rename src->bpnet

kundajelab · Feb 24, 2023 · 766da17 · 766da17
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diff --git a/src/basepairmodels/__init__.py → bpnet/__init__.py b/src/basepairmodels/__init__.py → bpnet/__init__.py
diff --git a/src/basepairmodels/api/__init__.py → bpnet/basepairmodels/__init__.py b/src/basepairmodels/api/__init__.py → bpnet/basepairmodels/__init__.py
diff --git a/src/basepairmodels/cli/__init__.py → bpnet/basepairmodels/api/__init__.py b/src/basepairmodels/cli/__init__.py → bpnet/basepairmodels/api/__init__.py
diff --git a/src/basepairmodels/api/bpnet.py → bpnet/basepairmodels/api/bpnet.py b/src/basepairmodels/api/bpnet.py → bpnet/basepairmodels/api/bpnet.py
diff --git a/src/basepairmodels/api/modisco.py → bpnet/basepairmodels/api/modisco.py b/src/basepairmodels/api/modisco.py → bpnet/basepairmodels/api/modisco.py
diff --git a/src/basepairmodels/api/motifinstance.py → bpnet/basepairmodels/api/motifinstance.py b/src/basepairmodels/api/motifinstance.py → bpnet/basepairmodels/api/motifinstance.py
diff --git a/src/basepairmodels/api/profilemodel.py → bpnet/basepairmodels/api/profilemodel.py b/src/basepairmodels/api/profilemodel.py → bpnet/basepairmodels/api/profilemodel.py
diff --git a/src/basepairmodels/common/__init__.py → bpnet/basepairmodels/cli/__init__.py b/src/basepairmodels/common/__init__.py → bpnet/basepairmodels/cli/__init__.py
diff --git a/src/basepairmodels/cli/argparsers.py → bpnet/basepairmodels/cli/argparsers.py b/src/basepairmodels/cli/argparsers.py → bpnet/basepairmodels/cli/argparsers.py
diff --git a/src/basepairmodels/cli/bigwig_helper.py → bpnet/basepairmodels/cli/bigwig_helper.py b/src/basepairmodels/cli/bigwig_helper.py → bpnet/basepairmodels/cli/bigwig_helper.py
diff --git a/src/basepairmodels/cli/bpnettrainer.py → bpnet/basepairmodels/cli/bpnettrainer.py b/src/basepairmodels/cli/bpnettrainer.py → bpnet/basepairmodels/cli/bpnettrainer.py
diff --git a/src/basepairmodels/cli/bpnetutils.py → bpnet/basepairmodels/cli/bpnetutils.py b/src/basepairmodels/cli/bpnetutils.py → bpnet/basepairmodels/cli/bpnetutils.py
diff --git a/src/basepairmodels/cli/counts_loss_weight.py → .../basepairmodels/cli/counts_loss_weight.py b/src/basepairmodels/cli/counts_loss_weight.py → .../basepairmodels/cli/counts_loss_weight.py
diff --git a/src/basepairmodels/cli/embeddings.py → bpnet/basepairmodels/cli/embeddings.py b/src/basepairmodels/cli/embeddings.py → bpnet/basepairmodels/cli/embeddings.py
diff --git a/src/basepairmodels/cli/exceptionhandler.py → bpnet/basepairmodels/cli/exceptionhandler.py b/src/basepairmodels/cli/exceptionhandler.py → bpnet/basepairmodels/cli/exceptionhandler.py
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diff --git a/src/basepairmodels/cli/motif_discovery.py → bpnet/basepairmodels/cli/motif_discovery.py b/src/basepairmodels/cli/motif_discovery.py → bpnet/basepairmodels/cli/motif_discovery.py
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diff --git a/src/basepairmodels/cli/shaputils.py → bpnet/basepairmodels/cli/shaputils.py b/src/basepairmodels/cli/shaputils.py → bpnet/basepairmodels/cli/shaputils.py
diff --git a/src/genomicsdlarchsandlosses/__init__.py → bpnet/basepairmodels/common/__init__.py b/src/genomicsdlarchsandlosses/__init__.py → bpnet/basepairmodels/common/__init__.py
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diff --git a/src/mseqgen_extra/docs/tutorial.html → bpnet/mseqgen_extra/docs/tutorial.html b/src/mseqgen_extra/docs/tutorial.html → bpnet/mseqgen_extra/docs/tutorial.html
