Add Spack configuration files.

Files for PROPKA, PDB2PQR, APBS.

Fixes #191.

docs/releases.rst

@@ -2,6 +2,15 @@
 Release history
 ===============
 
+----------------------------
+Current version (unreleased)
+----------------------------
+
+^^^^^^^^^^^^^
+Minor Updates
+^^^^^^^^^^^^^
+
+* Added `Spack <https://spack.io/>`_` configuration file to ``tools/spack`` directory.  See `#191 <https://github.com/Electrostatics/apbs/issues/191>_` for more information.
 
 ---------------------
 APBS 3.4.1 (Apr 2022)

docs/using/tools.rst

@@ -49,6 +49,14 @@ benchmark
 Benchmark file I/O for reading/writing scalar data.
 Found in :file:`tools/mesh`
 
+^^^^^
+spack
+^^^^^
+
+`Spack <https://spack.io/>`_` configuration files for APBS, PROPKA, and PDB2PQR.
+See `#191 <https://github.com/Electrostatics/apbs/issues/191>_` for more information.
+Found in :file:`tools/spack`
+
 ^^^^^^^^^^^^
 uhbd_asc2bin
 ^^^^^^^^^^^^

tools/spack/README.md

@@ -0,0 +1,3 @@
+# Spack configuration files
+
+This directory contains [Spack](https://spack.io/) configuration files for APBS, PROPKA, and PDB2PQR provided by [Stefan Richter](https://github.com/StefanGIT).

tools/spack/packages/apbs/package.py

@@ -0,0 +1,46 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Apbs(CMakePackage):
+    """
+    APBS (Adaptive Poisson-Boltzmann Solver) solves the equations of continuum electrostatics
+    for large biomolecular assemblages. This software was designed "from the ground up"
+    using modern design principles to ensure its ability to interface with other computational
+    packages and evolve as methods and applications change over time. The APBS code is
+    accompanied by extensive documentation for both users and programmers and is supported
+    by a variety of utilities for preparing calculations and analyzing results.
+    Finally, the free, open-source APBS license ensures its accessibility to the entire
+    biomedical community.
+    """
+
+    # Homepage and Github URL.
+    homepage = "https://www.poissonboltzmann.org/"
+    url      = "https://github.com/Electrostatics/apbs/archive/refs/tags/v3.4.0.tar.gz"
+
+    # List of GitHub accounts to notify when the package is updated.
+    maintainers = ['thielblz', 'richtesn']
+
+    # SHA256 checksum.
+    version('3.4.0', sha256='572ff606974119430020ec948c78e171d8525fb0e67a56dad937a897cac67461')
+
+    # Dependencies.
+    depends_on('cmake@3.19', type='build')
+    depends_on('python@3.8:3.10', type=('build', 'run'))
+    depends_on('blas', type=('build', 'run'))
+    depends_on('suite-sparse', type=('build', 'run'))
+    depends_on('maloc', type=('build', 'run'))
+
+    def cmake_args(self):
+        # Min and max Python versions need to be set as variables to pass tests.
+        # See tests/CMakeLists.txt lines 6-14.
+        args = [
+                '-DPYTHON_MIN_VERSION=3.8',
+                '-DPYTHON_MAX_VERSION=3.10',
+                ]
+        return args

tools/spack/packages/py-pdb2pqr/package.py

@@ -0,0 +1,34 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPdb2pqr(PythonPackage):
+    """
+    PDB2PQR - determining titration states,
+    adding missing atoms, and assigning
+    charges/radii to biomolecules.
+    """
+
+    # Url for the package's homepage.
+    homepage = "http://www.poissonboltzmann.org/"
+    pypi     = "pdb2pqr/pdb2pqr-3.5.2.tar.gz"
+
+    # List of GitHub accounts to
+    # notify when the package is updated.
+    maintainers = ['richtesn', 'thielblz']
+
+    version('3.5.2', sha256='9d145ff3797a563ce818f9d2488413ac339f66c58230670c2455b2572cccd957')
+    
+    depends_on('python@3.8:', type=('build','run'))
+    depends_on('py-docutils@:0.18', type=('build','run'))
+    depends_on('py-mmcif-pdbx@1.1.2:', type=('build','run'))
+    depends_on('py-numpy', type=('build','run'))
+    depends_on('py-propka@3.2:', type=('build','run'))
+    depends_on('py-requests', type=('build','run'))
+    depends_on('py-setuptools', type=('build','run'))
+

tools/spack/packages/py-propka/package.py

@@ -0,0 +1,32 @@
+
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPropka(PythonPackage):
+    """
+    PROPKA predicts the pKa values of ionizable
+    groups in proteins (version 3.0) and protein-ligand
+    complexes (version 3.1 and later) based on the 3D
+    structure.
+    For proteins without ligands both version should
+    produce the same result.
+    """
+
+    # Url for the package's homepage.
+    homepage = "http://propka.org/"
+    pypi     = "propka/propka-3.4.0.tar.gz"
+
+    # List of GitHub accounts to
+    # notify when the package is updated.
+    maintainers = ['richtesn', 'thielblz']
+
+    version('3.4.0', sha256='f19c2e145faa7eab000ce056a9058b8a30adba6970705047bb4fb7ba7570b020')
+
+    depends_on('py-setuptools', type=('build','run'))
+