Use declarative setup for SnapPy

install_usermodule_r8.sh

@@ -52,11 +52,9 @@ install_snappy() {
     )
 
     (
-        export VERSION="$SNAPPY_VERSION"
         # Pip install messes up shebang: https://github.com/pypa/setuptools/issues/494
         # pip install ./utils/SnapPy/
-        cd utils/SnapPy || exit 2
-        python3 setup.py install
+        pip install ./utils/SnapPy
     )
 }
 
@@ -70,14 +68,8 @@ install_bsnap() {
 main() {
     if [ -z "$1" ]; then
         MODULE_VERSION="TEST"
-        SNAPPY_VERSION="0.0.0.dev0"
     else
         MODULE_VERSION="$1"
-        if [ -z "$2" ]; then
-            SNAPPY_VERSION="$MODULE_VERSION"
-        else
-            SNAPPY_VERSION="$2"
-        fi
     fi
 
     MODULE_PREFIX=/modules/rhel8/user-apps/fou-modules/SnapPy/"$MODULE_VERSION"/

src/naccident/Makefile

@@ -15,9 +15,8 @@ clean: clean_links
 distclean: clean
 	rm -f bsnap_naccident create_naccident_input create_naccident_output
 
-install: bsnap_naccident ../../utils/SnapPy/Snappy/AddToa.py
+install: bsnap_naccident
 	install bsnap_naccident $(BINDIR)/
-	install ../../utils/SnapPy/Snappy/AddToa.py $(BINDIR)/snapAddToa
 
 
 .PHONY: all clean distclean install

utils/SnapPy/Snappy/AddToa.py

@@ -94,7 +94,7 @@ def add_toa_to_nc(nc: netCDF4.Dataset):
                 totalVar[:] = total
 
 
-if __name__ == "__main__":
+def main():
     import argparse
 
     parser = argparse.ArgumentParser()
@@ -103,3 +103,7 @@ def add_toa_to_nc(nc: netCDF4.Dataset):
 
     with netCDF4.Dataset(args.snapNc, "a") as nc:
         add_toa_to_nc(nc)
+
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/debian.bionic/control

@@ -2,13 +2,13 @@ Source: snap-py
 Maintainer: Heiko Klein <[email protected]>
 Section: python
 Priority: optional
-Build-Depends: python3-all, python3-netcdf4, debhelper (>= 7.4.3)
+Build-Depends: python3-all, python3-setuptools, debhelper (>= 7.4.3)
 Standards-Version: 3.9.7
 
 
 Package: snap-py
 Architecture: all
-Depends: ${misc:Depends}, ${python3:Depends}, bsnap (>= 2.1.2), python3-pyqt5, python3-pyqt5.qtwebkit
+Depends: ${misc:Depends}, ${python3:Depends}, bsnap (>= 2.1.2), python3-pyqt5, python3-pyqt5.qtwebkit, python3-netcdf4, python3-numpy
 Description: SNAP GUI in python
 
 

utils/SnapPy/debian.bionic/rules

@@ -19,11 +19,11 @@ override_dh_auto_build:
 
 
 override_dh_auto_install:
-	python3 setup.py install --force --root=debian/snap-py --no-compile -O0 --install-layout=deb
+	python3 setup.py install --force --root=debian/snap-py --no-compile -O0 --install-layout=deb --prefix=/usr
 
 
 
 override_dh_python2:
-	echo "omit: dh_python2 --no-guessing-versions"
+	dh_python2 --no-guessing-versions
 
 

utils/SnapPy/setup.cfg

@@ -0,0 +1,45 @@
+[metadata]
+name = Snappy
+version = 2.3.0
+description = SNAP utilities in python
+url = https://gitlab.met.no/emep/snap
+author = Heiko Klein
+author_email = [email protected]
+license = GPL-3.0-only
+
+[options]
+zip_safe = False
+include_package_data = True
+packages = find:
+setup_requires =
+    setuptools
+install_requires =
+    netCDF4
+    numpy
+
+[options.package_data]
+Snappy =
+    resources/*
+Snappy.EEMEP =
+    resources/*
+
+[options.entry_points]
+gui_scripts =
+    snapPy = snapscripts.snapPy:main
+console_scripts =
+    snap4rimsterm = snapscripts.snap4rimsterm:main
+    snapAddToa = snappy.AddToa:main
+    snapCombineInverse = snapscripts.snapCombineInverse:main
+    snapNc2grib = snapscripts.snapNc2grib:main
+    snapRunnerNpps = snapscripts.snapRunnerNpps:main
+    snapRunnerNpp = snapscripts.snapRunnerNpp:main
+    eemepModelRunner = snapscripts.eemepModelRunner:main
+    snapRemoteRunner = snapscripts.snapRemoteRunner:main
+    snapEnsPlot = snapscripts.snapEnsPlot:main
+
+
+[options.extras_require]
+gui =
+    cartopy
+    # PyQt5
+    # PyQtWebKit

utils/SnapPy/setup.py

@@ -1,46 +1,4 @@
-#!/usr/bin/env python3
-#
-# SNAP: Servere Nuclear Accident Programme
-# Copyright (C) 1992-2017   Norwegian Meteorological Institute
-#
-# This file is part of SNAP. SNAP is free software: you can
-# redistribute it and/or modify it under the terms of the
-# GNU General Public License as published by the
-# Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <https://www.gnu.org/licenses/>.
-#
+#! /usr/bin/env python3
+from setuptools import setup
 
