discotoolkit 1.1.4__tar.gz → 1.2.0__tar.gz

discotoolkit-1.2.0/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+include requirements.txt

discotoolkit-1.2.0/PKG-INFO

@@ -0,0 +1,140 @@
+Metadata-Version: 2.4
+Name: discotoolkit
+Version: 1.2.0
+Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
+Home-page: https://disco.bii.a-star.edu.sg/
+Author: Li Mengwei, Rom Uddamvathanak
+Author-email: uddamvathanak_rom@immunol.a-star.edu.sg
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: numpy>=1.21.6
+Requires-Dist: scanpy>=1.9.3
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: joblib>=1.1.0
+Requires-Dist: pandarallel>=1.6.5
+Requires-Dist: requests>=2.28.1
+Requires-Dist: colorcet>=3.0.1
+Requires-Dist: leidenalg
+Requires-Dist: h5py>=3.8
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: seaborn>=0.12
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<!--
+ * @Descripttion: 
+ * @version: 
+ * @Author: Mengwei Li
+ * @Date: 2023-04-16 21:20:42
+ * @LastEditors: Mengwei Li
+ * @LastEditTime: 2023-04-16 21:22:03
+-->
+[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
+
+# DISCOtoolkit 1.2.0
+
+DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation at [discotoolkit-py.readthedocs.io](https://discotoolkit-py.readthedocs.io/en/latest/).
+
+- Filter and download DISCO data based on sample metadata and cell type information
+- Gene search: a gene's expression across cell types and tissues
+- CELLiD: cell type annotation
+- scEnrichment: gene set enrichment using DISCO DEGs
+
+> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+
+## Quickstart (Google Colab)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+Installs, checks the server, filters, downloads and plots in about ten cells, with nothing to set up locally.
+
+## Installation
+
+Python 3.9 or newer. In your current environment:
+
+```
+pip install discotoolkit
+```
+
+To try the latest development version straight from GitHub:
+
+```
+pip install "git+https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git"
+```
+
+To work on the code, or to test changes before they are released, install from a local clone. `-e` links the install to the folder, so edits take effect without reinstalling:
+
+```
+git clone https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git
+cd DISCOtoolkit_py
+pip install -e .
+```
+
+`pip install discotoolkit` and a local install give the same code when the versions match. The difference is the source: PyPI delivers a released, packaged copy, while a local install uses the files in your folder.
+
+Dependencies (installed automatically): numpy, pandas, scanpy, scipy, joblib, pandarallel, requests, colorcet, leidenalg, h5py, matplotlib, seaborn.
+
+We recommend a virtual environment, for example with miniconda:
+
+```
+conda create --name disco python=3.10
+conda activate disco
+conda install ipykernel
+python -m ipykernel install --user --name disco --display-name "disco"
+python -m pip install -U discotoolkit
+```
+
+## Choosing a server
+
+```python
+import discotoolkit as dt
+
+dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
+dt.set_server("v2")                   # DISCO v2
+dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+```
+
+or set the `DISCO_API_URL` environment variable before importing the package.
+
+## Testing
+
+Two small test files need nothing beyond `requests`, so they run anywhere, including Colab:
+
+```
+python tests/test_settings.py           # offline: server selection logic
+python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
+python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
+python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+```
+
+GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release is published.
+
+`test_server_contract.py` checks status codes and the shape of each response (the columns and file types the toolkit reads). It only samples the large reference files, it does not download them.
+
+## Basic Usage
+Example in Jupyter notebook.
+
+<em>please select disco as the kernel for running the jupyter notebook</em>
+
+### [Quickstart for DISCO v1](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
+
+### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
+
+### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
+
+## Citation
+1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
+2. [Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen, Sebastian Maurer-Stroh, Jinmiao Chen. "Rediscovering publicly available single-cell data with the DISCO platform." Nucleic Acids Research (2024): gkae1108](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1108/7899529)
+
+## Follow us on our social media!
+- [HSCRM2](https://twitter.com/HSCRM2)
+- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)

