Merge pull request #152 from zktuong/refactor_generate_network

Speed upgrade - Refactor generate network

.github/workflows/formatting.yaml

@@ -0,0 +1,38 @@
+name: Code style checks
+
+on: [pull_request]
+
+jobs:
+  black:
+    name: Check black compliance.
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+
+      - name: Install black
+        run: python -m pip install black
+
+      - name: Run black
+        run: black --config pyproject.toml --check .
+
+  docstring:
+    name: Check docstring compliance.
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+
+      - name: Install interrogate
+        run: python -m pip install interrogate
+
+      - name: Run interrogate
+        run: interrogate .

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://github.com/psf/black
+    rev: 21.10b0
+    hooks:
+    -   id: black
+-   repo: https://github.com/kynan/nbstripout
+    rev: 0.5.0
+    hooks:
+    -   id: nbstripout

README.md

@@ -67,6 +67,9 @@ conda install seaborn scikit-learn statsmodels numba pytables
 conda install -c conda-forge python-igraph leidenalg
 pip install scanpy
 
+# with version >=0.3.0, it is reccomended to install graph-tool to enable hyperfast layout calculations
+conda install -c conda-forge graph-tool
+
 # skip if doing pre-processing via container
 conda install -c bioconda igblast blast # if this doesn't work, download them manually (see below)
 
@@ -144,6 +147,7 @@ pytables>=3.6.1 (conda-forge)
 seaborn>=0.10.1 (conda-forge)
 leidenalg>=0.8.0 (conda-forge)
 plotnine>=0.6.0 (conda-forge)
+graph-tool>=2.3.5 (conda-forge) # optional
 
 # Other executables (through conda)
 blast>=2.10.1 (bioconda)

conftest.py

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+# @Author: Kelvin
+# @Date:   2021-06-18 13:03:14
+# @Last Modified by:   Kelvin
+# @Last Modified time: 2022-06-18 15:20:37
+"""conftest"""