DiExpress 0.0.2__tar.gz

diexpress-0.0.2/DiExpress.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: DiExpress
+Version: 0.0.2
+Summary: A sample python package to start sharing your code with the world
+Home-page: https://github.com/HySonLab/DiExpress
+Author: Phuc Pham
+Author-email: phuc.phamhuythienai@gmail.com
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: trafilatura
+Dynamic: license-file
+
+# Differential Gene Expression (DGE) 

diexpress-0.0.2/DiExpress.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.cfg
+DiExpress.egg-info/PKG-INFO
+DiExpress.egg-info/SOURCES.txt
+DiExpress.egg-info/dependency_links.txt
+DiExpress.egg-info/requires.txt
+DiExpress.egg-info/top_level.txt
+code/__init__.py
+code/datetime_intel.py
+code/gadget.py

diexpress-0.0.2/DiExpress.egg-info/dependency_links.txt

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+

diexpress-0.0.2/DiExpress.egg-info/requires.txt

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+trafilatura

diexpress-0.0.2/DiExpress.egg-info/top_level.txt

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+code

diexpress-0.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2023 mrthinh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

diexpress-0.0.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: DiExpress
+Version: 0.0.2
+Summary: A sample python package to start sharing your code with the world
+Home-page: https://github.com/HySonLab/DiExpress
+Author: Phuc Pham
+Author-email: phuc.phamhuythienai@gmail.com
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: trafilatura
+Dynamic: license-file
+
+# Differential Gene Expression (DGE) 

diexpress-0.0.2/README.md

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+# Differential Gene Expression (DGE) 

diexpress-0.0.2/code/__init__.py

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+# Copyright 2022 Phuc Pham @ GitHub
+# See LICENSE for details.
+
+__author__ = "Phuc Pham @phuc-pham in GitHub"
+__version__ = "0.0.1"
+
+from .gadget import *
+from .datetime_intel import *

diexpress-0.0.2/code/datetime_intel.py

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+# Copyright 2022 Thinh Vu @ GitHub
+
+from datetime import datetime, date
+from datetime import timedelta
+import pandas as pd
+
+def date_from_today(days_delta, format='%Y-%m-%d', backward = True):
+    """
+    Return a DateTime value using today's DateTime as the base.
+    Args:
+        days_delta (:obj:`int`, required): How many days to add or subtract from today's
+        format (:obj:`str`, required): Datetime format of the output. Ex: "%Y-%m-%d". Concatnate the output string with 'T00:00:00Z' or 'T23:59:59Z' if you need.
+        format (:obj:`boolean`, optional): True to get dates in the past, False to get the future ones
+    """
+    today_val = datetime.now()
+    if backward == True:
+        target = (today_val - timedelta(days_delta)).strftime(format)
+    elif backward == False:
+        target = (today_val + timedelta(days_delta)).strftime(format)
+    else:
+        pass
+    return target
+
+
+def date_start_end(periods, freq, format='%Y-%m-%d'):
+    """
+    Return a DateTime value using today's DateTime as the base.
+    Args:
+        format (:obj:`str`, required): Datetime format of the output. Ex: "%Y-%m-%d"
+        periods (:obj:`int`, required): How many periods from today
+        freq (:obj:`str`, required): datetime frequency code. Ex: 'MS' for Month Start and 'M' for Month End. See more at: 
+    """
+    today = datetime.now().strftime('%Y-%m-%d')
+    target = pd.date_range(end=today, periods=periods, freq=freq)[0]\
+                .strftime(format)
+    return target
+
+
+# generate week value
+def weeknum_intel(datetime_now):
+    """ Generate weeknum for the report, consider the lag time of ICT and PST timezone
+    """
+    if datetime_now.strftime('%a') == 'Mon':
+        this_week = int(datetime_now.strftime('%U'))-1
+        last_week = this_week - 1
+    else:
+        this_week = int(datetime_now.strftime('%U'))
+        last_week = this_week - 1
+    return this_week, last_week
+
+
+def month_intel(datetime_now, end_date):
+  "Input value should be assigned with datetime.now() value"
+  if datetime_now.day == 1 and datetime_now.month < 2: # month = 1
+      this_month = 'Dec'
+      last_month = 'Nov'
+      return this_month, last_month
+  elif datetime_now.day > 1 and datetime_now.month < 2 : # month = 1
+      this_month = 'Jan'
+      last_month = 'Dec'
+      return this_month, last_month
+  if datetime_now.day == 1 and datetime_now.month == 2:
+      this_month = 'Jan'
+      last_month = 'Dec'
+      return this_month, last_month
+  elif datetime_now.day == 1 and datetime_now.month > 2:
+      this_month = datetime(datetime_now.year, int(datetime.strptime(end_date, '%Y-%m-%d').strftime('%m')), 1).strftime('%b')
+      last_month = datetime(datetime_now.year, int(datetime.strptime(end_date, '%Y-%m-%d').strftime('%m'))-1, 1).strftime('%b')
+      return this_month, last_month
+  else:
+      this_month = datetime_now.strftime('%b')
+      last_month = datetime(datetime_now.year, int(datetime.strptime(end_date, '%Y-%m-%d').strftime('%m'))-1, 1).strftime('%b')
+      return this_month, last_month
+
+def quarter_intel(datetime_now):
+  """ Return this quarter, last quarter base on the datetime value of today"""
+  if datetime_now.day == 1 and datetime_now.month in [1, 2, 3, 4]:
+      this_quarter = 'Q1'
+      last_quarter = 'Q4'
+      return this_quarter, last_quarter
+  elif datetime_now.day > 1 and datetime_now.month in [1, 2, 3]:
+      this_quarter = 'Q1'
+      last_quarter = 'Q4'
+      return this_quarter, last_quarter
+  elif datetime_now.day ==  1 and datetime_now.month in [7, 10]:
+      this_quarter = f'Q{(datetime_now.month-1)//3}'
+      last_quarter = f'Q{(datetime_now.month-1)//3-1}'
+      return this_quarter, last_quarter
+  else:
+      this_quarter = f'Q{(datetime_now.month-1)//3+1}'
+      last_quarter = f'Q{(datetime_now.month-1)//3}'
+      return this_quarter, last_quarter
+
+def last_quarter_date (current_quarter):
+    """Return the last date of a specific quarter"""
+    if current_quarter == 1:
+        last_qdate = '03-31'
+    elif current_quarter == 2:
+        last_qdate = '06-30'
+    elif current_quarter == 3:
+        last_qdate = '09-30'
+    elif current_quarter == 4:
+        last_qdate = '12-31'
+    return last_qdate
+
+def weeknum_gen():
+    if today_val.strftime('%a') == 'Mon':
+        this_week = int(today_val.strftime('%U'))-1
+        last_week = this_week - 1
+    else:
+        this_week = int(today_val.strftime('%U'))
+        last_week = this_week - 1
+    return this_week, last_week