discotoolkit-1.2.0/README.md

@@ -0,0 +1,110 @@
+<!--
+ * @Descripttion: 
+ * @version: 
+ * @Author: Mengwei Li
+ * @Date: 2023-04-16 21:20:42
+ * @LastEditors: Mengwei Li
+ * @LastEditTime: 2023-04-16 21:22:03
+-->
+[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
+
+# DISCOtoolkit 1.2.0
+
+DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation at [discotoolkit-py.readthedocs.io](https://discotoolkit-py.readthedocs.io/en/latest/).
+
+- Filter and download DISCO data based on sample metadata and cell type information
+- Gene search: a gene's expression across cell types and tissues
+- CELLiD: cell type annotation
+- scEnrichment: gene set enrichment using DISCO DEGs
+
+> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+
+## Quickstart (Google Colab)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+Installs, checks the server, filters, downloads and plots in about ten cells, with nothing to set up locally.
+
+## Installation
+
+Python 3.9 or newer. In your current environment:
+
+```
+pip install discotoolkit
+```
+
+To try the latest development version straight from GitHub:
+
+```
+pip install "git+https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git"
+```
+
+To work on the code, or to test changes before they are released, install from a local clone. `-e` links the install to the folder, so edits take effect without reinstalling:
+
+```
+git clone https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git
+cd DISCOtoolkit_py
+pip install -e .
+```
+
+`pip install discotoolkit` and a local install give the same code when the versions match. The difference is the source: PyPI delivers a released, packaged copy, while a local install uses the files in your folder.
+
+Dependencies (installed automatically): numpy, pandas, scanpy, scipy, joblib, pandarallel, requests, colorcet, leidenalg, h5py, matplotlib, seaborn.
+
+We recommend a virtual environment, for example with miniconda:
+
+```
+conda create --name disco python=3.10
+conda activate disco
+conda install ipykernel
+python -m ipykernel install --user --name disco --display-name "disco"
+python -m pip install -U discotoolkit
+```
+
+## Choosing a server
+
+```python
+import discotoolkit as dt
+
+dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
+dt.set_server("v2")                   # DISCO v2
+dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+```
+
+or set the `DISCO_API_URL` environment variable before importing the package.
+
+## Testing
+
+Two small test files need nothing beyond `requests`, so they run anywhere, including Colab:
+
+```
+python tests/test_settings.py           # offline: server selection logic
+python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
+python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
+python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+```
+
+GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release is published.
+
+`test_server_contract.py` checks status codes and the shape of each response (the columns and file types the toolkit reads). It only samples the large reference files, it does not download them.
+
+## Basic Usage
+Example in Jupyter notebook.
+
+<em>please select disco as the kernel for running the jupyter notebook</em>
+
+### [Quickstart for DISCO v1](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
+
+### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
+
+### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
+
+## Citation
+1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
+2. [Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen, Sebastian Maurer-Stroh, Jinmiao Chen. "Rediscovering publicly available single-cell data with the DISCO platform." Nucleic Acids Research (2024): gkae1108](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1108/7899529)
+
+## Follow us on our social media!
+- [HSCRM2](https://twitter.com/HSCRM2)
+- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit/CELLiD.py

@@ -18,7 +18,7 @@ from pandarallel import pandarallel  # multiprocessing library
 pd.options.mode.chained_assignment = None
 
 # import variable and class from other script
-from .GlobalVariable import logging, prefix_disco_url, timeout
+from .GlobalVariable import logging, api_url, timeout
 from .DiscoClass import FilterData, Filter
 from .GetMetadata import check_in_list
 
@@ -77,7 +77,7 @@ def get_atlas(ref_data=None, ref_path=None):
             if not (os.path.exists(ref_path + "/ref_data.pkl")):
                 logging.info("Downloading reference dataset...")
                 response = requests.get(
-                    url=prefix_disco_url + "toolkit/getRef?type=pkl", timeout=timeout
+                    url=api_url("toolkit/getRef?type=pkl"), timeout=timeout
                 )
                 open(ref_path + "/ref_data.pkl", "wb").write(response.content)
             ref_data = pd.read_pickle(
@@ -89,6 +89,42 @@ def get_atlas(ref_data=None, ref_path=None):
     return list(set(all_atlas))
 
 
+def _load_geneset(ref_path: str) -> pd.DataFrame:
+    """Get the gene-set reference (columns logfc, gene, atlas, name), downloading it once.
+
+    DISCO v1 serves it as plain CSV (`toolkit/getGeneSet?format=csv`), which is read with
+    pandas.read_csv. Older servers only offer a pickle (`getGeneSetPkl`); that is used as a
+    fallback, with a warning, because unpickling data from a network is only safe if the
+    server is trusted.
+    """
+    csv_file = ref_path + "/ref_geneset.csv"
+    pkl_file = ref_path + "/ref_geneset.pkl"
+
+    if os.path.exists(csv_file):
+        return pd.read_csv(csv_file)
+    if os.path.exists(pkl_file):
+        return pd.read_pickle(pkl_file, compression={"method": "gzip", "compresslevel": 6})
+
+    logging.info("Downloading gene set reference...")
+    response = requests.get(
+        url=api_url("toolkit/getGeneSet"), params={"format": "csv"}, timeout=timeout
+    )
+    if response.status_code == 200:
+        with open(csv_file, "wb") as handle:
+            handle.write(response.content)
+        return pd.read_csv(csv_file)
+
+    logging.warning(
+        "This server has no CSV gene set (HTTP %s); falling back to the pickle download.",
+        response.status_code,
+    )
+    response = requests.get(url=api_url("getGeneSetPkl"), timeout=timeout)
+    response.raise_for_status()
+    with open(pkl_file, "wb") as handle:
+        handle.write(response.content)
+    return pd.read_pickle(pkl_file, compression={"method": "gzip", "compresslevel": 6})
+
+
 def CELLiD_cluster(
     rna,
     ref_data: pd.DataFrame = None,
@@ -144,7 +180,7 @@ def CELLiD_cluster(
             if not (os.path.exists(ref_path + "/ref_data.pkl")):
                 logging.info("Downloading reference dataset...")
                 response = requests.get(
-                    url=prefix_disco_url + "toolkit/getRef?type=pkl", timeout=timeout
+                    url=api_url("toolkit/getRef?type=pkl"), timeout=timeout
                 )
                 open(ref_path + "/ref_data.pkl", "wb").write(response.content)
             ref_data = pd.read_pickle(
@@ -157,7 +193,7 @@ def CELLiD_cluster(
             if not (os.path.exists(ref_path + "/ref_deg.pkl")):
                 logging.info("Downloading deg dataset...")
                 response = requests.get(
-                    url=prefix_disco_url + "toolkit/getRefDeg?type=pkl", timeout=timeout
+                    url=api_url("toolkit/getRefDeg?type=pkl"), timeout=timeout
                 )
                 open(ref_path + "/ref_deg.pkl", "wb").write(response.content)
             ref_deg = pd.read_pickle(
@@ -347,24 +383,7 @@ def CELLiD_enrichment(
         if not os.path.exists(ref_path):
             os.mkdir(ref_path)
 
