resolved the awful merge commit from combining wall_tests and add_tor…

…ques.

.github/workflows/ci.yml

@@ -25,8 +25,9 @@ jobs:
           - name: Linux (CUDA 12)
     steps:
     - name: Check out
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
+        fetch-depth: 0
         submodules: recursive
 
     - name: Show dependency file
@@ -87,7 +88,8 @@ jobs:
         micromamba activate libmobility
         # install conda-build
         micromamba install -c conda-forge conda-build
-        conda build conda
+        export CUDA_VERSION=12
+        conda build devtools/conda-build
       shell: bash -el {0}
 
     - name: Install via pip

.github/workflows/conda.yaml

@@ -0,0 +1,44 @@
+name: Build and upload conda packages
+
+on:
+  release:
+    types: ['released', 'prereleased']
+  # lets add on PR for testing
+  # pull_request:
+  #   types: ['opened', 'edited', 'reopened', 'synchronize']
+
+  workflow_dispatch:        # Un comment line if you also want to trigger action manually
+
+jobs:
+  conda_deployment_with_new_tag:
+    name: Conda deployment of package with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        cuda-version: ["12.1", "12.6"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Conda environment creation and activation
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: devtools/conda-envs/build_env.yaml    # Path to the build conda environment
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+      - name: Build and upload the conda packages
+        uses: uibcdf/action-build-and-upload-conda-packages@v1.3.0
+        # Export cuda-version as an environment variable
+        env:
+          CUDA_VERSION: ${{ matrix.cuda-version }}
+        with:
+          meta_yaml_dir: devtools/conda-build
+          python-version: ${{ matrix.python-version }} # Values previously defined in `matrix`
+          user: stochasticHydroTools
+          label: auto
+          overwrite: true
+          token: ${{ secrets.ANACONDA_TOKEN }}

README.md

@@ -25,7 +25,7 @@ This repository is organized into the following directories:
 
 - **include/**: Includes the essential C++ base classes and utility files needed to construct the modules.  
 
-- **conda/**: Contains a meta.yaml file to build a conda package for libMobility using conda-build.  
+- **devtools/**: Contains dev specific scripts and files, like a meta.yaml file to build a conda package for libMobility using conda-build.  
 
 - **docs/**: Contains the source files for the documentation.  
 
@@ -70,12 +70,23 @@ The solvers constructor will check the provided configuration and throw an error
 
 
 ## How to use this repo
+
+### Installation
+
+#### Installing a pre-built binary
+
+You can install libMobility latest release through our conda channel:
+
+```shell
+$ conda install -c conda-forge -c stochasticHydroTools libmobility
+```
+
+#### Compiling from source
+
 Be sure to clone this repository recursively (using ```git clone --recurse```).  
 
 After compilation (see below) you will have all the tools mentioned above available for each solver.
 
-## Compilation
-
 We recommend working with a [conda](https://docs.conda.io/en/latest/) environment. The file environment.yml contains the necessary dependencies to compile and use the library.
 
 You can create the environment with:
@@ -108,7 +119,7 @@ The following variables are available to customize the compilation process:
   * DOUBLEPRECISION : If this variable is defined libMobility is compiled in double precision (single by default).  
 
 
-## Python Usage
+### Python Usage
 
 Importing libMobility will make available any module under "solvers".  
 
