From 00f6bf48f36ef0a1db8a068d24b01fb1db9cc4c9 Mon Sep 17 00:00:00 2001
From: Genaro Camele <genarocamele@hotmail.com>
Date: Sun, 7 Jul 2024 13:34:24 -0300
Subject: [PATCH] Updated CI

---
 .github/workflows/ci.yml | 39 ++++++++++++++++++++++++++++-----------
 README.md                | 16 +++-------------
 2 files changed, 31 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6043b03..4d2e7b9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -24,24 +24,41 @@ jobs:
     runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
+        python-version: [
+          "pypy-3.10",
+          "pypy-3.9",
+          "3.8",
+          "3.9",
+          "3.10",
+          "3.11",
+          "3.12",
+          "3.13",
+          "3",
+          "3.x",
+        ]
         platform:
           - runner: ubuntu-latest
             target: x86_64
-          - runner: ubuntu-latest
-            target: x86
-          - runner: ubuntu-latest
-            target: aarch64
-          - runner: ubuntu-latest
-            target: armv7
-          - runner: ubuntu-latest
-            target: s390x
-          - runner: ubuntu-latest
-            target: ppc64le
+          # - runner: ubuntu-latest
+          #   target: x86
+          # - runner: ubuntu-latest
+          #   target: aarch64
+          # - runner: ubuntu-latest
+          #   target: armv7
+          # - runner: ubuntu-latest
+          #   target: s390x
+          # - runner: ubuntu-latest
+          #   target: ppc64le
     steps:
       - uses: actions/checkout@v4
+      # Set up Python to avoid cache and include modern versions
+      # Read more at (https://github.com/PyO3/maturin-action/discussions/218)
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+          cache: pip
+          cache-dependency-path: .github/workflows/ci.yml
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
diff --git a/README.md b/README.md
index 8ffda2a..68a290d 100644
--- a/README.md
+++ b/README.md
@@ -144,19 +144,8 @@ All kind of help is welcome! Feel free o submit an issue or a PR. There are some
 
 We provide a Docker image to execute all the commands listed below:
 
-- Build for rust: cargo build [--release]
-- Build for Python (uses Maturin):
-	1. First of all, remove the `target/wheels` folder: `rm -rf ./target/wheels`
-	1. Build wheels: `docker run --rm -v $(pwd):/io jwaresolutions/ggca-build:0.3.0 maturin build --release --skip-auditwheel --manylinux=2014`
-	1. Repair wheels to include some missing `.so` files: `docker run --rm -v $(pwd):/io jwaresolutions/ggca-build:0.3.0 ./repair-wheels.sh`
-- Only for development:
-	- To run the examples you must run with this command due to [an issue][pyo3-issue] with Pyo3: `cargo run [--release] --example <example>`
-	- In Python you can test with Maturin:
-		- Maturin develop (installs the package in your current virtualenv): `maturin develop`
-		- Maturin build (just builds the wheel for your current Python version): `maturin build --manylinux=1-unchecked`
-- To publish in PyPi:
-	1. Install twine: `pip install twine`
-	1. Upload: `twine upload ./target/wheels/wheelhouse/*`
+- Build for rust: `cargo build [--release]`
+- Build for Python (uses Maturin) and it's generated by CI [maturin-actions][maturin-actions]
 
 
 ### Tests
@@ -202,4 +191,5 @@ If you use any part of our code, or the tool itself is useful for your research,
 [colorectal-dataset]: https://cbioportal-datahub.s3.amazonaws.com/coadread_tcga_pub.tar.gz
 [multiomix]: https://www.multiomix.org
 [env-logger]: https://docs.rs/env_logger/latest/env_logger/
+[maturin-actions]: https://github.com/PyO3/maturin-action
 [criterion]: https://github.com/bheisler/criterion.rs