-from distutils.core import setup
-import os
-
-version = os.getenv("VERSION", "0.5")
-
-setup(
-    name="Snappy",
-    version=version,
-    description="SNAP GUI in python",
-    author="Heiko Klein",
-    author_email="[email protected]",
-    url="https://gitlab.met.no/emep/snap",
-    packages=["Snappy", "Snappy.EEMEP", "METNO"],
-    package_dir={"Snappy": "Snappy", "Snappy.EEMEP": "Snappy/EEMEP"},
-    package_data={"Snappy": ["resources/*"], "Snappy.EEMEP": ["resources/*"]},
-    scripts=[
-        "snapPy",
-        "snap4rimsterm",
-        "snapCombineInverse",
-        "snapNc2grib.py",
-        "snapRunnerNpps",
-        "snapRunnerNpp",
-        "eemepModelRunner",
-        "snapRemoteRunner.py",
-    ],
-)
+setup()

utils/SnapPy/eemepModelRunner → utils/SnapPy/snapscripts/eemepModelRunner.py

@@ -176,7 +176,7 @@ def __init__(self, directory, hpc, directory2, dryrun=False):
 
 
 
-if __name__ == '__main__':
+def main():
     os.umask(0)
     import argparse
     parser = argparse.ArgumentParser(description="Search for volcano.xml/npp.xml files in the top-level directory, take the newest one and run the model on a HPC machine")
@@ -197,3 +197,7 @@ def __init__(self, directory, hpc, directory2, dryrun=False):
             delete_oldfiles(args.dir, args.cleanup)
         if dir2 and dirIsWritable(dir2):
             delete_oldfiles(dir2, args.cleanup)
+
+
+if __name__ == '__main__':
+    main()

utils/SnapPy/snap4rimsterm → utils/SnapPy/snapscripts/snap4rimsterm.py

@@ -245,7 +245,7 @@ def snap4rimsterm(rimsterm, argosrequest, basedir, ident, met_model, bitmapCompr
 
 
 
-if __name__ == "__main__":
+def main():
     os.umask(0) # make sure files can be deleted later
     import argparse
     parser = argparse.ArgumentParser(description="run snap from a rimsterm.xml file and convert to grib-files named ident_conc, ident_depo ident_wetd ident_dose ident_tofa")
@@ -261,3 +261,7 @@ def snap4rimsterm(rimsterm, argosrequest, basedir, ident, met_model, bitmapCompr
         snap4rimsterm(args.rimsterm, args.argosrequest, args.dir, args.ident, args.metmodel, bitmapCompress=args.bitmapCompress)
     else:
         print("need rimsterm option", file=sys.stderr)
+
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/snapCombineInverse → utils/SnapPy/snapscripts/snapCombineInverse.py

@@ -135,21 +135,25 @@ def initializeNc(ncFile, outNcFile, isotope):
 
 
 
-parser = argparse.ArgumentParser()
-parser.add_argument("-i", required=True, action="append", help="one or more snap.nc file from an inverse run to a measurement")
-parser.add_argument("-n", action="append", help="zero or more snap.nc file from an inverse run to a stations without measurement")
-parser.add_argument("-o", required=True, help="output nc file")
-parser.add_argument("-I", default="I131", help="isotope (default: I131)")
-args = parser.parse_args()
-
-(times, out_nc, conc, prob) = initializeNc(args.i[0], args.o, args.I)
-# remove first input
-args.i.pop(0)
-for i in args.i:
-    (conc, prob) = addFile(i, args.I, times, conc, prob)
-
-if args.n:
-    for i in args.n:
-        (conc, prob) = addFile(i, args.I, times, conc, prob, False)
-
-finishOutput(out_nc, args.I, times, conc, prob)
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", required=True, action="append", help="one or more snap.nc file from an inverse run to a measurement")
+    parser.add_argument("-n", action="append", help="zero or more snap.nc file from an inverse run to a stations without measurement")
+    parser.add_argument("-o", required=True, help="output nc file")
+    parser.add_argument("-I", default="I131", help="isotope (default: I131)")
+    args = parser.parse_args()
+
+    (times, out_nc, conc, prob) = initializeNc(args.i[0], args.o, args.I)
+    # remove first input
+    args.i.pop(0)
+    for i in args.i:
+        (conc, prob) = addFile(i, args.I, times, conc, prob)
+
+    if args.n:
+        for i in args.n:
+            (conc, prob) = addFile(i, args.I, times, conc, prob, False)
+
+    finishOutput(out_nc, args.I, times, conc, prob)
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/snapEnsPlot.py → utils/SnapPy/snapscripts/snapEnsPlot.py

