Merge pull request #49 from simpeg/pyproject_update

Switch to pyproject.toml based install

Author: jcapriot

.bumpversion.cfg

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.coveragerc

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.git_archival.txt

@@ -62,10 +62,17 @@ jobs:
       run: |
         make coverage
 
+    - name: Generate Source Distribution
+      if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == '3.11') }}
+      run: |
+        pip install build twine
+        python -m build --sdist .
+        twine check dist/*
+
     - name: Test Documentation
       if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == '3.11') }}
       run: |
-        pip install -r requirements_docs.txt
+        pip install .[docs]
         cd docs
         make html
         cd ..
@@ -79,38 +86,41 @@ jobs:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   distribute:
-    name: Distributing from 3.8
+    name: Distributing
     needs: build-and-test
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
+    env:
+      PYTHON_VERSION: '3.11'
 
     steps:
     - uses: actions/checkout@v4
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
         auto-update-conda: true
-        activate-environment: dev
-        python-version: 3.8
+        channels: conda-forge
+        python-version: ${{ env.PYTHON_VERSION }}
 
-    - name: Install Env
+    - name: Install Base Env
       run: |
         conda info
         conda list
         conda config --show
-        conda install --quiet --yes -c conda-forge pip numpy scipy pydiso
-        pip install -r requirements_docs.txt
+        conda install --quiet --yes pip numpy scipy
 
     - name: Install Our Package
       run: |
-        pip install -v -e .
+        pip install -v -e .[docs]
 
     - name: Generate Source Distribution
       run: |
-        python setup.py sdist
+        pip install build twine
+        python -m build --sdist .
+        twine check dist/*
 
     - name: Build Documentation
       run: |
@@ -119,15 +129,16 @@ jobs:
         cd ..
 
     - name: GitHub Pages
-      uses: crazy-max/ghaction-github-pages@v2.5.0
+      uses: crazy-max/ghaction-github-pages@v4
       with:
         build_dir: docs/_build/html
         jekyll: false
+        keep_history: true
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: pypi-publish
-      uses: pypa/gh-action-pypi-publish@v1.4.2
+      uses: pypa/gh-action-pypi-publish@v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

.gitattributes

@@ -1,5 +1,6 @@
 .coverage
 coverage.xml
+coverage_html_report/
 *.pyc
 *.so
 build/

.github/workflows/python-package-conda.yml

@@ -0,0 +1,5 @@
+prune .github
+prune docs
+prune tests
+exclude .gitignore MANIFEST.in .pre-commit-config.yaml
+exclude .git_archival.txt .gitattributes Makefile

.gitignore

@@ -1,28 +1,11 @@
-.PHONY: build coverage lint graphs tests docs mumps mumps_mac mumps_install_mac
-
-build:
-	python setup.py build_ext --inplace
+.PHONY: coverage tests docs
 
 coverage:
-	pytest --cov-config=.coveragerc --cov-report=xml --cov=pymatsolver -s -v
-
-lint:
-	pylint --output-format=html pymatsolver > pylint.html
-
-graphs:
-	pyreverse -my -A -o pdf -p pymatsolver pymatsolver/**.py pymatsolver/**/**.py
+	pytest --cov --cov-config=pyproject.toml -s -v
+	coverage xml
 
 tests:
 	pytest
 
 docs:
 	cd docs;make html
-
-mumps:
-	cd pymatsolver/mumps;make build
-
-mumps_mac:
-	cd pymatsolver/mumps;make build_mac
-
-mumps_install_mac:
-	brew install mumps --with-scotch5 --without-mpi

MANIFEST.in

@@ -9,7 +9,7 @@ pymatsolver
     :target: https://github.com/simpeg/pymatsolver/blob/master/LICENSE
     :alt: MIT license.
 
