feat(train_model): add atac layer argument #542

AlexanderAivazidis · 2024-07-08T21:32:16Z

No description provided.

github-actions · 2024-07-10T21:35:10Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (ad74106) to multiomeModel (f0703a6).

Target branch (beta):

commit ad74106635031ade275db1ef3ce411ada8445b04 (HEAD -> beta, tag: v0.2.0-beta.21, origin/beta)
Author: semantic-release-bot <[email protected]>
Date:   Wed Jul 10 19:54:47 2024 +0000

    chore(release): 0.2.0-beta.21

Pull request (multiomeModel):

commit f0703a6fd545a0a1998a7d700e4fde92a96a4856 (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Wed Jul 10 20:39:13 2024 +0000

    feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
    
    Signed-off-by: Alexander Aivazidis <[email protected]>

Can't fast forward beta (ad74106) to multiomeModel (f0703a6). beta (ad74106) is not a direct ancestor of multiomeModel (f0703a6). Branches appear to have diverged at 4429882:

* f0703a6fd545a0a1998a7d700e4fde92a96a4856 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* 377688bc2a844414ca016be136b2b5eda32ba062 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* 960282db4ae2b46221512f34b779c86bbe5d0d2f feat(VelocityTrainingMixin): Added atac data to train_faster method
* 9c06e3f4b0bc8ea7a22fd9947e6b62935dbe1679 fix[PyroVelocity]: missing colon in Args description
* 2cdcc3a46ce9361429ce37d3ccf054cc4f366245 feat[PyroVelocity]: added atac_data to setup_anndata method
* 11507a1dee873f40bf634de3d0d2238bd080adad corrected ATAC argument type from layer name to anndata object
* fae543bcbc88a75960c588378ce7a71d7846cb10 fix(vscode): disable automatic python env activation
* eb4981652ecc7ac84f6add83f86e477882c4048d added atac_layer argument to train_model tasks and made tests for it
| * ad74106635031ade275db1ef3ce411ada8445b04 chore(release): 0.2.0-beta.21
| * a9bacf3f0deef25349c9728e7852d91a6b919f50 fix(cid): set semantic release token variable
| * 1e43b3068eb59908ef8732360b0f3a0331a4e677 fix(make): add commands to set fast forward variables
| * 5c9ebf88894cd4b512a91cbc968afbb6acf1e196 fix(cid): pass mode to build-nix-images workflow
| * 12ba002aca593d31b2a50580a2127a3eb206aeec fix(build-nix-images): skip build in dev mode
| * ad09bc9b5218426db4879cbfe8008239fe0fe2a5 fix(pr-merge): declare explicit github actor and pat
| * fecedfff0f749f0dc230c935e203ef0311cba205 fix(mergify): remove conditions from queue_rules
| * cf2641ff702cd92be0a1772d420dcb74cd85a1b7 fix(cid): use `github.ref_name` in all concurrency group keys
| * 904cf1a958e953242f3f84e70c3a0c3e44a8d244 chore(flake): sync lock
| * 3af29eb38adba0290f6a9050f6a529ae3b68240c fix(cid): reenable all image builds
| * d85c34bd1043f613ce85e08067e6b958ab8eb9f8 fix(build-nix-images): disable cache
| * 9dfcd8d42bfe905afa0fcaf46dd1a1d7b9a4e607 fix(build-nix-images): pin actions cache to v4 hash
| * 09b1e73ab14e1cf997b656e7ab73ef3e2660553c chore(conda): build `0.2.0b20`
| * 43dc8d070d0f810750f9c7ac3c34f4963783e1c3 chore(version): `0.2.0b21`
| * 59daeb538f0e482c105507f47fc62e1066549306 fix(cid): only test workflow image build by default
| * 416acc8aa4464075ef7f234440f2d2275fa8a897 fix(build-nix-images): cache argo cli
| * 974021365f1c5f9f02a0600a732430d976290099 test(cid): build image subset without cache
| * 221c0733d316d2ce6538085c82fa3e58a2a45c10 fix(cid): migrate build-images reusable action usage to source
| * 051350790260d79140ae9862d5be2edbd87fbc83 fix(cid): reenable cachix for release job
| * 691c25aec7666e2a54e4830993ae5fe31f780ed9 refactor(cid): migrate composite action-based image build usage to action source
| * c6dec80303437945053229ca0902ab30ccb5616d fix(build-nix-images): preserve JSON list-formatted images argument
| * e477c5b8a436de73e839938dbbedad38c2f5ad14 fix(cid): include checkout_rev in set-variables outputs
| * 850afe8d728628fb620cbd145e499ba9077e09d5 fix(cid): disable containerfile image builds
| * dc224bdc7cdd0f6a994571b367aefc844ca409fe fix(cid): enable reusable workflow to build nix images
| * 33ab84f4abbb9fd3b2595144a49803a5f48eb028 feat(github): add reusable workflow to build nix images
| * 8c2179b125773ac6861e2aa66b7d24a5a2762964 feat(argo): add nix image build Workflow resource
| * 43172b72531474b8e9640498b465835909892873 fix(containers): set default scrollback
| * af62669a7143f728d56dcf04a21ac8fe151468e9 fix(vscode): remove unavailable workspace setting
| * 9150817c584eaf80811b8e71362615323d6bc9b5 fix(flake): reenable upstream flocken
| * 50b2a795da53189cc1a38614fbacd9f24b8f6dd3 fix(containers): update SHELL path
| * 257c5d786ba3cb565f92898d0910c8c1c88a8000 fix(containers): update code extensions
| * b6e57081f03bb78d55f1fd060b57afa7b165990f fix(pkgs): add bazel-buildtools to coreDevPackages
| * 14e6cbae2d940db804e5ed257cad0f69e6f534da fix(vscode): disable python-environment-manager
|/  
* 4429882dd1ed17cfc303ac8ae09e5d904eaf19c8 chore(release): 0.2.0-beta.20