diff --git a/src/mseqgen_extra/example/test.py → bpnet/mseqgen_extra/example/test.py b/src/mseqgen_extra/example/test.py → bpnet/mseqgen_extra/example/test.py
diff --git a/src/mseqgen_extra/requirements.txt → bpnet/mseqgen_extra/requirements.txt b/src/mseqgen_extra/requirements.txt → bpnet/mseqgen_extra/requirements.txt
diff --git a/src/mseqgen_extra/setup.py → bpnet/mseqgen_extra/setup.py b/src/mseqgen_extra/setup.py → bpnet/mseqgen_extra/setup.py
diff --git a/...seqgen_extra/tests/GRCh38_EBV.chrom.sizes → ...seqgen_extra/tests/GRCh38_EBV.chrom.sizes b/...seqgen_extra/tests/GRCh38_EBV.chrom.sizes → ...seqgen_extra/tests/GRCh38_EBV.chrom.sizes
diff --git a/...en_extra/tests/batchgen_params_peaks.json → ...en_extra/tests/batchgen_params_peaks.json b/...en_extra/tests/batchgen_params_peaks.json → ...en_extra/tests/batchgen_params_peaks.json
diff --git a/...n_extra/tests/batchgen_params_random.json → ...n_extra/tests/batchgen_params_random.json b/...n_extra/tests/batchgen_params_random.json → ...n_extra/tests/batchgen_params_random.json
diff --git a/...tra/tests/batchgen_params_sequential.json → ...tra/tests/batchgen_params_sequential.json b/...tra/tests/batchgen_params_sequential.json → ...tra/tests/batchgen_params_sequential.json
diff --git a/src/mseqgen_extra/tests/bpnet_params.json → bpnet/mseqgen_extra/tests/bpnet_params.json b/src/mseqgen_extra/tests/bpnet_params.json → bpnet/mseqgen_extra/tests/bpnet_params.json
diff --git a/...ra/tests/input-stranded_with_control.json → ...ra/tests/input-stranded_with_control.json b/...ra/tests/input-stranded_with_control.json → ...ra/tests/input-stranded_with_control.json
diff --git a/src/mseqgen_extra/tests/input.json → bpnet/mseqgen_extra/tests/input.json b/src/mseqgen_extra/tests/input.json → bpnet/mseqgen_extra/tests/input.json
diff --git a/src/mseqgen_extra/tests/input2.json → bpnet/mseqgen_extra/tests/input2.json b/src/mseqgen_extra/tests/input2.json → bpnet/mseqgen_extra/tests/input2.json
diff --git a/src/mseqgen_extra/tests/input3.json → bpnet/mseqgen_extra/tests/input3.json b/src/mseqgen_extra/tests/input3.json → bpnet/mseqgen_extra/tests/input3.json
diff --git a/src/mseqgen_extra/tests/input_data.json → bpnet/mseqgen_extra/tests/input_data.json b/src/mseqgen_extra/tests/input_data.json → bpnet/mseqgen_extra/tests/input_data.json
diff --git a/...ata_new_tasks_format_background_loci.json → ...ata_new_tasks_format_background_loci.json b/...ata_new_tasks_format_background_loci.json → ...ata_new_tasks_format_background_loci.json
diff --git a/...qgen_extra/tests/test_data/background.bed → ...qgen_extra/tests/test_data/background.bed b/...qgen_extra/tests/test_data/background.bed → ...qgen_extra/tests/test_data/background.bed
diff --git a/src/mseqgen_extra/tests/test_data/loci.bed → bpnet/mseqgen_extra/tests/test_data/loci.bed b/src/mseqgen_extra/tests/test_data/loci.bed → bpnet/mseqgen_extra/tests/test_data/loci.bed
diff --git a/...nded_with_controls/task0/control_minus.bw → ...nded_with_controls/task0/control_minus.bw b/...nded_with_controls/task0/control_minus.bw → ...nded_with_controls/task0/control_minus.bw
diff --git a/...anded_with_controls/task0/control_plus.bw → ...anded_with_controls/task0/control_plus.bw b/...anded_with_controls/task0/control_plus.bw → ...anded_with_controls/task0/control_plus.bw
diff --git a/...ask/stranded_with_controls/task0/minus.bw → ...ask/stranded_with_controls/task0/minus.bw b/...ask/stranded_with_controls/task0/minus.bw → ...ask/stranded_with_controls/task0/minus.bw
diff --git a/...sk/stranded_with_controls/task0/peaks.bed → ...sk/stranded_with_controls/task0/peaks.bed b/...sk/stranded_with_controls/task0/peaks.bed → ...sk/stranded_with_controls/task0/peaks.bed
