some refactoring of directories

kundajelab · Feb 24, 2023 · 56dd684 · 56dd684
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diff --git a/...basepairmodels/basepairmodels/__init__.py → src/basepairmodels/__init__.py b/...basepairmodels/basepairmodels/__init__.py → src/basepairmodels/__init__.py
diff --git a/...pairmodels/basepairmodels/api/__init__.py → src/basepairmodels/api/__init__.py b/...pairmodels/basepairmodels/api/__init__.py → src/basepairmodels/api/__init__.py
diff --git a/...asepairmodels/basepairmodels/api/bpnet.py → src/basepairmodels/api/bpnet.py b/...asepairmodels/basepairmodels/api/bpnet.py → src/basepairmodels/api/bpnet.py
diff --git a/...epairmodels/basepairmodels/api/modisco.py → src/basepairmodels/api/modisco.py b/...epairmodels/basepairmodels/api/modisco.py → src/basepairmodels/api/modisco.py
diff --git a/...odels/basepairmodels/api/motifinstance.py → src/basepairmodels/api/motifinstance.py b/...odels/basepairmodels/api/motifinstance.py → src/basepairmodels/api/motifinstance.py
diff --git a/...models/basepairmodels/api/profilemodel.py → src/basepairmodels/api/profilemodel.py b/...models/basepairmodels/api/profilemodel.py → src/basepairmodels/api/profilemodel.py
diff --git a/...pairmodels/basepairmodels/cli/__init__.py → src/basepairmodels/cli/__init__.py b/...pairmodels/basepairmodels/cli/__init__.py → src/basepairmodels/cli/__init__.py
diff --git a/...irmodels/basepairmodels/cli/argparsers.py → src/basepairmodels/cli/argparsers.py b/...irmodels/basepairmodels/cli/argparsers.py → src/basepairmodels/cli/argparsers.py
diff --git a/...odels/basepairmodels/cli/bigwig_helper.py → src/basepairmodels/cli/bigwig_helper.py b/...odels/basepairmodels/cli/bigwig_helper.py → src/basepairmodels/cli/bigwig_helper.py
diff --git a/...models/basepairmodels/cli/bpnettrainer.py → src/basepairmodels/cli/bpnettrainer.py b/...models/basepairmodels/cli/bpnettrainer.py → src/basepairmodels/cli/bpnettrainer.py
diff --git a/...irmodels/basepairmodels/cli/bpnetutils.py → src/basepairmodels/cli/bpnetutils.py b/...irmodels/basepairmodels/cli/bpnetutils.py → src/basepairmodels/cli/bpnetutils.py
diff --git a/.../basepairmodels/cli/counts_loss_weight.py → src/basepairmodels/cli/counts_loss_weight.py b/.../basepairmodels/cli/counts_loss_weight.py → src/basepairmodels/cli/counts_loss_weight.py
diff --git a/...irmodels/basepairmodels/cli/embeddings.py → src/basepairmodels/cli/embeddings.py b/...irmodels/basepairmodels/cli/embeddings.py → src/basepairmodels/cli/embeddings.py
diff --git a/...ls/basepairmodels/cli/exceptionhandler.py → src/basepairmodels/cli/exceptionhandler.py b/...ls/basepairmodels/cli/exceptionhandler.py → src/basepairmodels/cli/exceptionhandler.py
diff --git a/...sepairmodels/basepairmodels/cli/logger.py → src/basepairmodels/cli/logger.py b/...sepairmodels/basepairmodels/cli/logger.py → src/basepairmodels/cli/logger.py
diff --git a/...els/basepairmodels/cli/motif_discovery.py → src/basepairmodels/cli/motif_discovery.py b/...els/basepairmodels/cli/motif_discovery.py → src/basepairmodels/cli/motif_discovery.py
diff --git a/...pairmodels/basepairmodels/cli/outliers.py → src/basepairmodels/cli/outliers.py b/...pairmodels/basepairmodels/cli/outliers.py → src/basepairmodels/cli/outliers.py
diff --git a/...epairmodels/basepairmodels/cli/predict.py → src/basepairmodels/cli/predict.py b/...epairmodels/basepairmodels/cli/predict.py → src/basepairmodels/cli/predict.py
diff --git a/...rmodels/basepairmodels/cli/shap_scores.py → src/basepairmodels/cli/shap_scores.py b/...rmodels/basepairmodels/cli/shap_scores.py → src/basepairmodels/cli/shap_scores.py
diff --git a/...airmodels/basepairmodels/cli/shaputils.py → src/basepairmodels/cli/shaputils.py b/...airmodels/basepairmodels/cli/shaputils.py → src/basepairmodels/cli/shaputils.py