commit 4429882dd1ed17cfc303ac8ae09e5d904eaf19c8 (tag: v0.2.0-beta.20)
Author: semantic-release-bot <[email protected]>
Date:   Mon Jul 8 06:00:51 2024 +0000

    chore(release): 0.2.0-beta.20

Rebase locally, and then force push to multiomeModel.

Signed-off-by: Alexander Aivazidis <[email protected]>

In the long run we should refactor code, so that training uses scvi-tools modules. Signed-off-by: Alexander Aivazidis <[email protected]>

Signed-off-by: Alexander Aivazidis <[email protected]>

…ome data Signed-off-by: Alexander Aivazidis <[email protected]>

Signed-off-by: Alexander Aivazidis <[email protected]>

…mics functions. Signed-off-by: Alexander Aivazidis <[email protected]>

Signed-off-by: Alexander Aivazidis <[email protected]>

github-actions · 2024-07-22T19:19:12Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (0a01b81) to multiomeModel (b5508f9).

Target branch (beta):

commit 0a01b81971e4ebdd05b3ba04918907df245a0562 (HEAD -> beta, origin/beta)
Author: Cameron Smith <[email protected]>
Date:   Sat Jul 20 00:53:25 2024 -0400

    chore(nbs): sync _freeze hash
    
    Signed-off-by: Cameron Smith <[email protected]>

Pull request (multiomeModel):

commit b5508f9bd5991bff2bd86806b76f0640220830b6 (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Mon Jul 22 19:11:41 2024 +0000

    feat(.gitignore): Added example_notebooks directory to .gitignore file.
    
    Signed-off-by: Alexander Aivazidis <[email protected]>

Can't fast forward beta (0a01b81) to multiomeModel (b5508f9). beta (0a01b81) is not a direct ancestor of multiomeModel (b5508f9). Branches appear to have diverged at 16c654c:

* b5508f9bd5991bff2bd86806b76f0640220830b6 feat(.gitignore): Added example_notebooks directory to .gitignore file.
* 8368ce0ae14f007c064e550f0ca6cf13030d0931 feat(_test_velocity_model): Unit tests for velocity model
* 5a4dbbe85892ae0429a55ff14e2d76444d937892 feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.
* a857453437a1bb055bd9e382c3e95e3585c77ba0 feat(_transcription_dynamics): Added function for multiome dynamics.
* 365ba7b70f8fbb59efd3d56c83f131146f1b7045 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* cfee3171e876d09b5b7c8abdf3c2014a7b962c53 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* a36cae79e069cfe282c641ad697099f06b5b6d0a feat(VelocityTrainingMixin): Added atac data to train_faster method
* 7b7818806b66b9478f3ef84caa4698049fdc3291 fix[PyroVelocity]: missing colon in Args description
* 112b44d916f5c36a7a9adb42283c0b0d283cbb54 feat[PyroVelocity]: added atac_data to setup_anndata method
* f16cc6d34733ee04f62e0a4f1daeb3c86ea0a60b corrected ATAC argument type from layer name to anndata object
* 81ed87c32ac36ce66c700346557f563c83838f31 fix(vscode): disable automatic python env activation
* 9d2f67d7b82f1de2b2c1268a0bdb812d410bcfbf added atac_layer argument to train_model tasks and made tests for it
| * 0a01b81971e4ebdd05b3ba04918907df245a0562 chore(nbs): sync _freeze hash
| * 5ea6e671daf4c89f88d6dbb411d5cda8eff3a1a4 chore(nbs): set min width for search
| * 0642924432508a0ac2868a5f668e6404f19d09ec chore(wrangler): add configuration
| * 9b8917a04e19eed0ea38da4a8505f43c18a5f05f chore(nbs): interlink introductory pages
| * a1e211824f199cabadbb1e60af89389bbbd582f0 chore(flake): set devshell quarto python
| * 888edb847ddb20bbb2fb2b95ca61cc9eb1644474 chore(nbs): update information links
| * fb76e68607907798f3f752bc47a098a4977ecdbe chore(nbs): disable source menu
| * c299bbd0108735767a9a09179784e053da4625c9 chore(nbs): resize navigation tool
| * f000e65ac9ff9f77b632464bdd3f192d78f3027f chore(nbs): use explicit grid sizes
| * bf3b1b1903c6799bedc691baf88b3d5cbb9f7c4b chore(nbs): increase navbar padding
| * f836ca85c6ba986b104c4aeb03ec1c32365c23ea chore(nbs): update color scheme toggle size
| * dfecdf8ed24dfe73238b3599ff894272da9ccaeb chore(nbs): add navbar border
| * 8ccc365e624b032d7b5efe489291e296f0bb6e12 chore(flake): unset devshell QUARTO_PYTHON
| * 61b7308c57741c60af2a8ac0692a861cdc1c1c94 chore(nbs): update theme defaults
| * f42c11f0a3396e10ce2050e4203167935e41ba49 chore(quarto): 1.5.40 -> 1.5.55
| * f4f4789e0d40b65154b80bdba9ec2029074f51ea nit(contributing): fix `development`
| * 8d34070cee2e8cbe777e04f46646ae36ebf1abba nit(installation): note requirement to activate virtual env
| * b7da6af2682c8b8ec8bca7065122b456041bc6d8 docs(contributing): improve notes regarding devshell usage
| * 706d8665616864258ddd405961910ce7b8f5b721 docs(guides): add note on dependency versions
|/  
* 16c654c93734911c3109e210990c48216b369b86 nit(contributing): remove extra PR list element