-.. image:: https://codecov.io/gh/simpeg/pymatsolver/branch/master/graph/badge.svg
+.. image:: https://codecov.io/gh/simpeg/pymatsolver/branch/main/graph/badge.svg?token=8uQoxzxf3r
     :target: https://codecov.io/gh/simpeg/pymatsolver
     :alt: Coverage status
 
@@ -32,68 +32,42 @@ All solvers work with :code:`scipy.sparse` matricies, and a single or multiple r
 
 * L/U Triangular Solves
 * Wrapping of SciPy matrix solvers (direct and indirect)
-* Pardiso solvers now that MKL comes with conda!
-* Mumps solver with nice error messages
+* Pardiso solvers
+* Mumps solvers
 
 
-Installing Mumps
-================
+Installing Solvers
+==================
+Often, there are faster solvers available for your system than the default scipy factorizations available.
+pymatsolver provides a consistent interface to both MKL's ``Pardiso`` routines and the ``MUMPS`` solver package. To
+make use of these we use intermediate wrappers for the libraries that must be installed separately.
 
-We have not been able to get the pip install to work because of multiple dependencies on fortran libraries.
-However, the linux and mac installs are relatively easy. Note that you must have mumps pre-installed,
-currently we have only got this working for the sequential version, so when you are installing,
-you will need to point to that one. You can also look at the `.travis.yml` file for how to get it working on TravisCI.
+Pardiso
+-------
+The Pardiso interface is recommended for Intel processor based systems. The interface is enabled by
+the ``pydiso`` python package, which can be installed through conda-forge as:
 
-Linux
------
-
-From a clean install on Ubuntu:
-
-.. code-block:: bash
-
-    apt-get update
-    apt-get -y install gcc gfortran git libopenmpi-dev libmumps-seq-dev libblas-dev liblapack-dev
-
-    # Install all the python you need!
-    wget http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh -O miniconda.sh;
-    chmod +x miniconda.sh
-    ./miniconda.sh -b
-    export PATH=/root/anaconda/bin:/root/miniconda/bin:$PATH
-    conda update --yes conda
-    conda install --yes numpy scipy matplotlib cython ipython pytest coverage
-
-    git clone https://github.com/rowanc1/pymatsolver.git
-    cd pymatsolver
-    make mumps
+.. code::
 
-Mac
----
+    conda install -c conda-forge pydiso
 
-This assumes that you have Brew and some python installed (numpy, scipy):
-
-.. code-block:: bash
-
-    brew install mumps --with-scotch5 --without-mpi
-
-    git clone https://github.com/rowanc1/pymatsolver.git
-    cd pymatsolver
-    make mumps_mac
-
-If you have problems you may have to go into the Makefile and update the pointers to Lib and Include for the various libraries.
+Mumps
+-----
+Mumps is available for all platforms. The mumps interface is enabled by installing the ``python-mumps``
+wrapper package. This can easily be installed through conda-forge with:
 
-This command is helpful for finding dependencies. You should also take note of have happens when brew installs mumps.
+.. code::
 
-.. code-block:: bash
+    conda install -c conda-forge python-mumps
 
-    mpicc --showme
 
 
 Code:
 https://github.com/simpeg/pymatsolver
 
 
 Tests:
-https://travis-ci.org/simpeg/pymatsolver
+https://github.com/simpeg/pymatsolver/actions
 
 
 Bugs & Issues:

Makefile

@@ -49,17 +49,6 @@
   Mumps
 """
 
-SolverHelp = {}
-AvailableSolvers = {
-    "Diagonal": True,
-    "Solver": True,
-    "SolverLU": True,
-    "SolverCG": True,
-    "Triangle": True,
-    "Pardiso": False,
-    "Mumps": False
-}
-
 # Simple solvers
 from .solvers import Diagonal, Triangle, Forward, Backward
 from .wrappers import wrap_direct, WrapDirect
@@ -71,35 +60,58 @@
 from .iterative import BiCGJacobi
 
