Merge pull request #36 from dnv-opensource/35-solve-errors-that-lead-…

…to-nightly-build-failing

35 solve errors that lead to nightly build failing

.gitattributes

@@ -30,3 +30,7 @@
 *.png -text
 *.gif -text
 *.ico -text
+
+# Denote all files that are truly binary and should not be modified.
+*.onnx binary
+*.fmu binary

.github/workflows/_build_and_publish_documentation.yml

@@ -17,7 +17,7 @@ jobs:
         with:
           lfs: true
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_build_package.yml

@@ -11,7 +11,7 @@ jobs:
         with:
           lfs: true
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_code_quality.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -28,7 +28,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -47,7 +47,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
@@ -66,7 +66,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"

.github/workflows/_test.yml

@@ -16,22 +16,21 @@ jobs:
           - version: '3.10'
           - version: '3.11'
           - version: '3.12'
+          - version: '3.13'
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          enable-cache: true
+          enable-cache: false
           cache-dependency-glob: "uv.lock"
       - name: Install Python ${{ matrix.python.version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python.version }}
       - name: Install the project
-        run: uv sync --upgrade -p ${{ matrix.python.version }} --no-dev
-      - name: Install pytest
-        run: |
-          uv pip install pytest
-          uv pip install pytest-cov
+        run: uv sync -p ${{ matrix.python.version }} -U --no-dev
       - name: Run pytest
-        run: uv run pytest --cov
+        run: >
+          uv run --with pytest --with pytest-cov
+          pytest --cov

.github/workflows/_test_future.yml

@@ -1,10 +1,10 @@
-name: Unit Tests (py313)
-# Test also with Python 3.13 (experimental; workflow will not fail on error.)
+name: Unit Tests (py314)
+# Test also with Python 3.14 (experimental; workflow will not fail on error.)
 
 on: workflow_call
 
 jobs:
-  test313:
+  test314:
     name: Test on ${{matrix.python.version}}-${{matrix.platform.runner}} (experimental)
     continue-on-error: true
     runs-on: ${{ matrix.platform.runner }}
@@ -14,24 +14,22 @@ jobs:
           - runner: ubuntu-latest
           - runner: windows-latest
         python:
-          - version: '3.13.0-alpha - 3.13.0'
-            uvpy: '3.13'
+          - version: '3.14.0-alpha - 3.14.0'
+            uvpy: '3.14'
     steps:
       - uses: actions/checkout@v4
       - name: Install uv
-        uses: astral-sh/setup-uv@v2
+        uses: astral-sh/setup-uv@v5
         with:
-          enable-cache: true
+          enable-cache: false
           cache-dependency-glob: "uv.lock"
       - name: Install Python ${{ matrix.python.version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python.version }}
       - name: Install the project
-        run: uv sync --upgrade -p ${{ matrix.python.uvpy }} --no-dev
-      - name: Install pytest
-        run: |
-          uv pip install pytest
-          uv pip install pytest-cov
+        run: uv sync -p ${{ matrix.python.uvpy }} -U --no-dev
       - name: Run pytest
-        run: uv run pytest --cov
+        run: >
+          uv run --with pytest --with pytest-cov
+          pytest --cov

.gitignore

@@ -156,5 +156,8 @@ demos/**/*.log
 demos/**/*.db
 demos/**/*.nc
 
+# Cmake generated files
+CMakeUserPresets.json
+
 # modules
-modules.txt
+modules.txt

.pre-commit-config.yaml

@@ -1,20 +1,20 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: mixed-line-ending
-        fix: auto
+        args: [--fix=auto]
       - id: trailing-whitespace
       - id: check-yaml
       - id: check-toml
       - id: check-merge-conflict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    rev: v0.9.2
     hooks:
-      - id: ruff
       - id: ruff-format
+      - id: ruff
   # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v1.9.0
+  #   rev: v1.14.1
   #   hooks:
   #     - id: mypy
-  #       exclude: tests/
+exclude: '(.venv|.*_cache)/.*'

.sourcery.yaml

@@ -50,6 +50,7 @@ rule_settings:
 
 metrics:
   quality_threshold: 20.0
+
 # github:
 #   labels: []
 #   ignore_labels:

.vscode/extensions.json

@@ -11,6 +11,8 @@
         "sourcery.sourcery",
         "njpwerner.autodocstring",
         "editorconfig.editorconfig",
+        "ms-toolsai.jupyter",
+        "ms-toolsai.jupyter-renderers",
         "ms-python.mypy-type-checker",
     ],
     // List of extensions recommended by VS Code that should not be recommended for users of this workspace.