diff --git a/...rmodels/basepairmodels/common/__init__.py → src/basepairmodels/common/__init__.py b/...rmodels/basepairmodels/common/__init__.py → src/basepairmodels/common/__init__.py
diff --git a/...pairmodels/basepairmodels/common/stats.py → src/basepairmodels/common/stats.py b/...pairmodels/basepairmodels/common/stats.py → src/basepairmodels/common/stats.py
diff --git a/...rmodels/basepairmodels/common/training.py → src/basepairmodels/common/training.py b/...rmodels/basepairmodels/common/training.py → src/basepairmodels/common/training.py
diff --git a/...irmodels/basepairmodels/reports/README.md → src/basepairmodels/reports/README.md b/...irmodels/basepairmodels/reports/README.md → src/basepairmodels/reports/README.md
diff --git a/...eports/cluster_motif_hits_and_peaks.ipynb → ...eports/cluster_motif_hits_and_peaks.ipynb b/...eports/cluster_motif_hits_and_peaks.ipynb → ...eports/cluster_motif_hits_and_peaks.ipynb
diff --git a/...airmodels/reports/model_performance.ipynb → ...airmodels/reports/model_performance.ipynb b/...airmodels/reports/model_performance.ipynb → ...airmodels/reports/model_performance.ipynb
diff --git a/...airmodels/basepairmodels/reports/moods.py → src/basepairmodels/reports/moods.py b/...airmodels/basepairmodels/reports/moods.py → src/basepairmodels/reports/moods.py
diff --git a/...eports/showcase_motifs_and_profiles.ipynb → ...eports/showcase_motifs_and_profiles.ipynb b/...eports/showcase_motifs_and_profiles.ipynb → ...eports/showcase_motifs_and_profiles.ipynb
diff --git a/...models/reports/summarize_motif_hits.ipynb → ...models/reports/summarize_motif_hits.ipynb b/...models/reports/summarize_motif_hits.ipynb → ...models/reports/summarize_motif_hits.ipynb
diff --git a/...irmodels/basepairmodels/reports/tomtom.py → src/basepairmodels/reports/tomtom.py b/...irmodels/basepairmodels/reports/tomtom.py → src/basepairmodels/reports/tomtom.py
diff --git a/...pairmodels/basepairmodels/reports/util.py → src/basepairmodels/reports/util.py b/...pairmodels/basepairmodels/reports/util.py → src/basepairmodels/reports/util.py
diff --git a/...dels/reports/view_tfmodisco_results.ipynb → ...dels/reports/view_tfmodisco_results.ipynb b/...dels/reports/view_tfmodisco_results.ipynb → ...dels/reports/view_tfmodisco_results.ipynb
diff --git a/...ls/basepairmodels/reports/viz_sequence.py → src/basepairmodels/reports/viz_sequence.py b/...ls/basepairmodels/reports/viz_sequence.py → src/basepairmodels/reports/viz_sequence.py
diff --git a/src/basepairmodels/.circleci/config.yml → ...basepairmodels_extra/.circleci/config.yml b/src/basepairmodels/.circleci/config.yml → ...basepairmodels_extra/.circleci/config.yml
diff --git a/src/basepairmodels/README.md → src/basepairmodels_extra/README.md b/src/basepairmodels/README.md → src/basepairmodels_extra/README.md
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diff --git a/...rmodels/docs/_images/tutorial-control.png → ...s_extra/docs/_images/tutorial-control.png b/...rmodels/docs/_images/tutorial-control.png → ...s_extra/docs/_images/tutorial-control.png
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diff --git a/...models/docs/_images/tutorial-idrpeaks.png → ..._extra/docs/_images/tutorial-idrpeaks.png b/...models/docs/_images/tutorial-idrpeaks.png → ..._extra/docs/_images/tutorial-idrpeaks.png
diff --git a/...odels/docs/_sources/documentation.rst.txt → ...extra/docs/_sources/documentation.rst.txt b/...odels/docs/_sources/documentation.rst.txt → ...extra/docs/_sources/documentation.rst.txt
diff --git a/...asepairmodels/docs/_sources/index.rst.txt → ...rmodels_extra/docs/_sources/index.rst.txt b/...asepairmodels/docs/_sources/index.rst.txt → ...rmodels_extra/docs/_sources/index.rst.txt
diff --git a/...models/docs/_sources/installation.rst.txt → ..._extra/docs/_sources/installation.rst.txt b/...models/docs/_sources/installation.rst.txt → ..._extra/docs/_sources/installation.rst.txt