-        # check if the file does not exist
-        if not (os.path.exists(ref_path + "/ref_geneset.pkl")):
-            # downloading the geneset data from disco database
-            response = requests.get(
-                url=prefix_disco_url + "/getGeneSetPkl", timeout=timeout
-            )
-            open(ref_path + "/ref_geneset.pkl", "wb").write(response.content)
-            reference = pd.read_pickle(
-                ref_path + "/ref_geneset.pkl",
-                compression={"method": "gzip", "compresslevel": 6},
-            )
-
-        else:
-            # read the data into pandas dataframe for subsequent analysis
-            reference = pd.read_pickle(
-                ref_path + "/ref_geneset.pkl",
-                compression={"method": "gzip", "compresslevel": 6},
-            )
+        reference = _load_geneset(ref_path)
 
     # rename the name data to include the reference atlas
     reference["name"] = reference["name"] + " in " + reference["atlas"]

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit/DownloadDiscoData.py

@@ -17,7 +17,7 @@ import hashlib
 import scanpy as sc
 
 # import variable and class from other script
-from .GlobalVariable import logging, prefix_disco_url
+from .GlobalVariable import logging, api_url
 from .DiscoClass import FilterData, Filter
 from .GetMetadata import check_in_list
 
@@ -52,11 +52,11 @@ def download_disco_data(metadata, output_dir: str = "DISCOtmp"):
         if os.path.exists(output_file):
             os.remove(output_file)
 
-        url = prefix_disco_url + "download/getRawH5/" + p + "/" + s
+        url = api_url("download/getRawH5/" + p + "/" + s)
         rna = sc.read_10x_h5(filename=output_file, backup_url=url)
 
         cell = pd.read_csv(
-            prefix_disco_url + "toolkit/" + "getCellTypeSample?sampleId=" + s,
+            api_url("toolkit/getCellTypeSample?sampleId=" + s),
             sep="\t",
             header=0,
         )

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit/GeneSearch.py

@@ -7,6 +7,8 @@ import numpy as np
 from typing import Union
 import colorcet as cc
 
+from .GlobalVariable import api_url
+
 
 def gene_search(gene : str, atlas : Union[str, list] = None, figsize : tuple = None, dpi : int = 300):
 
@@ -27,8 +29,8 @@ def gene_search(gene : str, atlas : Union[str, list] = None, figsize : tuple = N
         atlas = [atlas]
 
     # url to get the API data
-    url = "https://www.immunesinglecell.org/api/vishuo/geneExp/getRefExp?gene=%s" % (gene)
-    response = requests.get(url)
+    response = requests.get(api_url("geneExp/getRefExp"), params={"gene": gene})
+    response.raise_for_status()
     data = response.json()
 
     # Extract relevant information from JSON data

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit/GetMetadata.py

@@ -11,7 +11,7 @@ import numpy as np
 from typing import Union
 
 # import variable and class from other script
-from .GlobalVariable import logging, prefix_disco_url
+from .GlobalVariable import logging, api_url
 from .DiscoClass import FilterData, Filter
 
 
@@ -35,7 +35,7 @@ def get_json(url: str, info_msg: str, error_msg: str, prefix: bool = True):
     if not prefix:
         response = requests.get(url)
     else:
-        response = requests.get(prefix_disco_url + url)
+        response = requests.get(api_url(url))
 
     # if the loading of JSON is successful, we get the text
     if response.status_code == 200:
@@ -51,9 +51,7 @@ def get_sample_ct_info():
     Returns:
         Pandas DataFrame: return pandas dataframe to the user
     """
-    temp = pd.read_csv(
-        prefix_disco_url + "toolkit/" + "getCellTypeSummary", sep="\t", header=0
-    )
+    temp = pd.read_csv(api_url("toolkit/getCellTypeSummary"), sep="\t", header=0)
     return temp  # return Dataframe of the JSON data
 
 
@@ -101,7 +99,7 @@ def get_disco_metadata():
     """
 
     metadata = pd.read_csv(
-        "https://immunesinglecell.org/disco_v3_api/toolkit/getSampleMetadata",
+        api_url("toolkit/getSampleMetadata"),
         sep="\t",
         header=0,
     )