.vscode/settings.json

@@ -30,6 +30,6 @@
     "python.terminal.activateEnvInCurrentTerminal": false,
     "mypy-type-checker.importStrategy": "fromEnvironment",
     "mypy-type-checker.reportingScope": "workspace",
-    "mypy-type-checker.preferDaemon": false,
+    "mypy-type-checker.preferDaemon": true,
     "ruff.configurationPreference": "filesystemFirst",
 }

CHANGELOG.md

@@ -5,22 +5,37 @@ The changelog format is based on [Keep a Changelog](https://keepachangelog.com/e
 
 ## [Unreleased]
 
+-/-
+
+
+## [0.4.1] - 2025-01-18
+
+### Added
+* Added support for Python 3.13
+* Added CITATION.cff
+* pyproject.toml : Added keywords
+
+### Solved
+* Resolved issues raised by `ruff` 0.9.2
+
 ### Dependencies
-* Updated to ruff>=0.8.3  (from ruff>=0.6.3)
-* Updated to pyright>=1.1.390  (from pyright>=1.1.378)
-* Updated to sourcery>=1.27  (from sourcery>=1.22)
+* Updated to ruff>=0.9.2  (from ruff>=0.6.3)
+* Updated to pyright>=1.1.392  (from pyright>=1.1.378)
+* Updated to sourcery>=1.31  (from sourcery>=1.22)
+* Updated to types-lxml>=2024.12  (from types-lxml>=2024.4)
+* Updated to sphinx-autodoc-typehints>=3.0  (from sphinx-autodoc-typehints>=2.2)
+* Updated to mypy>=1.14  (from mypy>=1.13)
+* Updated to setup-uv@v5  (from setup-uv@v2)
 * Updated to lxml>=5.3  (from lxml>=5.2)
-* Updated to types-lxml>=2024.11  (from types-lxml>=2024.4)
 * Updated to jupyter>=1.1  (from jupyter>=1.0)
 * Updated to pytest-cov>=6.0  (from pytest-cov>=5.0)
 * Updated to Sphinx>=8.1  (from Sphinx>=8.0)
 * Updated to sphinx-argparse-cli>=1.19  (from sphinx-argparse-cli>=1.17)
-* Updated to sphinx-autodoc-typehints>=2.5  (from sphinx-autodoc-typehints>=2.2)
 * Updated to pre-commit>=4.0  (from pre-commit>=3.8)
-* Updated to mypy>=1.13  (from mypy>=1.11.1)
-
-### Solved
-* Resolved issues raised by `ruff`
+* Updated to mypy>=1.14  (from mypy>=1.11.1)
+* numpy: As Python 3.13 requires numpy 2.x, made minimum required numpy version in pyproject.toml dependent on Python version:
+  * "numpy>=1.26; python_version < '3.13'",
+  * "numpy>=2.2; python_version >= '3.13'",
 
 
 ## [0.4.0] - 2024-11-11
@@ -360,7 +375,8 @@ This removes the need to manually add /src to the PythonPath environment variabl
 * Added support for Python 3.10
 
 <!-- Markdown link & img dfn's -->
-[unreleased]: https://github.com/dnv-opensource/dictIO/compare/v0.4.0...HEAD
+[unreleased]: https://github.com/dnv-opensource/dictIO/compare/v0.4.1...HEAD
+[0.4.1]: https://github.com/dnv-opensource/dictIO/compare/v0.4.0...v0.4.1
 [0.4.0]: https://github.com/dnv-opensource/dictIO/compare/v0.3.4...v0.4.0
 [0.3.4]: https://github.com/dnv-opensource/dictIO/compare/v0.3.3...v0.3.4
 [0.3.3]: https://github.com/dnv-opensource/dictIO/compare/v0.3.2...v0.3.3

