update readme

Let it be aligned with newest paper script.
batmen-lab · Sep 25, 2024 · 38669ee · 38669ee
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diff --git a/README.md b/README.md
@@ -5,13 +5,13 @@
   <h1 style="margin: 0; white-space: nowrap;">BioMANIA</h1>
 </div>
 
-[![Paper](https://img.shields.io/badge/Paper-burgundy?style=flat&logo=arxiv)](https://www.biorxiv.org/content/10.1101/2023.10.29.564479v1)
+[![Paper](https://img.shields.io/badge/Paper-burgundy?style=flat&logo=arxiv)](https://www.biorxiv.org/content/10.1101/2023.10.29.564479)
 [![GitHub stars](https://img.shields.io/github/stars/batmen-lab/BioMANIA?style=social)](https://github.com/batmen-lab/BioMANIA)
 [![Documentation Status](https://img.shields.io/readthedocs/biomania/latest?style=flat&logo=readthedocs&label=Doc)](https://biomania.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/badge/license-Apache%203.0-blue?style=flat&logo=open-source-initiative)](https://github.com/batmen-lab/BioMANIA/blob/main/LICENSE)
 [![Docker Version](https://img.shields.io/badge/Docker-v1.1.9-blue?style=flat&logo=docker)](https://hub.docker.com/repositories/chatbotuibiomania)
-[![Railway](https://img.shields.io/badge/Railway-purple?style=flat&logo=railway)](https://railway.app/template/qaQEvv)
 [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/14K4562oeesEz5qMoXmjv9gW_4VeLh6_U?usp=sharing)
+<!--[![Railway](https://img.shields.io/badge/Railway-purple?style=flat&logo=railway)](https://railway.app/template/qaQEvv)-->
 <!--[![Python unit tests](https://github.com/batmen-lab/BioMANIA/actions/workflows/python-test-unit.yml/badge.svg)](https://github.com/batmen-lab/BioMANIA/actions/workflows/python-test-unit.yml)-->
 
 
@@ -21,8 +21,9 @@ Welcome to the BioMANIA! This guide provides detailed instructions on how to set
 Project Overview:
 
 <!--![](./images/overview_v2.jpg)-->
-![](./images/Motivation.jpg)
-![](./images/Methods.jpg)
+<!--![](./images/Motivation.jpg)-->
+<!--![](./images/Methods.jpg)-->
+![](./images/overview.jpg)
 
 
 🌟 We warmly invite you to share your trained models and datasets in our [issues section](https://github.com/batmen-lab/BioMANIA/issues/2), making it easier for others to utilize and extend your work, thus amplifying its impact. Feel free to explore and provide feedback on tools shared by other contributors as well! 🚀🔍
@@ -39,9 +40,9 @@ We also offer a command-line interface (CLI) demo through the terminal.
 
 <img src="examples/cli.gif" style="width:800px;height:500px;animation: play 0.05s steps(100) infinite;">
 
-We also offer a GPTs demo (under developing).
+<!--We also offer a GPTs demo (under developing).
 
-<img src="examples/GPTs.gif" style="width:800px;height:450px;animation: play 1s steps(10) infinite;">
+<img src="examples/GPTs.gif" style="width:800px;height:450px;animation: play 1s steps(10) infinite;">-->
 
 # Web access online demo
 
@@ -109,11 +110,11 @@ ngrok http 3000
 
 then get the url like `https://[ngrok_id].ngrok-free.app` and copy it to chrome to start!
 
-## Run with Railway
+<!--## Run with Railway
 
 [![Deploy on Railway](https://railway.app/button.svg)](https://railway.app/template/qaQEvv)
 
-To use railway, you'll need to fill in the `OpenAI_API_KEY` in the Variables page of the biomania-backend service. Then, manually enable `Public Domain` in the Settings/Networking session for both front-end and back-end service. Copy the url from back-end as `https://[copied url]` and paste it in `BACKEND_URL` in front-end Variables page. For front-end url, paste it to the browser to access the frontend.
+To use railway, you'll need to fill in the `OpenAI_API_KEY` in the Variables page of the biomania-backend service. Then, manually enable `Public Domain` in the Settings/Networking session for both front-end and back-end service. Copy the url from back-end as `https://[copied url]` and paste it in `BACKEND_URL` in front-end Variables page. For front-end url, paste it to the browser to access the frontend.-->
 
