cleanup build scripts

MANIFEST.in

@@ -1,5 +1,5 @@
-include src/gui/DAMARIS.png
+include src/gui/DAMARIS3.png
-include src/gui/DAMARIS.ico
+include src/gui/DAMARIS3.ico
 include src/gui/damaris.glade
 include src/gui/damaris.gladep
 include doc/index.html

debian/control

@@ -2,7 +2,7 @@ Source: python3-damaris
 Section: science
 Priority: optional
 Maintainer: Markus Rosenstihl <markus.rosenstihl@pkm.tu-darmstadt.de>
-Build-Depends: python3, debhelper, python3-dev, dh-sequence-python3, dpkg-dev
+Build-Depends: python3, debhelper, python3-dev, dh-sequence-python3, dpkg-dev, pybuild-plugin-pyproject
 Standards-Version: 3.7.3
 X-Python3-Version: >= 3.5
 Rules-Requires-Root: no

debian/files

@@ -0,0 +1,2 @@
+python3-damaris_0.19_all.deb science optional
+python3-damaris_0.19_amd64.buildinfo science optional

debian/rules

@@ -10,7 +10,10 @@ PACKAGE_NAME=python3-damaris
 PYBUILD_NAME=python3-damaris
 MODULE_NAME=damaris3
 PYBASE=$(CURDIR)/debian/${PACKAGE_NAME}
-DH_ALWAYS_EXCLUDE=CVS:.git:venv
+DH_ALWAYS_EXCLUDE=CVS:.git:venv:.venv:*.h5
 
 %:
 	dh $@ --buildsystem=pybuild
+
+override_dh_auto_test:
+	PYBUILD_TEST_ARGS="-v $(CURDIR)/tests" dh_auto_test

pyproject.toml

@@ -1,23 +1,63 @@
 [build-system]
-requires = ["setuptools"]
+requires = [
+    "setuptools>=61.0",   # provides the "setuptools.build_meta" backend
+    "wheel"               # needed for the wheel building step
+]
 build-backend = "setuptools.build_meta"
 
 [project]
 requires-python = ">= 3.9"
 name = "python3-damaris"
-dynamic = ["version", 
+version = "0.19"
-	"dependencies",
+description = "Python version 3 frontend for DAMARIS (DArmstadt MAgnetic Resonance Instrument Software)"
-	"classifiers",
+license = "GPL-2.0"
-	"keywords",
+keywords = ["NMR", "data-processing"]
-	"license",
+readme = {file = "README", content-type = "text/plain"}
-	"readme",
+dependencies = [
+    "scipy >= 0.14.0",
+    "numpy >= 1.8.2, < 2.0",
+    "tables >= 3.1.1",
+    "matplotlib >= 1.4.1, <= 3.6",
+    "pyxdg",
+    "PyGObject >= 3.14.0, <= 3.51.0"
 ]
 authors = [
   {name = "Achim Gädke"},
   {name = "Christopher Schmitt"},
   {name = "Christian Tacke"},
-  {name = "Markus Rosenstihl", email = "markus.rosenstihl@pkm.tu-darmstadt.de"},
+  {name = "Joachim Beerwerth"},
+  {name = "Markus Rosenstihl", email = "markus.rosenstihl@pkm.tu-darmstadt.de"}
 ]
 maintainers = [
   {name = "Markus Rosenstihl", email = "markus.rosenstihl@pkm.tu-darmstadt.de"}
 ]
+
+[project.scripts]
+DAMARIS3 = "damaris.__main__:main"
+
+
+[tool.setuptools]
+packages = [
+    "damaris",
+    "damaris.data",
+    "damaris.experiments",
+    "damaris.gui",
+    "damaris.tools"
+]
+
+[tool.setuptools.package-dir]
+"damaris" = "src"
+"damaris.data" = "src/data"
+"damaris.experiments" = "src/experiments"
+"damaris.gui" = "src/gui"
+"damaris.tools" = "src/tools"
+
+[tool.setuptools.package-data]
+"damaris.gui" = ["DAMARIS3.png", "DAMARIS3.ico", "damaris.xml", "python.xml"]
+
+[tool.setuptools.data-files]
+"share/python3-damaris/images" = ["src/gui/DAMARIS3.png", "src/gui/DAMARIS3.ico"]
+"share/python3-damaris/doc" = ["doc/index.html"]
+"share/python3-damaris/doc/reference-html" = ["doc/reference-html/*"]
+"share/python3-damaris/doc/tutorial-html" = ["doc/tutorial-html/*"]
+

