Doc and pixi regression test

.github/workflows/ci.yml

@@ -258,3 +258,37 @@ jobs:
           bash run.sh
           cd ../../
 
+  Regression-Test-OF-pixi:
+    name: Regression-Test-OF-pixi (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-22.04']
+    defaults:
+      run:
+        shell: bash -l {0}
+        working-directory: ${{github.workspace}}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: gerlero/setup-openfoam@v1
+        with:
+          openfoam-version: 9
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          pixi-version: v0.62.2
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+      - name: Compile solver
+        run: |
+          cd OFsolvers/birdmultiphaseEulerFoam
+          export WM_COMPILE_OPTION=Debug
+          ./Allwmake
+          cd ../../
+      - name: Run bubble column tutorial
+        run: |
+          cd tutorial_cases/bubble_column_20L
+          bash run_pixi.sh 
+          cd ../../
+

bird/version.py

@@ -1,3 +1,3 @@
 """Bio reactor design version"""
 
-__version__ = "0.0.53"
+__version__ = "0.0.54"

docs/source/bubbleColumn.rst

@@ -20,7 +20,14 @@ To simply run the entire tutorial, do:
    cd ${BCE_CASE}
    bash run.sh
 
-This test is run as part of the continuous integration
+If you use pixi, make sure to run ``pixi shell`` first or 
+
+.. code-block:: console
+
+   cd ${BCE_CASE}
+   bash run_pixi.sh
+
+These tests are run as part of the continuous integration
 
 Geometry
 ------------

docs/source/contribute.rst

@@ -14,7 +14,15 @@ You can automatically enforce the formatting guidelines with
 
    pip install nox
    nox -s lint -- write 
+   nox -s spell -- write 
 
+If you use pixi, you can run 
+
+.. code-block:: console
+
+   pixi shell 
+   pixi run lint-write
+   pixi run spell-write
 
 Tests
 ------------
@@ -30,6 +38,15 @@ To run the unit tests
    cd ${BIRD_HOME}/../
    pytest .
 
+If you use pixi
+
+.. code-block:: console
+
+   pixi shell
+   BIRD_HOME=`python -c "import bird; print(bird.BIRD_DIR)"`
+   cd ${BIRD_HOME}/../
+   pixi run test
+
 To run the regression tests
 
 .. code-block:: console

docs/source/quickstart.rst

@@ -4,7 +4,7 @@ Quick start
 
 .. _installation_dev:
 
-Installation of python package for developers
+Installation of python package for developers (recommended)
 ------------
 
 
@@ -18,6 +18,23 @@ Installation of python package for developers
 
 .. _installation_users:
 
+Installation of python package for developers (with pixi)
+------------
+
+This requires installing pixi. If it is not available on your machine, follow `Pixi Installation <https://pixi.prefix.dev/latest/installation/>`_
+Once installed, pixi does not require the conda environment creation and pip install gymnastics, and can be used as 
+
+.. code-block:: console
+
+   git clone https://github.com/NREL/BioReactorDesign.git
+   cd BioReactorDesign
+   pixi shell
+
+This will activate an environment for you (equivalent to ``pip install -e .``)
+Alternatively to the ``pixi shell``, in any directory of BiRD, you can use ``pixi run python myscript.py`` instead of ``python myscript.py``
+
+.. _installation_users:
+
 Installation of python package for users
 ------------
 
@@ -64,3 +81,10 @@ Run an example
    cd tutorial_cases/bubble_column_20L
    bash run.sh
 
+If you run with pixi
+
+.. code-block:: console
+
+   cd tutorial_cases/bubble_column_20L
+   bash run_pixi.sh
+

tutorial_cases/bubble_column_20L/run_pixi.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+# Clean case
+./Allclean
+
+set -e  # Exit on any error
+# Define what to do on error
+trap 'echo "ERROR: Something failed! Running cleanup..."; ./Allclean' ERR
+
+
+echo PRESTEP 1
+# Generate blockmeshDict
+pixi run python ../../applications/write_block_cyl_mesh.py -i system/mesh.json -t system/topology.json -o system
+
+# Generate boundary stl
+pixi run python ../../applications/write_stl_patch.py -i system/inlets_outlets.json
+
+# Generate species thermo properties
+pixi run python ../../applications/write_species_thermo_prop.py -cf .
+
+
+echo PRESTEP 2
+# Mesh gen
+blockMesh -dict system/blockMeshDict
+transformPoints "rotate=((0 0 1) (0 1 0))"
+transformPoints "scale=(0.001 0.001 0.001)"
+
+# Inlet BC
+surfaceToPatch -tol 1e-3 inlets.stl
+export newmeshdir=$(foamListTimes -latestTime)
+rm -rf constant/polyMesh/
+cp -r $newmeshdir/polyMesh ./constant
+rm -rf $newmeshdir
+cp constant/polyMesh/boundary /tmp
+sed -i -e 's/inlets\.stl/inlet/g' /tmp/boundary
+cat /tmp/boundary > constant/polyMesh/boundary
+
+# setup IC
+cp -r 0.orig 0
+setFields
+
+# Scale
+transformPoints "scale=(0.19145161188225573 0.19145161188225573 0.19145161188225573)"
+
+# Setup mass flow rate
+# Get inlet area
+postProcess -func 'patchIntegrate(patch="inlet", field="alpha.gas")'
+postProcess -func writeCellVolumes
+writeMeshObj
+
+echo PRESTEP 3
+pixi run python writeGlobalVars.py
+cp constant/phaseProperties_pbe constant/phaseProperties
+
+
+echo RUN
+birdmultiphaseEulerFoam