GiMattia · GiMattia · Oct 27, 2025 · Sep 17, 2025 · Sep 17, 2025 · Sep 17, 2025
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
@@ -17,10 +17,10 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@v4
         with:
-          python-version: 3.13
+          python-version: 3.14
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/test_linux.yml b/.github/workflows/test_linux.yml
@@ -1,4 +1,4 @@
-name: Tests on Linux
+name: Linux Tests
 
 on:
   push:
@@ -9,36 +9,39 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os:
-          - ubuntu-22.04
-          - ubuntu-24.04
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-22.04, ubuntu-24.04]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
 
       - name: Clean untracked files & bytecode
-        shell: pwsh
-        run: |
-          git clean -xfd
+        run: git clean -xfd
 
+      # --- Setup Python ---
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements_dev.txt
+      # --- Install UV (replaces pip + virtualenv) ---
+      - name: Install uv
+        run: pip install uv
 
-      - name: Install pyPLUTO in editable mode
+      # --- Create virtual environment with uv ---
+      - name: Create uv environment
         run: |
-          pip uninstall -y pyPLUTO || true
-          pip install -e .
+          uv venv .venv
+          source .venv/bin/activate
 
+      # --- Sync environment (fast + reproducible) ---
+      - name: Install dependencies with uv
+        run: uv pip install -r requirements_dev.txt
+
+      # --- Run tests ---
       - name: Run Tests
-        run: pytest -v
-        working-directory: ./Tests
+        run: uv run pytest -v ./Tests
+
diff --git a/.github/workflows/test_macos.yml b/.github/workflows/test_macos.yml
@@ -13,7 +13,7 @@ jobs:
         os:
           - macOS-14
           - macOS-15
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout repository

diff --git a/.github/workflows/test_windows.yml b/.github/workflows/test_windows.yml
@@ -13,7 +13,7 @@ jobs:
         os:
           - windows-2022
           - windows-2025
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - name: Checkout repository

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -30,12 +30,12 @@ repos:
   #      files: \.py$
 
   # 2. Docformatter (formats docstrings)
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.7
-    hooks:
-      - id: docformatter
-        args: ["--in-place", "--black", "--blank"]
-        files: \.py$
+  #- repo: https://github.com/PyCQA/docformatter
+  #  rev: v1.7.7
+  #  hooks:
+  #    - id: docformatter
+  #      args: ["--in-place", "--black", "--blank"]
+  #      files: \.py$
 
