Default clip_to_obs to False (#63)

* docs: update documentations * docs: add a link of binary installers * perf(main): Command line tool supports a new input: filtered_feature_bc_matrix.h5 * docs(main): update documentation for .h5 file * docs(main): update dependencies * docs(main): add link to anndata and scanpy * docs: update dependencies * docs: update documentations * docs: update dependencies * docs: update dependency * add myst_parser * add sphinx_tabs * autodocsumm==0.2.8 * 0.4.4 Automatically generated by python-semantic-release * chore: add an option to support Mac M1 and M2 processors You need to install Mac specific version of Pytorch to allow M1/M2 acceleration. Though, support for this accelerator is still experimental in Pytorch, set device='cpu' upon any errors. * chore(docs): correct a wrong link * chore(docs): fix a typo * feat(model): add an option to clip the prediction * chore(docs):revise the docs * feat(*): remove tensorboard parameter * remove tensorboard from the command line tool * change email address, change default training epochs to 400 * 0.5.0 Automatically generated by python-semantic-release * feat: estimate ambient_profile_all * fix: fix setupdata * feat: print message * feat: print message * feat: support AnnData object as the input * default clip_to_obs to False, as it leads to overall over-correction * default clip_to_obs to False, as it leads to overall over-correction, change docs * default clip_to_obs to False, as it leads to overall over-correction, change __main__.py * Update python-semantic-release * 0.6.0 Automatically generated by python-semantic-release * make a new release 0.5.1 * feat(setup): change sample and n_batch parameters * docs(tutorials): update tutorials * chore(release_note): manually add release note * docs(tutorial): update hyperlinks for tutorials --------- Co-authored-by: Sheng, Caibin <[email protected]> Co-authored-by: github-actions <[email protected]> Co-authored-by: Caibin Sheng <[email protected]> Co-authored-by: github-actions <[email protected]>
Novartis · Mar 2, 2023 · 3e66569 · 3e66569
1 parent 77559cd
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diff --git a/docs/Release_notes.md b/docs/Release_notes.md
@@ -2,7 +2,7 @@
 
 ## TODO List
 * Multiple ambient profiles
-* Tutorial for snRNAseq (to be added since version v0.4.5)
+* Tutorial for snRNAseq (to be added since version v0.5.2)
 * Batch processing
 * Transfer learning
 * Early stopping
@@ -13,6 +13,22 @@
 
 <!--next-version-placeholder-->
 
+## v0.5.1 (2023-03-01)
+### Feature
+* Update dependencies ([`40e906e`](https://github.com/Novartis/scar/commit/40e906e2789509eaa493658d0775f074d571f04c))
+* Default clip_to_obs to False, as it leads to overall over-correction ([`944f09a`](https://github.com/Novartis/scar/commit/944f09aef2a1d9b97200fa90efb4a19eacaa7160))
+* Support AnnData object as the input ([`24a1ab6`](https://github.com/Novartis/scar/commit/24a1ab67b64d870f4a785ad8ca13dbb4b45c8293))
+* Print message ([`7659672`](https://github.com/Novartis/scar/commit/76596727389acc484c3dce78d6f2a262dec33a0e))
+* Print message ([`203687f`](https://github.com/Novartis/scar/commit/203687fb03f098a1bd2f1f3940d49c7e83421f22))
+* Estimate the ambient profile for all features all together, add ambient_profile_all to adata.uns ([`e1913fd`](https://github.com/Novartis/scar/commit/e1913fd15fdf5546619f750c23e03debbcf1d63e))
+
+### Fix
+* **setup:** Change sample and n_batch parameters to allow using all droplets by default ([`4f5e05f`](https://github.com/Novartis/scar/commit/4f5e05fa5bf6aa413287fb2be73d6ad01a3fc9b3))
+* **setup:** Fix setupdata ([`63afe9d`](https://github.com/Novartis/scar/commit/63afe9dd8fbc701360715e1a4318f6be8f07e58b))
+
+### Documentation
+* **tutorials:** Update tutorials ([`a21e2ec`](https://github.com/Novartis/scar/commit/a21e2ecd507f0c2b9f0e876af04a477927443205))
+
 ## v0.5.0 (2023-02-04)
 ### Feature
 * ***:** Remove tensorboard parameter ([`98717e7`](https://github.com/Novartis/scar/commit/98717e7c55f4c4184309cb6d3956097fde661046))

diff --git a/docs/conf.py b/docs/conf.py
@@ -15,12 +15,12 @@
 
 sys.path.insert(0, os.path.abspath("."))
 sys.path.insert(0, os.path.abspath(".."))
-from scar.main.__version__ import __version__, _copyright
+from scar.main.__version__ import __version__, _copyright, _author
 