setup.cfg

@@ -1,26 +0,0 @@
-[metadata]
-name = python3-damaris
-version = 0.18.0
-author = Achim Gädke, Christian, Tacke, Joachim Berwerth, Christopher Schmitt, Markus Rosenstihl
-author_email = markus.rosenstihl@þkm.tu-darmstadt.de
-url = https://gitea.pkm.physik.tu-darmstadt.de/IPKM/python3-damaris
-description = DArmstadt MAgnetic Resonance Instrumentation Software
-long_description = file: README.md
-long_description_content_type = text/markdown
-keywords = science, instrumentation
-license = BSD 3-Clause License
-classifiers =
-    License :: OSI Approved :: BSD License
-    Programming Language :: Python :: 3
-
-[options]
-packages = find:
-zip_safe = True
-include_package_data = True
-install_requires =
-    scipy >= 0.14.0
-    numpy (>= 1.8.2 , < 2.0)
-    tables >= 3.1.1
-    matplotlib (>= 1.4.1, <= 3.6)
-    pyxdg
-    PyGObject (>= 3.14.0, <= 3.51.0) # girepository2.0-dev not available on bookworm

setup.py

@@ -1,120 +0,0 @@
-#!/usr/bin/env python
-
-import shutil
-import os
-import os.path
-import sys
-from distutils.core import setup
-from distutils.command.build_scripts import build_scripts as _build_scripts
-from distutils import log
-from distutils.util import convert_path
-from distutils.dep_util import newer
-
-#if sys.version_info < (2, 5, 3):
-#    log.error("**** ERROR: Install manually: python setup.py install ****")
-#    raise ValueError
-
-class build_damaris_scripts(_build_scripts):
-
-    #user_options=_build_scripts.user_options[:]
-    #user_options.append(('install-dir=', 'd', "directory to install scripts to"))
-
-    def initialize_options (self):
-        _build_scripts.initialize_options(self)
-        self.damaris_dir = None
-
-    def finalize_options (self):
-        _build_scripts.finalize_options(self)
-        self.set_undefined_options('install',
-                                   ('install_lib', 'damaris_dir'))
-
-    def run (self):
-        "change PYTHON_PATH for DAMARIS executable"
-        _build_scripts.run(self)
-        script="scripts/DAMARIS3"
-        script = convert_path(script)
-        outfile = os.path.join(self.build_dir, os.path.basename(script))
-        self.damaris_dir=os.path.normpath(self.damaris_dir)
-        if self.damaris_dir in sys.path:
-            log.debug("not changing %s (this path is on standard path)", script)
-            # nothing to do for us
-            return
-
-        # now change PATH in DAMARIS script
-        # copy backup
-        log.info("adapting DAMARIS script to use local installation")
-        shutil.copyfile(outfile, outfile+".bak")
-        # the file should keep all its attributes (executable...)
-        inf=open(outfile+".bak","r")
-        outf=open(outfile,"w")
-        l=inf.readline()
-        while not l.startswith("import sys") and l!="":
-            outf.write(l)
-            l=inf.readline()
-
-        if l!="":
-            outf.write(l)
