diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 5ecb4fb..f219f4d 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -7,44 +7,32 @@ jobs: run-pymm-local: permissions: contents: read - pull-requests: write timeout-minutes: 30 - runs-on: ubuntu-latest + runs-on: ubuntu-26.04 steps: - - uses: actions/checkout@v2 - with: - fetch-depth: 0 + - uses: actions/checkout@v5 - - name: Set up Python 3.14 - uses: actions/setup-python@v2 - with: - python-version: 3.14 - - - name: Install OpenFOAM + - name: Install OpenFOAM and gmsh run: | sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key > /etc/apt/trusted.gpg.d/openfoam.asc" - sudo add-apt-repository http://dl.openfoam.org/ubuntu - sudo apt-get update - sudo apt -y install openfoam14 - - - name: Install gmsh - run: | + sudo add-apt-repository "http://dl.openfoam.org/ubuntu main dev" + sudo sed -i "s/^\(deb\).*\(http\)/\1 [arch=amd64] \2/" /etc/apt/sources.list.d/*dl_openfoam_org*list sudo apt-get update - sudo apt-get -y install gmsh + sudo apt -y install openfoam14 gmsh - - name: Install test dependecies + - name: Install pymm and python requirements run: | + python3.14 -m venv vpymm + . vpymm/bin/activate + echo "$PWD/vpymm/bin" >> $GITHUB_PATH pip install --upgrade pip setuptools wheel - pip install -r dev-requirements.txt - - - name: Install pymm - run: | pip install . + pip install -r dev-requirements.txt - name: Check code style and linting run: | - black --target-version py312 src/ tests/ --check + black --target-version py314 src/ tests/ --check pylint src/ tests/ ruff check src/ tests/ mypy --ignore-missing-imports src/ tests/ @@ -59,4 +47,4 @@ jobs: - name: Build documentation run: | pushd docs - make html + make html SPHINXOPTS="-W" diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8a8385b..e1f4600 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -13,13 +13,13 @@ Contributions are more than welcome using the fork and pull request approach 1. Work on your own fork of the main repo 1. In the main repo execute: 1. **pip install -r dev-requirements.txt** (this installs the [_dev-requirements.txt_](https://github.com/cssr-tools/pymm/blob/main/dev-requirements.txt)) - 1. **black --target-version py312 src/ tests/** (this formats the code) + 1. **black --target-version py314 src/ tests/** (this formats the code) 1. **pylint src/ tests/** (this analyses the code, and might rise issues that need to be fixed before the pull request) 1. **ruff check src/ tests/** (this also analyses the code, and might rise issues that need to be fixed before the pull request) 1. **mypy --ignore-missing-imports src/ tests/** (this is a static checker, and might rise issues that need to be fixed before the pull request) 1. **pytest --cov=pymm --cov-report term-missing tests/ -n auto** (this runs locally the tests, and might rise issues that need to be fixed before the pull request) 1. **pushd docs & make html** (this generates the documentation, and might rise issues that need to be fixed before the pull request; if the build succeeds and if the contribution changes the documentation, then copy all content from the docs/_build/html/ folder and replace the files in the [_docs_](https://github.com/cssr-tools/pymm/tree/main/docs) folder) - * Tip: See the [_CI.yml_](https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml) script and the [_Actions_](https://github.com/cssr-tools/pymm/actions) for installation of _pymm_, as well as the execution of the six previous steps in Ubuntu 24.04 using Python 3.12. + * Tip: See the [_CI.yml_](https://github.com/cssr-tools/pymm/blob/main/.github/workflows/CI.yml) script and the [_Actions_](https://github.com/cssr-tools/pymm/actions) for installation of _pymm_, as well as the execution of the six previous steps in Ubuntu 26.04 using Python 3.14. 1. Squash your commits into a single commit (see this [_nice tutorial_](https://gist.github.com/lpranam/4ae996b0a4bc37448dc80356efbca7fa) if you are not familiar with this) 1. Push your commit and make a pull request 1. The maintainers will review the pull request, and if the contribution is accepted, then it will be merge to the main repo diff --git a/docs/_sources/contributing.rst.txt b/docs/_sources/contributing.rst.txt index 0bc74e7..296bc25 100644 --- a/docs/_sources/contributing.rst.txt +++ b/docs/_sources/contributing.rst.txt @@ -22,7 +22,7 @@ Contribute to the software #. In the main repo execute: #. **pip install -r dev-requirements.txt** (this installs the `dev-requirements.txt `_) - #. **black \-\-target-version py312 src/ tests/** (this formats the code) + #. **black \-\-target-version py314 src/ tests/** (this formats the code) #. **pylint src/ tests/** (this analyses the code, and might rise issues that need to be fixed before the pull request) #. **ruff check src/ tests/** (this also analyses the code, and might rise issues that need to be fixed before the pull request) #. **mypy \-\-ignore-missing-imports src/ tests/** (this is a static checker, and might rise issues that need to be fixed before the pull request) @@ -30,7 +30,7 @@ Contribute to the software #. **pushd docs & make html** (this generates the documentation, and might rise issues that need to be fixed before the pull request; if the build succeeds and if the contribution changes the documentation, then copy all content from the docs/_build/html/ folder and replace the files in the `docs `_ folder) .. tip:: - See the `CI.yml `_ script and the `Actions `_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.04. + See the `CI.yml `_ script and the `Actions `_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 26.04 and Python 3.14. #. Squash your commits into a single commit (see this `nice tutorial `_ if you are not familiar with this) #. Push your commit and make a pull request diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt index b737495..b0ba1e9 100644 --- a/docs/_sources/installation.rst.txt +++ b/docs/_sources/installation.rst.txt @@ -45,7 +45,7 @@ install the Python requirements in a virtual environment with the following comm OpenFOAM -------- -See the `OpenFOAM page `_, where from OpenFOAM-12 the simulator is available via apt get, +See the `OpenFOAM page `_, where from OpenFOAM-12 the simulator is available via apt get, and OpenFOAM-14 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal: .. code-block:: console @@ -62,4 +62,4 @@ See the `Gmsh page `_. .. tip:: See the `CI.yml `_ script - for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu using Python 3.14. + for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu 26.04 using Python 3.14. diff --git a/docs/contributing.html b/docs/contributing.html index 005f200..1f14de7 100644 --- a/docs/contributing.html +++ b/docs/contributing.html @@ -107,7 +107,7 @@

Contribute to the software

  • pip install -r dev-requirements.txt (this installs the dev-requirements.txt)

    • -

  • black --target-version py312 src/ tests/ (this formats the code)

    • +

  • black --target-version py314 src/ tests/ (this formats the code)

  • pylint src/ tests/ (this analyses the code, and might rise issues that need to be fixed before the pull request)

  • ruff check src/ tests/ (this also analyses the code, and might rise issues that need to be fixed before the pull request)

  • mypy --ignore-missing-imports src/ tests/ (this is a static checker, and might rise issues that need to be fixed before the pull request)

    • @@ -116,7 +116,7 @@

    Contribute to the software

    Tip

    -

    See the CI.yml script and the Actions for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.04.

    +

    See the CI.yml script and the Actions for installation of pymm, as well as the execution of the six previous steps in Ubuntu 26.04 and Python 3.14.

    diff --git a/docs/installation.html b/docs/installation.html index 0ffe05e..d02a352 100644 --- a/docs/installation.html +++ b/docs/installation.html @@ -123,7 +123,7 @@

    Python package

    OpenFOAM

    -

    See the OpenFOAM page, where from OpenFOAM-12 the simulator is available via apt get, +

    See the OpenFOAM page, where from OpenFOAM-12 the simulator is available via apt get, and OpenFOAM-14 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:

    source /opt/openfoam14/etc/bashrc
 foamRun -help
@@ -136,7 +136,7 @@ 
    Gmsh<
 
    
 
    Tip
    
 
    See the CI.yml script
-for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu using Python 3.14.
    
+for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu 26.04 using Python 3.14.
    
