feat: Initial source code

BREAKING CHANGE: No longer in beta development state

Author: Rapsssito

.github/workflows/docs.yml

@@ -0,0 +1,28 @@
+name: Build docs
+
+on: workflow_dispatch
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/setup-python@v2
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
+    - uses: py-actions/py-dependency-install@v3
+      with:
+        path: "./requirements.txt"
+        update-pip: "false"
+        update-setuptools: "false"
+        update-wheel: "false"
+    - name: Build and Commit
+      uses: sphinx-notes/pages@v2
+      with:
+        documentation_path: './docs/source'
+        requirements_path: './requeriments_docs.txt'
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        branch: gh-pages

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+name: Semantic Release
+
+on: workflow_dispatch
+
+jobs:
+  release:
+    environment:
+        name: pypi
+        url: https://pypi.org/p/plink-bed-reader
+      permissions:
+        id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    runs-on: ubuntu-latest
+    concurrency: release
+
+    steps:
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 0
+
+    - name: Python Semantic Release
+      id: release
+      uses: relekang/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+    
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      # The following line is required to ensure that the package is only published to PyPI when a new version is released.
+      # NOTE: DO NOT wrap the conditional in ${{ }} as it will always evaluate to true.
+      # See https://github.com/actions/runner/issues/1173
+      if: steps.release.outputs.released == 'true'
+
+    - name: Publish package distributions to GitHub Releases
+      uses: python-semantic-release/[email protected]
+      if: steps.release.outputs.released == 'true'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -0,0 +1,40 @@
+# PLINK BED reader<!-- omit in toc -->
+**Lightweight and memory efficient reader for PLINK BED files**. It supports both SNP-major and individual-major formats. Written in pure Python. Check the [available documentation](https://computational-genomics-bsc.github.io/plink-bed-reader/) for more information.
+
+## Table of contents<!-- omit in toc -->
+- [Getting started](#getting-started)
+  - [Installation](#installation)
+- [Usage](#usage)
+- [Dependencies](#dependencies)
+
+
+## Getting started
+### Installation
+VariantExtractor is available on PyPI and can be installed using `pip`:
+```bash
+pip install plink-bed-reader
+```
+
+## Usage
+```python
+# Import the package
+from plink_bed_reader import PLINKBEDReader, BEDMode
+
+# Load the PLINK BED file (we include the mode for sanity check, but it is optional)
+bed = PLINKBEDReader('./input_test_data/test.bed', mode=BEDMode.SNP_MAJOR)
+
+# Print the number of SNPs and samples
+print('Number of SNPs:', bed.snp_count)
+print('Number of samples:', bed.sample_count)
+# Print the first SNP
+first_snp = bed[0]
+print('First SNP:', first_snp, first_snp.dtype)
+# Print the first 3 SNPs
+print('First 3 SNPs:', bed[:3])
+```
+
+## Dependencies
+
+The dependencies are covered by their own respective licenses as follows:
+
+* [Python/NumPy package](https://numpy.org/)

examples/example.py

@@ -6,9 +6,10 @@
     import os
     import sys
     sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)) + '/../src/')
+    # Import the package
     from plink_bed_reader import PLINKBEDReader, BEDMode
 
-    # Load the PLINK BED file
+    # Load the PLINK BED file (we include the mode for sanity check, but it is optional)
     bed = PLINKBEDReader('./input_test_data/test.bed', mode=BEDMode.SNP_MAJOR)
 
     # Print the number of SNPs and samples