[auto] Update benchmark results by github-actions[bot] · Pull Request #368 · openproblems-bio/openproblems

github-actions · 2022-04-21T02:43:46Z

Automated changes by create-pull-request GitHub action

* upstream/main: Run `test_benchmark` on a self-hosted runner (openproblems-bio#373) Jamboree label_projection task (openproblems-bio#313) Only cleanup AWS on success (openproblems-bio#371) Jamboree dimensionality reduction methods (openproblems-bio#318) Update benchmark results # ci skip (openproblems-bio#368) remove citeseq cbmc from DR (openproblems-bio#367) Ignore AWS warning and clean up s3 properly (openproblems-bio#366) docker images separate PR (openproblems-bio#354) Allow codecov to fail on forks remove scot altogether (openproblems-bio#363)

* Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com>

* Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) * Install libgeos-dev Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com>

* Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com>

* label docker images * fix syntax * Delete run_benchmark.yml * Update from main (#378) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * Install libgeos-dev (#377) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) * Install libgeos-dev Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * Install libgeos-dev * Update test_docker (#379) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * clean up dockerfile Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com>

* Fix rgeos install (#380) * label docker images * fix syntax * Delete run_benchmark.yml * Update from main (#378) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * Install libgeos-dev (#377) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) * Install libgeos-dev Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * Install libgeos-dev * Update test_docker (#379) * Label docker images based on build location (#351) * label docker images * fix syntax * Run benchmark only after unittests (#349) * run benchmark after unittests * always run cleanup * cleanup * If using GH actions image, test for git diff on dockerfile (#350) * if using gh actions image, test for git diff on dockerfile * allow empty tag for now * decode * if image doesn't exist, automatically github actions * fix quotes * fix parsing and committing of results on tag (#356) * Import SCOT (#333) * import SCOT * pre-commit * scran requires R * check that aligned spaces are finite * exclude unbalanced SCOT for now Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> * fix coverage badge # ci skip (#358) * fix gh actions badge link # ci skip (#359) * store results in /tmp (#361) * Remove scot unbalanced (#360) * Fix benchmark commit (#362) * store results in /tmp * add skip_on_empty * class doesn't have skip on empty * remove scot altogether (#363) * Allow codecov to fail on forks * docker images separate PR (#354) * docker images separate PR * all R requirements in r_requirements.txt * move github r packages to requirements file * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Ignore AWS warning and clean up s3 properly (#366) * ci cleanup * ignore aws batch warning * remove citeseq cbmc from DR (#367) Co-authored-by: Scott Gigante <scott.gigante@immunai.com> * Update benchmark results # ci skip (#368) Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> * Jamboree dimensionality reduction methods (#318) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Remove ivis * pre-commit Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Only cleanup AWS on success (#371) * only cleanup on success * pre-commit Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Jamboree label_projection task (#313) * Add scvi-tools docker image * add scanvi * hvg command use 2000 * update scvi-tools version; use image * train size * scanvi mask test labels * move import * hvg on train only, fix hvg command * add scarches scanvi * use string labels in testing * enforce batch metadata in dataset * add batch metadata in pancreas random * use train adata for scarches * Add majority vote simple baseline * test_mode * use test instead of test mode, update contributing * update contributing guide * Added helper function to introduce label noise * Actually return data with label noise * Only introduce label noise on training data * Made a pancreas dataset with label nosie * Reformat docstring * Added reference to example label noise dataset in datasets __init__.py * Add cengen C elegans data loader (#2) * add CeNGEN C elegans neuron dataset * add CeNGEN C elegans dataset for global tasks and for label_projection task * fix lines being too long * Reformat cengen