 
    
 
 
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 1c4b386..35acc6b 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/text/contributing.rst b/docs/text/contributing.rst
index 0bc74e7..296bc25 100644
--- a/docs/text/contributing.rst
+++ b/docs/text/contributing.rst
@@ -22,7 +22,7 @@ Contribute to the software
 #. In the main repo execute:
 
     #. **pip install -r dev-requirements.txt** (this installs the `dev-requirements.txt `_)
-    #. **black \-\-target-version py312 src/ tests/** (this formats the code)
+    #. **black \-\-target-version py314 src/ tests/** (this formats the code)
     #. **pylint src/ tests/** (this analyses the code, and might rise issues that need to be fixed before the pull request)
     #. **ruff check src/ tests/** (this also analyses the code, and might rise issues that need to be fixed before the pull request)
     #. **mypy \-\-ignore-missing-imports src/ tests/** (this is a static checker, and might rise issues that need to be fixed before the pull request)
@@ -30,7 +30,7 @@ Contribute to the software
     #. **pushd docs & make html** (this generates the documentation, and might rise issues that need to be fixed before the pull request; if the build succeeds and if the contribution changes the documentation, then copy all content from the docs/_build/html/ folder and replace the files in the `docs `_ folder)
     
     .. tip::
-        See the `CI.yml `_ script and the `Actions `_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 24.04.
+        See the `CI.yml `_ script and the `Actions `_ for installation of pymm, as well as the execution of the six previous steps in Ubuntu 26.04 and Python 3.14.
 
 #. Squash your commits into a single commit (see this `nice tutorial `_ if you are not familiar with this)
 #. Push your commit and make a pull request
diff --git a/docs/text/installation.rst b/docs/text/installation.rst
index b737495..b0ba1e9 100644
--- a/docs/text/installation.rst
+++ b/docs/text/installation.rst
@@ -45,7 +45,7 @@ install the Python requirements in a virtual environment with the following comm
 OpenFOAM
 --------
 
-See the `OpenFOAM page `_, where from OpenFOAM-12 the simulator is available via apt get,
+See the `OpenFOAM page `_, where from OpenFOAM-12 the simulator is available via apt get,
 and OpenFOAM-14 is the latest release. To test if OpenFoam is installed and working, you could type in the terminal:
 
 .. code-block:: console
@@ -62,4 +62,4 @@ See the `Gmsh page `_.
 .. tip::
 
     See the `CI.yml `_ script 
-    for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu using Python 3.14.
+    for installation of pymm, gmsh, and OpenFOAM-14 in Ubuntu 26.04 using Python 3.14.
diff --git a/src/pymm/core/pymm.py b/src/pymm/core/pymm.py
index 743c24b..d7d69a1 100644
--- a/src/pymm/core/pymm.py
+++ b/src/pymm/core/pymm.py
@@ -5,24 +5,25 @@
 """Main script for pymm"""
 
 import argparse
-import sys
-import subprocess
 import shutil
-from pathlib import Path
-from dataclasses import dataclass
-from contextlib import nullcontext
+import subprocess
+import sys
 import tomllib
+from contextlib import nullcontext
+from dataclasses import dataclass
+from pathlib import Path
 from typing import Any
-import numpy as np
-from numpy.typing import NDArray
-import skimage.transform
-from skimage import io, measure
-from skimage.morphology import remove_small_objects
+
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-from matplotlib.collections import LineCollection
+import numpy as np
+import skimage.transform
 from alive_progress import alive_bar
 from mako.template import Template
+from matplotlib.collections import LineCollection
+from numpy.typing import NDArray
+from skimage import io, measure
+from skimage.morphology import remove_small_objects
 
 ADD_BORDER = 50  # Add arbitrary border to extract the image boundaries
 
diff --git a/tests/test_device.py b/tests/test_device.py
index 2ce8a99..ea6ec4e 100644
--- a/tests/test_device.py
+++ b/tests/test_device.py
@@ -3,8 +3,8 @@
 
 """Test the device mode functionality"""
 
-from pathlib import Path
 import subprocess
+from pathlib import Path
 
 
 def test_device(tmp_path, monkeypatch):
diff --git a/tests/test_image.py b/tests/test_image.py
index 5e7406a..43b6dee 100644
--- a/tests/test_image.py
+++ b/tests/test_image.py
@@ -3,8 +3,9 @@
 
 """Test the image mode functionality"""
 
-from pathlib import Path
 import shutil
+from pathlib import Path
+
 from pymm.core.pymm import main
 
 
diff --git a/tests/test_single_grain.py b/tests/test_single_grain.py
index 8dd1ef4..df09667 100644
--- a/tests/test_single_grain.py
+++ b/tests/test_single_grain.py
@@ -3,8 +3,8 @@
 
 """Test in a single grain"""
 
-from pathlib import Path
 import subprocess
+from pathlib import Path
 
 
 def test_single_grain(tmp_path, monkeypatch):