 ## Run with script
 
@@ -231,8 +232,8 @@ model.run_pipeline(user_input, library, top_k=1, files=[], conversation_started=
 
 Please refer to the separate README for tutorials that supporting converting different coding tools to our APP.
 - [For PyPI Tools](./docs/PyPI2APP.md)
-- [For Python Source Code from Git Repo](./docs/Git2APP.md)
-- [For R Package](./docs/R2APP.md) (231123-Still under developing)
+- [For Python Source Code from Git Repo](./docs/Git2APP.md) (240925-Under developing)
+- [For R Package](./docs/R2APP.md) (231123-Under developing)
 
 ## Share your APP!
 
@@ -269,10 +270,9 @@ Thank you for choosing BioMANIA. We hope this guide assists you in navigating th
 
 
 ## **Version History**
-- v1.1.11 (2024-06)
- - Include task planning, execution correction into the logic.
- - Polish prompt.
- - Wrap backend service to be compatible for newer UI
+- v1.1.12 (2024-09-25)
+ - Update code scripts which are aligned with paper.
+ - Will renew the data, docker, scripts for generating report, documents for Git2APP, R2APP soon.
 
 view [version_history](./docs/version_history.md) for more details!
 

diff --git a/docs/Report_Generation.md b/docs/Report_Generation.md
@@ -11,7 +11,7 @@ Firstly, press `export chat` button on UI to get the chat json data. Convert the
 # cd src
 python report/Chat2Py.py report/demo_Preprocessing_and_clustering_3k_PBMCs.json
 ```
-![](./images/pyfile.jpg)
+![](https://github.com/batmen-lab/BioMANIA/tree/main/images/pyfile.jpg)
 
 
 ### For chat report
@@ -22,7 +22,7 @@ Convert the chat JSON into an [ipynb report](https://github.com/batmen-lab/BioMA
 # cd src
 python report/Chat2jupyter.py report/demo_Preprocessing_and_clustering_3k_PBMCs.json
 ```
-![](./images/jupyter.jpg)
+![](https://github.com/batmen-lab/BioMANIA/tree/main/images/jupyter.jpg)
 
 
 ### For performance report
@@ -36,7 +36,7 @@ python report/PNG2report.py scanpy
 
 Please note that the generation of this report must be based on the premise that the retriever models have already been trained, and the gpt baseline has already been tested. You need to first obtain the results of each model before running this script. Here is a reference for a [demo report](https://github.com/batmen-lab/BioMANIA/tree/main/src/report/performance_report.pdf).
 
-![](./images/performance_report.jpg)
+![](https://github.com/batmen-lab/BioMANIA/tree/main/images/performance_report.jpg)
 
 
 ### For common issue report
@@ -51,6 +51,9 @@ python report/Py2report.py scanpy
 The output files are located in the ./report folder.
 
 
+![](https://github.com/batmen-lab/BioMANIA/tree/main/images/error_category.jpg)
+
+
 TODO:
 
 We will provide the below files and the data of more tools later

diff --git a/docs/version_history.md b/docs/version_history.md
@@ -1,5 +1,10 @@
 
 ## Version History
+
+- v1.1.11 (2024-06)
+ - Include task planning, execution correction into the logic.
+ - Polish prompt.
+ - Wrap backend service to be compatible for newer UI
 - v1.1.9 (2023-12-24)
   - Add Drive URL installation feature for convenient uploading of large files by users.
   - Real-time informative displays for API execution, and enable image zoom and download features.

