docs/source/benchmark/diff/simulated.py b/docs/source/benchmark/diff/simulated.py
diff --git a/docs/source/benchmark/diff/timing.py b/docs/source/benchmark/diff/timing.py
diff --git a/docs/source/benchmark/index.md b/docs/source/benchmark/index.md
diff --git a/docs/source/index.md b/docs/source/index.md
diff --git a/docs/source/javascripts/reference.js b/docs/source/javascripts/reference.js
diff --git a/docs/source/quickstart/0_install.py b/docs/source/quickstart/0_install.py
diff --git a/docs/source/quickstart/1_data.py b/docs/source/quickstart/1_data.py
diff --git a/docs/source/quickstart/2_pred.py b/docs/source/quickstart/2_pred.py
diff --git a/docs/source/quickstart/3_diff.py b/docs/source/quickstart/3_diff.py
diff --git a/docs/source/reference/.pages b/docs/source/reference/.pages
diff --git a/docs/source/reference/data/clustering.md b/docs/source/reference/data/clustering.md
diff --git a/docs/source/reference/data/folds.md b/docs/source/reference/data/folds.md
diff --git a/docs/source/reference/data/fragments.md b/docs/source/reference/data/fragments.md
diff --git a/docs/source/reference/data/motifscan.md b/docs/source/reference/data/motifscan.md
diff --git a/docs/source/reference/data/regions.md b/docs/source/reference/data/regions.md
diff --git a/docs/source/reference/data/transcriptome.md b/docs/source/reference/data/transcriptome.md
diff --git a/docs/source/reference/index.md b/docs/source/reference/index.md
diff --git a/docs/source/reference/loaders/fragments.md b/docs/source/reference/loaders/fragments.md
diff --git a/docs/source/reference/models/diff/interpret.md b/docs/source/reference/models/diff/interpret.md
diff --git a/docs/source/reference/models/diff/model.md b/docs/source/reference/models/diff/model.md
diff --git a/docs/source/reference/models/diff/plot.md b/docs/source/reference/models/diff/plot.md
diff --git a/docs/source/reference/models/pred/interpret.md b/docs/source/reference/models/pred/interpret.md
diff --git a/docs/source/reference/models/pred/model.md b/docs/source/reference/models/pred/model.md
diff --git a/docs/source/reference/models/pred/plot.md b/docs/source/reference/models/pred/plot.md
diff --git a/docs/source/static/comparison.gif b/docs/source/static/comparison.gif
diff --git a/docs/source/static/eu.png b/docs/source/static/eu.png
diff --git a/docs/source/static/favicon.ai b/docs/source/static/favicon.ai
diff --git a/docs/source/static/favicon.png b/docs/source/static/favicon.png
diff --git a/docs/source/static/logo.ai b/docs/source/static/logo.ai
diff --git a/docs/source/static/logo.png b/docs/source/static/logo.png
diff --git a/docs/source/static/models/diff/1x/logo.png b/docs/source/static/models/diff/1x/logo.png
diff --git a/docs/source/static/models/diff/logo.pdf b/docs/source/static/models/diff/logo.pdf
diff --git a/docs/source/static/models/dime/logo.pdf b/docs/source/static/models/dime/logo.pdf
diff --git a/docs/source/static/models/dime/logo.png b/docs/source/static/models/dime/logo.png
diff --git a/docs/source/static/models/pred/1x/logo.png b/docs/source/static/models/pred/1x/logo.png
diff --git a/docs/source/static/models/pred/logo.pdf b/docs/source/static/models/pred/logo.pdf
diff --git a/docs/source/static/models/time/logo.pdf b/docs/source/static/models/time/logo.pdf
diff --git a/docs/source/static/models/time/logo.png b/docs/source/static/models/time/logo.png
diff --git a/docs/source/stylesheets/extra-reference.css b/docs/source/stylesheets/extra-reference.css
diff --git a/docs/source/stylesheets/extra.css b/docs/source/stylesheets/extra.css