commit 16c654c93734911c3109e210990c48216b369b86
Author: Cameron Smith <[email protected]>
Date:   Mon Jul 15 10:32:37 2024 -0400

    nit(contributing): remove extra PR list element
    
    Signed-off-by: Cameron Smith <[email protected]>

Rebase locally, and then force push to multiomeModel.

Signed-off-by: Alexander Aivazidis <[email protected]>

… data Signed-off-by: Alexander Aivazidis <[email protected]>

github-actions · 2024-07-22T21:52:13Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (0a01b81) to multiomeModel (e349bb7).

Target branch (beta):

commit 0a01b81971e4ebdd05b3ba04918907df245a0562 (HEAD -> beta, origin/beta)
Author: Cameron Smith <[email protected]>
Date:   Sat Jul 20 00:53:25 2024 -0400

    chore(nbs): sync _freeze hash
    
    Signed-off-by: Cameron Smith <[email protected]>

Pull request (multiomeModel):

commit e349bb7aab710c6d1619faa8da25ad3aad8a54be (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Mon Jul 22 21:51:49 2024 +0000

    fix(_velocity_model): LogNormal instead of Normal likelihood for atac data
    
    Signed-off-by: Alexander Aivazidis <[email protected]>

Can't fast forward beta (0a01b81) to multiomeModel (e349bb7). beta (0a01b81) is not a direct ancestor of multiomeModel (e349bb7). Branches appear to have diverged at 16c654c:

* e349bb7aab710c6d1619faa8da25ad3aad8a54be fix(_velocity_model): LogNormal instead of Normal likelihood for atac data
* e2080852523680e75e9406b7fd0b4ca612525108 fix(_velocity): Save existence of atac data in adata
* fe53c90470e9d414cca482c09cf2f6f390d3583d fix[_trainer_]: checking for existence of atac data
* b5508f9bd5991bff2bd86806b76f0640220830b6 feat(.gitignore): Added example_notebooks directory to .gitignore file.
* 8368ce0ae14f007c064e550f0ca6cf13030d0931 feat(_test_velocity_model): Unit tests for velocity model
* 5a4dbbe85892ae0429a55ff14e2d76444d937892 feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.
* a857453437a1bb055bd9e382c3e95e3585c77ba0 feat(_transcription_dynamics): Added function for multiome dynamics.
* 365ba7b70f8fbb59efd3d56c83f131146f1b7045 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* cfee3171e876d09b5b7c8abdf3c2014a7b962c53 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* a36cae79e069cfe282c641ad697099f06b5b6d0a feat(VelocityTrainingMixin): Added atac data to train_faster method
* 7b7818806b66b9478f3ef84caa4698049fdc3291 fix[PyroVelocity]: missing colon in Args description
* 112b44d916f5c36a7a9adb42283c0b0d283cbb54 feat[PyroVelocity]: added atac_data to setup_anndata method
* f16cc6d34733ee04f62e0a4f1daeb3c86ea0a60b corrected ATAC argument type from layer name to anndata object
* 81ed87c32ac36ce66c700346557f563c83838f31 fix(vscode): disable automatic python env activation
* 9d2f67d7b82f1de2b2c1268a0bdb812d410bcfbf added atac_layer argument to train_model tasks and made tests for it
| * 0a01b81971e4ebdd05b3ba04918907df245a0562 chore(nbs): sync _freeze hash
| * 5ea6e671daf4c89f88d6dbb411d5cda8eff3a1a4 chore(nbs): set min width for search
| * 0642924432508a0ac2868a5f668e6404f19d09ec chore(wrangler): add configuration
| * 9b8917a04e19eed0ea38da4a8505f43c18a5f05f chore(nbs): interlink introductory pages
| * a1e211824f199cabadbb1e60af89389bbbd582f0 chore(flake): set devshell quarto python
| * 888edb847ddb20bbb2fb2b95ca61cc9eb1644474 chore(nbs): update information links
| * fb76e68607907798f3f752bc47a098a4977ecdbe chore(nbs): disable source menu
| * c299bbd0108735767a9a09179784e053da4625c9 chore(nbs): resize navigation tool
| * f000e65ac9ff9f77b632464bdd3f192d78f3027f chore(nbs): use explicit grid sizes
| * bf3b1b1903c6799bedc691baf88b3d5cbb9f7c4b chore(nbs): increase navbar padding
| * f836ca85c6ba986b104c4aeb03ec1c32365c23ea chore(nbs): update color scheme toggle size
| * dfecdf8ed24dfe73238b3599ff894272da9ccaeb chore(nbs): add navbar border
| * 8ccc365e624b032d7b5efe489291e296f0bb6e12 chore(flake): unset devshell QUARTO_PYTHON
| * 61b7308c57741c60af2a8ac0692a861cdc1c1c94 chore(nbs): update theme defaults
| * f42c11f0a3396e10ce2050e4203167935e41ba49 chore(quarto): 1.5.40 -> 1.5.55
| * f4f4789e0d40b65154b80bdba9ec2029074f51ea nit(contributing): fix `development`
| * 8d34070cee2e8cbe777e04f46646ae36ebf1abba nit(installation): note requirement to activate virtual env
| * b7da6af2682c8b8ec8bca7065122b456041bc6d8 docs(contributing): improve notes regarding devshell usage
| * 706d8665616864258ddd405961910ce7b8f5b721 docs(guides): add note on dependency versions
|/  
* 16c654c93734911c3109e210990c48216b369b86 nit(contributing): remove extra PR list element

