Bump peter-evans/create-pull-request from 3 to 4 #4
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 3 to 4. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v3...v4) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
dependabot
bot
added
dependencies
scottgigante-immunai
added a commit
that referenced
this pull request
Oct 13, 2022
* init spatial * spatial decomposition * init cleanup * run precommit * README update * updated readme * api update * pre-commit * readme update * api stylefix * pre-commit * metrics update * linting * pre-commit * black * linting fix * pre-commit * cleanup * cleanup * linting * linting * task name change * Rctd (#6) Co-authored-by: almaan <[email protected]> * add stereoscope - nnls - nusvr - vanillanmf - nmfreg (#4) Co-authored-by: Hirak Sarkar <[email protected]> * Seurat (#8) Co-authored-by: almaan <[email protected]> * adding simulation (#7) Co-authored-by: giovp <[email protected]> Co-authored-by: almaan <[email protected]> * reorder requirements * Update mse.py * update R2 description * review comments, populated __init__.py files for import * update import statements * fix label dataset * Specify image * fix random * fix labels * pre-commit * add test=False * add synth data from destVI * remove logger * return spatial reference in correct format * specify cell type label * add destVI simulation to datasets * fix random * fix nusvr * fix stereoscope * added destvi * added destvi * try fix data generation * fix from previous delete * add scvitools version * Synthetic data generation (#9) * tangram first * tangram first * tangram first * tangram first * flake8 + isort _destvi_utils * tangram update; pancreas add string index * tangram update; pancreas add string index * tangram update; pancreas add string index; n_obs = 1000 in synth data * tangram update; pancreas add string index; n_obs = 1000 in synth data * new synth * add tangram-sc to docker * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * new synth approach * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * pancreas subset integer; comment pancreas dataset [skip actions] * merge and split sc and st data * merged anndata in methods * merged anndata in methods * fix destvi * add code reference * shorten * Update openproblems/tasks/spatial_decomposition/_utils.py Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * Update openproblems/tasks/spatial_decomposition/datasets/_sc_to_sp_utils.py [skip actions] Co-authored-by: Giovanni Palla <[email protected]> * comment fix * comment fix * fix pancreas dataset * update readme * fix destvi genertaion * fix sparse * minor fix * drop csr_matrix; fix double merge of anndata; update seurat v3 * updates * fix test for sparse arrays * test=False * add geos to r-extras * geos before r install * add software-properties-common * add python-software-properties * add RUN before command * rm geos from r-base * fix merging of anndata by pinning higher version * revert back anndata * fix obs_names and pin anndata * try to add swap * reduce number of spatial spots * remove swap * reduce obs * remove swap * remove step in CI * decrease dataset size * remove sparse * remove copy * remove datasets * remove datasets from init * address scott comments * skip all pancreas * fix import * remove destiv * Merge `main` into `synthetic-data-generation` (#10) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> * change test * fix from_cache * pre-commit * update data generation to remove inf * change test * check task * resolve suggestions from scott Co-authored-by: almaan <[email protected]> Co-authored-by: Giovanni Palla <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> * Remove duplicate line * Fill in baseline decorator * Check R version of seurat * pre-commit * Remove reference to __from_cache__ * Clean up proportions assert * pre-commit * set merge='unique' to retain uns * fixes from scott comments * Fix code_version for new API * Set `max_epochs` on `test` * pre-commit * Temporarily remove destvi * Add dataset metadata fields * Add task summary * Temporarily remove steroscope * pre-commit * Fix typo * Copy `uns` * fix uns_merge to include _from_cache * convert NaNs in categorical dtypes * convert string dtypes * bump tangram-sc * fix string dtypes * convert strings to categoricals inside pancreas * change api label to str * obsm cannot be pd.DataFrame * revert anndata change * fix rctd * fix R2 * fix lots of things * fix nmfreg and sample method * address scott comments * add metadata attribute decorator * Update r_requirements.txt * Handle comments in `r_requirements.txt` * Rename spacexr * Move API below metrics * Rename NNLS * Fix RCTD code URL * Set n_pcs in RCTD python call * Revert 2077c35 * Set n_pca in seuratv3.py * use `n_pcs` in seuratv3.R * Split string rather than skipping QA * Shorten line lengths * shorten line lengths * Clean up comment * Delete pbmc3k_raw.h5ad * Rename R2.py to r2.py * Fix reference to r2.py * pre-commit * Rename sc_to_sp.py to pancreas.py * Rename _sc_and_sp_utils.py to utils.py * rename _utils.py to utils.py * pre-commit * import all pancreas datasets * fix typo * fix namespace clash * need to pass test arg * fix method name (0_1 -> 0_5) * check tower auth explicitly * filter genes and cells * filter_genes_cells is in-place * remaining todos from scott * add destvi dataset * delete scvi models and dataset * fix shell string * one more syntactic fix * Add tangram to readme * Specify cell types in description * pre-commit * Better dataset descriptors * Clean up * Split don't skip * handle random_state * Fix doi URL * Move import inside * Shorten line lengths * Remove commented imports * Shorten descriptors * Fix seuratv3 URL * Remove unused projection_type arg * Remove unused toarray * Remove unused toarray * Update vanillanmf.py * Remove unused DataFrame handler * Remove unused categorical handler * Remove unused pandas import * update nmfreg * fix nmfreg * fix vanilla * fix nmf * fix alpha * rctd * pre-commit * add dataset_reference * shorten line lengths * document PYTEST_MAX_RETRIES * Allow 429 too many requests Co-authored-by: almaan <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Alma Andersson <[email protected]> Co-authored-by: Hirak Sarkar <[email protected]> Co-authored-by: Daniel Burkhardt <[email protected]> Co-authored-by: Scott Gigante <[email protected]> Co-authored-by: MalteDLuecken <[email protected]> Co-authored-by: SingleCellOpenProblems <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel Strobl <[email protected]> Co-authored-by: Scott Gigante <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Bumps peter-evans/create-pull-request from 3 to 4.
Release notes
Sourced from peter-evans/create-pull-request's releases.
... (truncated)
Commits
923ad83force tryFetch (#1189)f094b77fix: avoid issue with case sensitivity of repo names (#1179)af7c021docs: shorten quote97872c4docs: update GA quote/ref in concepts-guidelines.md (#1169)bd72e1bfix: use full name for head branch to allow for repo renaming (#1164)f1a7646build: update distribution (#1157)15b68d1fix: strip optional '.git' suffix from https server remote name. (#1153)0dfc93cbuild(deps): bump peter-evans/create-pull-request from 3 to 4 (#1150)252fb19build(deps): bump peter-evans/slash-command-dispatch from 2 to 3 (#1122)4b867c4build(deps): bump actions/setup-node from 2 to 3 (#1123)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
@dependabot rebase.Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR:
@dependabot rebasewill rebase this PR@dependabot recreatewill recreate this PR, overwriting any edits that have been made to it@dependabot mergewill merge this PR after your CI passes on it@dependabot squash and mergewill squash and merge this PR after your CI passes on it@dependabot cancel mergewill cancel a previously requested merge and block automerging@dependabot reopenwill reopen this PR if it is closed@dependabot closewill close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually@dependabot ignore this major versionwill close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this minor versionwill close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)@dependabot ignore this dependencywill close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)