diff --git a/examples/result_demo_ehrapy.png b/examples/result_demo_ehrapy.png
diff --git a/examples/result_demo_ehrapy_all.png b/examples/result_demo_ehrapy_all.png
diff --git a/examples/result_demo_scanpy_indiv.png b/examples/result_demo_scanpy_indiv.png
diff --git a/examples/result_demo_scanpy_plan.png b/examples/result_demo_scanpy_plan.png
diff --git a/examples/result_demo_snapatac2.png b/examples/result_demo_snapatac2.png
diff --git a/examples/result_demo_squidpy.png b/examples/result_demo_squidpy.png
diff --git a/images/Methods.jpg b/images/Methods.jpg
diff --git a/images/Motivation.jpg b/images/Motivation.jpg
diff --git a/images/demo_full.jpg b/images/demo_full.jpg
diff --git a/images/error_category.jpg b/images/error_category.jpg
diff --git a/images/overview.jpg b/images/overview.jpg
diff --git a/images/overview_v2.jpg b/images/overview_v2.jpg
diff --git a/src/configs/Base_cheatsheet.py b/src/configs/Base_cheatsheet.py
@@ -1,74 +1,90 @@
 CHEATSHEET = {
-    "numpy": [
-        "numpy.array"
-    ],
-    "pandas": [
-        "pandas.read_csv",
-        "pandas.read_excel",
-        "pandas.DataFrame.to_csv",
-        "pandas.DataFrame",
-        "pandas.concat",
-        "pandas.DataFrame.groupby"
-    ],
-    "matplotlib": [
-        "matplotlib.pyplot.plot",
-        "matplotlib.pyplot.subplots",
-        "matplotlib.pyplot.imshow",
-        "matplotlib.pyplot.hist",
-        "matplotlib.pyplot.scatter",
-        "matplotlib.pyplot.bar",
-        "matplotlib.pyplot.pie",
-        "matplotlib.pyplot.boxplot",
-        "matplotlib.pyplot.violinplot"
-    ],
-    "sklearn": [
-        "sklearn.preprocessing.StandardScaler",
-        "sklearn.preprocessing.StandardScaler.fit",
-        "sklearn.preprocessing.OneHotEncoder",
-        "sklearn.preprocessing.OneHotEncoder.fit",
-        "sklearn.preprocessing.normalize",
-        "sklearn.model_selection.train_test_split",
-        "sklearn.metrics.accuracy_score",
-        "sklearn.metrics.precision_score",
-        "sklearn.metrics.recall_score",
-        "sklearn.metrics.mean_squared_error",
-        "sklearn.decomposition.PCA",
-        "sklearn.decomposition.PCA.fit",
-        "sklearn.manifold.TSNE",
-        "sklearn.manifold.TSNE.fit",
-        "sklearn.decomposition.NMF",
-        "sklearn.decomposition.NMF.fit"
-    ],
-    "scipy": [
-        "scipy.sparse.csr_matrix"
-    ],
-    "torch": [
-        "torch.tensor"
-    ],
-    "json":["json.dump",
-        "json.load",
-        "json.loads"
-    ],
-    "statsmodels": [
-        "statsmodels.formula.api.ols"
-    ],
-    "pynndescent": [
-        "pynndescent.NNDescent.query"
-    ],
-    "anndata": [
-        "anndata.read_csv",
-        "anndata.AnnData.write_csvs"
-    ],
-    "pooch":[
-        "pooch.retrieve"
-    ],
-    "math":[
-        "math.ceil"
-    ],
-    "urllib":[
-        "urllib.request.urlretrieve"
-    ],
-    "tabulate":[
-        "tabulate.tabulate"
+    #"numpy": [
+    #    "numpy.array"
+    #],
+    #"pandas": [
+    #    "pandas.read_csv",
+    #    "pandas.read_excel",
+    #    "pandas.DataFrame.to_csv",
+    #    "pandas.DataFrame",
+    #    "pandas.concat",
+    #    "pandas.DataFrame.groupby"
+    #],
+    #"matplotlib": [