commit 16c654c93734911c3109e210990c48216b369b86
Author: Cameron Smith <[email protected]>
Date:   Mon Jul 15 10:32:37 2024 -0400

    nit(contributing): remove extra PR list element
    
    Signed-off-by: Cameron Smith <[email protected]>

Rebase locally, and then force push to multiomeModel.

github-actions · 2024-07-26T14:21:05Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (0a01b81) to multiomeModel (21a83ac).

Target branch (beta):

commit 0a01b81971e4ebdd05b3ba04918907df245a0562 (HEAD -> beta, origin/beta)
Author: Cameron Smith <[email protected]>
Date:   Sat Jul 20 00:53:25 2024 -0400

    chore(nbs): sync _freeze hash
    
    Signed-off-by: Cameron Smith <[email protected]>

Pull request (multiomeModel):

commit 21a83ace01cd1cc21728b7f24ee34f7fc4bc5f36 (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Fri Jul 26 14:20:43 2024 +0000

    fix(_trainer.py): Properly processing atac data

Can't fast forward beta (0a01b81) to multiomeModel (21a83ac). beta (0a01b81) is not a direct ancestor of multiomeModel (21a83ac). Branches appear to have diverged at 16c654c:

* 21a83ace01cd1cc21728b7f24ee34f7fc4bc5f36 fix(_trainer.py): Properly processing atac data
* e349bb7aab710c6d1619faa8da25ad3aad8a54be fix(_velocity_model): LogNormal instead of Normal likelihood for atac data
* e2080852523680e75e9406b7fd0b4ca612525108 fix(_velocity): Save existence of atac data in adata
* fe53c90470e9d414cca482c09cf2f6f390d3583d fix[_trainer_]: checking for existence of atac data
* b5508f9bd5991bff2bd86806b76f0640220830b6 feat(.gitignore): Added example_notebooks directory to .gitignore file.
* 8368ce0ae14f007c064e550f0ca6cf13030d0931 feat(_test_velocity_model): Unit tests for velocity model
* 5a4dbbe85892ae0429a55ff14e2d76444d937892 feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.
* a857453437a1bb055bd9e382c3e95e3585c77ba0 feat(_transcription_dynamics): Added function for multiome dynamics.
* 365ba7b70f8fbb59efd3d56c83f131146f1b7045 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* cfee3171e876d09b5b7c8abdf3c2014a7b962c53 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* a36cae79e069cfe282c641ad697099f06b5b6d0a feat(VelocityTrainingMixin): Added atac data to train_faster method
* 7b7818806b66b9478f3ef84caa4698049fdc3291 fix[PyroVelocity]: missing colon in Args description
* 112b44d916f5c36a7a9adb42283c0b0d283cbb54 feat[PyroVelocity]: added atac_data to setup_anndata method
* f16cc6d34733ee04f62e0a4f1daeb3c86ea0a60b corrected ATAC argument type from layer name to anndata object
* 81ed87c32ac36ce66c700346557f563c83838f31 fix(vscode): disable automatic python env activation
* 9d2f67d7b82f1de2b2c1268a0bdb812d410bcfbf added atac_layer argument to train_model tasks and made tests for it
| * 0a01b81971e4ebdd05b3ba04918907df245a0562 chore(nbs): sync _freeze hash
| * 5ea6e671daf4c89f88d6dbb411d5cda8eff3a1a4 chore(nbs): set min width for search
| * 0642924432508a0ac2868a5f668e6404f19d09ec chore(wrangler): add configuration
| * 9b8917a04e19eed0ea38da4a8505f43c18a5f05f chore(nbs): interlink introductory pages
| * a1e211824f199cabadbb1e60af89389bbbd582f0 chore(flake): set devshell quarto python
| * 888edb847ddb20bbb2fb2b95ca61cc9eb1644474 chore(nbs): update information links
| * fb76e68607907798f3f752bc47a098a4977ecdbe chore(nbs): disable source menu
| * c299bbd0108735767a9a09179784e053da4625c9 chore(nbs): resize navigation tool
| * f000e65ac9ff9f77b632464bdd3f192d78f3027f chore(nbs): use explicit grid sizes
| * bf3b1b1903c6799bedc691baf88b3d5cbb9f7c4b chore(nbs): increase navbar padding
| * f836ca85c6ba986b104c4aeb03ec1c32365c23ea chore(nbs): update color scheme toggle size
| * dfecdf8ed24dfe73238b3599ff894272da9ccaeb chore(nbs): add navbar border
| * 8ccc365e624b032d7b5efe489291e296f0bb6e12 chore(flake): unset devshell QUARTO_PYTHON
| * 61b7308c57741c60af2a8ac0692a861cdc1c1c94 chore(nbs): update theme defaults
| * f42c11f0a3396e10ce2050e4203167935e41ba49 chore(quarto): 1.5.40 -> 1.5.55
| * f4f4789e0d40b65154b80bdba9ec2029074f51ea nit(contributing): fix `development`
| * 8d34070cee2e8cbe777e04f46646ae36ebf1abba nit(installation): note requirement to activate virtual env
| * b7da6af2682c8b8ec8bca7065122b456041bc6d8 docs(contributing): improve notes regarding devshell usage
| * 706d8665616864258ddd405961910ce7b8f5b721 docs(guides): add note on dependency versions
|/  
* 16c654c93734911c3109e210990c48216b369b86 nit(contributing): remove extra PR list element