discotoolkit-1.2.0/discotoolkit/GlobalVariable.py

@@ -0,0 +1,81 @@
+"""
+Settings shared by the rest of the package: logging, the request timeout and --
+most importantly -- which DISCO server the toolkit talks to.
+
+By default the toolkit talks to DISCO v1 (https://disco.bii.a-star.edu.sg). To use
+another server:
+
+    import discotoolkit as dt
+    dt.set_server("v2")                          # a named preset
+    dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+
+or set the DISCO_API_URL environment variable before importing the package.
+"""
+
+import logging
+import os
+
+logging.basicConfig(level=logging.INFO)
+
+# seconds to wait for the server; the reference downloads are tens of MB
+timeout = 600
+
+# The API roots the toolkit knows by name. Both serve the same `toolkit/...` endpoints.
+SERVERS = {
+    "v1": "https://disco.bii.a-star.edu.sg/disco_v3_api/",
+    "v2": "https://immunesinglecell.org/disco_v3_api/",
+}
+DEFAULT_SERVER = "v1"
+
+
+def _normalise(server: str) -> str:
+    """Turn a preset name or a URL into an API root that ends with exactly one '/'."""
+    if not isinstance(server, str) or not server.strip():
+        raise ValueError("server must be a preset name (%s) or a URL" % ", ".join(SERVERS))
+    server = server.strip()
+    if server.lower() in SERVERS:
+        return SERVERS[server.lower()]
+    if not server.lower().startswith(("http://", "https://")):
+        raise ValueError(
+            "unknown server %r: use one of %s or a full http(s):// URL" % (server, ", ".join(SERVERS))
+        )
+    return server.rstrip("/") + "/"
+
+
+_server = _normalise(os.environ.get("DISCO_API_URL") or DEFAULT_SERVER)
+
+
+def set_server(server: str) -> str:
+    """Choose which DISCO server the toolkit uses for the rest of the session.
+
+    Args:
+        server (str): "v1", "v2", or the full URL of an API root such as
+            "https://disco.bii.a-star.edu.sg/disco_v3_api/".
+
+    Returns:
+        str: the API root now in use.
+    """
+    global _server
+    _server = _normalise(server)
+    logging.info("DISCOtoolkit is using %s", _server)
+    return _server
+
+
+def get_server() -> str:
+    """The API root the toolkit is currently using."""
+    return _server
+
+
+def api_url(path: str) -> str:
+    """Full URL for an API path, e.g. api_url("toolkit/getSampleMetadata").
+
+    Looked up on every call, so set_server() takes effect immediately everywhere.
+    """
+    return _server + path.lstrip("/")
+
+
+def __getattr__(name):
+    # `prefix_disco_url` was a plain variable in earlier releases; keep it readable.
+    if name == "prefix_disco_url":
+        return _server
+    raise AttributeError("module %r has no attribute %r" % (__name__, name))

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit/__init__.py

@@ -3,5 +3,6 @@ from .DiscoClass import *
 from .DownloadDiscoData import *
 from .CELLiD import *
 from .GeneSearch import *
+from .GlobalVariable import set_server, get_server
 
-__version__ = "1.1.4"
+__version__ = "1.2.0"

discotoolkit-1.2.0/discotoolkit.egg-info/PKG-INFO

@@ -0,0 +1,140 @@
+Metadata-Version: 2.4
+Name: discotoolkit
+Version: 1.2.0
+Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
+Home-page: https://disco.bii.a-star.edu.sg/
+Author: Li Mengwei, Rom Uddamvathanak
+Author-email: uddamvathanak_rom@immunol.a-star.edu.sg
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: pandas>=1.4.2
+Requires-Dist: numpy>=1.21.6
+Requires-Dist: scanpy>=1.9.3
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: joblib>=1.1.0
+Requires-Dist: pandarallel>=1.6.5
+Requires-Dist: requests>=2.28.1
+Requires-Dist: colorcet>=3.0.1
+Requires-Dist: leidenalg
+Requires-Dist: h5py>=3.8
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: seaborn>=0.12
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<!--
+ * @Descripttion: 
+ * @version: 
+ * @Author: Mengwei Li
+ * @Date: 2023-04-16 21:20:42
+ * @LastEditors: Mengwei Li
+ * @LastEditTime: 2023-04-16 21:22:03
+-->
+[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
+
+# DISCOtoolkit 1.2.0
+
+DISCOtoolkit is a Python package for accessing the data and tools of the [DISCO database](https://disco.bii.a-star.edu.sg/) (DISCO v1). Read the documentation at [discotoolkit-py.readthedocs.io](https://discotoolkit-py.readthedocs.io/en/latest/).
+
+- Filter and download DISCO data based on sample metadata and cell type information
+- Gene search: a gene's expression across cell types and tissues
+- CELLiD: cell type annotation
+- scEnrichment: gene set enrichment using DISCO DEGs
+
+> **DISCO v1 and v2.** The toolkit talks to **DISCO v1** by default. DISCO v2 has its own R package ([DISCOtoolkit](https://github.com/JinmiaoChenLab/DISCOtoolkit)); the Python package can still be pointed at a v2 server, see [Choosing a server](#choosing-a-server).
+
+## Quickstart (Google Colab)
+
+[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+Installs, checks the server, filters, downloads and plots in about ten cells, with nothing to set up locally.
+
+## Installation
+
+Python 3.9 or newer. In your current environment:
+
+```
+pip install discotoolkit
+```
+
+To try the latest development version straight from GitHub:
+
+```
+pip install "git+https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git"
+```
+
+To work on the code, or to test changes before they are released, install from a local clone. `-e` links the install to the folder, so edits take effect without reinstalling:
+
+```
+git clone https://github.com/JinmiaoChenLab/DISCOtoolkit_py.git
+cd DISCOtoolkit_py
+pip install -e .
+```
+
+`pip install discotoolkit` and a local install give the same code when the versions match. The difference is the source: PyPI delivers a released, packaged copy, while a local install uses the files in your folder.
+
+Dependencies (installed automatically): numpy, pandas, scanpy, scipy, joblib, pandarallel, requests, colorcet, leidenalg, h5py, matplotlib, seaborn.
+
+We recommend a virtual environment, for example with miniconda:
+
+```
+conda create --name disco python=3.10
+conda activate disco
+conda install ipykernel
+python -m ipykernel install --user --name disco --display-name "disco"
+python -m pip install -U discotoolkit
+```
+
+## Choosing a server
+
+```python
+import discotoolkit as dt
+
+dt.get_server()                       # 'https://disco.bii.a-star.edu.sg/disco_v3_api/'  (DISCO v1, the default)
+dt.set_server("v2")                   # DISCO v2
+dt.set_server("https://my.server/disco_v3_api/")   # any server with the same API
+```
+
+or set the `DISCO_API_URL` environment variable before importing the package.
+
+## Testing
+
+Two small test files need nothing beyond `requests`, so they run anywhere, including Colab:
+
+```
+python tests/test_settings.py           # offline: server selection logic
+python tests/test_version.py            # offline: setup.py and __init__.py agree on the version
+python tests/test_server_contract.py    # online: does the server answer everything the toolkit needs?
+python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # check another server
+```
+
+GitHub Actions runs these, and installs the package on Python 3.9-3.12, on every push. Maintainers: see [RELEASING.md](RELEASING.md) for how a release is published.
+
+`test_server_contract.py` checks status codes and the shape of each response (the columns and file types the toolkit reads). It only samples the large reference files, it does not download them.
+
+## Basic Usage
+Example in Jupyter notebook.
+
+<em>please select disco as the kernel for running the jupyter notebook</em>
+
+### [Quickstart for DISCO v1](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/quickstart_disco_v1.ipynb)
+
+### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
+
+### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
+
+### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
+
+## Citation
+1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
+2. [Mengwei Li, Kok Siong Ang, Brian Teo, Uddamvathanak Rom, Minh N Nguyen, Sebastian Maurer-Stroh, Jinmiao Chen. "Rediscovering publicly available single-cell data with the DISCO platform." Nucleic Acids Research (2024): gkae1108](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1108/7899529)
+
+## Follow us on our social media!
+- [HSCRM2](https://twitter.com/HSCRM2)
+- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit.egg-info/SOURCES.txt

