diff options
| -rw-r--r-- | .SRCINFO | 5 | ||||
| -rw-r--r-- | PKGBUILD | 14 | ||||
| -rw-r--r-- | fix_entrypoint.patch | 74 |
3 files changed, 89 insertions, 4 deletions
@@ -1,17 +1,20 @@ pkgbase = python-pdb2pqr pkgdesc = Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation. pkgver = 3.0.1 - pkgrel = 1 + pkgrel = 2 url = http://pypi.python.org/pypi/pdb2pqr arch = any license = BSD + makedepends = patch depends = python>=3.5 depends = python-propka>=3.2 depends = python-pandas>=1.0 depends = python-pytest>=5.4.1 options = !emptydirs source = https://files.pythonhosted.org/packages/source/p/pdb2pqr/pdb2pqr-3.0.1.tar.gz + source = fix_entrypoint.patch sha256sums = 15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0 + sha256sums = bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211 pkgname = python-pdb2pqr @@ -3,16 +3,24 @@ pkgname=python-pdb2pqr _name=${pkgname#python-} pkgver=3.0.1 -pkgrel=1 +pkgrel=2 pkgdesc="Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation." arch=(any) url="http://pypi.python.org/pypi/${_name}" license=(BSD) depends=('python>=3.5' 'python-propka>=3.2' 'python-pandas>=1.0' 'python-pytest>=5.4.1') -source=("https://files.pythonhosted.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz") -sha256sums=('15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0') +makedepends=(patch) +source=("https://files.pythonhosted.org/packages/source/${_name::1}/${_name}/${_name}-${pkgver}.tar.gz" + "fix_entrypoint.patch") +sha256sums=('15ac0ce77dc17fb459092aca12cc7c2c070904f77914f1197282e28f418b6bd0' + 'bb177e8fb9a31f2486e5682ae97139ebf87948fb4dc33dc892e90ff606df7211') options=(!emptydirs) +prepare() { + cd "${srcdir}/${_name}-${pkgver}" + patch -Np0 -i "${srcdir}/fix_entrypoint.patch" +} + build() { cd "${srcdir}/${_name}-${pkgver}" python setup.py build diff --git a/fix_entrypoint.patch b/fix_entrypoint.patch new file mode 100644 index 000000000000..cb004817eb72 --- /dev/null +++ b/fix_entrypoint.patch @@ -0,0 +1,74 @@ +--- pdb2pqr/__init__.py 2020-07-03 20:02:43.000000000 +0300 ++++ pdb2pqr/__init__.py 2020-08-25 20:48:59.940600307 +0300 +@@ -6,11 +6,11 @@ + For more information, see http://www.poissonboltzmann.org/
+ """
+ import logging
+ from sys import version_info
+ assert version_info >= (3, 5)
+-from .main import main, build_parser
++from .main import main_driver, build_parser
+
+
+ _LOGGER = logging.getLogger(__name__)
+ logging.captureWarnings(True)
+
+@@ -18,6 +18,6 @@ + if __name__ == "__main__":
+ logging.basicConfig(level=logging.DEBUG)
+ logging.captureWarnings(True)
+ parser = build_parser()
+ args = parser.parse_args()
+- main(args)
++ main_driver(args)
+--- pdb2pqr/__main__.py 2020-07-03 20:02:43.000000000 +0300 ++++ pdb2pqr/__main__.py 2020-08-25 20:49:15.213902523 +0300 +@@ -6,11 +6,11 @@ + For more information, see http://www.poissonboltzmann.org/
+ """
+ import logging
+ from sys import version_info
+ assert version_info >= (3, 5)
+-from pdb2pqr.main import main, build_parser
++from pdb2pqr.main import main_driver, build_parser
+
+
+ _LOGGER = logging.getLogger(__name__)
+ logging.captureWarnings(True)
+
+@@ -18,6 +18,6 @@ + if __name__ == "__main__":
+ logging.basicConfig(level=logging.DEBUG)
+ logging.captureWarnings(True)
+ parser = build_parser()
+ args = parser.parse_args()
+- main(args)
++ main_driver(args)
+--- pdb2pqr/main.py 2020-07-03 20:02:43.000000000 +0300 ++++ pdb2pqr/main.py 2020-08-25 20:50:27.673754924 +0300 +@@ -533,11 +533,11 @@ + lines = io.print_protein_atoms(matched_atoms, args.keep_chain)
+
+ return {"lines": lines, "header": header, "missed_residues": missing_atoms}
+
+
+-def main(args):
++def main_driver(args):
+ """Main driver for running program from the command line.
+
+ Validate inputs, launch PDB2PQR, handle output.
+
+ Args:
+@@ -581,5 +581,12 @@ + missing_lines=results["missed_residues"], is_cif=is_cif)
+
+ if args.apbs_input:
+ raise NotImplementedError("Missing argument for APBS input file.")
+ io.dump_apbs(args.output_pqr)
++
++
++def main():
++ """Hook for command-line usage."""
++ parser = build_parser()
++ args = parser.parse_args()
++ main_driver(args)
|