fix overflow errors numpy v2

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/docs.yml

@@ -29,34 +29,28 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Mambaforge
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-            python-version: '3.11'
-            miniforge-variant: Mambaforge
-            miniforge-version: latest
-            use-mamba: true
-
-      - name: Setup env
-        run: |
-          python make_env.py full -p 3.11 -n pyflwdir -o environment-doc.yml
-          mamba env create -f environment-doc.yml
-          mamba run -n pyflwdir pip install -e .
+          pixi-version: "v0.39.2"
+          environments: default
+          locked: false
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       # if we're not publishing we don't have to write them, so we might as well
       # save ourself a bunch of IO time
       - name: Build dummy docs
         if: ${{ github.event_name == 'pull_request' }}
         run: |
-          mamba run -n pyflwdir sphinx-build ./docs ./docs/_build -b dummy -W
+          pixi run docs-dummy
 
       - name: Build html docs
         if: ${{ github.event_name != 'pull_request' }}
         run: |
-          mamba run -n pyflwdir sphinx-build -M html ./docs ./docs/_build -W
-          echo "DOC_VERSION=$(mamba run -n pyflwdir python -c 'from pyflwdir import __version__ as v; print("dev" if "dev" in v else "v"+v)')" >> $GITHUB_ENV
+          pixi run docs-html
+          echo "DOC_VERSION=$(pixi run version)" >> $GITHUB_ENV
 
       - name: Upload to GitHub Pages
         if: ${{ github.event_name != 'pull_request'}}

.github/workflows/test_cov.yml

@@ -29,32 +29,19 @@ jobs:
       cancel-in-progress: true
     steps:
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        id: pip
+      - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          # caching, see https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
-          python-version: '3.11'
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
-
-      # true if cache-hit occurred on the primary key
-      - name: Cache hit
-        run: echo '${{ steps.pip.outputs.cache-hit }}'
-
-      # build environment with pip
-      - name: Install pyflwdir
-        run: |
-          pip install --upgrade pip
-          pip install .[test]
-          pip list
+          pixi-version: "v0.39.2"
+          environments: test-py312
+          locked: false
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       # run test
       - name: Test
-        run: |
-          export NUMBA_DISABLE_JIT=1
-          python -m pytest --verbose --cov=pyflwdir --cov-report xml
+        run: pixi run -e test-py312 test-cov-xml
 
       # upload coverage
       - uses: codecov/codecov-action@v3

.github/workflows/tests.yml

@@ -24,39 +24,24 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.9', '3.10','3.11']
+        python-version: ['39', '310','311', '312']
     runs-on: ubuntu-latest
     timeout-minutes: 30
     concurrency:
       group: ${{ github.workflow }}-${{ matrix.python-version }}-${{ github.ref }}
       cancel-in-progress: true
     steps:
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        id: pip
+      - uses: prefix-dev/setup-pixi@v0.8.1
         with:
-          # caching, see https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
-
-      # true if cache-hit occurred on the primary key
-      - name: Cache hit
-        run: echo '${{ steps.pip.outputs.cache-hit }}'
-
-      # build environment with pip
-      - name: Install pyflwdir
-        run: |
-          pip install --upgrade pip
-          pip install .[test]
-          pip list
+          pixi-version: "v0.39.2"
+          environments: test-py${{ matrix.python-version }}
+          locked: false
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       # run test
       - name: Test
-        run: |
-          python -m pytest --verbose --cov=pyflwdir --cov-report xml
-
-      # upload coverage
-      - uses: codecov/codecov-action@v3
+        run: pixi run -e test-py${{ matrix.python-version }} test

.gitignore

@@ -100,9 +100,6 @@ venv.bak/
 .spyderproject
 .spyproject
 
-# VScode
-.vscode
-
 # PyCharm
 .idea
 
@@ -128,4 +125,7 @@ _pyflwdir
 scripts
 
 pyflwdir*.yml
-pixi.lock
+
+# pixi environments
+.pixi
+*.egg-info

.pre-commit-config.yaml

@@ -8,7 +8,6 @@ repos:
       - id: check-yaml
       - id: check-added-large-files
       - id: check-ast
-      - id: check-json
       - id: debug-statements
       - id: mixed-line-ending
   # make sure notebooks are stripped of output before committing

.vscode/launch.json

@@ -0,0 +1,21 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+
+        {
+            "name": "Python Debugger: Current File with Arguments",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "args": [
+                "${command:pickArgs}"
+            ],
+            "env": {"NUMBA_DISABLE_JIT": "1"},
+
+        }
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

CHANGELOG.rst

@@ -5,7 +5,13 @@ Change Log
 in development
 **************
 
+0.6.0  (19-12-2024)
+********************
+* Fixed numpy 2.0 compatibility issues
+* Fixed bug in strahler stream order method when more than two streams meet.
 * Fixed support for interger type DEMs in `from_dem` and `dem.fill_depressions` methods
+* Add support for py 3.12
+* Add support for pixi
 