@@ -1,5 +1,7 @@
 MANIFEST.in
 README.md
+pyproject.toml
+requirements.txt
 setup.py
 discotoolkit/CELLiD.py
 discotoolkit/CellMapper.py
@@ -14,4 +16,7 @@ discotoolkit.egg-info/PKG-INFO
 discotoolkit.egg-info/SOURCES.txt
 discotoolkit.egg-info/dependency_links.txt
 discotoolkit.egg-info/requires.txt
-discotoolkit.egg-info/top_level.txt
+discotoolkit.egg-info/top_level.txt
+tests/test_server_contract.py
+tests/test_settings.py
+tests/test_version.py

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/discotoolkit.egg-info/requires.txt

@@ -6,3 +6,7 @@ joblib>=1.1.0
 pandarallel>=1.6.5
 requests>=2.28.1
 colorcet>=3.0.1
+leidenalg
+h5py>=3.8
+matplotlib>=3.5
+seaborn>=0.12

discotoolkit-1.2.0/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"

discotoolkit-1.2.0/requirements.txt

@@ -0,0 +1,12 @@
+pandas>=1.4.2
+numpy>=1.21.6
+scanpy>=1.9.3
+scipy>=1.10.1
+joblib>=1.1.0
+pandarallel>=1.6.5
+requests>=2.28.1
+colorcet>=3.0.1
+leidenalg
+h5py>=3.8
+matplotlib>=3.5
+seaborn>=0.12

{discotoolkit-1.1.4 → discotoolkit-1.2.0}/setup.py

@@ -6,16 +6,15 @@ with open("requirements.txt", "r") as f:
 
 setup(
     name='discotoolkit',
-    version="1.1.4",
-    url='http://www.immunesinglecell.org/',
+    version="1.2.0",
+    url='https://disco.bii.a-star.edu.sg/',
     author='Li Mengwei, Rom Uddamvathanak',
     author_email='uddamvathanak_rom@immunol.a-star.edu.sg',
     description='DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.',
     packages=find_packages(include=["discotoolkit", "discotoolkit.*"]),
     install_requires=requirements,
-    python_requires = '>=3.8.16',
+    python_requires = '>=3.9',
     include_package_data=True,
-    long_description="DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database. \
-        It provides the following functions\nFilter and download DISCO data based on sample metadata and cell type information\nCELLiD: \
-            cell type annotation\nscEnrichment: geneset enrichment using DISCO DEGs",
+    long_description=open("README.md", encoding="utf-8").read(),
+    long_description_content_type="text/markdown",
 )

