Repository for the manuscript Fischer, D. S., Schaar, A. C. and Theis, F. Learning cell communication from spatial graphs of cells. 2021.
You can install ncem via pip from PyPI:
$ pip install ncem
This package was created with cookietemple using Cookiecutter based on Hypermodern_Python_Cookiecutter.
Question Hello, Thank you for creating ncem. I wanted to ask if the Custom data loader also accepts tangram mapped adata. In specific: what should obsm node_types, proportions consist of ?
questionI am appreciated by your excellent work. I plan to use 'NCEM' package with my CODEX image data. Yet, I failed to load my data referring the tutorial code. I find there are a lot of prefix like 'zhang','Hartmann' to build a dataloader. I don't know how to choose them. May I request for a help?
questionHi Anna and David,
I am interested to apply ncem for one of the MERFISH data. But I do not understand how to make dataloader for this data. It would be very grateful if you can help me to built the initial inputs for the ncem then I can see what useful information I get from ncem. The link of data files are following. Thanks. https://www.dropbox.com/sh/w4c98xryzdjsffd/AACSCptc-0ekCeptCC9OLK32a?dl=0
Question
Hi, thank you for developing this great package. I am just wondering have you tried to run it on sequencing-based ST data, and do we need some special set up to make it work?
questionHi, I am running your example of following two notebooks data_exploration_melc_tonsils.ipynb, and model_benchmarks_melc_tonsils.ipynb In the first one I get the error at step "Supp. Fig. 7: Ligand–receptor permutation test"
TypeError: init() got an unexpected keyword argument 'allowed_methods'
And from the other notebook at step "Figure 1 (d): Modeling cell communication as spatial cell state dependencies"
FileNotFoundError: [Errno 2] No such file or directory: '.210419_INTERACTIONS_BASELINE_NONE_NODES_PATIENT_1_pascualreguanttonsil/results/'
Can you please let me know what I am missing here? Thanks.
questionBumps actions/cache from 2.1.6 to 3.2.1.
Sourced from actions/cache's releases.
v3.2.1
What's Changed
- Release compression related changes for windows by
@Phantsurein actions/cache#1039- Upgrade codeql to v2 by
@Phantsurein actions/cache#1023Full Changelog: https://github.com/actions/cache/compare/v3.2.0...v3.2.1
v3.2.0
What's Changed
- fix wrong timeout env var key in README.md by
@walterddrin actions/cache#959- Updated release doc with correct env variable by
@kotewarin actions/cache#960- Create pull_request_template.md by
@pdotlin actions/cache#963- Update README with clearer info about cache-hit and its value by
@kotewarin actions/cache#961- Change datadog/squid to Ubuntu/squid in CI check by
@bishal-pdMSFTin actions/cache#976- Add more details to version section in readme by
@bishal-pdMSFTin actions/cache#971- Update hashFiles documentation reference by
@asaf400in actions/cache#979- Updated link for cache segment download info by
@kotewarin actions/cache#986- Readme update for deleting caches by
@t-dedahin actions/cache#981- Add oncall logic to assign issues and PRs by
@vsvipulin actions/cache#997- Bump minimatch from 3.0.4 to 3.1.2 by
@dependabotin actions/cache#998- Revert "Bump minimatch from 3.0.4 to 3.1.2" by
@vsvipulin actions/cache#1005- Fix npm vulnerability by
@Phantsurein actions/cache#1007- refactor: Use early return pattern to avoid nested conditions by
@jongwoooin actions/cache#1013- Use cache in check-dist.yml by
@jongwoooin actions/cache#1004- chore: Use built-in cache action to cache dependencies by
@jongwoooin actions/cache#1014- Updated node example by
@t-dedahin actions/cache#1008- Fix: Node npm doc example by
@apascualmin actions/cache#1026- docs: fix an invalid link in workarounds.md by
@teatimeguestin actions/cache#929- General Availability release for granular cache by
@kotewarin actions/cache#1035 More details here on beta release.New Contributors
@walterddrmade their first contribution in actions/cache#959@asaf400made their first contribution in actions/cache#979@jongwooomade their first contribution in actions/cache#1013@apascualmmade their first contribution in actions/cache#1026@teatimeguestmade their first contribution in actions/cache#929Full Changelog: https://github.com/actions/cache/compare/v3...v3.2.0
v3.2.0-beta.1
What's Changed
- Actions Cache Granular Control Implementation by
@kotewarin actions/cache#1006v3.1.0-beta.3
What's Changed
- Bug fixes for bsdtar fallback, if gnutar not available, and gzip fallback, if cache saved using old cache action, on windows.
Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.2...v3.1.0-beta.3
... (truncated)
Sourced from actions/cache's changelog.
3.2.1
- Update
@actions/cacheon windows to use gnu tar and zstd by default and fallback to bsdtar and zstd if gnu tar is not available. (issue)- Added support for fallback to gzip to restore old caches on windows.
- Added logs for cache version in case of a cache miss.
![[DEPENDABOT]: Bump actions/cache from 2.1.6 to 3.2.1](https://avatars.githubusercontent.com/in/29110?v=4)
c1a5de8 Upgrade codeql to v2 (#1023)9b0be58 Release compression related changes for windows (#1039)c17f4bf GA for granular cache (#1035)ac25611 docs: fix an invalid link in workarounds.md (#929)dc097e3 Update examples.md (#1026)fb86cbf Updated node example (#1008)a57932f Merge pull request #1014 from jongwooo/chore/use-built-in-cache-action04b13ca chore: Use built-in cache action to cache dependencies941bc71 Merge pull request #1004 from jongwooo/chore/use-cache-in-check-dist08d8639 Merge branch 'main' into chore/use-cache-in-check-distDependabot 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.
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Sourced from actions/cache's releases.
v3.2.0
What's Changed
- fix wrong timeout env var key in README.md by
@walterddrin actions/cache#959- Updated release doc with correct env variable by
@kotewarin actions/cache#960- Create pull_request_template.md by
@pdotlin actions/cache#963- Update README with clearer info about cache-hit and its value by
@kotewarin actions/cache#961- Change datadog/squid to Ubuntu/squid in CI check by
@bishal-pdMSFTin actions/cache#976- Add more details to version section in readme by
@bishal-pdMSFTin actions/cache#971- Update hashFiles documentation reference by
@asaf400in actions/cache#979- Updated link for cache segment download info by
@kotewarin actions/cache#986- Readme update for deleting caches by
@t-dedahin actions/cache#981- Add oncall logic to assign issues and PRs by
@vsvipulin actions/cache#997- Bump minimatch from 3.0.4 to 3.1.2 by
@dependabotin actions/cache#998- Revert "Bump minimatch from 3.0.4 to 3.1.2" by
@vsvipulin actions/cache#1005- Fix npm vulnerability by
@Phantsurein actions/cache#1007- refactor: Use early return pattern to avoid nested conditions by
@jongwoooin actions/cache#1013- Use cache in check-dist.yml by
@jongwoooin actions/cache#1004- chore: Use built-in cache action to cache dependencies by
@jongwoooin actions/cache#1014- Updated node example by
@t-dedahin actions/cache#1008- Fix: Node npm doc example by
@apascualmin actions/cache#1026- docs: fix an invalid link in workarounds.md by
@teatimeguestin actions/cache#929- General Availability release for granular cache by
@kotewarin actions/cache#1035 More details here on beta release.New Contributors
@walterddrmade their first contribution in actions/cache#959@asaf400made their first contribution in actions/cache#979@jongwooomade their first contribution in actions/cache#1013@apascualmmade their first contribution in actions/cache#1026@teatimeguestmade their first contribution in actions/cache#929Full Changelog: https://github.com/actions/cache/compare/v3...v3.2.0
v3.2.0-beta.1
What's Changed
- Actions Cache Granular Control Implementation by
@kotewarin actions/cache#1006v3.1.0-beta.3
What's Changed
- Bug fixes for bsdtar fallback, if gnutar not available, and gzip fallback, if cache saved using old cache action, on windows.
Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.2...v3.1.0-beta.3
v3.1.0-beta.2
What's Changed
- Updated node example by
@t-dedahin actions/cache#1008- Release cache
3.1.0-beta.2with gzip fallback for old cache by@Phantsurein actions/cache#1022Full Changelog: https://github.com/actions/cache/compare/v3.1.0-beta.1...v3.1.0-beta.2
... (truncated)
c17f4bf GA for granular cache (#1035)ac25611 docs: fix an invalid link in workarounds.md (#929)dc097e3 Update examples.md (#1026)fb86cbf Updated node example (#1008)a57932f Merge pull request #1014 from jongwooo/chore/use-built-in-cache-action04b13ca chore: Use built-in cache action to cache dependencies941bc71 Merge pull request #1004 from jongwooo/chore/use-cache-in-check-dist08d8639 Merge branch 'main' into chore/use-cache-in-check-dista2f324e Merge pull request #1013 from jongwooo/refactor/use-early-return-pattern-to-a...35f4702 refactor: Use early return pattern to avoid nested conditionsDependabot 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.
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@dependabot rebase will rebase this PR@dependabot recreate will recreate this PR, overwriting any edits that have been made to it@dependabot merge will merge this PR after your CI passes on it@dependabot squash and merge will squash and merge this PR after your CI passes on it@dependabot cancel merge will cancel a previously requested merge and block automerging@dependabot reopen will reopen this PR if it is closed@dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually@dependabot ignore this major version will 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 version will 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 dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)Bumps actions/cache from 2.1.6 to 3.0.11.
Sourced from actions/cache's releases.
v3.0.11
What's Changed
- Call out cache not saved on hit by
@Phantsurein actions/cache#946- Update
@actions/coreto 1.10.0 by@rentziassin actions/cache#950- Update cache to use
@actions/core@^1.10.0 by@pdotlin actions/cache#956New Contributors
@rentziassmade their first contribution in actions/cache#950Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.11
v3.0.10
- Fix a bug with sorting inputs.
- Update definition for
restore-keysin README.mdv3.0.9
- Enhanced the warning message for cache unavailability in case of GHES.
v3.0.8
What's Changed
- Fix
zstdnot working for windows on gnu tar in issues.- Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable
SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.v3.0.7
What's Changed
- Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.
v3.0.6
What's Changed
- Add example for clojure lein project dependencies by
@shivamarora1in PR actions/cache#835- Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by
@pdotlin PR actions/cache#887- Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
- Fix issue #833 where cache save was not working for caching github workspace directory
New Contributors
@shivamarora1made their first contribution in actions/cache#835@pdotlmade their first contribution in actions/cache#887Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6
v3.0.5
Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.
v3.0.4
In this release, we have fixed the tar creation error while trying to create it with path as
~/home folder onubuntu-latest.v3.0.3
Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)
v3.0.2
... (truncated)
Sourced from actions/cache's changelog.
3.0.11
- Update toolkit version to 3.0.5 to include
@actions/core@^1.10.0- Update
@actions/cacheto use updatedsaveStateandsetOutputfunctions from@actions/core@^1.10.0
9b0c1fc Merge pull request #956 from actions/pdotl-version-bump18103f6 Fix licensed status error3e383cd Update RELEASES43428ea toolkit versioon update and version bump for cache1c73980 3.0.11a3f5edc Merge pull request #950 from rentziass/rentziass/update-actions-core831ee69 Update licensesb9c8bfe Update @actions/core to 1.10.00f20846 Merge pull request #946 from actions/Phantsure-patch-2862fc14 Update README.mdDependabot 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.
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Sourced from actions/cache's releases.
v3.0.10
- Fix a bug with sorting inputs.