@@ -14,14 +14,16 @@
 import sys
 
 import numpy as np
+import logging
 
 # suppress some warnings
 warnings.filterwarnings("ignore", category=UserWarning,
                         message="Warning: 'partition' will ignore the 'mask' of the MaskedArray.")
 # shapefile.py uses root logger :-( and warns a lot about GSHHS
-import logging
 logging.root.setLevel(logging.ERROR)
 
+
+
 def plotMap(data, x, y, ax, title="", title_loc="center", clevs=[10,100,300,1000,3000,10000,30000,100000, 300000, 10000000], colors=None, extend='max'):
     ax.add_feature(cartopy.feature.GSHHSFeature(scale='low', facecolor='none', edgecolor='whitesmoke', linewidth=.2), zorder=100)
     ax.add_feature(cartopy.feature.BORDERS, edgecolor="lightgray", linewidth=.5, zorder=100) 
@@ -266,9 +268,8 @@ def snapens(ncfiles, hour, outfile):
     fig.subplots_adjust(hspace=0.12, wspace=0.01)
     fig.savefig(outfile, bbox_inches='tight')
 
-
 
-if __name__ == "__main__":
+def main():
     os.umask(0o002)
 
     parser = argparse.ArgumentParser(
@@ -281,4 +282,8 @@ def snapens(ncfiles, hour, outfile):
     parser.add_argument('SNAPNC', help="snap*.nc filenames", nargs='+')
     args = parser.parse_args()
 
-    snapens(args.SNAPNC, args.hour, args.out)
+    snapens(args.SNAPNC, args.hour, args.out)
+
+
+if __name__ == "main":
+    main()

utils/SnapPy/snapNc2grib.py → utils/SnapPy/snapscripts/snapNc2grib.py

@@ -21,7 +21,7 @@ def getIsotopesFromFile(filename):
     print(f"converting isotopes: {', '.join(isotop_names)}", file=sys.stderr)
     return isotopes
 
-if __name__ == "__main__":
+def main():
     parser = argparse.ArgumentParser(description="convert a snap.nc output-file to grib, should be run after snapAddToa")
     parser.add_argument("--nc", help="snap.nc filename", required=True)
     parser.add_argument("--ident", help="output-file identifier", required=True)
@@ -37,3 +37,6 @@ def getIsotopesFromFile(filename):
         bitmapCompress= True
     dirname = os.path.dirname(ncfile)
     snapNc_convert_to_grib(ncfile, dirname, ident, isotopes, bitmapCompress=bitmapCompress)
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/snapPy → utils/SnapPy/snapscripts/snapPy.py

@@ -26,7 +26,7 @@
 import Snappy.EEMEP.Resources
 import Snappy.EEMEP.Controller
 
-if __name__ == "__main__":
+def main():
     app = QtWidgets.QApplication(sys.argv)
     tabs = QtWidgets.QTabWidget()
     snap = SnapController()
@@ -42,3 +42,6 @@
 
 
     sys.exit(app.exec_())
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/snapRemoteRunner.py → utils/SnapPy/snapscripts/snapRemoteRunner.py

@@ -403,7 +403,7 @@ def _check_and_unpack_new_files(self):
             self.ssh.syscall("rm", delete_upload_files, 30)
 
 
-if __name__ == "__main__":
+def main():
     os.umask(0o002)
     import argparse
 
@@ -482,3 +482,7 @@ def _check_and_unpack_new_files(self):
             delete_oldfiles(args.dir, args.cleanup)
         if dir2 and dirIsWritable(dir2):
             delete_oldfiles(dir2, args.cleanup)
+
+
+if __name__ == "__main__":
+    main()

utils/SnapPy/snapRunnerNpp → utils/SnapPy/snapscripts/snapRunnerNpp.py

@@ -345,7 +345,7 @@ def runsnap(npp, met_model, outdir, release_dt, runtime, plot_from_file=None):
 
 
 
-if __name__ == "__main__":
+def main():
     os.umask(0o002)
 
     parser = argparse.ArgumentParser(
@@ -373,3 +373,7 @@ def runsnap(npp, met_model, outdir, release_dt, runtime, plot_from_file=None):
     if (args.store):
         os.environ["STORE"] = args.store
     runsnap(outdir=args.outdir, met_model=args.metmodel, runtime=int(args.runtime), npp=args.npp, release_dt=release_dt, plot_from_file=plot_from_file)
+
+
+if __name__ == "__main__":
+    main()