diexpress-0.0.2/code/gadget.py

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+import shutil
+import os
+import subprocess
+import requests
+from trafilatura import fetch_url, extract
+import yaml
+import gc
+import torch
+
+# Working with file systems
+def lmt_detect():
+    """Detect the running OS and return file path delimiter"""
+    if os.name == 'nt':
+        lmt = '\\'
+    else:
+        lmt = '/'
+    return lmt
+
+ROOT_DIR = os.path.abspath(os.curdir)
+LMT = lmt_detect()
+
+def file_ls(directory=ROOT_DIR):
+    """List all file in the root directory"""
+    data = []
+    for entry in os.listdir(directory):
+        if os.path.isfile(os.path.join(directory, entry)):
+            data.append(entry)
+    return data
+
+def subdir_ls(basepath=ROOT_DIR):
+    """List all subdirectories in the root folder"""
+    data = []
+    for entry in os.listdir(basepath):
+        if os.path.isdir(os.path.join(basepath, entry)):
+            data.append(entry)
+    return data
+
+def newest_file(path=ROOT_DIR):
+    files = os.listdir(path)
+    paths = [os.path.join(path, basename) for basename in files]
+    return max(paths, key=os.path.getctime)
+
+# Credentials reading
+def yaml_cred(item_name, cred_path):
+    """Read YAML config file"""
+    with open(cred_path) as file: 
+        documents = yaml.full_load(file)
+        for item, doc in documents.items():
+            if item == item_name:
+                return doc
+
+# run cmd commands
+def env_setup(command_ls):
+    """Run the cmd command. Use the pipe `|` to separate each command"""
+    os.system(command_ls)
+
+def runcmd(cmd, verbose = False, *args, **kwargs):
+    """Run cmd commands"""
+    process = subprocess.Popen(
+        cmd,
+        stdout = subprocess.PIPE,
+        stderr = subprocess.PIPE,
+        text = True,
+        shell = True
+    )
+    std_out, std_err = process.communicate()
+    if verbose:
+        print(std_out.strip(), std_err)
+    pass
+
+# Data loading
+def read_txt(path_to_file):
+    """Read a plain text file"""
+    with open(path_to_file) as f:
+        content = f.read()
+    return content
+
+# Memory cleaning
+def memory_cleaner():
+    """Free up memory from large model data"""
+
+    gc.collect()
+    torch.cuda.empty_cache()
+
+
+# API Request
+def api_request(url, payload={}, method='GET'):
+    """Request any API endpoints with a default User-Agent"""
+    headers = {
+        'accept-language': 'en-US,en;q=0.9',
+        'sec-ch-ua': '"Google Chrome";v="107", "Chromium";v="107", "Not=A?Brand";v="24"',
+        'sec-ch-ua-platform': '"macOS"',
+        'user-agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/107.0.0.0 Safari/537.36'
+        }
+    response = requests.request(f"{method}", url, headers=headers, data=payload)
+    return response.json()
+
+# Get Google font
+def get_google_font(font_family):
+    """Download & extract a Google font to local folder"""
+    lmt = lmt_detect()
+    font_url = 'https://fonts.google.com/download?family={}'.format(font_family)
+    response = requests.get(font_url)
+    file_name = ROOT_DIR + lmt + '{}.zip'.format(font_family)
+    with open(file_name, 'wb') as f:
+        f.write(response.content)
+    shutil.unpack_archive(file_name, lmt.join([ROOT_DIR, 'font', font_family]))
+
+# Convert Web to text
+def web_to_text(url):
+    downloaded = fetch_url(url)
+    result = extract(downloaded)
+    return result

diexpress-0.0.2/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "DiExpress"
+description = "A sample python package to start sharing your code with the world"
+version = "0.0.2"
+readme = "README.md"
+requires-python = ">=3.7"
+dependencies = [
+                "trafilatura"
+                ]

diexpress-0.0.2/setup.cfg

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+[metadata]
+name = DiExpress
+version = 0.0.2
+author = Phuc Pham
+author_email = phuc.phamhuythienai@gmail.com
+description = A sample python package to start sharing your code with the world
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/HySonLab/DiExpress
+classifiers = 
+	Programming Language :: Python :: 3
+	License :: OSI Approved :: MIT License
+	Operating System :: OS Independent
+
+[options]
+package_dir = 
+packages = find:
+python_requires = >=3.7
+
+[egg_info]
+tag_build = 
+tag_date = 0
+