- Update definition for
restore-keysin README.mdv3.0.9
- Enhanced the warning message for cache unavailability in case of GHES.
v3.0.8
What's Changed
- Fix
zstdnot working for windows on gnu tar in issues.- Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable
SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.v3.0.7
What's Changed
- Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.
v3.0.6
What's Changed
- Add example for clojure lein project dependencies by
@shivamarora1in PR actions/cache#835- Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by
@pdotlin PR actions/cache#887- Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
- Fix issue #833 where cache save was not working for caching github workspace directory
New Contributors
@shivamarora1made their first contribution in actions/cache#835@pdotlmade their first contribution in actions/cache#887Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6
v3.0.5
Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.
v3.0.4
In this release, we have fixed the tar creation error while trying to create it with path as
~/home folder onubuntu-latest.v3.0.3
Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)
v3.0.2
This release adds the support for dynamic cache size cap on GHES.
v3.0.1
- Added support for caching from GHES 3.5.
- Fixed download issue for files > 2GB during restore.
v3.0.0
This change adds a minimum runner version(node12 -> node16), which can break users using an out-of-date/fork of the runner. This would be most commonly affecting users on GHES 3.3 or before, as those runners do not support node16 actions and they can use actions from github.com via github connect or manually copying the repo to their GHES instance.
Few dependencies and cache action usage examples have also been updated.
... (truncated)
Sourced from actions/cache's changelog.
Releases
3.0.0
- Updated minimum runner version support from node 12 -> node 16
3.0.1
- Added support for caching from GHES 3.5.
- Fixed download issue for files > 2GB during restore.
3.0.2
- Added support for dynamic cache size cap on GHES.
3.0.3
- Fixed avoiding empty cache save when no files are available for caching. (issue)
3.0.4
- Fixed tar creation error while trying to create tar with path as
~/home folder onubuntu-latest. (issue)3.0.5
- Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit. (PR)
3.0.6
- Fixed #809 - zstd -d: no such file or directory error
- Fixed #833 - cache doesn't work with github workspace directory
3.0.7
- Fixed #810 - download stuck issue. A new timeout is introduced in the download process to abort the download if it gets stuck and doesn't finish within an hour.
3.0.8
- Fix zstd not working for windows on gnu tar in issues #888 and #891.
- Allowing users to provide a custom timeout as input for aborting download of a cache segment using an environment variable
SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.3.0.9
- Enhanced the warning message for cache unavailablity in case of GHES.
56461b9 Merge pull request #931 from ELHoussineT/patch-1f85d12c Merge branch 'main' into patch-198044e4 Update README.mdedc4989 Merge pull request #942 from actions/vsvipul/fix-sort68d9698 Remove sort logic from inputsac80757 Actions/cache release 3.0.9 (#930)0ff0597 Update examples.md (#920)1268184 Update README.md (#936)3238536 Update README.md1a78ace Updated the GHES warning message (#925)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.
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Sourced from actions/cache's releases.
v3.0.9
- Enhanced the warning message for cache unavailability in case of GHES.
v3.0.8
What's Changed
- Fix
zstdnot working for windows on gnu tar in issues.- Allow users to provide a custom timeout as input for aborting cache segment download using the environment variable
SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.v3.0.7
What's Changed
- Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.
v3.0.6
What's Changed
- Add example for clojure lein project dependencies by
@shivamarora1in PR actions/cache#835- Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by
@pdotlin PR actions/cache#887- Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
- Fix issue #833 where cache save was not working for caching github workspace directory
New Contributors
@shivamarora1made their first contribution in actions/cache#835@pdotlmade their first contribution in actions/cache#887Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6
v3.0.5
Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit.
v3.0.4
In this release, we have fixed the tar creation error while trying to create it with path as
~/home folder onubuntu-latest.v3.0.3
Fixed avoiding empty cache save when no files are available for caching. (actions/cache#624)
v3.0.2
This release adds the support for dynamic cache size cap on GHES.
v3.0.1
- Added support for caching from GHES 3.5.