@@ -119,12 +130,13 @@ Calling
 ```
 will provide more in depth information about the solver.  
 
-## C++ Usage
+### C++ Usage
 
 In order to use a module called SolverName, the header solvers/SolverName/mobility.h must be included.  
 If the module has been compiled correctly the definitions required for the functions in mobility.h will be available at solvers/SolverName/mobility.so.  
 An example is available in cpp/example.cpp.  
-## Adding a new solver
+
+### Adding a new solver
 
 Solvers must be added following the ```libmobility::Mobility``` directives (see include/MobilityInterface). This C++ base class joins every solver under a common interface. When the C++ interface is prepared, the python bindings can be added automagically by using ```pythonify.h``` (a tool under MobilityInterface).  
 

conda/meta.yaml → devtools/conda-build/meta.yaml

@@ -1,25 +1,29 @@
 package:
   name: libmobility
-  version: 0.1.0
+  version: {{ GIT_DESCRIBE_TAG }}
 
 source:
-  path: ../  # Path to your project's source code
+  git_url: ../../
+
+build:
+  number: 0
+  string: cuda{{ CUDA_VERSION }}py{{ CONDA_PY }}h{{ PKG_HASH }}_{{ PKG_BUILDNUM }}
 
 requirements:
 
   build:
     - cmake >=3.22
-    - cuda-version 12.*
+    - cuda-version {{ CUDA_VERSION }}
     - gxx
     - cuda-libraries-dev
     - cuda-nvcc 
     - make
     - mkl-devel
     - pybind11
-    - python 3.11.*
+    - python
   run:
-    - python 3.11.*
-    - cuda-version 12.*
+    - python
+    - cuda-version >={{ CUDA_VERSION }}
     - numpy
     - cuda-libraries
     - mkl
@@ -33,7 +37,7 @@ test:
   source_files:
     - tests
   commands:
-    - pytest -vs -k SelfMobility tests/test_*py
+    - pytest -vs -k "SelfMobility and not fluct" tests/test_*py
 
 about:
   home: https://github.com/stochasticHydroTools/libmobility

devtools/conda-envs/build_env.yaml

@@ -0,0 +1,7 @@
+channels:    # write here the list of channels to look for your library dependencies
+  - conda-forge
+  - default
+
+dependencies:   # Keep this block with only these two packages
+  - anaconda-client
+  - conda-build

docs/source/installation.rst

@@ -1,11 +1,32 @@
 Installation
 ============
 
-We recommend working with a `conda <https://docs.conda.io/en/latest/>`_ environment. The file ``environment.yml`` contains the necessary dependencies to compile and use the library.
+We recommend working with a `conda <https://docs.conda.io/en/latest/>`_ environment.
+
+You can install libMobility's latest release through our conda channel:
+
+.. code-block:: shell
+
+    $ conda install -c conda-forge -c stochasticHydroTools libmobility
+
+
+
+Compilation from source
+~~~~~~~~~~~~~~~~~~~~~~~
+
+If you want to compile the library from source, you can clone the repository with:
+
+.. code-block:: shell
+
+    $ git clone --recursive https://github.com/stochasticHydroTools/libMobility
+
+The ``--recursive`` flag is necessary to clone the submodules of the repository.
 
 Getting dependencies
 --------------------
 
+The file ``environment.yml`` contains the necessary dependencies to compile and use the library.
+
 You can create the environment with:
 
 .. code-block:: shell
@@ -20,21 +41,39 @@ Then, activate the environment with:
 
 .. hint:: At the moment we offer several installation methods: via pip, conda or building from source. We recommend using pip or conda first, resorting to building from source only if the other methods do not work for you.
 
+Building from source
+--------------------
+
+CMake is used for compilation under the hood. After installing the dependencies you can compile and install everything with:
+
+.. code-block:: shell
+
+    $ mkdir build && cd build
+    $ cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX ..
+    $ make all install
+
+It is advisable to install the library in the conda environment, so that the python bindings are available. The environment variable ``$CONDA_PREFIX`` is set to the root of the conda environment.
+
+After compilation, the python bindings will be available in the conda environment under the name ``libMobility``. See :ref:`usage` for more information.
+
+The following variables are available to customize the compilation process:
+
+- ``DOUBLEPRECISION``: If this variable is defined, libMobility is compiled in double precision (single by default).
 
-Installing via pip
-------------------
+Alternative: Installing via pip
+-------------------------------
 
 After installing the dependencies, you can install the library with pip. Go to the root of the repository and run:
 
 .. code-block:: shell
 
     $ pip install .
     
+   
+Alternative: Building a conda package
+-------------------------------------
 
-Building a conda package
-------------------------
-
-Building the conda package only requires the conda-build package. You can install it with:
+Building the conda package only requires the conda-build package (dependencies will be fetched automatically). You can install it with:
 
 .. code-block:: shell
 
@@ -44,7 +83,7 @@ You can build a conda package with the following command from the root of the re
 
 .. code-block:: shell
 		
-    $ conda build conda
+    $ conda build devtools/conda-build
 
 This will build and test the package, which you can install in any environment with:
 
@@ -55,22 +94,3 @@ This will build and test the package, which you can install in any environment w
 Conda will automatically install all the dependencies needed to run the library.
 
 
-Building from source
---------------------
-
-
-CMake is used for compilation, you can compile and install everything with:
-
-.. code-block:: shell
-
-    $ mkdir build && cd build
-    $ cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX ..
-    $ make all install
-
-It is advisable to install the library in the conda environment, so that the python bindings are available. The environment variable ``$CONDA_PREFIX`` is set to the root of the conda environment.
-
-After compilation, the python bindings will be available in the conda environment under the name ``libMobility``. See :ref:`usage` for more information.
-
-The following variables are available to customize the compilation process:
-
-- ``DOUBLEPRECISION``: If this variable is defined, libMobility is compiled in double precision (single by default).

setup.py

@@ -4,6 +4,16 @@
 import os
 import sys
 
+try:
+    version = (
+        subprocess.check_output(["git", "describe", "--abbrev=0", "--tags"])
+        .strip()
+        .decode("utf-8")
+    )
+except:
+    print("Failed to retrieve the current version, defaulting to 0")
+    version = "0"
+
 
 class CMakeExtension(Extension):
     def __init__(self, name, sourcedir=""):
@@ -50,7 +60,7 @@ def build_extension(self, ext):
 
 setup(
     name="libMobility",
-    version="0.1.0",
+    version=version,
     packages=find_packages(),
     ext_modules=[CMakeExtension("libMobility")],
     cmdclass=dict(build_ext=CMakeBuild),

solvers/DPStokes/extra/poly_fits.h

@@ -1,7 +1,25 @@
+/* Ryker Fish 2024. Helpers to compute values of c^{-1} from [1].
+
+The ES kernel has a function c(beta) that provides a relationship between the hydrodynamic radius and the kernel
+parameters alpha and beta. There is no closed form for c, but we can approximate c and c^{-1} with a polynomial fit.
+
+We have rH = h*w*c(beta), where rH is the hydrodynamic radius, h is the grid spacing, and w is the width of the kernel. 
+Thus, we can write c^{-1}(rH/(h*w)) = beta.
+
+References:
+[1] Computing hydrodynamic interactions in confined doubly periodic geometries in linear time.
+A. Hashemi et al. J. Chem. Phys. 158, 154101 (2023) https://doi.org/10.1063/5.0141371
+ */
+
 #include <vector>
 
 namespace dpstokes_polys{
 
+  /* Evaluates a polynomial at x with coefficients in descending order, so the highest order coefficients
+  are at the start of polyCoeffs.
+  e.g. for a polynomial of order n, this computes 
+      polyCoeffs[n+1] + polyCoeffs[n]*x + polyCoeffs[n-2]*x^2 + ... + polyCoeffs[0]*x^n
+  */
   double polyEval(std::vector<double> polyCoeffs, double x){
 
     int order = polyCoeffs.size() - 1;
@@ -15,6 +33,7 @@ namespace dpstokes_polys{
     return accumulator;
   }
 
+  // Coefficients for the polynomial fit of c^{-1} from [1]
   std::vector<double> cbetam_inv = {
   4131643418.193291,
   -10471683395.26777,