diff --git a/...odels/docs/_sources/miscellaneous.rst.txt → ...extra/docs/_sources/miscellaneous.rst.txt b/...odels/docs/_sources/miscellaneous.rst.txt → ...extra/docs/_sources/miscellaneous.rst.txt
diff --git a/...epairmodels/docs/_sources/modules.rst.txt → ...odels_extra/docs/_sources/modules.rst.txt b/...epairmodels/docs/_sources/modules.rst.txt → ...odels_extra/docs/_sources/modules.rst.txt
diff --git a/...pairmodels/docs/_sources/tutorial.rst.txt → ...dels_extra/docs/_sources/tutorial.rst.txt b/...pairmodels/docs/_sources/tutorial.rst.txt → ...dels_extra/docs/_sources/tutorial.rst.txt
diff --git a/src/basepairmodels/docs/_static/basic.css → ...sepairmodels_extra/docs/_static/basic.css b/src/basepairmodels/docs/_static/basic.css → ...sepairmodels_extra/docs/_static/basic.css
diff --git a/...airmodels/docs/_static/css/badge_only.css → ...els_extra/docs/_static/css/badge_only.css b/...airmodels/docs/_static/css/badge_only.css → ...els_extra/docs/_static/css/badge_only.css
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diff --git a/src/mseqgen/requirements.txt → src/mseqgen_extra/requirements.txt b/src/mseqgen/requirements.txt → src/mseqgen_extra/requirements.txt
diff --git a/src/mseqgen/setup.py → src/mseqgen_extra/setup.py b/src/mseqgen/setup.py → src/mseqgen_extra/setup.py
diff --git a/src/mseqgen/tests/GRCh38_EBV.chrom.sizes → ...seqgen_extra/tests/GRCh38_EBV.chrom.sizes b/src/mseqgen/tests/GRCh38_EBV.chrom.sizes → ...seqgen_extra/tests/GRCh38_EBV.chrom.sizes
diff --git a/src/mseqgen/tests/batchgen_params_peaks.json → ...en_extra/tests/batchgen_params_peaks.json b/src/mseqgen/tests/batchgen_params_peaks.json → ...en_extra/tests/batchgen_params_peaks.json
diff --git a/...mseqgen/tests/batchgen_params_random.json → ...n_extra/tests/batchgen_params_random.json b/...mseqgen/tests/batchgen_params_random.json → ...n_extra/tests/batchgen_params_random.json
diff --git a/...gen/tests/batchgen_params_sequential.json → ...tra/tests/batchgen_params_sequential.json b/...gen/tests/batchgen_params_sequential.json → ...tra/tests/batchgen_params_sequential.json
diff --git a/src/mseqgen/tests/bpnet_params.json → src/mseqgen_extra/tests/bpnet_params.json b/src/mseqgen/tests/bpnet_params.json → src/mseqgen_extra/tests/bpnet_params.json
diff --git a/...en/tests/input-stranded_with_control.json → ...ra/tests/input-stranded_with_control.json b/...en/tests/input-stranded_with_control.json → ...ra/tests/input-stranded_with_control.json
diff --git a/src/mseqgen/tests/input.json → src/mseqgen_extra/tests/input.json b/src/mseqgen/tests/input.json → src/mseqgen_extra/tests/input.json
diff --git a/src/mseqgen/tests/input2.json → src/mseqgen_extra/tests/input2.json b/src/mseqgen/tests/input2.json → src/mseqgen_extra/tests/input2.json
diff --git a/src/mseqgen/tests/input3.json → src/mseqgen_extra/tests/input3.json b/src/mseqgen/tests/input3.json → src/mseqgen_extra/tests/input3.json
diff --git a/src/mseqgen/tests/input_data.json → src/mseqgen_extra/tests/input_data.json b/src/mseqgen/tests/input_data.json → src/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/src/mseqgen/tests/test_data/background.bed → ...qgen_extra/tests/test_data/background.bed b/src/mseqgen/tests/test_data/background.bed → ...qgen_extra/tests/test_data/background.bed
diff --git a/src/mseqgen/tests/test_data/loci.bed → src/mseqgen_extra/tests/test_data/loci.bed b/src/mseqgen/tests/test_data/loci.bed → src/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/tests/test_generators.py → src/mseqgen_extra/tests/test_generators.py b/src/mseqgen/tests/test_generators.py → src/mseqgen_extra/tests/test_generators.py
diff --git a/src/mseqgen/tests/test_sequtils.py → src/mseqgen_extra/tests/test_sequtils.py b/src/mseqgen/tests/test_sequtils.py → src/mseqgen_extra/tests/test_sequtils.py