-            l=inf.readline()
-            while l.endswith("# inserted by setup.py\n"):
-                l=inf.readline()
-            outf.write("sys.path.insert(0,\"%s\") # inserted by setup.py\n"%self.damaris_dir)
-            outf.write(l)
-        outf.writelines(inf.readlines())
-        inf.close()
-        outf.close()
-        os.remove(outfile+".bak")
-
-# create doc data file information
-distribution_doc_prefix=os.path.join("share","python3-damaris","doc")
-distribution_data_files = [[ "share", []],
-                           [os.path.join("share", "python3-damaris", "images"),
-                            ["src/gui/DAMARIS3.png", "src/gui/DAMARIS3.ico"]],
-                           [os.path.join("share", "python3-damaris"), []],
-                           [distribution_doc_prefix, ['doc/index.html']]]
-
-if os.path.isdir(os.path.join("doc","reference-html")):
-    # no subdirs, work can be done in simple way
-    distribution_data_files.append([os.path.join(distribution_doc_prefix, 'reference-html'),
-                                    [os.path.join('doc', 'reference-html', f)
-                                     for f in os.listdir(os.path.join('doc', 'reference-html'))]])
-
-if os.path.isdir(os.path.join("doc","tutorial-html")):
-    # here, modern style file and attachment directories should be handled
-    for d in os.walk(os.path.join("doc","tutorial-html")):
-        distribution_data_files.append([os.path.join(os.path.dirname(distribution_doc_prefix),d[0]),
-                                        [os.path.join(d[0], f) for f in d[2]]])
-
-LONG_DESCRIPTION="""
-DArmstadt MAgnetic Resonance Instrument Software
-"""
-
-GPL_LICENCE = "feed licence here"
-
-setup (
-    name = 'python3-damaris',
-    version = "0.18.2",
-    description = 'python frontend for DAMARIS (DArmstadt MAgnetic Resonance Instrument Software)',
-    long_description = LONG_DESCRIPTION,
-    author = 'Achim Gaedke',
-    author_email = 'Achim.Gaedke@physik.tu-darmstadt.de',
-    maintainer = 'Achim Gaedke',
-    maintainer_email = 'markus.rosenstihl@pkm.tu-darmstadt.de',
-    url = 'http://www.fkp.physik.tu-darmstadt.de/damaris/',
-    license = GPL_LICENCE,
-    platforms = ['Any',],
-    keywords = ['NMR', 'data-processing'],
-    packages = [ 'damaris',
-                 'damaris.data',
-                 'damaris.experiments',
-                 'damaris.gui',
-                 'damaris.tools' ],
-    package_dir = { 'damaris': 'src',
-                    'damaris.data': 'src/data',
-                    'damaris.experiments': 'src/experiments',
-                    'damaris.gui': 'src/gui',
-                    'damaris.tools': 'src/tools' },
-    package_data = { 'damaris.gui': ['DAMARIS3.png', 'DAMARIS3.ico', 'damaris.xml', 'python.xml']},
-    scripts = ['scripts/DAMARIS3'],
-    cmdclass={"build_scripts": build_damaris_scripts},
-    data_files = distribution_data_files
-    )