 # -- Project information -----------------------------------------------------
 project = "scAR"
 copyright = _copyright
-author = "Caibin Sheng"
+author = _author
 release = __version__
 
 

diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -11,7 +11,8 @@ Run scar with Python API
    scAR_tutorial_sgRNA_assignment
    scAR_tutorial_identity_barcode
    scAR_tutorial_denoising_CITEseq
-   scAR_tutorial_mRNA_denoising
+   scAR_tutorial_denoising_scRNAseq
+   scAR_tutorial_denoising_snRNAseq
 
 Run scar with the command line tool
 ---------------------------------

diff --git a/docs/tutorials/scAR_tutorial_ambient_profile.ipynb b/docs/tutorials/scAR_tutorial_ambient_profile.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "292f4a7a-8578-4bda-9a15-186db1e448fe",
    "metadata": {},
@@ -17,9 +18,9 @@
     "\n",
     "Note\n",
     "\n",
-    "You need to install [scar](https://scar-tutorials.readthedocs.io/en/latest/) to run this notebook on your own device. \n",
+    "To run this notebook on your device, you need to install [![scAR](https://img.shields.io/badge/install-scar-brightgreen)](https://scar-tutorials.readthedocs.io/en/latest/Installation.html). \n",
     "\n",
-    "You can also run it on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_ambient_profile.ipynb)\n",
+    "Alternatively, you can also run this notebook on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_ambient_profile.ipynb)\n",
     "\n",
     "</div>"
    ]
@@ -863,9 +864,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "scar",
+   "display_name": "scar-gpu",
    "language": "python",
-   "name": "scar"
+   "name": "scar-gpu"
   },
   "language_info": {
    "codemirror_mode": {
@@ -877,7 +878,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.8.15"
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/scAR_tutorial_denoising_CITEseq.ipynb b/docs/tutorials/scAR_tutorial_denoising_CITEseq.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "88bc1132-b643-4372-ace5-853fa1b5620f",
    "metadata": {},
@@ -15,9 +16,9 @@
     "<div class=\"alert alert-info\">\n",
     "Note\n",
     "\n",
-    "You need to install [scar](https://scar-tutorials.readthedocs.io/en/latest/) to run this notebook on your own device. \n",
+    "To run this notebook on your device, you need to install [![scAR](https://img.shields.io/badge/install-scar-brightgreen)](https://scar-tutorials.readthedocs.io/en/latest/Installation.html). \n",
     "\n",
-    "You can also run it on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_denoising_CITEseq.ipynb)\n",
+    "Alternatively, you can also run this notebook on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_denoising_CITEseq.ipynb)\n",
     "    \n",
     "</div>"
    ]
@@ -1288,7 +1289,7 @@
   "kernelspec": {
    "display_name": "scar-gpu",
    "language": "python",
-   "name": "scar-gpu"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1301,6 +1302,11 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.8.15"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "6d40340ff8365112c27c9e1a45c88437ccb67b4e448376c6c9ce1e8299da967d"
+   }
   }
  },
  "nbformat": 4,

diff --git a/docs/tutorials/scAR_tutorial_denoising_scRNAseq.ipynb b/docs/tutorials/scAR_tutorial_denoising_scRNAseq.ipynb
diff --git a/docs/tutorials/scAR_tutorial_identity_barcode.ipynb b/docs/tutorials/scAR_tutorial_identity_barcode.ipynb
@@ -1,6 +1,7 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "f041069a-5e79-4341-8109-6bdb881a6d7e",
    "metadata": {},
@@ -16,9 +17,9 @@
     "\n",
     "Note\n",
     "\n",
-    "You need to install [scar](https://scar-tutorials.readthedocs.io/en/latest/) to run this notebook on your own device. \n",
+    "To run this notebook on your device, you need to install [![scAR](https://img.shields.io/badge/install-scar-brightgreen)](https://scar-tutorials.readthedocs.io/en/latest/Installation.html). \n",
     "\n",
-    "You can also run it on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_identity_barcode.ipynb)\n",
+    "Alternatively, you can also run this notebook on Colab [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Novartis/scAR/blob/main/docs/tutorials/scAR_tutorial_identity_barcode.ipynb)\n",
     "\n",
     "</div>"
    ]
@@ -802,9 +803,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "scar",
+   "display_name": "general",
    "language": "python",
-   "name": "scar"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -816,7 +817,12 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.10.8"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "bd32a3866492c9301d636a0fa4a9c1d709d3d15d440921553e00b19e0db36c6b"
+   }
   }
  },
  "nbformat": 4,