discotoolkit-1.2.0/tests/test_server_contract.py

@@ -0,0 +1,160 @@
+"""
+Does a DISCO server answer everything discotoolkit needs?
+
+Needs only `requests`, so it runs anywhere -- including a fresh Colab notebook:
+
+    !pip install requests
+    !python tests/test_server_contract.py                                # DISCO v1 (default)
+    !python tests/test_server_contract.py https://immunesinglecell.org/disco_v3_api/   # another server
+
+or with pytest:  DISCO_API_URL=<api root> pytest tests/test_server_contract.py
+
+It checks status codes and the *shape* of each response (the columns and file types the
+toolkit reads), not the science. Large reference files are only sampled (first bytes), never
+downloaded in full.
+"""
+import os
+import sys
+
+import requests
+
+DEFAULT = "https://disco.bii.a-star.edu.sg/disco_v3_api/"
+BASE = (sys.argv[1] if len(sys.argv) > 1 and sys.argv[1].startswith("http") else os.environ.get("DISCO_API_URL", DEFAULT)).rstrip("/") + "/"
+TIMEOUT = 120
+
+
+def url(path):
+    return BASE + path.lstrip("/")
+
+
+def first_lines(path, n=3, **params):
+    """First n text lines of a (possibly huge) response, without downloading the rest."""
+    with requests.get(url(path), params=params, stream=True, timeout=TIMEOUT) as r:
+        assert r.status_code == 200, "HTTP %s for %s" % (r.status_code, path)
+        # Downloads are served as application/octet-stream, which has no charset, so without
+        # this requests would hand back bytes instead of text.
+        r.encoding = "utf-8"
+        lines = []
+        for line in r.iter_lines(decode_unicode=True):
+            lines.append(line)
+            if len(lines) >= n:
+                break
+        return lines
+
+
+def first_bytes(path, n=8, **params):
+    with requests.get(url(path), params=params, stream=True, timeout=TIMEOUT) as r:
+        assert r.status_code == 200, "HTTP %s for %s" % (r.status_code, path)
+        size = r.headers.get("Content-Length")
+        return next(r.iter_content(chunk_size=n)), (int(size) if size else None)
+
+
+def columns(line):
+    return line.split("\t")
+
+
+# ---- metadata the Filter / FilterData classes work on ------------------------------------
+
+def test_sample_metadata_has_the_filter_columns():
+    header, row = first_lines("toolkit/getSampleMetadata", 2)
+    need = {"sample_id", "project_id", "sample_type", "tissue", "disease", "platform", "cell_number"}
+    missing = need - set(columns(header))
+    assert not missing, "getSampleMetadata lacks columns: %s" % sorted(missing)
+    assert len(columns(row)) == len(columns(header)), "rows are not tab-aligned with the header"
+
+
+def test_cell_type_summary_columns():
+    header, row = first_lines("toolkit/getCellTypeSummary", 2)
+    assert columns(header) == ["sample_id", "cell_type", "cell_type_score", "cell_number"], columns(header)
+    float(columns(row)[2]); int(columns(row)[3])
+
+
+def test_cell_ontology_is_a_list_of_cell_name_and_parent():
+    r = requests.get(url("toolkit/getCellOntology"), timeout=TIMEOUT)
+    assert r.status_code == 200
+    data = r.json()
+    assert isinstance(data, list) and len(data) > 100
+    assert {"cell_name", "parent"} <= set(data[0]), data[0]
+
+
+# ---- per-sample download (download_disco_data) ---------------------------------------------
+
+def _a_sample():
+    header, row = first_lines("toolkit/getSampleMetadata", 2)
+    cols = columns(header)
+    values = columns(row)
+    return values[cols.index("project_id")], values[cols.index("sample_id")]
+
+
+def test_cell_type_labels_for_one_sample():
+    project, sample = _a_sample()
+    header, row = first_lines("toolkit/getCellTypeSample", 2, sampleId=sample)
+    cols = columns(header)
+    # the toolkit reads columns 0, 2 and 5 by position, so their order matters
+    assert cols[0] == "cell_id" and cols[2] == "cell_type" and cols[5] == "cell_type_score", cols
+
+
+def test_raw_10x_h5_is_downloadable_and_is_hdf5():
+    project, sample = _a_sample()
+    head, size = first_bytes("download/getRawH5/%s/%s" % (project, sample))
+    assert head.startswith(b"\x89HDF"), "not an HDF5 file: %r" % head
+    assert size is None or size > 1000
+
+
+# ---- CELLiD / scEnrichment reference data ---------------------------------------------------
+
+def test_cellid_reference_is_a_gzip_pickle():
+    head, size = first_bytes("toolkit/getRef", type="pkl")
+    assert head[:2] == b"\x1f\x8b", "getRef is not gzip data: %r" % head
+    assert size is None or size > 1_000_000
+
+
+def test_cellid_deg_reference_is_a_gzip_pickle():
+    head, size = first_bytes("toolkit/getRefDeg", type="pkl")
+    assert head[:2] == b"\x1f\x8b", "getRefDeg is not gzip data: %r" % head
+
+
+def test_gene_set_reference_is_available_as_plain_csv():
+    header, row = first_lines("toolkit/getGeneSet", 2, format="csv")
+    cols = [c.strip('"') for c in header.split(",")]
+    assert cols == ["logfc", "gene", "atlas", "name"], cols
+
+
+# ---- gene_search ------------------------------------------------------------------------------
+
+def test_gene_reference_expression_rows_have_the_shape_gene_search_reads():
+    r = requests.get(url("geneExp/getRefExp"), params={"gene": "CD4"}, timeout=TIMEOUT)
+    assert r.status_code == 200
+    rows = r.json()
+    assert rows, "no reference expression for CD4"
+    # entry[0] ';'-separated values, entry[1] cell type, entry[3] atlas / tissue
+    assert isinstance(rows[0][0], str) and ";" in rows[0][0]
+    assert isinstance(rows[0][1], str) and isinstance(rows[0][3], str)
+
+
+# ---- housekeeping ---------------------------------------------------------------------------------
+
+def test_server_reports_a_toolkit_version_and_api_url():
+    v = requests.get(url("getToolkitVersion"), timeout=TIMEOUT).json()
+    assert v.get("version"), v
+    u = requests.get(url("getToolkitUrl"), timeout=TIMEOUT).json()
+    assert u.get("url", "").startswith("http"), u
+
+
+def _run_all():
+    tests = [(n, f) for n, f in sorted(globals().items()) if n.startswith("test_") and callable(f)]
+    print("DISCO toolkit contract test against %s\n" % BASE)
+    failed = 0
+    for name, fn in tests:
+        try:
+            fn()
+            print("  PASS  %s" % name)
+        except Exception as error:   # report every failure, do not stop at the first
+            failed += 1
+            print("  FAIL  %s\n          %s: %s" % (name, type(error).__name__, error))
+    print("\n%d/%d passed" % (len(tests) - failed, len(tests)))
+    return 1 if failed else 0
+
+
+if __name__ == "__main__":
+    sys.exit(_run_all())