diff --git a/docs/tex/overview.tex b/docs/tex/overview.tex
diff --git a/mkdocs.yml b/mkdocs.yml
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/scripts/benchmark/datasets/pbmc10k/1-download.py b/scripts/benchmark/datasets/pbmc10k/1-download.py
diff --git a/scripts/benchmark/datasets/pbmc10k/2-process_all.py b/scripts/benchmark/datasets/pbmc10k/2-process_all.py
diff --git a/scripts/benchmark/datasets/pbmc10k/3-process_large.py b/scripts/benchmark/datasets/pbmc10k/3-process_large.py
diff --git a/scripts/benchmark/datasets/pbmc10k/4-process_tiny.py b/scripts/benchmark/datasets/pbmc10k/4-process_tiny.py
diff --git a/scripts/benchmark/datasets/pbmc10k/5-process_wide.py b/scripts/benchmark/datasets/pbmc10k/5-process_wide.py
diff --git a/scripts/cythonize.sh b/scripts/cythonize.sh
diff --git a/scripts/dist.sh b/scripts/dist.sh
diff --git a/scripts/followup/miff/fit_negbinom.py b/scripts/followup/miff/fit_negbinom.py
diff --git a/scripts/followup/miff/layers_linear_spline.py b/scripts/followup/miff/layers_linear_spline.py
diff --git a/scripts/followup/miff/quadratic.py b/scripts/followup/miff/quadratic.py
diff --git a/scripts/followup/miff/truncated_normal.py b/scripts/followup/miff/truncated_normal.py
diff --git a/scripts/install.sh b/scripts/install.sh
diff --git a/scripts/test.py b/scripts/test.py
diff --git a/setup.py b/setup.py
diff --git a/src/chromatinhd/__init__.py b/src/chromatinhd/__init__.py
diff --git a/src/chromatinhd/biomart/__init__.py b/src/chromatinhd/biomart/__init__.py
diff --git a/src/chromatinhd/biomart/cache.py b/src/chromatinhd/biomart/cache.py
diff --git a/src/chromatinhd/biomart/dataset.py b/src/chromatinhd/biomart/dataset.py
@@ -246,5 +246,11 @@ def from_genome(self, genome):
                 "http://www.ensembl.org/biomart/martservice?",
                 "ENSEMBL_MART_ENSEMBL",
             )
+        elif genome in ["GRCz11"]:
+            return Dataset(
+                "drerio_gene_ensembl",
+                "http://www.ensembl.org/biomart/martservice?",
+                "ENSEMBL_MART_ENSEMBL",
+            )
         else:
             raise ValueError("Genome not supported")
diff --git a/src/chromatinhd/biomart/homology.py b/src/chromatinhd/biomart/homology.py
diff --git a/src/chromatinhd/biomart/tss.py b/src/chromatinhd/biomart/tss.py
diff --git a/src/chromatinhd/data/__init__.py b/src/chromatinhd/data/__init__.py
diff --git a/src/chromatinhd/data/associations/__init__.py b/src/chromatinhd/data/associations/__init__.py
diff --git a/src/chromatinhd/data/associations/associations.py b/src/chromatinhd/data/associations/associations.py
diff --git a/src/chromatinhd/data/associations/plot.py b/src/chromatinhd/data/associations/plot.py
diff --git a/src/chromatinhd/data/clustering/__init__.py b/src/chromatinhd/data/clustering/__init__.py
diff --git a/src/chromatinhd/data/clustering/clustering.py b/src/chromatinhd/data/clustering/clustering.py
diff --git a/src/chromatinhd/data/examples/pbmc10ktiny/fragments.tsv.gz b/src/chromatinhd/data/examples/pbmc10ktiny/fragments.tsv.gz
diff --git a/src/chromatinhd/data/examples/pbmc10ktiny/fragments.tsv.gz.tbi b/src/chromatinhd/data/examples/pbmc10ktiny/fragments.tsv.gz.tbi
diff --git a/src/chromatinhd/data/examples/pbmc10ktiny/transcriptome.h5ad b/src/chromatinhd/data/examples/pbmc10ktiny/transcriptome.h5ad
diff --git a/src/chromatinhd/data/folds/__init__.py b/src/chromatinhd/data/folds/__init__.py
diff --git a/src/chromatinhd/data/folds/folds.py b/src/chromatinhd/data/folds/folds.py
