Merge pull request #38 from abearab/master

easy installation through pip

.github/workflows/python-publish.yml

@@ -0,0 +1,63 @@
+name: Publish PyPI
+
+on:
+  release:
+    types: [published]
+
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os-version }}
+    name: ${{ matrix.os-version }} (${{ matrix.python-version }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os-version: ["ubuntu-latest"]
+        python-version: ["3.9"] # ["3.8", "3.9", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: "Set up Python ${{ matrix.python-version }}"
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: "Install flake8"
+      run: |
+        pip install flake8
+    - name: "Lint with flake8"
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: "Install miniconda"
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        mamba-version: "*"
+        python-version: ${{ matrix.python-version }}
+        channels: conda-forge,bioconda
+        environment-file: environment.yml
+    - name: "Install pytest"
+      shell: bash -l {0}
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel build pytest
+        pip install twine
+    - name: "Test with pytest"
+      shell: bash -l {0}
+      run: |
+        pytest -s
+    - name: Build package
+      shell: bash -l {0}
+      run: | 
+        python setup.py bdist_wheel --universal
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_TOKEN }}

CanDI/__version__.py

@@ -0,0 +1 @@
+version = "0.1.1"

CanDI/candi/__init__.py

@@ -1,4 +1,4 @@
-from CanDI.candi import data
+from . import data
 data = data.Data() #Global object data instantiated on import required for access by GeneQuery Objects
-from CanDI.candi.candi import (Gene, CellLine, Organelle, Cancer, CellLineCluster, GeneCluster)
+from . import (Gene, CellLine, Organelle, Cancer, CellLineCluster, GeneCluster)
 

CanDI/candi/candi.py

@@ -4,8 +4,8 @@
 import itertools as it
 import pandas as pd
 import numpy as np
-from CanDI.candi import data, grabber
-from CanDI.structures import entity
+from . import data, grabber
+from . import entity
 
 class SubsetHandler(object):
 

CanDI/candi/grabber.py

@@ -1,6 +1,6 @@
 import numpy as np
 from pathlib import Path
-from CanDI.candi import data
+from . import data
 
 class Grabber:
     """"Grabber class handles all bulk data retrival from the CanDI Classes.

CanDI/setup/install.py

@@ -1,20 +1,21 @@
 import argparse
-from manager import Manager
+from .manager import Manager
 
-if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("--source", help="Specify the download source", default="dataverse")
+    parser.add_argument("--data_dir", help="Specify the data directory", default=None)
     args = parser.parse_args()
 
     if args.source == 'dataverse':
         print("Downloading data from Dataverse")
-        m = Manager(download_source=args.source)
+        m = Manager(download_source=args.source, data_dir=args.data_dir)
         m.download_reformatted_data()
         m.write_config(m.cfig_path, m.parser)
 
     elif args.source == 'depmap':        
         print("Downloading data from DepMap")
-        m = Manager(download_source=args.source)
+        m = Manager(download_source=args.source, data_dir=args.data_dir)
         m.get_depmap_info()
         m.write_config(m.cfig_path, m.parser)
         m.download_defaults()
@@ -23,4 +24,7 @@
         m.write_config(m.cfig_path, m.parser)
 
     else:
-        raise ValueError("Invalid source. Please specify either 'dataverse' or 'depmap'")
+        raise ValueError("Invalid source. Please specify either 'dataverse' or 'depmap'")
+
+if __name__ == "__main__":
+    main()

CanDI/setup/manager.py

@@ -8,16 +8,20 @@
 from time import sleep
 from pathlib import Path
 from concurrent.futures import ThreadPoolExecutor
-from dataverse import depmap_dataverse_download
+from .dataverse import depmap_dataverse_download
 
 class Manager(object):
     """The Manager class handles interations with the datasources
     and the config file. It is used to setup of the config file upon installation.
     All data downloading is done by Manager
     """
-    def __init__(self, download_source=None):
+    def __init__(self, download_source=None, data_dir=None):
 
-        manager_path = os.path.dirname(os.path.realpath(__file__))
+        if data_dir:
+            manager_path = data_dir
+        else:
+            manager_path = os.path.dirname(os.path.realpath(__file__))
+
         cfig_path = manager_path + "/data/config.ini"
         parser = configparser.ConfigParser()
         parser.read(cfig_path.replace(".ini", ".draft.ini"))
@@ -218,6 +222,12 @@ def format_depmap_data(self, df, path):
 
 
     def download_reformatted_data(self, depmap_release=''):
+        if not os.path.exists(self.manager_path + '/data/'):
+            os.makedirs(self.manager_path + '/data/')
+
+        if not os.path.exists(self.manager_path + '/data/depmap/'):
+            os.makedirs(self.manager_path + '/data/depmap/')
+
         if self.download_source == "dataverse":
             urls, file_names = depmap_dataverse_download(
                 self.manager_path + '/data/depmap/', 

CanDI/setup/reset_config.py

@@ -1,7 +1,7 @@
 import os
 import configparser
 import json
-from manager import Manager
+from .manager import Manager
 
 
 def main():

CanDI/structures/entity.py

@@ -1,5 +1,5 @@
 import pandas as pd
-from CanDI.structures import handlers
+from . import handlers
 
 class Entity(object):
 

README.rst

@@ -8,20 +8,19 @@ CanDI - A global cancer data integrator
 Package Installation
 --------------------
 
-First, you need to clone this repository to use CanDI.
+CanDI is now available on `PyPI <https://pypi.org/project/CanDI/>`_ and can be installed with pip:
 
 .. code:: bash
 
-   git clone https://github.com/GilbertLabUCSF/CanDI.git
+   pip install CanDI
 
-We suggest to use `Conda <https://docs.conda.io/en/latest/>`__ as a
-package manager and environment management system. You can create a
-fresh conda environment with all ``CanDI``\ ’s requirements using bellow
-command:
+___
+For the latest version (development version) install from GitHub:
 
 .. code:: bash
+   
+   pip install git+https://github.com/GilbertLabUCSF/CanDI.git
 
-   conda env create -f CanDI/environment.yml -n candi
 
 Prepare Datasets
 ~~~~~~~~~~~~~~~~
@@ -59,22 +58,10 @@ Package Usage
 Import CanDI into python
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-To import ``CanDI``, your active directory in python must be same as the
-cloned folder.
-
 .. code:: python
 
    from CanDI import candi
 
-**OR**, you can add path to the `CanDI` directory if you want to use it from other directories.
-
-.. code:: python
-
-   import sys
-   sys.path.append("path-to-candi-directory")
-
-   from CanDI import candi
-
 CanDI Objects
 ~~~~~~~~~~~~~
 

setup.py

@@ -0,0 +1,31 @@
+from setuptools import setup, find_packages
+from CanDI.__version__ import version
+
+from pathlib import Path
+
+this_directory = Path(__file__).parent
+
+setup(
+    name='CanDI',
+    description='A cancer data integration package',
+    version=version,
+    packages=find_packages(),
+    python_requires='>=3.9',
+    install_requires=[
+        "pandas",
+        "configparser",
+        "requests",
+        "tqdm",
+    ],
+    url = 'https://github.com/GilbertLabUCSF/CanDI',
+    entry_points={
+        'console_scripts': [
+            'candi-install = CanDI.setup.install:main',
+        ],
+    },
+    classifiers=[
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3',
+    ],
+)