commit 16c654c93734911c3109e210990c48216b369b86
Author: Cameron Smith <[email protected]>
Date:   Mon Jul 15 10:32:37 2024 -0400

    nit(contributing): remove extra PR list element
    
    Signed-off-by: Cameron Smith <[email protected]>

Rebase locally, and then force push to multiomeModel.

…n functions. Signed-off-by: Alexander Aivazidis <[email protected]>

Signed-off-by: Alexander Aivazidis <[email protected]>

…cause they caused dimension errors during posterior sampling. Signed-off-by: Alexander Aivazidis <[email protected]>

Signed-off-by: Alexander Aivazidis <[email protected]>

github-actions · 2024-07-26T14:25:05Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (0a01b81) to multiomeModel (c03a247).

Target branch (beta):

commit 0a01b81971e4ebdd05b3ba04918907df245a0562 (HEAD -> beta, origin/beta)
Author: Cameron Smith <[email protected]>
Date:   Sat Jul 20 00:53:25 2024 -0400

    chore(nbs): sync _freeze hash
    
    Signed-off-by: Cameron Smith <[email protected]>

Pull request (multiomeModel):

commit c03a24752aa3e8839f6a2c969241228af2847a44 (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Fri Jul 26 14:24:43 2024 +0000

    fix(train): Ensure atac data is handled properly.
    
    Signed-off-by: Alexander Aivazidis <[email protected]>

Can't fast forward beta (0a01b81) to multiomeModel (c03a247). beta (0a01b81) is not a direct ancestor of multiomeModel (c03a247). Branches appear to have diverged at 16c654c:

* c03a24752aa3e8839f6a2c969241228af2847a44 fix(train): Ensure atac data is handled properly.
* d9f0636c24dc1b996aa3d6786aa83788ff55ebcd fix(_velocity_module): Removed rates from multivariateNormalGuide, because they caused dimension errors during posterior sampling.
* d5dcc987aa09189866a9c71281a0075436266608 fix(_velocity): Handling atac data.
* 7a04607a4d114e059c3f9e5aa1008bfe57836a9b fix(_transcription_dynamics): Ensuring no inplace tensor operations in functions.
* 21a83ace01cd1cc21728b7f24ee34f7fc4bc5f36 fix(_trainer.py): Properly processing atac data
* e349bb7aab710c6d1619faa8da25ad3aad8a54be fix(_velocity_model): LogNormal instead of Normal likelihood for atac data
* e2080852523680e75e9406b7fd0b4ca612525108 fix(_velocity): Save existence of atac data in adata
* fe53c90470e9d414cca482c09cf2f6f390d3583d fix[_trainer_]: checking for existence of atac data
* b5508f9bd5991bff2bd86806b76f0640220830b6 feat(.gitignore): Added example_notebooks directory to .gitignore file.
* 8368ce0ae14f007c064e550f0ca6cf13030d0931 feat(_test_velocity_model): Unit tests for velocity model
* 5a4dbbe85892ae0429a55ff14e2d76444d937892 feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.
* a857453437a1bb055bd9e382c3e95e3585c77ba0 feat(_transcription_dynamics): Added function for multiome dynamics.
* 365ba7b70f8fbb59efd3d56c83f131146f1b7045 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* cfee3171e876d09b5b7c8abdf3c2014a7b962c53 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* a36cae79e069cfe282c641ad697099f06b5b6d0a feat(VelocityTrainingMixin): Added atac data to train_faster method
* 7b7818806b66b9478f3ef84caa4698049fdc3291 fix[PyroVelocity]: missing colon in Args description
* 112b44d916f5c36a7a9adb42283c0b0d283cbb54 feat[PyroVelocity]: added atac_data to setup_anndata method
* f16cc6d34733ee04f62e0a4f1daeb3c86ea0a60b corrected ATAC argument type from layer name to anndata object
* 81ed87c32ac36ce66c700346557f563c83838f31 fix(vscode): disable automatic python env activation
* 9d2f67d7b82f1de2b2c1268a0bdb812d410bcfbf added atac_layer argument to train_model tasks and made tests for it
| * 0a01b81971e4ebdd05b3ba04918907df245a0562 chore(nbs): sync _freeze hash
| * 5ea6e671daf4c89f88d6dbb411d5cda8eff3a1a4 chore(nbs): set min width for search
| * 0642924432508a0ac2868a5f668e6404f19d09ec chore(wrangler): add configuration
| * 9b8917a04e19eed0ea38da4a8505f43c18a5f05f chore(nbs): interlink introductory pages
| * a1e211824f199cabadbb1e60af89389bbbd582f0 chore(flake): set devshell quarto python
| * 888edb847ddb20bbb2fb2b95ca61cc9eb1644474 chore(nbs): update information links
| * fb76e68607907798f3f752bc47a098a4977ecdbe chore(nbs): disable source menu
| * c299bbd0108735767a9a09179784e053da4625c9 chore(nbs): resize navigation tool
| * f000e65ac9ff9f77b632464bdd3f192d78f3027f chore(nbs): use explicit grid sizes
| * bf3b1b1903c6799bedc691baf88b3d5cbb9f7c4b chore(nbs): increase navbar padding
| * f836ca85c6ba986b104c4aeb03ec1c32365c23ea chore(nbs): update color scheme toggle size
| * dfecdf8ed24dfe73238b3599ff894272da9ccaeb chore(nbs): add navbar border
| * 8ccc365e624b032d7b5efe489291e296f0bb6e12 chore(flake): unset devshell QUARTO_PYTHON
| * 61b7308c57741c60af2a8ac0692a861cdc1c1c94 chore(nbs): update theme defaults
| * f42c11f0a3396e10ce2050e4203167935e41ba49 chore(quarto): 1.5.40 -> 1.5.55
| * f4f4789e0d40b65154b80bdba9ec2029074f51ea nit(contributing): fix `development`
| * 8d34070cee2e8cbe777e04f46646ae36ebf1abba nit(installation): note requirement to activate virtual env
| * b7da6af2682c8b8ec8bca7065122b456041bc6d8 docs(contributing): improve notes regarding devshell usage
| * 706d8665616864258ddd405961910ce7b8f5b721 docs(guides): add note on dependency versions
|/  
* 16c654c93734911c3109e210990c48216b369b86 nit(contributing): remove extra PR list element

commit 16c654c93734911c3109e210990c48216b369b86
Author: Cameron Smith <[email protected]>
Date:   Mon Jul 15 10:32:37 2024 -0400

    nit(contributing): remove extra PR list element
    
    Signed-off-by: Cameron Smith <[email protected]>

Rebase locally, and then force push to multiomeModel.

…delling stochastic gene activation. Signed-off-by: Alexander Aivazidis <[email protected]>

…ng stochastic gene activation. Signed-off-by: Alexander Aivazidis <[email protected]>

…screte parameter for gene state. Signed-off-by: Alexander Aivazidis <[email protected]>

github-actions · 2024-07-26T17:42:33Z

Triggered from #542 by @AlexanderAivazidis.

Checking if we can fast forward beta (0a01b81) to multiomeModel (54cb35c).

Target branch (beta):

commit 0a01b81971e4ebdd05b3ba04918907df245a0562 (HEAD -> beta, origin/beta)
Author: Cameron Smith <[email protected]>
Date:   Sat Jul 20 00:53:25 2024 -0400

    chore(nbs): sync _freeze hash
    
    Signed-off-by: Cameron Smith <[email protected]>

Pull request (multiomeModel):

commit 54cb35c808d21d4beb5ca34e6017e012e7eaf2b4 (pull_request/multiomeModel)
Author: Alexander Aivazidis <[email protected]>
Date:   Fri Jul 26 17:42:12 2024 +0000

    feat(_test_transcription_dynamics): Adapted test to include latent discrete parameter for gene state.
    