diff --git a/src/chromatinhd/data/fragments/__init__.py b/src/chromatinhd/data/fragments/__init__.py
diff --git a/src/chromatinhd/data/fragments/fragments.py b/src/chromatinhd/data/fragments/fragments.py
diff --git a/src/chromatinhd/data/fragments/view.py b/src/chromatinhd/data/fragments/view.py
diff --git a/src/chromatinhd/data/genotype/__init__.py b/src/chromatinhd/data/genotype/__init__.py
diff --git a/src/chromatinhd/data/genotype/genotype.py b/src/chromatinhd/data/genotype/genotype.py
diff --git a/src/chromatinhd/data/gradient/__init__.py b/src/chromatinhd/data/gradient/__init__.py
diff --git a/src/chromatinhd/data/gradient/gradient.py b/src/chromatinhd/data/gradient/gradient.py
diff --git a/src/chromatinhd/data/motifscan/__init__.py b/src/chromatinhd/data/motifscan/__init__.py
diff --git a/src/chromatinhd/data/motifscan/download.py b/src/chromatinhd/data/motifscan/download.py
diff --git a/src/chromatinhd/data/motifscan/motifcount.py b/src/chromatinhd/data/motifscan/motifcount.py
diff --git a/src/chromatinhd/data/motifscan/motifscan.py b/src/chromatinhd/data/motifscan/motifscan.py
diff --git a/src/chromatinhd/data/motifscan/motiftrack.py b/src/chromatinhd/data/motifscan/motiftrack.py
diff --git a/src/chromatinhd/data/motifscan/plot.py b/src/chromatinhd/data/motifscan/plot.py
diff --git a/src/chromatinhd/data/motifscan/scan_helpers.c b/src/chromatinhd/data/motifscan/scan_helpers.c
diff --git a/src/chromatinhd/data/motifscan/scan_helpers.html b/src/chromatinhd/data/motifscan/scan_helpers.html
diff --git a/src/chromatinhd/data/motifscan/scan_helpers.pyx b/src/chromatinhd/data/motifscan/scan_helpers.pyx
diff --git a/src/chromatinhd/data/motifscan/view.py b/src/chromatinhd/data/motifscan/view.py
diff --git a/src/chromatinhd/data/peakcounts/__init__.py b/src/chromatinhd/data/peakcounts/__init__.py
diff --git a/src/chromatinhd/data/peakcounts/peakcounts.py b/src/chromatinhd/data/peakcounts/peakcounts.py
diff --git a/src/chromatinhd/data/peakcounts/plot.py b/src/chromatinhd/data/peakcounts/plot.py
diff --git a/src/chromatinhd/data/regions.py b/src/chromatinhd/data/regions.py
diff --git a/src/chromatinhd/data/transcriptome/__init__.py b/src/chromatinhd/data/transcriptome/__init__.py
diff --git a/src/chromatinhd/data/transcriptome/timetranscriptome.py b/src/chromatinhd/data/transcriptome/timetranscriptome.py
diff --git a/src/chromatinhd/data/transcriptome/transcriptome.py b/src/chromatinhd/data/transcriptome/transcriptome.py
diff --git a/src/chromatinhd/device.py b/src/chromatinhd/device.py
diff --git a/src/chromatinhd/embedding.py b/src/chromatinhd/embedding.py
diff --git a/src/chromatinhd/flow/__init__.py b/src/chromatinhd/flow/__init__.py
diff --git a/src/chromatinhd/flow/flow.py b/src/chromatinhd/flow/flow.py
diff --git a/src/chromatinhd/flow/flow_template.jinja2 b/src/chromatinhd/flow/flow_template.jinja2
diff --git a/src/chromatinhd/flow/linked.py b/src/chromatinhd/flow/linked.py
diff --git a/src/chromatinhd/flow/objects.py b/src/chromatinhd/flow/objects.py
diff --git a/src/chromatinhd/flow/sparse.py b/src/chromatinhd/flow/sparse.py
diff --git a/src/chromatinhd/flow/tensorstore.py b/src/chromatinhd/flow/tensorstore.py
diff --git a/src/chromatinhd/flow/tipyte.py b/src/chromatinhd/flow/tipyte.py
diff --git a/src/chromatinhd/grid/__init__.py b/src/chromatinhd/grid/__init__.py
diff --git a/src/chromatinhd/grid/broken.py b/src/chromatinhd/grid/broken.py
diff --git a/src/chromatinhd/grid/grid.py b/src/chromatinhd/grid/grid.py
diff --git a/src/chromatinhd/loaders/__init__.py b/src/chromatinhd/loaders/__init__.py