data loader * Create tabula_muris_senis.py Need dataframe containing sample information in './tabula_muris_senis_data_objects/tabula_muris_senis_data_objects.csv' load_tabula_muris_senis(method_list, organ_list) takes in methods and organs to extract data from and combines into one anndata object. If method_list or organ_list = None, do not filter based on that input. EX: load_tabula_muris_senis(method_list=['facs'], organ_list = None) returns all facs experiments for all organs in one anndata object. * pre-commit * Modify anndata in place in add_label_noise rather than copy * Added CSV file with tabula muris senis data links * Update tabula_muris_senis.py * Add random_labels baseline to label_projection task * Update tabula_muris_senis.py * Update tabula_muris_senis.py * pre-commit * Update tabula_muris_senis.py * pre-commit * fix missing labels at prediction time * Handle test flag through tests and docker, pass to methods * If test method run, use 1 max_epoch for scvi-tools * Use only 2 batches for sample dataset for label_projection * Remove zebrafish random dataset * Fix decorator dependency to <5.0.0 * Remove functools.wraps from docker decorator for test parameterization * Fix cengen missing batch info * Use functools.update_wrapper for docker test * Add batch to pancreas_random_label_noise * Make cengen test dataset have more cells per batch * Set span=0.8 for hvg call for scanvi_hvg methods * Set span=0.8 for HVG selection only in test mode for scvi * Revert "Handle test flag through tests and docker, pass to methods" This reverts commit 3b940c0. * Add test parameter to label proj baselines * Fix flake remove unused import * Revert "Remove zebrafish random dataset" This reverts commit 3915798. * Update scVI setup_anndata to new version * pre-commit * Reformat and rerun tests * Add code_url and code_version for baseline label proj methods * Fallback HVG flavor for label projection task * pre-commit * Fix unused import * Fix using highly_variable_genes * Pin scvi-tools to 0.15.5 * Unpin scvi-tools, pin jax==0.3.6, see optuna/optuna-examples#99 * Add scikit-misc as requirement for scvi docker * Pin jaxlib as well * pin jaxlib along with jax * Set paper_year to year of implementation * Set random zebrafish split to 0.8+0.2 * Add tabula_muris_senis_lung_random dataset to label_projection * pre-commit * Add tabula muris senis datasets csv * Fix loading tabula muris csv * pre-commit * Test loader for tabula muris senis Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * Run `test_benchmark` on a self-hosted runner (#373) * set up cirun * use ubuntu standard AMI * run nextflow on the self-hosted machine * add to CONTRIBUTING * update ami * install unzip * set up docker * install docker from curl * use t2.micro not nano * use custom AMI * pythonLocation * add scripts to path * larger disk size * new image again * chown for now * chmod 755 * fixed permissions * use tower workspace * test nextflow * try again * nextflow -q * redirect stderr * increase memory * cleanup * sudo install * name * try setting pythonpath * fix branch env * another fix * fix run name * typo * fix pythonpath: * don't use pushd * pass pythonpath * set nousersite * empty * sudo install * run attempt * revert temporary changes * cleanup * fix contributing * add instructions for tower * fix repo name * move ami setup into script * Import Olsson 2016 dataset for dimred task (#352) * Import Olsson 2016 dataset for dimred task * Fix path to Olsson dataset loader * Filter genes cells before subsetting Olsson data in test * Use highly expressed genes for test Olsson dataset Test dataset is now 700 genes by 300 cells (was 500 x 500) * Add ivis dimred method (#369) * add densMAP package to python-extras * pre-commit * Add Ivis method * Explicitly mention it's CPU implementation * Add forgotten import in __init__ * Remove redundant filtering * Move ivis inside the function * Make var names unique, add ivis[cpu] to README * Pin tensorflow version * Add NeuralEE skeleton * Implement method * added densmap and densne * Fix typo pytoch -> torch * pre-commit * remove densne * Add forgotten detach/cpu/numpy * formatting * pre-commit * formatting * formatting * pre-commit * formatting * formatting * formatting * pre-commit * formatting * umap-learn implementation * pre-commit * Add docker image * Add skeleton method * formatting * Implement method * Fix some small bugs * Add preprocessing * Change batch size to 1k cells for aff. matrix * Add new preprocessing * Add new preprocessing * Fix preprocessing * Fix preprocessing * pre-commit * updated template for PR with PR evaluation checks (#314) * Update alra.py (#304) * Update alra.py Fix pre-processing and transformation back into the original space * pre-commit * Update alra.py * make sure necessary methods are imported Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> * Add scanpy preprocessing to densmap dimred method * Rename preprocess_scanpy() to preprocess_logCPM_1kHVG() * Add preprocessing suffix to dimred methods * Subset object in preprocess_logCPM_1kHVG() * Use standard names for input * Add neuralee_logCPM_1kHVG method * Add densmap_pca method * Fix preprocess_logCPM_1kHVG() Now returns an AnnData rather than acting in place - Subsetting wasn't working in place Also set HVG flavor to "cell_ranger" * Add test argument to dimred methods * Move preprocess_logCPM_1kHVG() to tools.normalize * Change name in python-method-scvis Docker README * Rename openproblems-python-method-scvis container Now called open-problems-python36 * Fix AnnData ref in merge * Copy object when subsetting in preprocess_logCPM_1kHVG() * Move PCA to dimred methods * Use preprocess_logCPM_1kHVG() in nn_ranking metrics * Fix path in python36 dockerfile * Add test kwarg to neuralee_default method * Add check for n_var to preprocess_logCPM_1kHVG() Should fix tests that were failing due to scverse/scanpy#2230 * Store raw counts in NeuralEE default method * Update dimred README * Replace X_input with PCA in ivis dimred method * Refactor preprocess_logCPM_1kHVG() to log_cpm_hvg() * Re-add ivis Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> * hotfix timeout-minutes (#374) * use branch of scprep to provide R traceback (#376) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * clean up dockerfile Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com> * only skip CI if command is in commit headline (#381) * only skip if ci skip is in commit headline * try using endsWith instead # ci skip * Fix CI skip (#382) * only skip if ci skip is in commit headline * try using endsWith instead # ci skip * make actions run * upgrade AMI (#384) * upgrade AMI * uncomment docker * uncomment tests * Revert "Run test_benchmark on a self-hosted runner (#373)" (#386) * revert 2d57868 * bash -x * /bin/bash * Bugfix CI (#387) * upgrade AMI * uncomment docker * uncomment tests * clean up testing * tighter diff for testing * more memory * Revert "Bugfix CI (#387)" (#388) This reverts commit b50a909. * pass test arg to methods through CLI (#390) * make scvi run faster on test mode (#385) * make scvi run faster on test mode * pass test argument through cli * dirty hack to fix docker_build (#391) * remove ivis temporarily (#392) * neuralee fix (#383) * build images before testing * try something different * needs * fewer linebreaks * try as string * move the if * remove one condition * fix * cancel more quickly * run benchmark * don't build on main in run_benchmark Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Scott Gigante <scottgigante@users.noreply.github.com> Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: SingleCellOpenProblems <singlecellopenproblems@protonmail.com> Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Ben DeMeo <bdemeo@mit.edu> Co-authored-by: Michal Klein <michal.klein@protonmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: bendemeo <45370700+bendemeo@users.noreply.github.com> Co-authored-by: MalteDLuecken <m.d.luecken@gmail.com> Co-authored-by: Wesley Lewis <59123674+wes-lewis@users.noreply.github.com> Co-authored-by: Daniel Burkhardt <burkhardt.d.b@gmail.com> Co-authored-by: Nikolay Markov <nikolai.markov@icloud.com> Co-authored-by: adamgayoso <adamgayoso@users.noreply.github.com> Co-authored-by: Valentine Svensson <v@nxn.se> Co-authored-by: Eduardo Beltrame <munfred@brandeis.edu> Co-authored-by: atchen <81202350+atchen@users.noreply.github.com>

Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.5.1 to 1.5.2. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](nf-core/setup-nextflow@v1.5.1...v1.5.2) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.5.1 to 1.5.2. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](nf-core/setup-nextflow@v1.5.1...v1.5.2) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 0baa112

Update benchmark results # ci skip

2c93db3

github-actions Bot requested review from dburkhardt and scottgigante April 21, 2022 02:43

scottgigante-immunai merged commit a9e7d0c into main Apr 21, 2022

scottgigante-immunai deleted the auto_update_benchmark_1779 branch April 21, 2022 13:08

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[auto] Update benchmark results - #368

[auto] Update benchmark results#368
scottgigante-immunai merged 1 commit into
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