Merge pull request #4 from remydubois/fix/license

Added license, improved readme and publish action

Author: remydubois

.github/workflows/publish-package.yaml

@@ -0,0 +1,29 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [published]
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade poetry
+        python -m poetry install --with dev
+    - name: Build package
+      run: python -m poetry build
+    - name: Publish package
+      run: python -m poetry publish -u __token__ -p ${{ secrets.PYPI_TOKEN }}

LICENSE

@@ -0,0 +1,13 @@
+Copyright 2025 Rémy Dubois
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

README.md

@@ -112,11 +112,7 @@ In order for benchmarks to run in a reasonable amount of time, the timings repor
 </p>
 
 ### Scalability
-TODO: this could clearly be improved with a smarter batching strategy
-`illico` scales reasonably well with your compute budget. Find below the processing time of the K562-essential dataset for both OVO and OVR tests, while increasing the number of threads used. Similarly as before, a benchmark is defined by:
-1. The data format (CSR, or dense) used to contain the expression matrix.
-2. The test performed: OVO (`reference="non-targeting"`) or OVR (`reference=None`).
-The example below shows spanning 8 threads instead of 1 brings a 7-folds speedup for the cell line k562.
+`illico` scales reasonably well with your compute budget. On the K562-essential dataset spanning 8 threads instead of 1 brings a 7-folds speedup.
 ```bash
 ---------------------- benchmark 'k562-dense-ovo': 4 tests -----------------------
 Name (time in s)                                                    Mean