diff --git a/src/chromatinhd/loaders/clustering.py b/src/chromatinhd/loaders/clustering.py
diff --git a/src/chromatinhd/loaders/clustering_fragments.py b/src/chromatinhd/loaders/clustering_fragments.py
diff --git a/src/chromatinhd/loaders/extraction/fragments.pyx b/src/chromatinhd/loaders/extraction/fragments.pyx
diff --git a/src/chromatinhd/loaders/extraction/motifs.pyx b/src/chromatinhd/loaders/extraction/motifs.pyx
diff --git a/src/chromatinhd/loaders/fragments.py b/src/chromatinhd/loaders/fragments.py
diff --git a/src/chromatinhd/loaders/fragments2.py b/src/chromatinhd/loaders/fragments2.py
diff --git a/src/chromatinhd/loaders/fragments_helpers.c b/src/chromatinhd/loaders/fragments_helpers.c
diff --git a/src/chromatinhd/loaders/fragments_helpers.html b/src/chromatinhd/loaders/fragments_helpers.html
diff --git a/src/chromatinhd/loaders/fragments_helpers.pyx b/src/chromatinhd/loaders/fragments_helpers.pyx
diff --git a/src/chromatinhd/loaders/minibatches.py b/src/chromatinhd/loaders/minibatches.py
diff --git a/src/chromatinhd/loaders/peakcounts.py b/src/chromatinhd/loaders/peakcounts.py
diff --git a/src/chromatinhd/loaders/pool.py b/src/chromatinhd/loaders/pool.py
diff --git a/src/chromatinhd/loaders/transcriptome.py b/src/chromatinhd/loaders/transcriptome.py
diff --git a/src/chromatinhd/loaders/transcriptome_fragments.py b/src/chromatinhd/loaders/transcriptome_fragments.py
diff --git a/src/chromatinhd/loaders/transcriptome_fragments2.py b/src/chromatinhd/loaders/transcriptome_fragments2.py
diff --git a/src/chromatinhd/loaders/transcriptome_fragments_time.py b/src/chromatinhd/loaders/transcriptome_fragments_time.py
diff --git a/src/chromatinhd/models/__init__.py b/src/chromatinhd/models/__init__.py
diff --git a/src/chromatinhd/models/diff/__init__.py b/src/chromatinhd/models/diff/__init__.py
diff --git a/src/chromatinhd/models/diff/interpret/__init__.py b/src/chromatinhd/models/diff/interpret/__init__.py
diff --git a/src/chromatinhd/models/diff/interpret/differential.py b/src/chromatinhd/models/diff/interpret/differential.py
diff --git a/src/chromatinhd/models/diff/interpret/enrichment/__init__.py b/src/chromatinhd/models/diff/interpret/enrichment/__init__.py
diff --git a/src/chromatinhd/models/diff/interpret/enrichment/enrichment.py b/src/chromatinhd/models/diff/interpret/enrichment/enrichment.py
diff --git a/src/chromatinhd/models/diff/interpret/performance.py b/src/chromatinhd/models/diff/interpret/performance.py
diff --git a/src/chromatinhd/models/diff/interpret/regionpositional.py b/src/chromatinhd/models/diff/interpret/regionpositional.py
diff --git a/src/chromatinhd/models/diff/interpret/slices.py b/src/chromatinhd/models/diff/interpret/slices.py
diff --git a/src/chromatinhd/models/diff/loader/__init__.py b/src/chromatinhd/models/diff/loader/__init__.py
diff --git a/src/chromatinhd/models/diff/loader/clustering_cuts.py b/src/chromatinhd/models/diff/loader/clustering_cuts.py
diff --git a/src/chromatinhd/models/diff/loader/clustering_fragments.py b/src/chromatinhd/models/diff/loader/clustering_fragments.py
diff --git a/src/chromatinhd/models/diff/model/__init__.py b/src/chromatinhd/models/diff/model/__init__.py
diff --git a/src/chromatinhd/models/diff/model/binary.py b/src/chromatinhd/models/diff/model/binary.py
diff --git a/src/chromatinhd/models/diff/model/cutnf.py b/src/chromatinhd/models/diff/model/cutnf.py
diff --git a/src/chromatinhd/models/diff/model/encoders.py b/src/chromatinhd/models/diff/model/encoders.py
diff --git a/src/chromatinhd/models/diff/model/playground.py b/src/chromatinhd/models/diff/model/playground.py