- Fixed download issue for files > 2GB during restore.
v3.0.0
This change adds a minimum runner version(node12 -> node16), which can break users using an out-of-date/fork of the runner. This would be most commonly affecting users on GHES 3.3 or before, as those runners do not support node16 actions and they can use actions from github.com via github connect or manually copying the repo to their GHES instance.
Few dependencies and cache action usage examples have also been updated.
v2.1.7
Support 10GB cache upload using the latest version
1.0.8of@actions/cache
Sourced from actions/cache's changelog.
3.0.9
- Enhanced the warning message for cache unavailablity in case of GHES.
ac80757 Actions/cache release 3.0.9 (#930)0ff0597 Update examples.md (#920)1268184 Update README.md (#936)1a78ace Updated the GHES warning message (#925)1bc650b Merge pull request #922 from actions/vsvipul/add-anurag92e01f4 Add anuragc617 to assigneesb195c99 Merge pull request #912 from actions/pdotl/readme-update-19f98a2f Merge branch 'main' into pdotl/readme-update-1471fb0c Move workarounds to a different filea213d1e Merge pull request #913 from actions/vsvipul-patch-2Dependabot 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.
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Sourced from actions/setup-python's releases.
Add check-latest input and bug fixes
In scope of this release we add the check-latest input. If check-latest is set to true, the action first checks if the cached version is the latest one. If the locally cached version is not the most up-to-date, the version will then be downloaded from python-versions repository. By default check-latest is set to false. For PyPy it will to try to reach https://downloads.python.org/pypy/versions.json
Example of usage:
steps: - uses: actions/[email protected] - uses: actions/[email protected] with: python-version: '3.9' check-latest: true - run: python --versionBesides, it includes such changes as
- Resolved logs for python-version and file inputs: actions/setup-python#465
- Added linux os release info to primary key: actions/setup-python#467
- Added fix to change Python versions for poetry: actions/setup-python#445
- Fix Tool Path handling for self-hosted runners: actions/setup-python#466
v4.1.0
In scope of this pull request we updated
actions/cachepackage as the new version contains fixes for caching error handling. Moreover, we added a new input update-environment. This option allows to specify if the action shall update environment variables (default) or not.Update-environment input
- name: setup-python 3.9 uses: actions/[email protected] with: python-version: 3.9 update-environment: falseBesides, we added such changes as:
- Allow python-version-file to be a relative path: actions/setup-python#431
- Added new environment variables for
Cmake: actions/setup-python#440- Updated error message for resolveVersion: actions/setup-python#450
- Assign default value of
AGENT_TOOLSDIRECTORYif not set: actions/setup-python#394v4.0.0
What's Changed
- Support for
python-version-fileinput: #336Example of usage:
- uses: actions/[email protected] with: python-version-file: '.python-version' # Read python version from a file - run: python my_script.py </tr></table>
... (truncated)
b55428b Merge pull request #472 from IvanZosimov/ReadmeUpdatee084fca Merge branch 'main' into ReadmeUpdate789730b Fix broken links in the text bodyc4e98b7 Fix broken linkscfcafa5 Fix review pointsc318b92 Fix review pointsa93d541 Merge pull request #466 from techman83/fix/tool_path72394d1 Fix typofe396d3 Revert changes853c012 Change advanced-usage.mdDependabot 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.
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... (truncated)
Sourced from actions/cache's changelog.
3.2.2
- Reverted the changes made in 3.2.1 to use gnu tar and zstd by default on windows.
4723a57 Revert compression changes related to windows but keep version logging (#1049)d1507cc Merge pull request #1042 from me-and/correct-readme-re-windows3337563 Merge branch 'main' into correct-readme-re-windows60c7666 save/README.md: Fix typo in example (#1040)b053f2b Fix formatting error in restore/README.md (#1044)501277c README.md: remove outdated Windows cache tip linkc1a5de8 Upgrade codeql to v2 (#1023)9b0be58 Release compression related changes for windows (#1039)c17f4bf GA for granular cache (#1035)ac25611 docs: fix an invalid link in workarounds.md (#929)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.
