Fix publish workflow; fix entrypoints

.github/workflows/publish.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: '3.11'
 
       - name: Install dependencies
         run: |
@@ -49,7 +49,7 @@ jobs:
 
       - uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.11"
 
       - name: Install package and dependencies
         run: |

docs/source/cli.rst

@@ -18,6 +18,12 @@ Generate HTML report
 --------------------
 Generate a report from MS²Rescore result file(s):
 
+.. code-block:: console
+
+    ms2rescore-report [OPTIONS] OUTPUT_PREFIX
+
+or
+
 .. code-block:: console
 
     python -m ms2rescore.report [OPTIONS] OUTPUT_PREFIX
@@ -28,6 +34,12 @@ Start graphical user interface
 ------------------------------
 Start the graphical user interface. For more info, see :ref:`Graphical user interface`.
 
+.. code-block:: console
+
+    ms2rescore-gui
+
+or
+
 .. code-block:: console
 
     python -m ms2rescore.gui

ms2rescore/gui/__main__.py

@@ -4,6 +4,13 @@
 
 from ms2rescore.gui.app import app
 
-if __name__ == "__main__":
+
+def main():
+    """Entrypoint for MS²Rescore GUI."""
     multiprocessing.freeze_support()
     app()
+
+
+if __name__ == "__main__":
+    main()
+    main()

pyproject.toml

@@ -73,8 +73,8 @@ CompOmics = "https://www.compomics.com"
 
 [project.scripts]
 ms2rescore = "ms2rescore.__main__:main"
-ms2rescore-gui = "ms2rescore.gui:main"
-ms2rescore-plotting = "ms2rescore.plotting:main"
+ms2rescore-gui = "ms2rescore.gui.__main__:main"
+ms2rescore-report = "ms2rescore.report.__main__:main"
 
 [build-system]
 requires = ["flit_core >=3.2,<4"]