diff --git a/src/chromatinhd/models/diff/model/spline.py b/src/chromatinhd/models/diff/model/spline.py
diff --git a/src/chromatinhd/models/diff/model/splines/__init__.py b/src/chromatinhd/models/diff/model/splines/__init__.py
diff --git a/src/chromatinhd/models/diff/model/splines/cubic.py b/src/chromatinhd/models/diff/model/splines/cubic.py
diff --git a/src/chromatinhd/models/diff/model/splines/linear.py b/src/chromatinhd/models/diff/model/splines/linear.py
diff --git a/src/chromatinhd/models/diff/model/splines/quadratic.py b/src/chromatinhd/models/diff/model/splines/quadratic.py
diff --git a/src/chromatinhd/models/diff/model/truncated_normal.py b/src/chromatinhd/models/diff/model/truncated_normal.py
diff --git a/src/chromatinhd/models/diff/plot/__init__.py b/src/chromatinhd/models/diff/plot/__init__.py
diff --git a/src/chromatinhd/models/diff/plot/differential.py b/src/chromatinhd/models/diff/plot/differential.py
diff --git a/src/chromatinhd/models/diff/plot/differential_expression.py b/src/chromatinhd/models/diff/plot/differential_expression.py
diff --git a/src/chromatinhd/models/diff/trainer/__init__.py b/src/chromatinhd/models/diff/trainer/__init__.py
diff --git a/src/chromatinhd/models/diff/trainer/trainer.py b/src/chromatinhd/models/diff/trainer/trainer.py
diff --git a/src/chromatinhd/models/miff/loader/__init__.py b/src/chromatinhd/models/miff/loader/__init__.py
diff --git a/src/chromatinhd/models/miff/loader/clustering.py b/src/chromatinhd/models/miff/loader/clustering.py
diff --git a/src/chromatinhd/models/miff/loader/combinations.py b/src/chromatinhd/models/miff/loader/combinations.py
diff --git a/src/chromatinhd/models/miff/loader/minibatches.py b/src/chromatinhd/models/miff/loader/minibatches.py
diff --git a/src/chromatinhd/models/miff/loader/motifcount.py b/src/chromatinhd/models/miff/loader/motifcount.py
diff --git a/src/chromatinhd/models/miff/loader/motifs.py b/src/chromatinhd/models/miff/loader/motifs.py
diff --git a/src/chromatinhd/models/miff/loader/motifs_fragments.py b/src/chromatinhd/models/miff/loader/motifs_fragments.py
diff --git a/src/chromatinhd/models/miff/model/__init__.py b/src/chromatinhd/models/miff/model/__init__.py
diff --git a/src/chromatinhd/models/miff/model/clustering/__init__.py b/src/chromatinhd/models/miff/model/clustering/__init__.py
diff --git a/src/chromatinhd/models/miff/model/clustering/distributions.py b/src/chromatinhd/models/miff/model/clustering/distributions.py
diff --git a/src/chromatinhd/models/miff/model/clustering/model.py b/src/chromatinhd/models/miff/model/clustering/model.py
diff --git a/src/chromatinhd/models/miff/model/clustering2/__init__.py b/src/chromatinhd/models/miff/model/clustering2/__init__.py
diff --git a/src/chromatinhd/models/miff/model/clustering2/distributions.py b/src/chromatinhd/models/miff/model/clustering2/distributions.py
diff --git a/src/chromatinhd/models/miff/model/clustering2/model.py b/src/chromatinhd/models/miff/model/clustering2/model.py
diff --git a/src/chromatinhd/models/miff/model/clustering3/__init__.py b/src/chromatinhd/models/miff/model/clustering3/__init__.py
diff --git a/src/chromatinhd/models/miff/model/clustering3/count.py b/src/chromatinhd/models/miff/model/clustering3/count.py
diff --git a/src/chromatinhd/models/miff/model/clustering3/model.py b/src/chromatinhd/models/miff/model/clustering3/model.py
diff --git a/src/chromatinhd/models/miff/model/clustering3/position.py b/src/chromatinhd/models/miff/model/clustering3/position.py
diff --git a/src/chromatinhd/models/miff/model/global_norm/__init__.py b/src/chromatinhd/models/miff/model/global_norm/__init__.py