+    #    "matplotlib.pyplot.plot",
+    #    "matplotlib.pyplot.subplots",
+    #    "matplotlib.pyplot.imshow",
+    #    "matplotlib.pyplot.hist",
+    #    "matplotlib.pyplot.scatter",
+    #    "matplotlib.pyplot.bar",
+    #    "matplotlib.pyplot.pie",
+    #    "matplotlib.pyplot.boxplot",
+    #    "matplotlib.pyplot.violinplot"
+    #],
+    #"sklearn": [
+    #    "sklearn.preprocessing.StandardScaler",
+    #    "sklearn.preprocessing.StandardScaler.fit",
+    #    "sklearn.preprocessing.OneHotEncoder",
+    #    "sklearn.preprocessing.OneHotEncoder.fit",
+    #    "sklearn.preprocessing.normalize",
+    #    "sklearn.model_selection.train_test_split",
+    #    "sklearn.metrics.accuracy_score",
+    #    "sklearn.metrics.precision_score",
+    #    "sklearn.metrics.recall_score",
+    #    "sklearn.metrics.mean_squared_error",
+    #    "sklearn.decomposition.PCA",
+    #    "sklearn.decomposition.PCA.fit",
+    #    "sklearn.manifold.TSNE",
+    #    "sklearn.manifold.TSNE.fit",
+    #    "sklearn.decomposition.NMF",
+    #    "sklearn.decomposition.NMF.fit"
+    #],
+    #"scipy": [
+    #    "scipy.sparse.csr_matrix"
+    #],
+    #"torch": [
+    #    "torch.tensor"
+    #],
+    #"json":["json.dump",
+    #    "json.load",
+    #    "json.loads"
+    #],
+    #"statsmodels": [
+    #    "statsmodels.formula.api.ols"
+    #],
+    #"pynndescent": [
+    #    "pynndescent.NNDescent.query"
+    #],
+    #"anndata": [
+    #    "anndata.read_csv",
+    #    "anndata.AnnData.write_csvs"
+    #],
+    #"pooch":[
+    #    "pooch.retrieve"
+    #],
+    #"math":[
+    #    "math.ceil"
+    #],
+    #"urllib":[
+    #    "urllib.request.urlretrieve"
+    #],
+    #"tabulate":[
+    #    "tabulate.tabulate"
+    #],
+    "cellrank":[
+        "cellrank.kernels.PseudotimeKernel",
+        "cellrank.kernels.PseudotimeKernel.compute_transition_matrix",
+        "cellrank.kernels.PseudotimeKernel.plot_random_walks",
+        "cellrank.kernels.PseudotimeKernel.plot_projection",
+        "cellrank.estimators.GPCCA",
+        "cellrank.estimators.GPCCA.fit",
+        "cellrank.estimators.GPCCA.macrostates_memberships",
+        "cellrank.estimators.GPCCA.plot_macrostates",
+        "cellrank.estimators.GPCCA.predict_terminal_states",
+        "cellrank.estimators.GPCCA.compute_fate_probabilities",
+        "cellrank.estimators.GPCCA.plot_fate_probabilities",
+        "cellrank.pl.circular_projection",
+        "cellrank.models.GAM",
+        "cellrank.pl.gene_trends"
     ]
 }
diff --git a/src/configs/Lib_cheatsheet.py b/src/configs/Lib_cheatsheet.py
@@ -1,4 +1,13 @@
 CHEATSHEET = {
+    "scanpy":{
+        "LIB":"scanpy",
+        "LIB_ALIAS":"scanpy",
+        "API_HTML_PATH": "scanpy.readthedocs.io/en/latest/api/index.html",
+        "GITHUB_LINK": "https://github.com/scverse/scanpy",
+        "READTHEDOC_LINK": "https://scanpy.readthedocs.io/",
+        "TUTORIAL_HTML_PATH":"scanpy.readthedocs.io/en/latest/tutorials",
+        "TUTORIAL_GITHUB":["https://github.com/scverse/scanpy_usage", "https://github.com/scverse/scanpy-tutorials"]
+    },
     "squidpy":{
         "LIB":"squidpy",
         "LIB_ALIAS":"squidpy",
@@ -8,14 +17,23 @@