CITATION.cff

@@ -0,0 +1,35 @@
+title: dictIO
+version: 0.4.1
+abstract: >-
+  Python package to read, write and manipulate dictionary text files.
+  Supports dictIOs native file format, as well as JSON, XML and OpenFOAM.
+type: software
+authors:
+  - name: DNV SE
+    address: 'Brooktorkai 18'
+    post-code: '20457'
+    city: Hamburg
+    country: DE
+    website: 'https://www.dnv.com/'
+  - given-names: Frank
+    family-names: Lumpitzsch
+    affiliation: DNV
+    email: frank.lumpitzsch@dnv.com
+    website: 'https://www.linkedin.com/in/frank-lumpitzsch-23013196/'
+  - given-names: Claas
+    family-names: Rostock
+    affiliation: DNV
+    email: claas.rostock@dnv.com
+    website: 'https://www.linkedin.com/in/claasrostock/?locale=en_US'
+  - given-names: Seunghyeon
+    family-names: Yoo
+    affiliation: DNV
+    email: seunghyeon.yoo@dnv.com
+    website: 'https://www.linkedin.com/in/seunghyeon-yoo-3625173b/'
+keywords:
+license: MIT
+license-url: 'https://dnv-opensource.github.io/dictIO/LICENSE.html'
+url: 'https://dnv-opensource.github.io/dictIO/README.html'
+repository-code: 'https://github.com/dnv-opensource/dictIO'
+message: 'Please cite this software using these metadata.'
+cff-version: 1.2.0

README.md

@@ -128,12 +128,21 @@ Clone the dictIO repository into your local development directory:
 ```sh
 git clone https://github.com/dnv-opensource/dictIO path/to/your/dev/dictIO
 ```
+Change into the project directory after cloning:
+```sh
+cd dictIO
+```
 
 ### 4. Install dependencies
 Run `uv sync` to create a virtual environment and install all project dependencies into it:
 ```sh
 uv sync
 ```
+> **Note**: Using `--no-dev` will omit installing development dependencies.
+
+> **Note**: `uv` will create a new virtual environment called `.venv` in the project root directory when running
+> `uv sync` the first time. Optionally, you can create your own virtual environment using e.g. `uv venv`, before running
+> `uv sync`.
 
 ### 5. (Optional) Activate the virtual environment
 When using `uv`, there is in almost all cases no longer a need to manually activate the virtual environment. <br>
@@ -163,6 +172,20 @@ uv run pre-commit install
 
 All pre-commit hooks configured in `.pre-commit-config.yaml` will now run each time you commit changes.
 
+pre-commit can also manually be invoked, at anytime, using:
+```sh
+uv run pre-commit run --all-files
+```
+
+To skip the pre-commit validation on commits (e.g. when intentionally committing broken code), run:
+```sh
+uv run git commit -m <MSG> --no-verify
+```
+
+To update the hooks configured in `.pre-commit-config.yaml` to their newest versions, run:
+```sh
+uv run pre-commit autoupdate
+```
 
 ### 7. Test that the installation works
 To test that the installation works, run pytest in the project root folder:
@@ -172,7 +195,7 @@ uv run pytest
 
 ## Meta
 
-Copyright (c) 2024 [DNV](https://www.dnv.com) SE. All rights reserved.
+Copyright (c) 2024 [DNV](https://www.dnv.com) AS. All rights reserved.
 
 Frank Lumpitzsch - [@LinkedIn](https://www.linkedin.com/in/frank-lumpitzsch-23013196/) - frank.lumpitzsch@dnv.com
 

STYLEGUIDE.md

@@ -372,9 +372,9 @@ If you are interested in the long story including the why‘s, read these discus
     import pandas as pd
     import numpy as np
 
-    import my_package
-    import my_package.my_module
-    from my_package.my_module import my_function, MyClass
+    import dictIO
+    import dictIO.my_module
+    from dictIO.my_module import my_function, MyClass
 ```
 
 * Even if a Python file is intended to be used as executable / script file only, it shall still be importable as a module, and its import should not have any side effects. Its main functionality shall hence be in a `main()` function, so that the code can be imported as a module for testing or being reused in the future:

docs/make.bat

@@ -10,8 +10,6 @@ if "%SPHINXBUILD%" == "" (
 set SOURCEDIR=source
 set BUILDDIR=build
 
-if "%1" == "" goto help
-
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.
@@ -25,6 +23,8 @@ if errorlevel 9009 (
 	exit /b 1
 )
 
+if "%1" == "" goto help
+
 %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -a -E
 goto end