discotoolkit-1.2.0/tests/test_settings.py

@@ -0,0 +1,90 @@
+"""Offline tests for choosing a DISCO server. No network, and no pandas/scanpy needed:
+GlobalVariable is loaded straight from its file, so this runs on any Python >= 3.9.
+
+    python tests/test_settings.py        or        pytest tests/test_settings.py
+"""
+import importlib.util
+import os
+import sys
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+PATH = os.path.join(HERE, "..", "discotoolkit", "GlobalVariable.py")
+
+
+def load(env=None):
+    """A fresh copy of GlobalVariable, as if the package had just been imported."""
+    saved = os.environ.get("DISCO_API_URL")
+    if env is None:
+        os.environ.pop("DISCO_API_URL", None)
+    else:
+        os.environ["DISCO_API_URL"] = env
+    try:
+        spec = importlib.util.spec_from_file_location("GlobalVariable_under_test", PATH)
+        module = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(module)
+        return module
+    finally:
+        if saved is None:
+            os.environ.pop("DISCO_API_URL", None)
+        else:
+            os.environ["DISCO_API_URL"] = saved
+
+
+def test_default_server_is_disco_v1():
+    g = load()
+    assert g.get_server() == "https://disco.bii.a-star.edu.sg/disco_v3_api/"
+
+
+def test_api_url_joins_paths_with_exactly_one_slash():
+    g = load()
+    assert g.api_url("toolkit/getSampleMetadata") == g.get_server() + "toolkit/getSampleMetadata"
+    assert g.api_url("/toolkit/getSampleMetadata") == g.get_server() + "toolkit/getSampleMetadata"
+
+
+def test_named_presets_and_urls():
+    g = load()
+    assert g.set_server("v2") == "https://immunesinglecell.org/disco_v3_api/"
+    assert g.api_url("x") == "https://immunesinglecell.org/disco_v3_api/x"      # takes effect at once
+    assert g.set_server("V1") == g.SERVERS["v1"]                                 # preset names are case-insensitive
+    assert g.set_server("https://example.org/api") == "https://example.org/api/"  # trailing slash added
+    assert g.set_server("http://localhost:8889/disco_v3_api///") == "http://localhost:8889/disco_v3_api/"
+
+
+def test_bad_servers_are_rejected_without_changing_the_current_one():
+    g = load()
+    before = g.get_server()
+    for bad in ["", "   ", "v3", "ftp://x", "disco.bii.a-star.edu.sg", None, 5]:
+        try:
+            g.set_server(bad)
+        except ValueError:
+            pass
+        else:
+            raise AssertionError("accepted %r" % (bad,))
+    assert g.get_server() == before
+
+
+def test_environment_variable_sets_the_starting_server():
+    assert load("v2").get_server() == "https://immunesinglecell.org/disco_v3_api/"
+    assert load("https://example.org/disco_v3_api").get_server() == "https://example.org/disco_v3_api/"
+
+
+def test_old_prefix_variable_still_readable():
+    g = load()
+    g.set_server("v2")
+    assert g.prefix_disco_url == "https://immunesinglecell.org/disco_v3_api/"
+
+
+def _run_all():
+    tests = [(n, f) for n, f in sorted(globals().items()) if n.startswith("test_") and callable(f)]
+    failed = 0
+    for name, fn in tests:
+        try:
+            fn(); print("  PASS  %s" % name)
+        except Exception as error:
+            failed += 1; print("  FAIL  %s\n          %s: %s" % (name, type(error).__name__, error))
+    print("\n%d/%d passed" % (len(tests) - failed, len(tests)))
+    return 1 if failed else 0
+
+
+if __name__ == "__main__":
+    sys.exit(_run_all())

discotoolkit-1.2.0/tests/test_version.py

@@ -0,0 +1,41 @@
+"""The version must be the same in setup.py and discotoolkit/__init__.py (and in the release tag).
+
+Pure text checks, so they need no dependencies:
+
+    python tests/test_version.py            # setup.py == __init__.py
+    python tests/test_version.py v1.2.0     # ... and equals the tag
+"""
+import os
+import re
+import sys
+
+ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
+
+
+def find(path, pattern):
+    with open(os.path.join(ROOT, path)) as handle:
+        match = re.search(pattern, handle.read())
+    assert match, "no version found in %s" % path
+    return match.group(1)
+
+
+def test_setup_and_init_agree():
+    setup_version = find("setup.py", r'version\s*=\s*"([^"]+)"')
+    init_version = find("discotoolkit/__init__.py", r'__version__\s*=\s*"([^"]+)"')
+    assert setup_version == init_version, "setup.py says %s, __init__.py says %s" % (setup_version, init_version)
+
+
+def main():
+    test_setup_and_init_agree()
+    version = find("setup.py", r'version\s*=\s*"([^"]+)"')
+    if len(sys.argv) > 1:
+        tag = sys.argv[1]
+        assert tag == "v" + version, "tag %s does not match package version %s (expected v%s)" % (tag, version, version)
+    print("version %s OK" % version)
+
+
+if __name__ == "__main__":
+    try:
+        main()
+    except AssertionError as error:
+        sys.exit("FAIL: %s" % error)