diff --git a/...task/stranded_with_controls/task0/plus.bw → ...task/stranded_with_controls/task0/plus.bw b/...task/stranded_with_controls/task0/plus.bw → ...task/stranded_with_controls/task0/plus.bw
diff --git a/...nded_with_controls/task1/control_minus.bw → ...nded_with_controls/task1/control_minus.bw b/...nded_with_controls/task1/control_minus.bw → ...nded_with_controls/task1/control_minus.bw
diff --git a/...anded_with_controls/task1/control_plus.bw → ...anded_with_controls/task1/control_plus.bw b/...anded_with_controls/task1/control_plus.bw → ...anded_with_controls/task1/control_plus.bw
diff --git a/...ask/stranded_with_controls/task1/minus.bw → ...ask/stranded_with_controls/task1/minus.bw b/...ask/stranded_with_controls/task1/minus.bw → ...ask/stranded_with_controls/task1/minus.bw
diff --git a/...sk/stranded_with_controls/task1/peaks.bed → ...sk/stranded_with_controls/task1/peaks.bed b/...sk/stranded_with_controls/task1/peaks.bed → ...sk/stranded_with_controls/task1/peaks.bed
diff --git a/...task/stranded_with_controls/task1/plus.bw → ...task/stranded_with_controls/task1/plus.bw b/...task/stranded_with_controls/task1/plus.bw → ...task/stranded_with_controls/task1/plus.bw
diff --git a/.../stranded_without_controls/task0/minus.bw → .../stranded_without_controls/task0/minus.bw b/.../stranded_without_controls/task0/minus.bw → .../stranded_without_controls/task0/minus.bw
diff --git a/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed b/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed
diff --git a/...k/stranded_without_controls/task0/plus.bw → ...k/stranded_without_controls/task0/plus.bw b/...k/stranded_without_controls/task0/plus.bw → ...k/stranded_without_controls/task0/plus.bw
diff --git a/.../stranded_without_controls/task1/minus.bw → .../stranded_without_controls/task1/minus.bw b/.../stranded_without_controls/task1/minus.bw → .../stranded_without_controls/task1/minus.bw
diff --git a/...stranded_without_controls/task1/peaks.bed → ...stranded_without_controls/task1/peaks.bed b/...stranded_without_controls/task1/peaks.bed → ...stranded_without_controls/task1/peaks.bed
diff --git a/...k/stranded_without_controls/task1/plus.bw → ...k/stranded_without_controls/task1/plus.bw b/...k/stranded_without_controls/task1/plus.bw → ...k/stranded_without_controls/task1/plus.bw
diff --git a/...with_controls/task0/control_unstranded.bw → ...with_controls/task0/control_unstranded.bw b/...with_controls/task0/control_unstranded.bw → ...with_controls/task0/control_unstranded.bw
diff --git a/.../unstranded_with_controls/task0/peaks.bed → .../unstranded_with_controls/task0/peaks.bed b/.../unstranded_with_controls/task0/peaks.bed → .../unstranded_with_controls/task0/peaks.bed
diff --git a/...tranded_with_controls/task0/unstranded.bw → ...tranded_with_controls/task0/unstranded.bw b/...tranded_with_controls/task0/unstranded.bw → ...tranded_with_controls/task0/unstranded.bw
diff --git a/...with_controls/task1/control_unstranded.bw → ...with_controls/task1/control_unstranded.bw b/...with_controls/task1/control_unstranded.bw → ...with_controls/task1/control_unstranded.bw
diff --git a/.../unstranded_with_controls/task1/peaks.bed → .../unstranded_with_controls/task1/peaks.bed b/.../unstranded_with_controls/task1/peaks.bed → .../unstranded_with_controls/task1/peaks.bed
diff --git a/...tranded_with_controls/task1/unstranded.bw → ...tranded_with_controls/task1/unstranded.bw b/...tranded_with_controls/task1/unstranded.bw → ...tranded_with_controls/task1/unstranded.bw