 # Scipy direct solvers
-from .direct import Solver
+from .direct import Solver, pardiso
 from .direct import SolverLU
 
-from .solvers import PymatsolverAccuracyError
+from .solvers import SolverAccuracyError
+from .direct import Pardiso, Mumps
+from .direct.pardiso import _available as _pardiso_available
+from .direct.mumps import _available as _mumps_available
+
+SolverHelp = {}
+AvailableSolvers = {
+    "Diagonal": True,
+    "Solver": True,
+    "SolverLU": True,
+    "SolverCG": True,
+    "Triangle": True,
+    "Pardiso": _pardiso_available,
+    "Mumps": _mumps_available,
+}
 
 BicgJacobi = BiCGJacobi  # backwards compatibility
+PardisoSolver = Pardiso  # backwards compatibility
 
-try:
-    from .direct import Pardiso
-    AvailableSolvers['Pardiso'] = True
-    PardisoSolver = Pardiso  # backwards compatibility
-except ImportError:
+if not AvailableSolvers["Pardiso"]:
     SolverHelp['Pardiso'] = """Pardiso is not working
 
 Ensure that you have pydiso installed, which may also require Python
 to be installed through conda.
 """
 
-try:
-    from .direct import Mumps
-    AvailableSolvers['Mumps'] = True
-except ImportError:
+if not AvailableSolvers["Mumps"]:
     SolverHelp['Mumps'] = """Mumps is not working.
 
 Ensure that you have python-mumps installed, which may also require Python
 to be installed through conda.
 """
 
-__version__ = '0.2.0'
 __author__ = 'SimPEG Team'
 __license__ = 'MIT'
 __copyright__ = '2013 - 2024, SimPEG Team, https://simpeg.xyz'
+
+from importlib.metadata import version, PackageNotFoundError
+
+# Version
+try:
+    # - Released versions just tags:       0.8.0
+    # - GitHub commits add .dev#+hash:     0.8.1.dev4+g2785721
+    # - Uncommitted changes add timestamp: 0.8.1.dev4+g2785721.d20191022
+    __version__ = version("pymatsolver")
+except PackageNotFoundError:
+    # If it was not installed, then we don't know the version. We could throw a
+    # warning here, but this case *should* be rare. discretize should be
+    # installed properly!
+    from datetime import datetime
+
+    __version__ = "unknown-" + datetime.today().strftime("%Y%m%d")

README.rst

@@ -1,18 +1,10 @@
-from ..wrappers import WrapDirect
 from scipy.sparse.linalg import spsolve, splu
 
+from ..wrappers import WrapDirect
+from .pardiso import Pardiso
+from .mumps import Mumps
+
 Solver = WrapDirect(spsolve, factorize=False, name="Solver")
 SolverLU = WrapDirect(splu, factorize=True, name="SolverLU")
 
-__all__ = ["Solver", "SolverLU"]
-try:
-    from .pardiso import Pardiso
-    __all__ += ["Pardiso"]
-except ImportError:
-    pass
-
-try:
-    from .mumps import Mumps
-    __all__ += ["Mumps"]
-except ImportError:
-    pass
+__all__ = ["Solver", "SolverLU", "Pardiso", "Mumps"]

pymatsolver/__init__.py

@@ -1,5 +1,10 @@
 from pymatsolver.solvers import Base
-from mumps import Context
+try:
+    from mumps import Context
+    _available = True
+except ImportError:
+    Context = None
+    _available = False
 
 class Mumps(Base):
     """The MUMPS direct solver.
@@ -33,6 +38,10 @@ class Mumps(Base):
     _transposed = False
 
     def __init__(self, A, ordering=None, is_symmetric=None, is_positive_definite=False, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+        if not _available:
+            raise ImportError(
+                "The Mumps solver requires the python-mumps package to be installed."
+            )
         is_hermitian = kwargs.pop('is_hermitian', False)
         super().__init__(A, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, is_hermitian=is_hermitian, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
         if ordering is None: