resolved conflicts

.github/workflows/ci.yml

@@ -11,21 +11,21 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-13]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Run image
-        uses: abatilo/actions-poetry@v2
+        uses: abatilo/actions-poetry@v2.3.0
         with:
-          poetry-version: 1.8.2
+          poetry-version: 1.8.3
       - name: Cache Poetry virtualenv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ~/.virtualenvs
@@ -40,11 +40,16 @@ jobs:
         run: poetry install
         if: steps.cache.outputs.cache-hit != 'true'
 
+      - name: list env contents
+        run: |
+          poetry show
+          pip list
+
       - name: Test with pytest
         run: poetry run pytest --cov . --cov-report xml:coverage-reports/coverage-hydrolib-core.xml --junitxml=xunit-reports/xunit-result-hydrolib-core.xml
 
       - name: Autoformat code if the check fails
-        if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.8) }}
+        if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == 3.12) }}
         run: |
           poetry run isort .
           poetry run black .

.github/workflows/docs.yml

@@ -7,19 +7,19 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.4.0
+          poetry-version: 1.8.3
       - name: Cache Poetry virtualenv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ~/.virtualenvs

.github/workflows/docs_release.yml

@@ -8,19 +8,19 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.4.0
+          poetry-version: 1.8.3
       - name: Cache Poetry virtualenv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ~/.virtualenvs

.github/workflows/integration.yml

@@ -13,26 +13,26 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.9]
+        python-version: [3.12]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.4.0
+          poetry-version: 1.8.3
 
       - name: Cache Poetry virtualenv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ~/.virtualenvs

.github/workflows/release.yml

@@ -29,26 +29,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Run image
         uses: abatilo/[email protected]
         with:
-          poetry-version: 1.4.0
+          poetry-version: 1.8.3
 
       - name: Cache Poetry virtualenv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ~/.virtualenvs
-          key: venv-ubuntu-latest-3.8-${{ hashFiles('**/poetry.lock') }}
+          key: venv-ubuntu-latest-${{ hashFiles('**/poetry.lock') }}
 
       - name: Set Poetry config
         run: |

docs/guides/contributing.md

@@ -34,7 +34,7 @@ When starting development on a branch, a pull request should be created for revi
 In the description text area on GitHub, use a [closing keyword](https://docs.github.com/articles/closing-issues-using-keywords) such that this PR will be automatically linked to the issue.
 For example: `Fixes #160`.
 
-During continuous integration, the checks will be run with python 3.8, 3.9 and 3.12 on Windows, Ubuntu and MacOS. The checks consist of running the tests, checking the code formatting and running SonarCloud. 
+During continuous integration, the checks will be run with several Python versions on Windows, Ubuntu and MacOS. The checks consist of running the tests, checking the code formatting and running SonarCloud. 
 We advise to use a draft pull request, to prevent the branch to be merged back before developement is finished. When the branch is ready for review, you can update the status of the pull request to "ready for review".
 
 ### Reviews

docs/guides/setup.md

@@ -16,7 +16,7 @@ pip install hydrolib-core
 
 If you want to create a fresh test environment for hydrolib-core, you could use the following command (only once):
 ``` bash
-conda create -n hydrolib python=3.8 -c conda-forge
+conda create -n hydrolib python=3.12 -c conda-forge
 ```
 Prior to the `pip install`, first activate the desired environment:
 ``` bash

pyproject.toml

@@ -14,42 +14,44 @@ homepage = "https://deltares.github.io/HYDROLIB-core"
 "issue tracker" = "https://github.com/Deltares/HYDROLIB-core/issues"
 
 [tool.poetry.dependencies]
-python = "^3.8"
-netCDF4 = "^1.5,!=1.7.*"
-numpy = [
-    { version = "^1.21", python = "^3.8" },
-    { version = "^1.25", python = "^3.12" }
-]
+python = "^3.9"
+# exclude yanked netcdf versions 1.7.0 and 1.7.1, but include 1.7.2 (first with python 3.12 support)
+netCDF4 = "^1.5,!=1.7.0,!=1.7.1"
+# no caret here, since numpy v2 is required for future python 3.13 support, but this is not yet widely supported by packages numpy v1 support is also still required.
+numpy = ">=1.25,<3"
 pydantic = "^2.5"
-lxml = ">=4.6"
-meshkernel = "^4.2.0"
+# lxml 5.0 is from December 2023
+lxml = "^5.0"
+meshkernel = "^5.0.1"
 strenum = "^0"
 
 [tool.poetry.dev-dependencies]
-pytest = "^6.2"
+pytest = "^8.0"
+pytest-cov = "^5.0"
 black = "^24.3"
 isort = "^5.8"
+devtools = "^0.6.1"
 mkdocs = "^1.2"
 mkdocs-material = "^8.0"
 mkdocstrings = "^0.16"
 mkdocs-autorefs = "^0.3, !=0.3.1"
 mkdocs-macros-plugin = "^0.6.3"
-pytest-cov = "^2.11"
+mkdocs-table-reader-plugin = "^0.6.1"
+mkdocs-jupyter = "^0.21.0"
 pymdown-extensions = "^9.1"
 commitizen = "^2.17"
 flake8 = "^3.9.2"
 mypy = "^0.910"
-devtools = "^0.6.1"
-matplotlib = "^3.4"
-mkdocs-table-reader-plugin = "^0.6.1"
 openpyxl = "^3.0.9"
 mike = "^1.1.2"
-jinja2 = "<4"
+jinja2 = "^3.0"
 markupsafe = "<2.1"
-mkdocs-jupyter = "^0.21.0"
 jupyter = "^1.0.0"
 ipykernel = "^6.15.0"
-xarray = ">=2023.0.0"
+# matplotlib >=3.8 supports numpy 2.0
+matplotlib = "^3.8"
+# xarray >=2024.6.0 supports numpy 2.0, but consider looser version if adding it as actual package dependencies
+xarray = ">=2024.6.0"
 # add minimal pandas version for python 3.13 to prevent 2.0.3 to be installed by poetry
 # if we do not combine it with the minimal version for py3.8 poetry tries to install 
 # pandas 2.2.3 for python 3.8 which will naturally fail. The >=1.3 dep comes from xarray.
@@ -73,7 +75,7 @@ changelog_file = "docs/changelog.md"
 
 [tool.black]
 line-length = 88
-target-version = ['py38', 'py39', 'py310', 'py311']
+target-version = ['py39', 'py310', 'py311', 'py312']
 exclude = '''
 (
   /(
@@ -99,6 +101,7 @@ line_length = 88
 
 [tool.pytest.ini_options]
 markers = ["plots", "docker"]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

sonar-project.properties

@@ -11,4 +11,4 @@ sonar.organization=deltares
 # Encoding of the source code. Default is default system encoding
 sonar.sourceEncoding=UTF-8
 
-sonar.python.version=3.8, 3.9
+sonar.python.version=3.9, 3.10, 3.11, 3.12

tests/dflowfm/test_net.py

@@ -232,8 +232,10 @@ def test_create_2d_multiple_grids():
     [
         (DeleteMeshOption.INSIDE_NOT_INTERSECTED, False, 22, 68, 13),
         (DeleteMeshOption.INSIDE_AND_INTERSECTED, False, 30, 98, 20),
+        (DeleteMeshOption.FACES_WITH_INCLUDED_CIRCUMCENTERS, False, 28, 90, 18),
         (DeleteMeshOption.INSIDE_NOT_INTERSECTED, True, 33, 100, 19),
         (DeleteMeshOption.INSIDE_AND_INTERSECTED, True, 20, 62, 12),
+        (DeleteMeshOption.FACES_WITH_INCLUDED_CIRCUMCENTERS, True, 23, 72, 14),
     ],
 )
 def test_create_clip_2d(deletemeshoption, inside, nnodes, nedgenodes, nfaces):