Merge branch 'release_0_5_0' into 'main'

[Project] Release 0.5.0

See merge request !242

.gitlab-ci.yml

@@ -121,7 +121,6 @@ tests (arch - conda - ogs custom latest) [M]:
     - pytest
   parallel:
     matrix:
-      - PYTHON_VERSION: "3.10"
       - PYTHON_VERSION: "3.11"
       - PYTHON_VERSION: "3.12"
       - PYTHON_VERSION: "3.13"
@@ -153,6 +152,8 @@ tests (win - pip) [R]:
   rules:
     - *regression-rules
   needs: []
+  variables:
+    MPLBACKEND: Agg  # non-interactive backend for matplotlib
   before_script:
     - python -m venv .venv
     - .venv\Scripts\Activate.ps1
@@ -193,7 +194,7 @@ docs preview [M]:
     - pip install -e .[docs]
     - *pip-setup-extra-headless
   script:
-    - make docs SPHINXOPTS="--keep-going -n -j 4" > sphinx_output.log 2>&1
+    - make docs SPHINXOPTS="--keep-going -n -j 4" | tee sphinx_output.log
     - echo "Counting warnings in Sphinx output..."
     # Count lines with "WARNING" in the Sphinx log
     - warning_count=$(grep -c "WARNING" sphinx_output.log || true)

docs/releases/index.md

@@ -5,6 +5,7 @@
 maxdepth: 3
 ---
 0.x (upcoming release)  <ogstools-0.x>
+0.5.0 <ogstools-0.5.0>
 0.4.0 <ogstools-0.4.0>
 0.3.1 <ogstools-0.3.1>
 0.3.0 <ogstools-0.3.0>

docs/releases/ogstools-0.5.0.md

+# OGSTools 0.5.0 Release Notes
+
+- Recommended OGS Version: 6.5.4
+
+## API breaking changes
+
+- MeshSeries.data --> MeshSeries.values
+- MeshSeries.clear --> MeshSeries.clear_cache
+- In aggregate functions func str is replaced by callables (e.g. numpy.min)
+- meshlib.gmsh_meshing.remesh_with_triangle --> meshlib.gmsh_meshing.remesh_with_triangles
+- msh2vtu python interface was replaced with meshes_from_gmsh
+  - CLI tool msh2vtu is not affected by this
+  - parameter keep_ids was removed (in our OGS world there is no reason to keep the gmsh data names and the wrong data types in the meshes, which would happen if k was used)
+  - parameter log_level was changed to log (True or False)
+- removed:
+  - MeshSeries.spatial_data_unit/spatial_output_unit/time_unit (see
+    MeshSeries.scale())
+  - plot.linesample/linesample_contourf
+  - meshlib.data_processing.interp_points/distance_in_profile/sample_polyline
+    (see updated line sample example)
+
+## Bugfixes
+
+- Failed sub library imports led to incomplete and unhandled package import
+- MeshSeries was unable to handle xdmf with just one timestep correctly
+- MeshSeries kept the hdf5 file handle open - parallel read access was not possible
+- OMP_NUM_THREADS was not working on Windows
+- Feflow mesh did not allow mixed celltypes
+- plot functions had sometimes different color schemes in the color bar
+- Tortuosity was not a medium property
+- BHE mesh (z coordinate negative)
+
+## Features
+
+- MeshSeries gets copy() method.
+- MeshSeries gets transform() method, that applies an arbitrary transformation function to all time steps.
+- MeshSeries get extract() method to select points or cells via ids
+- MeshSeries can be sliced to get new MeshSeries with the selected subset of timesteps
+- MeshSeries gets a modify function that applies arbitrary function to all timestep - meshes.
+- difference() between two meshes is now possible even with different topologies
+- Project write_input, path can be specified
+- MeshSeries gets scale() method to scale spatially or temporally
+- variables.get_preset will now return a Variable corresponding to the spatial
+  coordinates if given "x", "y" or "z"
+- plot module gets line() function as a general purpose 1D plotting function
+- plot.setup get spatial_unit and time_unit which are used for labeling
+
+## Infrastructure
+
+- Python 3.13 support (CI testing)
+- Testing of all supported Python version 3.10-3.13 (pip and conda)
+- Testing with pinned dependencies in regression tests and with open dependencies in maintenance tests
+- msh2vtu - complete overhaul
+
+## Examples
+
+- All examples use `import ogstools as ot`. To not be confused with ogs python bindings
+
+# Footnotes
+
+- All related Merge requests are tagged with 0.5.0 Release https://gitlab.opengeosys.org/ogs/tools/ogstools/-/merge_requests?scope=all&state=merged&milestone_title=0.5.0%20Release

docs/releases/ogstools-0.x.md

@@ -4,35 +4,8 @@ This is not released yet!
 
 ## API breaking changes
 
-- MeshSeries.data --> MeshSeries.values
-- MeshSeries.clear --> MeshSeries.clear_cache
-- meshlib.gmsh_meshing.remesh_with_triangle --> meshlib.gmsh_meshing.remesh_with_triangles
-- msh2vtu python interface was replaced with meshes_from_gmsh
-  - CLI tool msh2vtu is not affected by this
-  - parameter keep_ids was removed (in our OGS world there is no reason to keep the gmsh data names and the wrong data types in the meshes, which would happen if k was used)
-  - parameter log_level was changed to log (True or False)
-- removed:
-  - MeshSeries.spatial_data_unit/spatial_output_unit/time_unit (see
-    MeshSeries.scale())
-  - plot.linesample/linesample_contourf
-  - meshlib.data_processing.interp_points/distance_in_profile/sample_polyline
-    (see update line sample example)
+## Bugfixes
 
 ## Features
 
-- MeshSeries gets copy() method.
-- MeshSeries gets transform() method, that applies an arbitrary transformation function to all time steps.
-- MeshSeries get extract() method to select points or cells via ids
-- MeshSeries can be sliced to get new MeshSeries with the selected subset of timesteps
-- difference() between two meshes is now possible even with different topologies
-- MeshSeries gets scale() method to scale spatially or temporally
-- variables.get_preset will now return a Variable corresponding to the spatial
-  coordinates if given "x", "y" or "z"
-- plot module gets line() function as a general purpose 1D plotting function
-- plot.setup get spatial_unit and time_unit which are used for labeling
-
 ## Infrastructure
-
-- Python 3.13 support (CI testing)
-- Testing of all supported Python version 3.10-3.13 (pip and conda)
-- Testing with pinned dependencies in regression tests and with open dependencies in maintenance tests

pyproject.toml

@@ -41,7 +41,7 @@ dependencies = [
   # meshing algorithm changed with this version
   "typeguard>=4.0.0",
   "lxml>=4.6.0",
-  "ogs>=6.5.3",
+  "ogs>=6.5.4",
   "pandas>=2.2.3",
 ]
 
@@ -139,7 +139,7 @@ pinned = [
   "nbformat==5.10.4",
   "nest-asyncio==1.6.0",
   "numpy==2.2.1",
-  "ogs==6.5.3",
+  "ogs==6.5.4",
   "overrides==7.7.0",
   "packaging==24.2",
   "pandamesh==0.2.2",