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Sourced from pre-commit's releases.
pre-commit v2.21.0
Features
- Require new-enough virtualenv to prevent 3.10 breakage
- #2467 PR by
@asottile.- Respect aliases with
SKIPfor environment install.- Allow
pre-commit run --filesagainst unmerged paths.
- #2484 PR by
@asottile.- Also apply regex warnings to
repo: localhooks.
- #2524 PR by
@chrisRedwine.- #2521 issue by
@asottile.rustis now a "first class" language -- supportinglanguage_versionand installation when not present.
- #2534 PR by
@Holzhaus.rnow uses more-reliable binary installation.
- #2460 PR by
@lorenzwalthert.GIT_ALLOW_PROTOCOLis now passed through for git operations.
- #2555 PR by
@asottile.GIT_ASKPASSis now passed through for git operations.- Remove
tomldependency by usingcargo adddirectly.- Support
dotnethooks which have dotted prefixes.Fixes
- Properly adjust
--commit-msg-filenameif run from a sub directory.
- #2459 PR by
@asottile.- Simplify
--intent-to-adddetection by usinggit diff.- Fix
R.exeselection on windows.
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@SInginc.- Skip default
nugetsource when installingdotnetpackages.pre-commit v2.20.0
Features
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sourceandobject-name(positional args) ofprepare-commit-msghook asPRE_COMMIT_COMIT_MSG_SOURCEandPRE_COMMIT_COMMIT_OBJECT_NAME.
- #2407 PR by
@M-Whitaker.- #2406 issue by
@M-Whitaker.Fixes
... (truncated)
Sourced from pre-commit's changelog.
2.21.0 - 2022-12-25
Features
- Require new-enough virtualenv to prevent 3.10 breakage
- #2467 PR by
@asottile.- Respect aliases with
SKIPfor environment install.- Allow
pre-commit run --filesagainst unmerged paths.
- #2484 PR by
@asottile.- Also apply regex warnings to
repo: localhooks.
- #2524 PR by
@chrisRedwine.- #2521 issue by
@asottile.rustis now a "first class" language -- supportinglanguage_versionand installation when not present.
- #2534 PR by
@Holzhaus.rnow uses more-reliable binary installation.
- #2460 PR by
@lorenzwalthert.GIT_ALLOW_PROTOCOLis now passed through for git operations.
- #2555 PR by
@asottile.GIT_ASKPASSis now passed through for git operations.- Remove
tomldependency by usingcargo adddirectly.- Support
dotnethooks which have dotted prefixes.Fixes
- Properly adjust
--commit-msg-filenameif run from a sub directory.
- #2459 PR by
@asottile.- Simplify
--intent-to-adddetection by usinggit diff.- Fix
R.exeselection on windows.
- #2605 PR by
@lorenzwalthert.- #2599 issue by
@SInginc.- Skip default
nugetsource when installingdotnetpackages.2.20.0 - 2022-07-10
Features
- Expose
sourceandobject-name(positional args) ofprepare-commit-msghook asPRE_COMMIT_COMIT_MSG_SOURCEandPRE_COMMIT_COMMIT_OBJECT_NAME.
- #2407 PR by
@M-Whitaker.- #2406 issue by
@M-Whitaker.Fixes
... (truncated)
40c5bda v2.21.0bb27ea3 Merge pull request #2642 from rkm/fix/dotnet-nuget-configc38e0c7 dotnet: ignore nuget source during tool installbce513f Merge pull request #2641 from rkm/fix/dotnet-tool-prefixe904628 fix dotnet hooks with prefixesd7b8b12 Merge pull request #2646 from pre-commit/pre-commit-ci-update-config94b6178 [pre-commit.ci] pre-commit autoupdateb474a83 Merge pull request #2643 from pre-commit/pre-commit-ci-update-configa179808 [pre-commit.ci] pre-commit autoupdate3aa6206 Merge pull request #2605 from lorenzwalthert/r/fix-exeDependabot 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.