diff --git a/src/chromatinhd/models/miff/model/global_norm/distributions.py b/src/chromatinhd/models/miff/model/global_norm/distributions.py
diff --git a/src/chromatinhd/models/miff/model/global_norm/model.py b/src/chromatinhd/models/miff/model/global_norm/model.py
diff --git a/src/chromatinhd/models/miff/model/local_norm/__init__.py b/src/chromatinhd/models/miff/model/local_norm/__init__.py
diff --git a/src/chromatinhd/models/miff/model/local_norm/distributions.py b/src/chromatinhd/models/miff/model/local_norm/distributions.py
diff --git a/src/chromatinhd/models/miff/model/local_norm/model.py b/src/chromatinhd/models/miff/model/local_norm/model.py
diff --git a/src/chromatinhd/models/miff/model/site_embedder.py b/src/chromatinhd/models/miff/model/site_embedder.py
diff --git a/src/chromatinhd/models/miff/model/zoom.py b/src/chromatinhd/models/miff/model/zoom.py
diff --git a/src/chromatinhd/models/model.py b/src/chromatinhd/models/model.py
diff --git a/src/chromatinhd/models/pred/__init__.py b/src/chromatinhd/models/pred/__init__.py
diff --git a/src/chromatinhd/models/pred/interpret/__init__.py b/src/chromatinhd/models/pred/interpret/__init__.py
diff --git a/src/chromatinhd/models/pred/interpret/censorers.py b/src/chromatinhd/models/pred/interpret/censorers.py
diff --git a/src/chromatinhd/models/pred/interpret/performance.py b/src/chromatinhd/models/pred/interpret/performance.py
diff --git a/src/chromatinhd/models/pred/interpret/regionmultiwindow.py b/src/chromatinhd/models/pred/interpret/regionmultiwindow.py
diff --git a/src/chromatinhd/models/pred/interpret/regionpairwindow.py b/src/chromatinhd/models/pred/interpret/regionpairwindow.py
diff --git a/src/chromatinhd/models/pred/interpret/regionsizewindow.py b/src/chromatinhd/models/pred/interpret/regionsizewindow.py
diff --git a/src/chromatinhd/models/pred/interpret/size.py b/src/chromatinhd/models/pred/interpret/size.py
diff --git a/src/chromatinhd/models/pred/model/__init__.py b/src/chromatinhd/models/pred/model/__init__.py
diff --git a/src/chromatinhd/models/pred/model/better.py b/src/chromatinhd/models/pred/model/better.py
diff --git a/src/chromatinhd/models/pred/model/encoders.py b/src/chromatinhd/models/pred/model/encoders.py
diff --git a/src/chromatinhd/models/pred/model/loss.py b/src/chromatinhd/models/pred/model/loss.py
diff --git a/src/chromatinhd/models/pred/model/multilinear.py b/src/chromatinhd/models/pred/model/multilinear.py
diff --git a/src/chromatinhd/models/pred/model/multiscale.py b/src/chromatinhd/models/pred/model/multiscale.py
diff --git a/src/chromatinhd/models/pred/model/peakcounts.py b/src/chromatinhd/models/pred/model/peakcounts.py
diff --git a/src/chromatinhd/models/pred/model/peakcounts_test.py b/src/chromatinhd/models/pred/model/peakcounts_test.py
diff --git a/src/chromatinhd/models/pred/model/shared.py b/src/chromatinhd/models/pred/model/shared.py
diff --git a/src/chromatinhd/models/pred/plot/__init__.py b/src/chromatinhd/models/pred/plot/__init__.py
diff --git a/src/chromatinhd/models/pred/plot/copredictivity.py b/src/chromatinhd/models/pred/plot/copredictivity.py
diff --git a/src/chromatinhd/models/pred/plot/effect.py b/src/chromatinhd/models/pred/plot/effect.py
diff --git a/src/chromatinhd/models/pred/plot/predictivity.py b/src/chromatinhd/models/pred/plot/predictivity.py
diff --git a/src/chromatinhd/models/pred/trainer/__init__.py b/src/chromatinhd/models/pred/trainer/__init__.py
diff --git a/src/chromatinhd/models/pred/trainer/trainer.py b/src/chromatinhd/models/pred/trainer/trainer.py