 0.5.8  (06-Oct-2023)
 ********************

CONTRIBUTING.rst

@@ -108,70 +108,56 @@ First, clone pyflwdir's ``git`` repo and navigate into the repository:
     $ git clone git@github.com:Deltares/pyflwdir.git
     $ cd pyflwdir
 
-Then, make and activate a new pyflwdir conda environment based on the environment.yml
-file contained in the repository:
+Install pixi from `pixi.sh <pixi.sh>`__ to manage the development environment.
+To install the package in development mode, use the following command:
 
 .. code-block:: console
 
-    $ conda env create -f envs/pyflwdir-dev.yml
-    $ conda activate pyflwdir-dev
+    $ pixi install
+    $ pixi run install-pre-commit
 
-Finally, build and install PyFlwDir:
-
-.. code-block:: console
-
-    $ pip install -e .
+This will install the package in development mode and install the required dependencies.
 
 Running the tests
 ^^^^^^^^^^^^^^^^^
 
 PyFlwDir's tests live in the tests folder and generally match the main package layout.
 Test should be run from the tests folder.
 
-Note that to get a coverage report we need to disable numba jit. This can be done
-by setting the environment variable ``NUMBA_DISABLE_JIT=1``, see
-`numba docs <https://numba.pydata.org/numba-doc/dev/reference/envvars.html#envvar-NUMBA_DISABLE_JIT>`_
-
-To run the entire suite and the code coverage report.
+To run the tests, use the following command:
 
 .. code-block:: console
 
-    $ python -m pytest --verbose --cov=pyflwdir --cov-report term-missing
+    $ pixi run test
+
+To run the tests with coverage, numba needs to be disabled.
+This is done by setting the environment variable NUMBA_DISABLE_JIT to 1.
+These arguments are combined in the following command:
 
 .. code-block:: console
 
-    $ python -m pytest --verbose --cov=pyflwdir --cov-report term-missing
+    $ pixi run test-cov
 
 A single test file:
 
 .. code-block:: console
 
-    $ python -m pytest --verbose test_pyflwdir.py
+    $ pixi run python -m pytest --verbose test_pyflwdir.py
 
 A single test:
 
 .. code-block:: console
 
-    $ python -m pytest --verbose test_pyflwdir.py::test_save
+    $ pixi run python -m pytest --verbose test_pyflwdir.py::test_save
 
 Running code format checks
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The code formatting will be checked based on the `black clode style
-<https://black.readthedocs.io/en/stable/the_black_code_style.html>`__ during ci.
-Make sure the check below returns *All done!* before commiting your edits.
-
-To check the formatting of your code:
-
-.. code-block:: console
-
-    $ black --check .
-
 To automatically reformat your code:
 
 .. code-block:: console
 
-    $ black .
+    $ pixi run lint
 
 Creating a release
 ^^^^^^^^^^^^^^^^^^
@@ -188,7 +174,8 @@ Creating a release
 
 .. code-block:: console
 
-    $ python setup.py sdist bdist_wheel
+    $ flit build
+    $ python -m twine check dist/*
 
 4. Then use twine to upload our wheels to pypi. It will prompt you for your username and password.
 

environment.yml

@@ -1,19 +1,18 @@
 name: pyflwdir
 
 channels:
-  - conda-forge
+- conda-forge
 
-# note that these are the developer dependencies,
-# if you only want the user dependencies, see
-# install_requires in setup.py
 dependencies:
-  # required
-  - python>=3.9
-  - pyflwdir
-  # optional for notebooks
-  - cartopy>=0.20
-  - descartes
-  - geopandas>=0.8
-  - jupyter
-  - matplotlib
-  - rasterio
+- affine
+- cartopy>=0.20
+- descartes
+- geopandas>0.8
+- jupyter
+- matplotlib
+- numba>=0.54,<1.0
+- numpy
+- pandoc
+- python~=3.12.0
+- rasterio
+- scipy

examples/basins.ipynb

@@ -253,7 +253,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.10.5 ('hydromt-dev')",
+   "display_name": "default",
    "language": "python",
    "name": "python3"
   },
@@ -267,12 +267,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "3808d5b5b54949c7a0a707a38b0a689040fa9c90ab139a050e41373880719ab1"
-   }
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,

examples/streams.ipynb

@@ -88,7 +88,8 @@
    "source": [
     "# vectorize stream order for plotting\n",
     "feats = flw.streams(stream_mask, strord=strahler)\n",
-    "gdf = gpd.GeoDataFrame.from_features(feats, crs=crs)"
+    "gdf = gpd.GeoDataFrame.from_features(feats, crs=crs)\n",
+    "gdf.to_file(\"rhine_strahler.geojson\", driver=\"GeoJSON\")"
    ]
   },
   {
@@ -171,11 +172,9 @@
   }
  ],
  "metadata": {
-  "interpreter": {
-   "hash": "1d6565df54f631b3318aa7a4d6d8532e5ca49bf98056c57553f6cb4464998323"
-  },
   "kernelspec": {
-   "display_name": "Python 3.9.7 64-bit ('pyflwdir': conda)",
+   "display_name": "default",
+   "language": "python",
    "name": "python3"
   },
   "language_info": {
@@ -188,7 +187,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,