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pre-commit-hooks v4.3.0
Features
check-executables-have-shebangs: usegit config core.fileModeto determine if it should querygit.
- #730 PR by
@Kurt-von-Laven.name-tests-test: add--pytest-test-firsttest convention.
- #779 PR by
@asottile.Fixes
check-shebang-scripts-are-executable: update windows instructions.
- #774 PR by
@mdeweerd.- #770 issue by
@mdeweerd.check-toml: use stdlibtomllibwhen available.
- #771 PR by
@DanielNoord.- #755 issue by
@sognetic.check-added-large-files: don't run on non-filestages.
- #778 PR by
@asottile.- #777 issue by
@skyj.pre-commit-hooks v4.2.0
Features
name-tests-test: updated display text.
- #713 PR by
@asottile.check-docstring-first: make output more parsable.
- #748 PR by
@asottile.check-merge-conflict: make output more parsable.
- #748 PR by
@asottile.debug-statements: make output more parsable.
- #748 PR by
@asottile.Fixes
check-merge-conflict: fix detection of======conflict marker on windows.
- #748 PR by
@asottile.Updating
- Drop python<3.7.
- #719 PR by
@asottile.- Changed default branch from
mastertomain.
- #744 PR by
@asottile.pre-commit-hooks v4.1.0
Features
debug-statements: addpdbrdebugger.
- #614 PR by
@cansarigol.detect-private-key: add detection for additional key types.check-executables-have-shebangs: improve messaging on windows.
- #689 PR by
@pujitm.- #686 issue by
@jmerdich.check-added-large-files: support--enforce-allwithgit-lfs.
- #674 PR by
@amartani.
... (truncated)
Sourced from pre-commit-hooks's changelog.
4.4.0 - 2022-11-23
Features
forbid-submodules: new hook which outright bans submodules.
- #815 PR by
@asottile.- #707 issue by
@ChiefGokhlayeh.4.3.0 - 2022-06-07
Features
check-executables-have-shebangs: usegit config core.fileModeto determine if it should querygit.
- #730 PR by
@Kurt-von-Laven.name-tests-test: add--pytest-test-firsttest convention.
- #779 PR by
@asottile.Fixes
check-shebang-scripts-are-executable: update windows instructions.
- #774 PR by
@mdeweerd.- #770 issue by
@mdeweerd.check-toml: use stdlibtomllibwhen available.
- #771 PR by
@DanielNoord.- #755 issue by
@sognetic.check-added-large-files: don't run on non-filestages.
- #778 PR by
@asottile.- #777 issue by
@skyj.4.2.0 - 2022-04-06
Features
name-tests-test: updated display text.
- #713 PR by
@asottile.check-docstring-first: make output more parsable.
- #748 PR by
@asottile.check-merge-conflict: make output more parsable.
- #748 PR by
@asottile.debug-statements: make output more parsable.
- #748 PR by
@asottile.Fixes
check-merge-conflict: fix detection of======conflict marker on windows.
- #748 PR by
@asottile.Updating
- Drop python<3.7.
- #719 PR by
@asottile.- Changed default branch from
mastertomain.
... (truncated)
f71fa2c v4.4.0afb705d Merge pull request #841 from pre-commit/pre-commit-ci-update-configa63d8f3 [pre-commit.ci] pre-commit autoupdateb4982b5 Merge pull request #840 from pre-commit/all-repos_autofix_no-implicit-optional360df52 remove no_implicit_optional5d205e6 Merge pull request #838 from pre-commit/pre-commit-ci-update-configc44770d [pre-commit.ci] pre-commit autoupdatec032263 Merge pull request #829 from pre-commit/pre-commit-ci-update-config0a7d3b7 [pre-commit.ci] pre-commit autoupdate4dcb74a Merge pull request #822 from pre-commit/pre-commit-ci-update-configDependabot 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.