    Signed-off-by: Alexander Aivazidis <[email protected]>

Can't fast forward beta (0a01b81) to multiomeModel (54cb35c). beta (0a01b81) is not a direct ancestor of multiomeModel (54cb35c). Branches appear to have diverged at 16c654c:

* 54cb35c808d21d4beb5ca34e6017e012e7eaf2b4 feat(_test_transcription_dynamics): Adapted test to include latent discrete parameter for gene state.
* 1e096dde9b99b2d8ad0c0cc031712edf198431b1 feat(_velocity_model): Sampling latent discrete parameter for modelling stochastic gene activation.
* 637588ae1cf6b89f30b3a7522e0b23ec1dcda860 feat(_transcription_dynamics): Added latent discrete parameter for modelling stochastic gene activation.
* c03a24752aa3e8839f6a2c969241228af2847a44 fix(train): Ensure atac data is handled properly.
* d9f0636c24dc1b996aa3d6786aa83788ff55ebcd fix(_velocity_module): Removed rates from multivariateNormalGuide, because they caused dimension errors during posterior sampling.
* d5dcc987aa09189866a9c71281a0075436266608 fix(_velocity): Handling atac data.
* 7a04607a4d114e059c3f9e5aa1008bfe57836a9b fix(_transcription_dynamics): Ensuring no inplace tensor operations in functions.
* 21a83ace01cd1cc21728b7f24ee34f7fc4bc5f36 fix(_trainer.py): Properly processing atac data
* e349bb7aab710c6d1619faa8da25ad3aad8a54be fix(_velocity_model): LogNormal instead of Normal likelihood for atac data
* e2080852523680e75e9406b7fd0b4ca612525108 fix(_velocity): Save existence of atac data in adata
* fe53c90470e9d414cca482c09cf2f6f390d3583d fix[_trainer_]: checking for existence of atac data
* b5508f9bd5991bff2bd86806b76f0640220830b6 feat(.gitignore): Added example_notebooks directory to .gitignore file.
* 8368ce0ae14f007c064e550f0ca6cf13030d0931 feat(_test_velocity_model): Unit tests for velocity model
* 5a4dbbe85892ae0429a55ff14e2d76444d937892 feat(_test_transcription_dynamics): Unit tests for transcription dynamics functions.
* a857453437a1bb055bd9e382c3e95e3585c77ba0 feat(_transcription_dynamics): Added function for multiome dynamics.
* 365ba7b70f8fbb59efd3d56c83f131146f1b7045 feat(_velocity_model): Added a MultiVelocityModelAuto class for multiome data
* cfee3171e876d09b5b7c8abdf3c2014a7b962c53 feat(_velocity_module): Added a MultiVelocityModule for multiome data.
* a36cae79e069cfe282c641ad697099f06b5b6d0a feat(VelocityTrainingMixin): Added atac data to train_faster method
* 7b7818806b66b9478f3ef84caa4698049fdc3291 fix[PyroVelocity]: missing colon in Args description
* 112b44d916f5c36a7a9adb42283c0b0d283cbb54 feat[PyroVelocity]: added atac_data to setup_anndata method
* f16cc6d34733ee04f62e0a4f1daeb3c86ea0a60b corrected ATAC argument type from layer name to anndata object
* 81ed87c32ac36ce66c700346557f563c83838f31 fix(vscode): disable automatic python env activation
* 9d2f67d7b82f1de2b2c1268a0bdb812d410bcfbf added atac_layer argument to train_model tasks and made tests for it
| * 0a01b81971e4ebdd05b3ba04918907df245a0562 chore(nbs): sync _freeze hash
| * 5ea6e671daf4c89f88d6dbb411d5cda8eff3a1a4 chore(nbs): set min width for search
| * 0642924432508a0ac2868a5f668e6404f19d09ec chore(wrangler): add configuration
| * 9b8917a04e19eed0ea38da4a8505f43c18a5f05f chore(nbs): interlink introductory pages
| * a1e211824f199cabadbb1e60af89389bbbd582f0 chore(flake): set devshell quarto python
| * 888edb847ddb20bbb2fb2b95ca61cc9eb1644474 chore(nbs): update information links
| * fb76e68607907798f3f752bc47a098a4977ecdbe chore(nbs): disable source menu
| * c299bbd0108735767a9a09179784e053da4625c9 chore(nbs): resize navigation tool
| * f000e65ac9ff9f77b632464bdd3f192d78f3027f chore(nbs): use explicit grid sizes
| * bf3b1b1903c6799bedc691baf88b3d5cbb9f7c4b chore(nbs): increase navbar padding
| * f836ca85c6ba986b104c4aeb03ec1c32365c23ea chore(nbs): update color scheme toggle size
| * dfecdf8ed24dfe73238b3599ff894272da9ccaeb chore(nbs): add navbar border
| * 8ccc365e624b032d7b5efe489291e296f0bb6e12 chore(flake): unset devshell QUARTO_PYTHON
| * 61b7308c57741c60af2a8ac0692a861cdc1c1c94 chore(nbs): update theme defaults
| * f42c11f0a3396e10ce2050e4203167935e41ba49 chore(quarto): 1.5.40 -> 1.5.55
| * f4f4789e0d40b65154b80bdba9ec2029074f51ea nit(contributing): fix `development`
| * 8d34070cee2e8cbe777e04f46646ae36ebf1abba nit(installation): note requirement to activate virtual env
| * b7da6af2682c8b8ec8bca7065122b456041bc6d8 docs(contributing): improve notes regarding devshell usage
| * 706d8665616864258ddd405961910ce7b8f5b721 docs(guides): add note on dependency versions
|/  
* 16c654c93734911c3109e210990c48216b369b86 nit(contributing): remove extra PR list element

commit 16c654c93734911c3109e210990c48216b369b86
Author: Cameron Smith <[email protected]>
Date:   Mon Jul 15 10:32:37 2024 -0400

    nit(contributing): remove extra PR list element
    
    Signed-off-by: Cameron Smith <[email protected]>

Rebase locally, and then force push to multiomeModel.