diff --git a/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed b/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed
diff --git a/...nded_without_controls/task0/unstranded.bw → ...nded_without_controls/task0/unstranded.bw b/...nded_without_controls/task0/unstranded.bw → ...nded_without_controls/task0/unstranded.bw
diff --git a/...stranded_without_controls/task1/peaks.bed → ...stranded_without_controls/task1/peaks.bed b/...stranded_without_controls/task1/peaks.bed → ...stranded_without_controls/task1/peaks.bed
diff --git a/...nded_without_controls/task1/unstranded.bw → ...nded_without_controls/task1/unstranded.bw b/...nded_without_controls/task1/unstranded.bw → ...nded_without_controls/task1/unstranded.bw
diff --git a/...nded_with_controls/task0/control_minus.bw → ...nded_with_controls/task0/control_minus.bw b/...nded_with_controls/task0/control_minus.bw → ...nded_with_controls/task0/control_minus.bw
diff --git a/...anded_with_controls/task0/control_plus.bw → ...anded_with_controls/task0/control_plus.bw b/...anded_with_controls/task0/control_plus.bw → ...anded_with_controls/task0/control_plus.bw
diff --git a/...ask/stranded_with_controls/task0/minus.bw → ...ask/stranded_with_controls/task0/minus.bw b/...ask/stranded_with_controls/task0/minus.bw → ...ask/stranded_with_controls/task0/minus.bw
diff --git a/...sk/stranded_with_controls/task0/peaks.bed → ...sk/stranded_with_controls/task0/peaks.bed b/...sk/stranded_with_controls/task0/peaks.bed → ...sk/stranded_with_controls/task0/peaks.bed
diff --git a/...task/stranded_with_controls/task0/plus.bw → ...task/stranded_with_controls/task0/plus.bw b/...task/stranded_with_controls/task0/plus.bw → ...task/stranded_with_controls/task0/plus.bw
diff --git a/.../stranded_without_controls/task0/minus.bw → .../stranded_without_controls/task0/minus.bw b/.../stranded_without_controls/task0/minus.bw → .../stranded_without_controls/task0/minus.bw
diff --git a/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed b/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed
diff --git a/...k/stranded_without_controls/task0/plus.bw → ...k/stranded_without_controls/task0/plus.bw b/...k/stranded_without_controls/task0/plus.bw → ...k/stranded_without_controls/task0/plus.bw
diff --git a/...with_controls/task0/control_unstranded.bw → ...with_controls/task0/control_unstranded.bw b/...with_controls/task0/control_unstranded.bw → ...with_controls/task0/control_unstranded.bw
diff --git a/.../unstranded_with_controls/task0/peaks.bed → .../unstranded_with_controls/task0/peaks.bed b/.../unstranded_with_controls/task0/peaks.bed → .../unstranded_with_controls/task0/peaks.bed
diff --git a/...tranded_with_controls/task0/unstranded.bw → ...tranded_with_controls/task0/unstranded.bw b/...tranded_with_controls/task0/unstranded.bw → ...tranded_with_controls/task0/unstranded.bw
diff --git a/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed b/...stranded_without_controls/task0/peaks.bed → ...stranded_without_controls/task0/peaks.bed
diff --git a/...nded_without_controls/task0/unstranded.bw → ...nded_without_controls/task0/unstranded.bw b/...nded_without_controls/task0/unstranded.bw → ...nded_without_controls/task0/unstranded.bw
diff --git a/src/mseqgen_extra/tests/test_generators.py → bpnet/mseqgen_extra/tests/test_generators.py b/src/mseqgen_extra/tests/test_generators.py → bpnet/mseqgen_extra/tests/test_generators.py
diff --git a/src/mseqgen_extra/tests/test_sequtils.py → bpnet/mseqgen_extra/tests/test_sequtils.py b/src/mseqgen_extra/tests/test_sequtils.py → bpnet/mseqgen_extra/tests/test_sequtils.py