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@dependabot rebase will rebase this PR@dependabot recreate will recreate this PR, overwriting any edits that have been made to it@dependabot merge will merge this PR after your CI passes on it@dependabot squash and merge will squash and merge this PR after your CI passes on it@dependabot cancel merge will cancel a previously requested merge and block automerging@dependabot reopen will reopen this PR if it is closed@dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually@dependabot ignore this major version will 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 version will 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 dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)I have a problem with installing ncem in my virtual environment.
My environment is pre-installed with jupyterlab-server 2.11.2 requiring jinja2>=3.0.3. When I tried to install ncem, I received an error message stating that it requires jinja2<3.0.0,>=2.11.3.
**Could you please update ncem to support Jinja2>=3.0.3? **
enhancementQuestion
Hi I want to use NCEM for CODEX data , but I could find any tutorial or how to prepare the data for this type of analysis.
Could please direct me if there is any tutorial or notebook that you could share with us ?
questionI am trying to install ncem on my machine: macOS Monterey 12.6.1 pip 22.2.2 from /Users/sei/opt/miniconda3/envs/test-env/lib/python3.8/site-packages/pip (python 3.8)
pip install ncem
When I do this I get the following error:
(test-env) [email protected] ~ % pip install ncem
Collecting ncem
Using cached ncem-0.1.4-py3-none-any.whl (119 kB)
Collecting click<8.0.0,>=7.1.2
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting patsy<0.6.0,>=0.5.1
Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB)
Collecting Jinja2<4.0.0,>=2.11.3
Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)
Collecting docrep<0.4.0,>=0.3.2
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py) ... done
Collecting matplotlib<4.0.0,>=3.4.2
Using cached matplotlib-3.6.1-cp38-cp38-macosx_11_0_arm64.whl (7.2 MB)
Collecting diffxpy<0.8.0,>=0.7.4
Using cached diffxpy-0.7.4-py3-none-any.whl (85 kB)
Collecting scipy<2.0.0,>=1.7.0
Using cached scipy-1.9.3-cp38-cp38-macosx_12_0_arm64.whl (28.5 MB)
Collecting scanpy<2.0.0,>=1.7.2
Using cached scanpy-1.9.1-py3-none-any.whl (2.0 MB)
Collecting squidpy<2.0.0,>=1.0.0
Using cached squidpy-1.2.3-py3-none-any.whl (180 kB)
Collecting PyYAML<6.0.0,>=5.4.1
Using cached PyYAML-5.4.1.tar.gz (175 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting louvain<0.8.0,>=0.7.0
Using cached louvain-0.7.2-cp38-cp38-macosx_11_0_arm64.whl (187 kB)
Collecting rich<11.0.0,>=10.1.0
Using cached rich-10.16.2-py3-none-any.whl (214 kB)
Collecting ncem
Using cached ncem-0.1.3-py3-none-any.whl (118 kB)
Using cached ncem-0.1.2-py3-none-any.whl (117 kB)
Using cached ncem-0.1.1-py3-none-any.whl (105 kB)
Using cached ncem-0.1.0-py3-none-any.whl (82 kB)
Collecting Jinja2<3.0.0,>=2.11.3
Using cached Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
ERROR: Cannot install ncem==0.1.0, ncem==0.1.1, ncem==0.1.2, ncem==0.1.3 and ncem==0.1.4 because these package versions have conflicting dependencies.
The conflict is caused by:
ncem 0.1.4 depends on tensorflow<3.0.0 and >=2.5.0
ncem 0.1.3 depends on tensorflow<3.0.0 and >=2.5.0
ncem 0.1.2 depends on tensorflow<3.0.0 and >=2.5.0
ncem 0.1.1 depends on tensorflow<3.0.0 and >=2.5.0
ncem 0.1.0 depends on tensorflow<3.0.0 and >=2.5.0
To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
Please let me know if there's anything else I should be doing beforehand. Thank you kindly for your help
Full Changelog: https://github.com/theislab/ncem/compare/0.1.1...0.1.2
Source code(tar.gz)Initial release of ncem package.
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