   # 3. Blackened-docs (formats code in docstrings)
   - repo: https://github.com/adamchainz/blacken-docs

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,25 +1,68 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+cff-version: "1.2.0"
 authors:
-  - name: Giancarlo Mattia
-    orcid: 0000-0003-1454-6226
-  - name: Daniele Crocco
-    orcid: 0009-0001-4284-9446
-  - name: David Melon Fuksman
-    orcid: 0000-0002-1697-6433
-  - name: Matteo Bugli
-    orcid: 0000-0002-7834-0422
-  - name: Vittoria Berta
-    orcid: 0000-0001-6305-6931
-  - name: Eleonora Puzzoni
-    orcid: 0009-0009-5314-348X
-  - name: Andrea Mignone
-    orcid: 0000-0002-8352-6635
-  - name: Bhargav Vaidya
-    orcid: 0000-0001-5424-0059
-
-title: 'PyPLUTO: a data analysis Python package for the PLUTO code'
-version: 1.0.0
-doi: 10.48550/arXiv.2501.09748
-date-released: 2025-12-17
-url: "https://github.com/GiMattia/PyPLUTO"
+- family-names: Mattia
+  given-names: Giancarlo
+  orcid: "https://orcid.org/0000-0003-1454-6226"
+- family-names: Crocco
+  given-names: Daniele
+  orcid: "https://orcid.org/0009-0001-4284-9446"
+- family-names: Melon Fuksman
+  given-names: David
+  orcid: "https://orcid.org/0000-0002-1697-6433"
+- family-names: Bugli
+  given-names: Matteo
+  orcid: "https://orcid.org/0000-0002-7834-0422"
+- family-names: Berta
+  given-names: Vittoria
+  orcid: "https://orcid.org/0000-0001-6305-6931"
+- family-names: Puzzoni
+  given-names: Eleonora
+  orcid: "https://orcid.org/0009-0009-5314-348X"
+- family-names: Mignone
+  given-names: Andrea
+  orcid: "https://orcid.org/0000-0002-8352-6635"
+- family-names: Vaidya
+  given-names: Bhargav
+  orcid: "https://orcid.org/0000-0001-5424-0059"
+doi: 10.5281/zenodo.17137196
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Mattia
+    given-names: Giancarlo
+    orcid: "https://orcid.org/0000-0003-1454-6226"
+  - family-names: Crocco
+    given-names: Daniele
+    orcid: "https://orcid.org/0009-0001-4284-9446"
+  - family-names: Melon Fuksman
+    given-names: David
+    orcid: "https://orcid.org/0000-0002-1697-6433"
+  - family-names: Bugli
+    given-names: Matteo
+    orcid: "https://orcid.org/0000-0002-7834-0422"
+  - family-names: Berta
+    given-names: Vittoria
+    orcid: "https://orcid.org/0000-0001-6305-6931"
+  - family-names: Puzzoni
+    given-names: Eleonora
+    orcid: "https://orcid.org/0009-0009-5314-348X"
+  - family-names: Mignone
+    given-names: Andrea
+    orcid: "https://orcid.org/0000-0002-8352-6635"
+  - family-names: Vaidya
+    given-names: Bhargav
+    orcid: "https://orcid.org/0000-0001-5424-0059"
+  date-published: 2025-09-17
+  doi: 10.21105/joss.08448
+  issn: 2475-9066
+  issue: 113
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 8448
+  title: "PyPLUTO: a data analysis Python package for the PLUTO code"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.08448"
+  volume: 10
+title: "PyPLUTO: a data analysis Python package for the PLUTO code"
diff --git a/Docs/Figures/__pycache__/test_gui_ot.cpython-312-pytest-8.3.4.pyc b/Docs/Figures/__pycache__/test_gui_ot.cpython-312-pytest-8.3.4.pyc
diff --git a/Docs/Figures/__pycache__/test_gui_sod.cpython-312-pytest-8.3.4.pyc b/Docs/Figures/__pycache__/test_gui_sod.cpython-312-pytest-8.3.4.pyc
diff --git a/Docs/Figures/pluto_ot_full.mp4 b/Docs/Figures/pluto_ot_full.mp4
diff --git a/Docs/Figures/pluto_ot_gui.mp4 b/Docs/Figures/pluto_ot_gui.mp4
diff --git a/Docs/Figures/pluto_sod_full.mp4 b/Docs/Figures/pluto_sod_full.mp4
diff --git a/Docs/Figures/pluto_sod_gui.mp4 b/Docs/Figures/pluto_sod_gui.mp4
diff --git a/Docs/Figures/test_gui_ot.py b/Docs/Figures/test_gui_ot.py
@@ -103,7 +103,7 @@ def postprocess_video():
         "-t",
         "23",
         "-vf",
-        "crop=1180:750:40:47",
+        "crop=1185:750:50:50",
         "-c:a",
         "copy",
         "pluto_ot_gui.mp4",

diff --git a/Docs/Figures/test_gui_sod.py b/Docs/Figures/test_gui_sod.py
@@ -98,7 +98,7 @@ def postprocess_video():
         "-t",
         "18",
         "-vf",
-        "crop=1180:750:40:47",
+        "crop=1185:750:50:50",
         "-c:a",
         "copy",
         "pluto_sod_gui.mp4",

diff --git a/Docs/source/_static/pluto_ot_gui.mp4 b/Docs/source/_static/pluto_ot_gui.mp4
diff --git a/Docs/source/_static/pluto_sod_gui.mp4 b/Docs/source/_static/pluto_sod_gui.mp4
diff --git a/Examples/test01_sod.py b/Examples/test01_sod.py
@@ -51,4 +51,4 @@
 # Saving the image and showing the plot in the Examples folder
 # (i.e., where the file test01_sod.py is located)
 Image.savefig("test01_sod.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test02_ot.png b/Examples/test02_ot.png
diff --git a/Examples/test02_ot.py b/Examples/test02_ot.py
@@ -42,4 +42,4 @@
 
 # Saving the image and showing the plot
 Image.savefig("test02_ot.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test03_rti.png b/Examples/test03_rti.png
diff --git a/Examples/test03_rti.py b/Examples/test03_rti.py
@@ -75,4 +75,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test03_rti.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test04_rotor.png b/Examples/test04_rotor.png
diff --git a/Examples/test04_rotor.py b/Examples/test04_rotor.py
@@ -91,4 +91,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test04_rotor.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test05_fieldloop.png b/Examples/test05_fieldloop.png
diff --git a/Examples/test05_fieldloop.py b/Examples/test05_fieldloop.py
@@ -95,4 +95,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test05_fieldloop.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test06_diskplanet.png b/Examples/test06_diskplanet.png
diff --git a/Examples/test06_diskplanet.py b/Examples/test06_diskplanet.py
@@ -76,4 +76,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test06_diskplanet.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test07_khi.png b/Examples/test07_khi.png
diff --git a/Examples/test07_khi.py b/Examples/test07_khi.py
@@ -94,4 +94,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test07_khi.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test08_torus.png b/Examples/test08_torus.png
diff --git a/Examples/test08_torus.py b/Examples/test08_torus.py
@@ -92,4 +92,4 @@
 
