From 26fa6ccdadf356bb9b4fab139140f85d68252a9d Mon Sep 17 00:00:00 2001
From: Thomas Cokelaer <cokelaer@gmail.com>
Date: Tue, 7 Apr 2026 10:14:30 +0200
Subject: [PATCH] Fix CI

---
 .github/workflows/main.yml | 13 +++++++++++--
 .github/workflows/pypi.yml | 11 ++++++-----
 environment.yml            |  6 +++---
 pyproject.toml             |  2 ++
 4 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cf1b432..490b376 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -9,7 +9,7 @@ on:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 1 * *'
+    - cron: '0 0 2 * *'
 
 jobs:
   build-linux:
@@ -17,11 +17,16 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.9, '3.10', '3.11']
+        python: ['3.10', '3.11', '3.12']
       fail-fast: false
 
     steps:
 
+    - name: install graphviz
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -y graphviz
+
     - name: checkout git repo
       uses: actions/checkout@v4
 
@@ -31,6 +36,8 @@ jobs:
           environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
     - name: install package itself
       shell: bash -l {0}
@@ -48,8 +55,10 @@ jobs:
         pytest -v --cov-report term-missing --cov=sequana_pipelines.demultiplex
 
     - name: coveralls
+      continue-on-error: true
       shell: bash -l {0}
       run: |
+        echo $COVERALLS_REPO_TOKEN
         coveralls --service=github
       env:
           GITHUB_TOKEN: ${{ github.token }}
diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
index 687b760..7f190b9 100644
--- a/.github/workflows/pypi.yml
+++ b/.github/workflows/pypi.yml
@@ -8,11 +8,13 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.11
 
@@ -26,14 +28,13 @@ jobs:
           poetry build
  
     - name: Publish distribution to Test PyPI
+      if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/environment.yml b/environment.yml
index 86896f5..6e5740a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,6 @@
 name: demultiplex
 channels:
-  - conda-forge
-  - defaults
+- conda-forge
+- defaults
 dependencies:
-  - pip
+- pulp>=2.7
diff --git a/pyproject.toml b/pyproject.toml
index 2176527..1c938a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,6 +40,8 @@ sequana-wrappers = ">=26.3.0"
 click-completion = ">=0.5.2"
 
 
+snakemake = ">=7.32"
+pulp = ">=2.7"
 [tool.poetry.scripts]
 sequana_demultiplex = "sequana_pipelines.demultiplex.main:main"