diff --git a/src/chromatinhd/models/pret/model/__init__.py b/src/chromatinhd/models/pret/model/__init__.py
diff --git a/src/chromatinhd/models/pret/model/better.py b/src/chromatinhd/models/pret/model/better.py
diff --git a/src/chromatinhd/models/pret/model/loss.py b/src/chromatinhd/models/pret/model/loss.py
diff --git a/src/chromatinhd/models/pret/model/peakcounts.py b/src/chromatinhd/models/pret/model/peakcounts.py
diff --git a/src/chromatinhd/models/pret/trainer/__init__.py b/src/chromatinhd/models/pret/trainer/__init__.py
diff --git a/src/chromatinhd/models/pret/trainer/trainer.py b/src/chromatinhd/models/pret/trainer/trainer.py
diff --git a/src/chromatinhd/optim.py b/src/chromatinhd/optim.py
diff --git a/src/chromatinhd/plot/__init__.py b/src/chromatinhd/plot/__init__.py
diff --git a/src/chromatinhd/plot/genome/__init__.py b/src/chromatinhd/plot/genome/__init__.py
diff --git a/src/chromatinhd/plot/genome/genes.py b/src/chromatinhd/plot/genome/genes.py
diff --git a/src/chromatinhd/plot/matshow45.py b/src/chromatinhd/plot/matshow45.py
diff --git a/src/chromatinhd/plot/patch.py b/src/chromatinhd/plot/patch.py
diff --git a/src/chromatinhd/plot/quasirandom.py b/src/chromatinhd/plot/quasirandom.py
diff --git a/src/chromatinhd/plot/tickers.py b/src/chromatinhd/plot/tickers.py
diff --git a/src/chromatinhd/scoring/prediction/filterers.py b/src/chromatinhd/scoring/prediction/filterers.py
diff --git a/src/chromatinhd/simulation/simulate.py b/src/chromatinhd/simulation/simulate.py
diff --git a/src/chromatinhd/sparse.py b/src/chromatinhd/sparse.py
diff --git a/src/chromatinhd/train.py b/src/chromatinhd/train.py
diff --git a/src/chromatinhd/utils/__init__.py b/src/chromatinhd/utils/__init__.py
diff --git a/src/chromatinhd/utils/ecdf.py b/src/chromatinhd/utils/ecdf.py
diff --git a/src/chromatinhd/utils/interleave.py b/src/chromatinhd/utils/interleave.py
diff --git a/src/chromatinhd/utils/intervals.py b/src/chromatinhd/utils/intervals.py
diff --git a/src/chromatinhd/utils/numpy.py b/src/chromatinhd/utils/numpy.py
diff --git a/src/chromatinhd/utils/scanpy.py b/src/chromatinhd/utils/scanpy.py
diff --git a/src/chromatinhd/utils/testing.py b/src/chromatinhd/utils/testing.py
diff --git a/src/chromatinhd/utils/timing.py b/src/chromatinhd/utils/timing.py
diff --git a/src/chromatinhd/utils/torch.py b/src/chromatinhd/utils/torch.py
diff --git a/tests/_test_sparse.py b/tests/_test_sparse.py
diff --git a/tests/biomart/conftest.py b/tests/biomart/conftest.py
diff --git a/tests/biomart/tss_test.py b/tests/biomart/tss_test.py
diff --git a/tests/conftest.py b/tests/conftest.py
diff --git a/tests/data/motifscan/test_motifscan.py b/tests/data/motifscan/test_motifscan.py
diff --git a/tests/loaders/test_fragment_helpers.py b/tests/loaders/test_fragment_helpers.py
diff --git a/tests/loaders/test_fragments.py b/tests/loaders/test_fragments.py
diff --git a/tests/loaders/test_transcriptome_fragments.py b/tests/loaders/test_transcriptome_fragments.py
diff --git a/tests/models/diff/loader/test_clustering_cuts.py b/tests/models/diff/loader/test_clustering_cuts.py
diff --git a/tests/models/diff/model/_test_spline.py b/tests/models/diff/model/_test_spline.py
diff --git a/tests/models/diff/model/test_diff_model.py b/tests/models/diff/model/test_diff_model.py
diff --git a/tests/models/miff/_test_zoom.py b/tests/models/miff/_test_zoom.py
diff --git a/tests/models/pred/model/test_pred_model.py b/tests/models/pred/model/test_pred_model.py
diff --git a/tests/utils/test_interleave.py b/tests/utils/test_interleave.py