discotoolkit-1.1.4/MANIFEST.in

@@ -1 +0,0 @@
-include README.md

discotoolkit-1.1.4/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: discotoolkit
-Version: 1.1.4
-Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
-Home-page: http://www.immunesinglecell.org/
-Author: Li Mengwei, Rom Uddamvathanak
-Author-email: uddamvathanak_rom@immunol.a-star.edu.sg
-Requires-Python: >=3.8.16
-
-DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.         It provides the following functions
-Filter and download DISCO data based on sample metadata and cell type information
-CELLiD:             cell type annotation
-scEnrichment: geneset enrichment using DISCO DEGs

discotoolkit-1.1.4/README.md

@@ -1,72 +0,0 @@
-<!--
- * @Descripttion: 
- * @version: 
- * @Author: Mengwei Li
- * @Date: 2023-04-16 21:20:42
- * @LastEditors: Mengwei Li
- * @LastEditTime: 2023-04-16 21:22:03
--->
-[![Documentation Status](https://readthedocs.org/projects/discotoolkit-py/badge/?version=latest)](https://discotoolkit-py.readthedocs.io/en/latest/?badge=latest) [![Downloads](https://static.pepy.tech/personalized-badge/discotoolkit?period=total&units=international_system&left_color=black&right_color=orange&left_text=Downloads)](https://pepy.tech/project/discotoolkit) [![PyPI version](https://img.shields.io/pypi/v/discotoolkit)](https://pypi.org/project/discotoolkit)
-
-# DISCOtoolkit 1.1.4
-
-DISCOtoolkit is an python package that allows users to access data and use the tools provided by the [DISCO database](https://www.immunesinglecell.org/). Read the documentation [DISCOtoolkit](https://discotoolkit-py.readthedocs.io/en/latest/). It provides the following functions:
-
-- Filter and download DISCO data based on sample metadata and cell type information
-- CELLiD: cell type annotation
-- scEnrichment: geneset enrichment using DISCO DEGs
-
-Dependency Requirements:
-
-- Numpy >= 1.21.6
-- Pandas >= 1.4.2
-- Scanpy >= 1.9.3
-- Scipy >= 1.8.0
-- joblib >= 1.1.0
-- pandarallel >= 1.6.5
-
-## Minimal installation:
-
-The DISCOtoolkit can be easily installed in the current Python environment using `pip`:
-
-```
-pip install discotoolkit
-```
-
-## Installation guide:
-
-we recommend to install miniconda first and install discotoolkit in virtual env
-
-```
-conda create --name disco python=3.8
-```
-```
-conda activate disco
-```
-```
-conda install ipykernel
-```
-```
-python -m ipykernel install --user --name disco --display-name "disco"
-```
-``` 
-python -m pip install discotoolkit # adding -U for installing the latest version
-```
-
-## Basic Usage
-Example in Jupyter notebook.
-
-<em>please select disco as the kernel for running the jupyter notebook</em>
-
-### [Filter and download DISCO data](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/download_data.ipynb)
-
-### [Cell Type Annotation using CELLiD](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/CELLiD_celltype_annotation.ipynb)
-
-### [scEnrichment](https://github.com/JinmiaoChenLab/DISCOtoolkit_py/blob/main/docs/scEnrichment.ipynb)
-
-## Citation
-1. [Li, Mengwei, et al. "DISCO: a database of Deeply Integrated human Single-Cell Omics data." Nucleic acids research 50.D1 (2022): D596-D602.](https://academic.oup.com/nar/article/50/D1/D596/6430491)
-
-## Follow us on our social media!
-- [HSCRM2](https://twitter.com/HSCRM2)
-- [JinmiaoChenLab Github repo](https://github.com/JinmiaoChenLab)

discotoolkit-1.1.4/discotoolkit/GlobalVariable.py

@@ -1,33 +0,0 @@
-'''
-Descripttion: 
-version: 
-Author: Mengwei Li
-Date: 2023-07-06 16:59:59
-LastEditors: Mengwei Li
-LastEditTime: 2024-10-23 15:52:29
-'''
-"""
-Global variable file to import for the subsequent script.
-
-Main purpose is for the logging to be imported to other script and getting the url
-"""
-
-import requests
-import json
-import logging
-# import random
-
-# setting the logging level
-# logger = logging.StreamHandler()
-# logger.setLevel(0)
-logging.basicConfig(level = logging.INFO)
-
-timeout = 600
-
-# Define package-level variable
-# response = requests.get("http://www.immunesinglecell.org/api/vishuo/getToolkitUrl")
-
-# if response.status_code == 200:
-#     prefix_disco_url = json.loads(response.text)["url"]
-# else:
-prefix_disco_url = "https://immunesinglecell.org/disco_v3_api/"

discotoolkit-1.1.4/discotoolkit.egg-info/PKG-INFO

@@ -1,13 +0,0 @@
-Metadata-Version: 2.1
-Name: discotoolkit
-Version: 1.1.4
-Summary: DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.
-Home-page: http://www.immunesinglecell.org/
-Author: Li Mengwei, Rom Uddamvathanak
-Author-email: uddamvathanak_rom@immunol.a-star.edu.sg
-Requires-Python: >=3.8.16
-
-DISCOtoolkit is an python package that allows users to access data and use the tools provided by the DISCO database.         It provides the following functions
-Filter and download DISCO data based on sample metadata and cell type information
-CELLiD:             cell type annotation
-scEnrichment: geneset enrichment using DISCO DEGs