Update branch with master

inbo · Oct 16, 2024 · af53a0e · af53a0e
2 parents 53523ac + 288b351
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diff --git a/.github/workflows/tests-coverage.yml b/.github/workflows/tests-coverage.yml
@@ -9,20 +9,24 @@ on:
 jobs:
   windows-conda-tests:
     runs-on: "windows-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
-          environment-file:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: PowerShell
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: true
+      - name: Run unit tests
         shell: powershell
         run: |
-          conda config --add channels conda-forge
-          conda config --set channel_priority strict
-          conda install pandas=1.5.3 pyyaml rasterio fiona
-          pip install -e .
+          pip install . --no-deps
           pip install -r dev-requirements.txt coverage
           pytest --cov niche_vlaanderen --cov-report xml --verbose --tb=long
       - name: Upload coverage
@@ -31,14 +35,15 @@ jobs:
             coveralls --service=github
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_PARALLEL: true 
+          COVERALLS_PARALLEL: true
+
   linux-pip-tests:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
         fail-fast: [false]
-
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -6,10 +6,10 @@ Windows
 =======
 
 The recommended way of installing niche_vlaanderen on windows uses miniconda_ for installation.
-The recommended version is `64 bit with Python 3.9`__.
+The currently recommended version is `64 bit with Python 3.11`__.
 
-__ https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Windows-x86_64.exe
-.. _Miniconda: https://conda.io/miniconda.html
+__ https://repo.anaconda.com/miniconda/Miniconda3-py311_24.7.1-0-Windows-x86_64.exe
+.. _Miniconda: https://docs.anaconda.com/miniconda/
 
 The installation can proceed without administrator rights, keep the default options. After miniconda is installed,
 we will proceed installing niche_vlaanderen in its own environment.
@@ -24,42 +24,57 @@ You will probably see something as:
   OR
     (base) C:\Users\myusername> 
 
-Create an environment (called niche in this example) that will contain niche_vlaanderen and its dependencies:
+For the remainder, we use ``(<CONDA-ENV-NAME>) C:\>`` to indicate the prompt.
 
-.. code-block:: shell
+.. Note::
+   If you do not use the installation of Miniconda with the default Python version of 3.11
+   (i.e. the python version in your ``base`` environment is not Python 3.11), you can still
+   create an environment with Python 3.11 by running the following command::
 
-    (C:\Users\myusername\Miniconda3) C:\Users\myusername> conda create --name niche
+       (base) C:\> conda create -n py311 python=3.11
+       (base) C:\> conda activate py311
+       (py311) C:\>
 
-Activate the niche environment:
+   By running the commands below from ``py311`` environment instead of ``base``, you will also install niche_vlaanderen in an environment
+   `niche` with Python 3.11.
+
+To install packages, conda used a dependency resolver. Make sure the ``libmamba`` solver is activated by running
+the following commands in the command prompt:
 
 .. code-block:: shell
 
-    (C:\Users\myusername\Miniconda3) C:\Users\myusername> conda activate niche
+    (base) C:\> conda config --show-sources
+    (base) C:\> conda config --set solver libmamba
 
-You will see that `(C:\\Users\\myusername\\Miniconda3)`/`(base)` will change into `(niche)`.
+Once the correct solver is set, create an environment (called ``niche``) that will contain niche_vlaanderen and its dependencies:
+
+.. code-block:: shell
+
+    (base) C:\> conda env create -f environment.yml
 
-Now install the niche_vlaanderen package and its dependencies within the niche environment:
+Activate the niche environment:
 
 .. code-block:: shell
 
-    (niche) C:\Users\myusername> conda install pandas pyyaml rasterio fiona
-    (niche) C:\Users\myusername> pip install niche_vlaanderen
+    (base) C:\> conda activate niche
+
+You will see that `(C:\\Users\\myusername\\Miniconda3)`/`(base)` will change into `(niche)`.
 
-It is strongly recommended to install also `matplotlib` (otherwise plotting
-will not work) and `jupyter` notebook, which allows interactive usage from a web browser.
+Now install the niche_vlaanderen package within the niche environment (with the option ``--no-deps``
+to avoid installing dependencies that are already in the environment):
 
 .. code-block:: shell
 
-    (niche) C:\Users\myusername> conda install matplotlib jupyter
+    (niche) C:\> pip install niche-vlaanderen --no-deps
 
 You can verify the installation was successful by running the command line interface.
 Note you must activate niche once more, because some changes were made during
 installation.
 
 .. code-block:: shell
 
-    (C:\Users\myusername\Miniconda3) C:\Users\myusername> conda activate niche
-    (niche) C:\Users\myusername> niche --help
+    (base) C:\> conda activate niche
+    (niche) C:\> niche --help
     Usage: niche [OPTIONS] CONFIG
 
       Command line interface to the NICHE vegetation model
@@ -77,8 +92,8 @@ from the Anaconda prompt).
 
 .. code-block:: shell
 
-    (C:\Users\myusername\Miniconda3) C:\Users\myusername> conda activate niche
-    (niche) C:\Users\myusername> pip install niche_vlaanderen --upgrade
+    (base) C:\> conda activate niche
+    (niche) C:\> pip install niche_vlaanderen --upgrade  --no-deps
     
 Note you might need to update other packages.
 
@@ -89,24 +104,5 @@ If you want to install a specific niche_vlaanderen version, you can install usin
 
 .. code-block:: shell
 
-    (C:\Users\myusername\Miniconda3) C:\Users\myusername> conda activate niche
-    (niche) C:\Users\myusername> pip install niche_vlaanderen==1.0
-
-Alternative installation
-========================
-It is possible to install niche_vlaanderen without using an environment. This is currently not
-the recommended installation as it requires setting an environment variable for
-opening some grid files. (See :ref:`missing_gcs` for instructions).
-
-.. code-block:: shell
-
-    conda install pandas pyyaml rasterio fiona
-    pip install niche_vlaanderen
-
-Like for the normal installation, it is strongly recommended to install also `matplotlib` (otherwise plotting
-will not work) and `jupyter` notebook, which allows interactive usage from a web browser.
-
-.. code-block:: shell
-
-    conda install matplotlib jupyter
-
+    (base) C:\> conda activate niche
+    (niche) C:\> pip install niche_vlaanderen==1.0
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,15 @@
+name: niche
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - geopandas
+  - numpy
+  - pandas
+  - pygeos
+  - pyyaml
+  - rasterio
+  - rasterstats>=0.17
+  - tqdm
+  - jupyter
+  - matplotlib