AlexanderAivazidis self-assigned this Jul 8, 2024

AlexanderAivazidis force-pushed the multiomeModel branch from f34196b to fae543b Compare July 8, 2024 21:50

AlexanderAivazidis added dev-mode Do not rebuild images and use branch name instead of git short SHA for image tags execute-workflow Control workflow execution on PRs labels Jul 8, 2024

AlexanderAivazidis force-pushed the multiomeModel branch from f0703a6 to b8224cc Compare July 10, 2024 21:51

cameronraysmith removed execute-workflow Control workflow execution on PRs dev-mode Do not rebuild images and use branch name instead of git short SHA for image tags labels Jul 10, 2024

AlexanderAivazidis force-pushed the multiomeModel branch 2 times, most recently from 7cc6355 to 41fa01b Compare July 12, 2024 02:27

cameronraysmith modified the milestones: 0.2.x, 0.3.x Jul 12, 2024

AlexanderAivazidis force-pushed the multiomeModel branch from 41fa01b to bef8f62 Compare July 12, 2024 17:39

AlexanderAivazidis added 6 commits July 15, 2024 15:08

added atac_layer argument to train_model tasks and made tests for it

9d2f67d

fix(vscode): disable automatic python env activation

81ed87c

corrected ATAC argument type from layer name to anndata object

f16cc6d

feat[PyroVelocity]: added atac_data to setup_anndata method

112b44d

fix[PyroVelocity]: missing colon in Args description

7b78188

Signed-off-by: Alexander Aivazidis <[email protected]>

feat(VelocityTrainingMixin): Added atac data to train_faster method

a36cae7

In the long run we should refactor code, so that training uses scvi-tools modules. Signed-off-by: Alexander Aivazidis <[email protected]>

AlexanderAivazidis force-pushed the multiomeModel branch from bef8f62 to d4c7f42 Compare July 15, 2024 15:08

AlexanderAivazidis added 6 commits July 22, 2024 19:04

feat(_velocity_module): Added a MultiVelocityModule for multiome data.

cfee317

Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_velocity_model): Added a MultiVelocityModelAuto class for multi…

365ba7b

…ome data Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_transcription_dynamics): Added function for multiome dynamics.

a857453

Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_test_transcription_dynamics): Unit tests for transcription dyna…

5a4dbbe

…mics functions. Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_test_velocity_model): Unit tests for velocity model

8368ce0

Signed-off-by: Alexander Aivazidis <[email protected]>

feat(.gitignore): Added example_notebooks directory to .gitignore file.

b5508f9

Signed-off-by: Alexander Aivazidis <[email protected]>

AlexanderAivazidis force-pushed the multiomeModel branch from d4c7f42 to b5508f9 Compare July 22, 2024 19:18

AlexanderAivazidis added 3 commits July 22, 2024 21:49

fix[_trainer_]: checking for existence of atac data

fe53c90

Signed-off-by: Alexander Aivazidis <[email protected]>

fix(_velocity): Save existence of atac data in adata

e208085

Signed-off-by: Alexander Aivazidis <[email protected]>

fix(_velocity_model): LogNormal instead of Normal likelihood for atac…

e349bb7

… data Signed-off-by: Alexander Aivazidis <[email protected]>

cameronraysmith added skip-ci Skip CI workflow enhancement New feature or request python Pull requests that update Python code and removed skip-ci Skip CI workflow labels Jul 23, 2024

fix(_trainer.py): Properly processing atac data

21a83ac

AlexanderAivazidis added 4 commits July 26, 2024 14:22

fix(_transcription_dynamics): Ensuring no inplace tensor operations i…

7a04607

…n functions. Signed-off-by: Alexander Aivazidis <[email protected]>

fix(_velocity): Handling atac data.

d5dcc98

Signed-off-by: Alexander Aivazidis <[email protected]>

fix(_velocity_module): Removed rates from multivariateNormalGuide, be…

d9f0636

…cause they caused dimension errors during posterior sampling. Signed-off-by: Alexander Aivazidis <[email protected]>

fix(train): Ensure atac data is handled properly.

c03a247

Signed-off-by: Alexander Aivazidis <[email protected]>

AlexanderAivazidis added 3 commits July 26, 2024 17:41

feat(_transcription_dynamics): Added latent discrete parameter for mo…

637588a

…delling stochastic gene activation. Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_velocity_model): Sampling latent discrete parameter for modelli…

1e096dd

…ng stochastic gene activation. Signed-off-by: Alexander Aivazidis <[email protected]>

feat(_test_transcription_dynamics): Adapted test to include latent di…

54cb35c

…screte parameter for gene state. Signed-off-by: Alexander Aivazidis <[email protected]>

cameronraysmith modified the milestones: 0.2.x, 0.3.x Jul 30, 2024

cameronraysmith modified the milestones: 0.3.x, 0.4.x Aug 14, 2024

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feat(train_model): add atac layer argument #542

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