src/__main__.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python3
+"""
+DAMARISi3 command-line interface.
+"""
+
+import sys
+import os
+import argparse
+import sqlite3
+
+# for numpy-1.1 and later: check the environment for LANG and LC_NUMERIC
+# see: http://projects.scipy.org/scipy/numpy/ticket/902
+if os.environ.get("LANG", "").startswith("de") or os.environ.get("LC_NUMERIC", "").startswith("de"):
+    os.environ["LC_NUMERIC"] = "C"
+
+
+def main():
+    """Main entry point for DAMARIS."""
+    parser = argparse.ArgumentParser(description='DArmstadt MAgnetic Resonance Instrumentation Software')
+
+    parser.add_argument("--run", action="store_true", help="run DAMARIS immediately with given scripts")
+    parser.add_argument("--clean", action="store_true", help="cleanup DAMARIS run files")
+    parser.add_argument("--debug", action="store_true", help="run DAMARIS with DEBUG flag set")
+    parser.add_argument("--mpl", help="run DAMARIS with matplotlib backend",
+                        choices=["GTK3Agg", "GTK3Cairo"], default="GTK3Agg")
+    parser.add_argument("exp_script", help="experiment script", nargs="?", metavar="EXP.py")
+    parser.add_argument("res_script", help="result script", nargs="?", metavar="RES.py")
+
+    args = parser.parse_args()
+
+    import matplotlib
+    if args.mpl:
+        matplotlib.use(args.mpl)
+
+    import damaris.gui.DamarisGUI
+
+    lockfile = os.path.expanduser('~/.damaris.lockdb')
+    if args.clean:
+        if os.path.exists(lockfile):
+            print("Removing lockfile: %s" % lockfile)
+            os.remove(lockfile)
+        else:
+            print("Lockfile does not exists: %s" % lockfile)
+    lockdb = sqlite3.connect(lockfile)
+
+    c = lockdb.cursor()
+    c.execute("CREATE TABLE IF NOT EXISTS damaris (uuid text, status text)")
+    lockdb.commit()
+
+    if args.debug:
+        damaris.gui.DamarisGUI.debug = True
+        print("debug flag set")
+        try:
+            import resource
+            resource.setrlimit(resource.RLIMIT_CORE, (-1, -1))
+        except ImportError:
+            pass
+
+    print(args)
+    d = damaris.gui.DamarisGUI.DamarisGUI(args.exp_script, args.res_script, start_immediately=args.run)
+    d.run()
+
+    sys.stdout = sys.__stdout__
+    sys.stderr = sys.__stderr__
+
+
+if __name__ == "__main__":
+    main()

src/tools/goniometer.py

@@ -56,7 +56,7 @@ class goniometer:
 
     def _recv(self):
         retstr = self.serial.readline().strip().replace("\x00","")
-        search_result = re.search("<(\d+)>", retstr)
+        search_result = re.search(r"<(\d+)>", retstr)
         if search_result != None:
             angle = float(search_result.group(1))/36.0
             self.current_angle = angle

tests/exp_test.py

@@ -1,11 +1,15 @@
-def test():
+import time
+
+def test(i):
     e=Experiment()
     e.ttl_pulse(length=1e-6, value=1)
     e.wait(1e-3)
     e.ttl_pulse(length=1e-6,value=1)
     e.record(samples=1024,frequency=1e6,sensitivity=1)
+    e.set_description("variable",i)
+    e.set_description("const", "test")
     return e
 
 def experiment():
     for i in range(10):
-        yield test()
+        yield test(i)

tests/res_test.py

@@ -1,8 +1,24 @@
+import tables
+
+r = MeasurementResult("test")
+
 def result():
+    try:
+        h5 = tables.open_file("test.h5", "w")
+    except:
+        print("h5 already opened")
     accu = Accumulation(error=False)
     for num,ts in enumerate(results):
         data["accu"] = accu
-        data["ts %i"%num] = ts+0
+        data["data/ts %i"%num] = ts+0
+        ts.write_to_hdf(h5, "/", f"adc_{num}", f"adc_{num}")
         data["fft"] = (ts+0).fft()
+        r[num] = ts.y[0][0]
+        data["test"] = r
         accu+=ts
-        print("ts")
+    accu.write_to_hdf(h5, "/", "name", "title")
+    print(accu)
+    try:
+        h5.close()
+    except:
+        print("h5 already closed")

tests/test_ADC_Result.py

@@ -4,7 +4,7 @@ import unittest
 from datetime import datetime
 
 import numpy as np
-from src.data.ADC_Result import ADC_Result
+from damaris.data.ADC_Result import ADC_Result
 
 
 class TestADCResult(unittest.TestCase):

tests/test_Accumulation.py

@@ -5,8 +5,8 @@ from datetime import datetime
 
 import numpy as np
 
-from src.data.ADC_Result import ADC_Result
+from damaris.data.ADC_Result import ADC_Result
-from src.data.Accumulation import Accumulation
+from damaris.data.Accumulation import Accumulation
 
 
 class TestAccumulation(unittest.TestCase):