 # Saving the image and showing the plots
 Image.savefig("test08_torus.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test09_blast.png b/Examples/test09_blast.png
diff --git a/Examples/test09_blast.py b/Examples/test09_blast.py
@@ -75,4 +75,4 @@ def plot_frame(Data, ax_idx: int, time_label: str):
 
 # Saving and showing
 Image.savefig("test09_blast.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test11_xpoint.png b/Examples/test11_xpoint.png
diff --git a/Examples/test11_xpoint.py b/Examples/test11_xpoint.py
@@ -97,4 +97,4 @@ def compute_gamma(dp):
 
 # --- Save and show ---
 Image.savefig("test11_xpoint.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test12_riemannlp.png b/Examples/test12_riemannlp.png
diff --git a/Examples/test12_riemannlp.py b/Examples/test12_riemannlp.py
@@ -62,4 +62,4 @@ class simultaneously and how to produce a scatter plot on a omplex axes
 
 # Saving the image and showing the plot
 Image.savefig("test12_riemannlp.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/Examples/test13_flowpastcyl.png b/Examples/test13_flowpastcyl.png
diff --git a/Examples/test13_flowpastcyl.py b/Examples/test13_flowpastcyl.py
@@ -54,4 +54,4 @@
 
 # Save and show the figure
 Image.savefig("test13_flowpastcyl.png", script_relative=True)
-pyPLUTO.show()
+# pyPLUTO.show()
diff --git a/README.md b/README.md
@@ -4,17 +4,13 @@
 | --- | --- |
 | Package | [![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) ![Python Versions](https://img.shields.io/badge/Python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-3776AB.svg?style=flat&logo=python&logoColor=white) ![GitHub release](https://img.shields.io/github/v/release/GiMattia/PyPLUTO?include_prereleases&label=Github%20Release) [![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) |
 | Tests | [![Windows Tests](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_windows.yml/badge.svg)](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_windows.yml) [![MacOS Tests](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_macos.yml/badge.svg)](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_macos.yml) [![Linux Tests](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_linux.yml/badge.svg)](https://github.com/GiMattia/PyPLUTO/actions/workflows/test_linux.yml) ![Coverage Report](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/GiMattia/384b1f3a3a3b74cdbd65c4e3dce0632f/raw/pytest-coverage-comment__main.json) |
-| Style | [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com//GiMattia/PyPLUTO/actions/workflows/pre-commit.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) ![Pylint](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/GiMattia/8fc3a521f1c5e59e41eb16d1197bf8c8/raw/pylint-score.json) ![Mypy](https://img.shields.io/badge/type_checking-mypy-brightgreen) |
-| Distribution | [![Arxiv](https://img.shields.io/badge/arXiv-2501.09748-8F1515?style=flat&logo=arxiv&logoColor=red)](https://doi.org/10.48550/arXiv.2501.09748) [![Documentation](https://readthedocs.org/projects/pypluto/badge/?version=latest)](https://pypluto.readthedocs.io/en/latest/?badge=latest) |
+| Style | [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com//GiMattia/PyPLUTO/actions/workflows/pre-commit.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) ![Pylint](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/GiMattia/8fc3a521f1c5e59e41eb16d1197bf8c8/raw/pylint-score.json) ![Mypy](https://img.shields.io/badge/type_checking-mypy-brightgreen) [![Documentation](https://readthedocs.org/projects/pypluto/badge/?version=latest)](https://pypluto.readthedocs.io/en/latest/?badge=latest) |
+| Distribution | [![DOI](https://joss.theoj.org/papers/10.21105/joss.08448/status.svg)](https://doi.org/10.21105/joss.08448) [![Arxiv](https://img.shields.io/badge/arXiv-2501.09748-8F1515?style=flat&logo=arxiv&logoColor=red)](https://doi.org/10.48550/arXiv.2501.09748) [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.17137196.svg)](https://doi.org/10.5281/zenodo.17137196) |
 
 <!-- ![Doc Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/GiMattia/cc212934fc58b93ddebda8c669dbb171/raw/interrogate-badge.svg) -->
 
 <!-- ![PyPI](https://img.shields.io/pypi/v/PyPLUTO) -->
 <!-- ![Conda](https://img.shields.io/badge/conda-available-brightgreen) -->
-<!-- ![Zenodo](https://img.shields.io/badge/zenodo-DATA-brightgreen) -->
-<!-- [![DOI](https://joss.theoj.org/papers/.../status.svg)](https://doi.org/...) -->
-
-
 
 PyPLUTO is a Python library which loads and plots the data obtain from the
 PLUTO code simulations.