         "TUTORIAL_HTML_PATH":"squidpy.readthedocs.io/en/latest/notebooks/tutorials",
         "TUTORIAL_GITHUB":"https://github.com/scverse/squidpy_notebooks"
     },
-    "scanpy":{
-        "LIB":"scanpy",
-        "LIB_ALIAS":"scanpy",
-        "API_HTML_PATH": "scanpy.readthedocs.io/en/latest/api/index.html",
-        "GITHUB_LINK": "https://github.com/scverse/scanpy",
-        "READTHEDOC_LINK": "https://scanpy.readthedocs.io/",
-        "TUTORIAL_HTML_PATH":"scanpy.readthedocs.io/en/latest/tutorials",
-        "TUTORIAL_GITHUB":["https://github.com/scverse/scanpy_usage", "https://github.com/scverse/scanpy-tutorials"]
+    "ehrapy": {
+        "LIB": "ehrapy",
+        "LIB_ALIAS": "ehrapy",
+        "API_HTML_PATH": "ehrapy.readthedocs.io/en/latest/usage/usage.html",
+        "GITHUB_LINK": "https://github.com/theislab/ehrapy",
+        "READTHEDOC_LINK": "https://ehrapy.readthedocs.io/",
+        "TUTORIAL_HTML_PATH": "https://ehrapy.readthedocs.io/en/latest/tutorials/index.html",
+        "TUTORIAL_GITHUB": "https://github.com/theislab/ehrapy-tutorials"
+    },
+    "snapatac2": {
+        "LIB": "snapatac2",
+        "LIB_ALIAS": "snapatac2",
+        "API_HTML_PATH": "kzhang.org/SnapATAC2/api/index.html", #kzhang.org/SnapATAC2/version/2.6/api/index.html
+        "GITHUB_LINK": "https://github.com/kaizhang/SnapATAC2",
+        "READTHEDOC_LINK": "https://kzhang.org/SnapATAC2",
+        "TUTORIAL_HTML_PATH": "https://kzhang.org/SnapATAC2/tutorials/index.html",
+        "TUTORIAL_GITHUB": "https://github.com/kaizhang/SnapATAC2"
     },
     "scanpy_subset":{
         "LIB":"scanpy_subset",
@@ -188,24 +206,6 @@
         "TUTORIAL_HTML_PATH": None,
         "TUTORIAL_GITHUB": None
     },
-    "ehrapy": {
-        "LIB": "ehrapy",
-        "LIB_ALIAS": "ehrapy",
-        "API_HTML_PATH": "ehrapy.readthedocs.io/en/latest/usage/usage.html",
-        "GITHUB_LINK": "https://github.com/theislab/ehrapy",
-        "READTHEDOC_LINK": "https://ehrapy.readthedocs.io/",
-        "TUTORIAL_HTML_PATH": "https://ehrapy.readthedocs.io/en/latest/tutorials/index.html",
-        "TUTORIAL_GITHUB": "https://github.com/theislab/ehrapy-tutorials"
-    },
-    "snapatac2": {
-        "LIB": "snapatac2",
-        "LIB_ALIAS": "snapatac2",
-        "API_HTML_PATH": "kzhang.org/SnapATAC2/api/index.html",
-        "GITHUB_LINK": "https://github.com/kaizhang/SnapATAC2",
-        "READTHEDOC_LINK": "https://kzhang.org/SnapATAC2",
-        "TUTORIAL_HTML_PATH": "https://kzhang.org/SnapATAC2/tutorials/index.html",
-        "TUTORIAL_GITHUB": "https://github.com/kaizhang/SnapATAC2"
-    },
     "cellrank": {
         "LIB": "cellrank",
         "LIB_ALIAS": "cellrank",
@@ -358,5 +358,14 @@
         "READTHEDOC_LINK": "https://scanpy-tutorials.readthedocs.io/en/latest/spatial/integration-scanorama.html",
         "TUTORIAL_HTML_PATH": "https://scanpy-tutorials.readthedocs.io/en/latest/spatial/integration-scanorama.html",
         "TUTORIAL_GITHUB": "https://github.com/brianhie/scanorama"
+    },
+    "base":{
+        "LIB": "base",
+        "LIB_ALIAS": "base",
+        "API_HTML_PATH": None,
+        "GITHUB_LINK": None,
+        "READTHEDOC_LINK": None,
+        "TUTORIAL_HTML_PATH": None,
+        "TUTORIAL_GITHUB": None
     }
 }