Improve cmdrun and testing

.github/workflows/ci-pixi-macos.yml

@@ -0,0 +1,37 @@
+name: mf6rtm continuous integration - macOS
+
+on:
+  schedule:
+    - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches: [main, develop, feature/**]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest]
+        python-version: ['310', '311', '312', '313']
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/[email protected]
+      with:
+        log-level: vvv
+        pixi-version: v0.41.4
+        cache: true
+        environments: py${{ matrix.python-version }}
+
+    - name: Install environment
+      run: pixi install -e py${{ matrix.python-version }}
+
+    - name: Run tests
+      run: pixi run -e py${{ matrix.python-version }} test
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci-pixi.yml

@@ -0,0 +1,70 @@
+name: mf6rtm continuous integration
+
+on:
+  schedule:
+    - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches: [main, develop, feature/**]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest, ubuntu-latest]
+        python-version: ['310', '311', '312', '313']
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.41.4
+        cache: true
+        environments: py${{ matrix.python-version }}
+
+    - name: Run tests
+      run: pixi run -e py${{ matrix.python-version }} test
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.41.4
+        cache: true
+
+    - name: Run linting
+      run: pixi run lint
+
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/[email protected]
+      with:
+        pixi-version: v0.41.4
+        cache: true
+        environments: py310
+
+    - name: Run tests with coverage
+      run: pixi run -e py310 test-cov
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Upload to Coveralls
+      run: pixi run -e py310 coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}

.gitignore

@@ -191,8 +191,7 @@ pyrightconfig.json
 *.png
 
 #Python pixi environments 
-pixi.lock
-pixi.toml
+.pixi/
 
 #Test output files
 /autotest/test01/*

README.md

@@ -29,18 +29,88 @@ Most options for each phreeqc block can be passed by adding list with options. H
 All dependencies and executables are included in this repo. This package extensively uses [modflowapi](https://github.com/MODFLOW-USGS/modflowapi) and [phreeqcrm](https://github.com/usgs-coupled/phreeqcrm)
 
 ## Installation
-The package can be installed through pip as:
+
+### Quick Start with pip
+
+The package can be installed via pip:
 
 ```commandline
 pip install mf6rtm
 ```
+
+### Manual Installation with Conda/Mamba
+
+If you prefer conda/mamba, create a dedicated environment:
+
+```commandline
+mamba env create -f env.yml
+mamba activate mf6rtm-dev
+```
+
+After activating the environment, install the MODFLOW6 executables:
+
+```commandline
+pip install modflow-devtools
+get-modflow --subset mf6,libmf6,gridgen :python
+```
+
+Once installed, the executables in `envs/[env-name]/bin` will be automatically invoked whenever mf6rtm runs within the environment.
+
+### Custom MODFLOW Versions
+
+If you need custom or older versions of mf6 (e.g., for running PESTPP on an HPC cluster), place them in a separate directory and use the provided utility to bring them to the model working directory:
+
+```Python
+from mf6rtm import utils
+
+utils.prep_bins(model_dir, src_path=path_to_bins)
+```
+### Running the benchmark notebooks
+We have provided some benchmarks in the form of Jupyter notebooks. We have also included the executables needed to run them out of the box. Nevertheless, they can also be run using the executables downloaded with modflow-devtools.
+
 ## Developing
-We recommend forking and cloning a local version of this repo. A development Conda environment is provided in the `env.yml` file, which should install all required dependencies to run tests and modify the package on the fly. To install the environment, use the following command:
+
+### With Pixi (Recommended)
+
+For development, we recommend using pixi for fast, reproducible environments:
+
+```commandline
+# Fork and clone the repository
+git clone https://github.com/YOUR-USERNAME/mf6rtm.git
+cd mf6rtm
+
+# Install development environment with all dependencies
+pixi install
+
+# Run tests
+pixi run test
+
+# Run tests with coverage
+pixi run test-cov
+
+# Run linting
+pixi run lint
+
+# Test with specific Python version
+pixi run -e py311 test
+
+```
+
+### With Conda/Mamba
+
+Alternatively, use conda/mamba with the provided environment file:
 
 ```commandline
+# Install environment
 conda env create -f env.yml
+conda activate mf6rtm-dev
+
+# Install development dependencies
+pip install -r requirements_dev.txt
 ```
 
+The development dependencies for testing are located in `requirements_dev.txt`. We have also provided dependencies with flopy and pyemu inside the repo but feel free to use your own distribution.
+
 ## Funding
 The developing of mf6rtm was kindly funded and supported by [Intera, Inc](https://www.intera.com).
 

autotest/pytest.ini

@@ -1,5 +1,5 @@
 [pytest]
-addopts = -rs -vvv --color=yes --cov=mf6rtm
+addopts = -ra --color=yes #--cov=mf6rtm
 log_cli = True
 log_cli_level = INFO