diff --git a/Tests/0test_examples.py b/Tests/0test_examples.py
@@ -0,0 +1,61 @@
+import subprocess
+from pathlib import Path
+
+import pytest
+from PIL import Image, ImageChops
+
+EXAMPLES_DIR = (Path(__file__).parent / "../Examples").resolve()
+REFERENCE_DIR = (Path(__file__).parent / "Ref_figs").resolve()
+
+
+def list_example_scripts():
+    """Return a list of Python scripts in ../Examples."""
+    scripts = sorted(EXAMPLES_DIR.glob("*.py"))
+    if not scripts:
+        pytest.skip("No example scripts found in ../Examples")
+    return scripts
+
+
+def run_example(script: Path):
+    """Run a single Python example script."""
+    subprocess.run(["python", str(script)], check=True)
+
+
+def images_identical(img1_path, img2_path) -> bool:
+    """Return True if two images are pixel-identical."""
+    with Image.open(img1_path) as img1, Image.open(img2_path) as img2:
+        if img1.size != img2.size or img1.mode != img2.mode:
+            return False
+        diff = ImageChops.difference(img1, img2)
+        return diff.getbbox() is None
+
+
+@pytest.mark.parametrize("script", list_example_scripts())
+def test_example(script):
+    """
+    Run one example script and compare its generated images
+    with the reference ones in the current directory.
+    Each example appears as a separate pytest test.
+    """
+    run_example(script)
+
+    generated_images = sorted(EXAMPLES_DIR.glob("*.png"))
+    reference_images = sorted(REFERENCE_DIR.glob("*.png"))
+
+    assert generated_images, f"No images generated by {script.name}"
+    assert reference_images, "No reference images found in current directory"
+    assert len(generated_images) == len(reference_images), (
+        f"{script.name}: different number of images "
+        f"({len(generated_images)} generated vs {len(reference_images)} reference)"
+    )
+
+    mismatches = []
+    for gen_img, ref_img in zip(
+        generated_images, reference_images, strict=False
+    ):
+        if not images_identical(gen_img, ref_img):
+            mismatches.append(gen_img.name)
+
+    assert (
+        not mismatches
+    ), f"{script.name}: mismatched images {', '.join(mismatches)}"
diff --git a/Tests/Ref_figs/test01_sod.png b/Tests/Ref_figs/test01_sod.png
diff --git a/Tests/Ref_figs/test02_ot.png b/Tests/Ref_figs/test02_ot.png
diff --git a/Tests/Ref_figs/test03_rti.png b/Tests/Ref_figs/test03_rti.png
diff --git a/Tests/Ref_figs/test05_fieldloop.png b/Tests/Ref_figs/test05_fieldloop.png
diff --git a/Tests/Ref_figs/test07_khi.png b/Tests/Ref_figs/test07_khi.png
diff --git a/Tests/Ref_figs/test08_torus.png b/Tests/Ref_figs/test08_torus.png
diff --git a/Tests/Ref_figs/test09_blast.png b/Tests/Ref_figs/test09_blast.png
diff --git a/Tests/Ref_figs/test11_xpoint.png b/Tests/Ref_figs/test11_xpoint.png
diff --git a/Tests/Ref_figs/test12_riemannlp.png b/Tests/Ref_figs/test12_riemannlp.png
diff --git a/Tests/test01_sod.png b/Tests/test01_sod.png
diff --git a/Tests/test02_ot.png b/Tests/test02_ot.png
diff --git a/Tests/test03_rti.png b/Tests/test03_rti.png
diff --git a/Tests/test04_rotor.png b/Tests/test04_rotor.png
diff --git a/Tests/test05_fieldloop.png b/Tests/test05_fieldloop.png
diff --git a/Tests/test06_diskplanet.png b/Tests/test06_diskplanet.png
diff --git a/Tests/test07_khi.png b/Tests/test07_khi.png
diff --git a/Tests/test08_torus.png b/Tests/test08_torus.png
diff --git a/Tests/test09_blast.png b/Tests/test09_blast.png
diff --git a/Tests/test10_riemann2d.gif b/Tests/test10_riemann2d.gif
diff --git a/Tests/test11_xpoint.png b/Tests/test11_xpoint.png
diff --git a/Tests/test12_riemannlp.png b/Tests/test12_riemannlp.png
diff --git a/Tests/test13_flowpastcyl.png b/Tests/test13_flowpastcyl.png
-Original file line number
+Diff line change
@@ Expand Up / @@ -103,7 +103,7 @@ def postprocess_video(): @@
             "-t",
             "23",
             "-vf",
-            "crop=1180:750:40:47",
+            "crop=1185:750:50:50",
             "-c:a",
             "copy",
             "pluto_ot_gui.mp4",
@@ Expand Down @@