IPKM/python3-damaris
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script for release added, pyrefly checks are fixed for now

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markusro committed 2026-10-21 00:48:06 +02:00
1 parent 428af30c30
commit dda8ae7df0
6 files changed
+179 -89
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.gitea/workflows/debian-build.yml
+13 -1
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@@ -22,13 +22,25 @@ jobs:
- name: Install Node.js and git
run: |
apt-get update
apt-get -y install nodejs git lsb-release jq
apt-get -y install nodejs git lsb-release jq devscripts
- name: Checkout repository
uses: actions/checkout@v3
with:
github-server-url: https://gitea.pkm.physik.tu-darmstadt.de
- name: Set package version from release tag
if: startsWith(gitea.ref, 'refs/tags/v')
env:
TAG: ${{ gitea.ref_name }}
run: |
set -euo pipefail
VERSION="${TAG#v}"
if [ "$(dpkg-parsechangelog --show-field Version)" != "$VERSION" ]; then
dch --newversion "$VERSION" --distribution stable --force-distribution --noquery "Release $TAG"
fi
sed -i -E "s/^(__version__ = \")([^\"]+)(\")$/\1${VERSION}\3/" src/damaris/__init__.py
- name: Install build dependencies
run: bash requirements.debian
scripts/release.sh
Executable
+65
View File
@@ -0,0 +1,65 @@
#!/usr/bin/env bash
set -euo pipefail
usage() {
echo "Usage: $0 VERSION (for example: 0.30)"
}
if [[ ${1:-} == "-h" || ${1:-} == "--help" ]]; then
usage
exit 0
fi
if [[ $# -ne 1 || ! $1 =~ ^[0-9]+\.[0-9]+(\.[0-9]+)?$ ]]; then
usage >&2
exit 2
fi
version=$1
tag="v$version"
root=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
cd "$root"
if [[ -n $(git status --porcelain) ]]; then
echo "Release requires a clean working tree." >&2
exit 1
fi
if git rev-parse -q --verify "refs/tags/$tag" >/dev/null; then
echo "Tag $tag already exists." >&2
exit 1
fi
command -v dch >/dev/null || { echo "Install devscripts to use dch." >&2; exit 1; }
command -v dpkg-parsechangelog >/dev/null || { echo "Install dpkg-dev to use dpkg-parsechangelog." >&2; exit 1; }
current_version=$(dpkg-parsechangelog --show-field Version)
if [[ $current_version == "$version" ]]; then
echo "debian/changelog already has version $version." >&2
exit 1
fi
dch --newversion "$version" --distribution stable --force-distribution
sed -i "s/^__version__ = .*/__version__ = \"$version\"/" src/damaris/__init__.py
if [[ $(dpkg-parsechangelog --show-field Version) != "$version" ]] ||
[[ $(sed -n 's/^__version__ = "\([^"]*\)"$/\1/p' src/damaris/__init__.py) != "$version" ]]; then
echo "Release version did not update consistently; inspect the changelog and package version." >&2
exit 1
fi
echo "About to commit the version bump and create tag $tag."
read -r -p "Continue? [y/N] " answer
if [[ ! $answer =~ ^[Yy]$ ]]; then
echo "Release preparation stopped; version and changelog edits were kept."
exit 1
fi
git add debian/changelog src/damaris/__init__.py
git commit -m "Release $tag"
git tag -a "$tag" -m "Release $tag"
echo "Created local release tag $tag. Push the commit and tag to start the package workflow."
echo " git push origin HEAD"
echo " git push origin $tag"
src/damaris/data/ADC_Result.py
+25 -33
View File
@@ -12,13 +12,14 @@ import numpy
import sys
import datetime
import tables
from typing import IO
from typing import IO, Any, Literal, cast
from scipy.signal import filtfilt, remez
_XArray = numpy.ndarray | list
_YChannels = list[numpy.ndarray]
_IndexList = list[tuple[int, int]]
_Description = dict[str, str]
_CompressionLibrary = Literal["blosc", "blosc2", "bzip2", "lzo", "zlib"]
#############################################################################
# #
# Name: Class ADC_Result #
@@ -377,13 +378,14 @@ class ADC_Result(MeasurementData, Resultable, Drawable, DamarisFFT, Signalpath):
def write_to_hdf(self, hdffile: tables.File, where: str, name: str, title: str, complib: str | None = None, complevel: int | None = None) -> None:
accu_group=hdffile.create_group(where=where,name=name,title=title)
accu_group._v_attrs.damaris_type="ADC_Result"
attrs = cast(Any, accu_group._v_attrs)
attrs.damaris_type="ADC_Result"
if self.contains_data():
self.lock.acquire()
try:
# save time stamps
if "job_date" in dir(self) and self.job_date is not None:
accu_group._v_attrs.time="%04d%02d%02d %02d:%02d:%02d.%03d"%(self.job_date.year,
attrs.time="%04d%02d%02d %02d:%02d:%02d.%03d"%(self.job_date.year,
self.job_date.month,
self.job_date.day,
self.job_date.hour,
@@ -393,15 +395,17 @@ class ADC_Result(MeasurementData, Resultable, Drawable, DamarisFFT, Signalpath):
if self.description is not None:
for (key,value) in self.description.items():
accu_group._v_attrs.__setattr__("description_"+key,str(value))
accu_group._v_attrs.__setattr__("sampling_rate",self.sampling_rate)
attrs.__setattr__("description_"+key,str(value))
attrs.__setattr__("sampling_rate",self.sampling_rate)
# save interval information
filter=None
if complib is not None:
if complevel is None:
complevel=9
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
filter=tables.Filters(complevel=complevel,
complib=cast(_CompressionLibrary, complib),
shuffle=True)
index_table=hdffile.create_table(where=accu_group,
name="indices",
@@ -414,7 +418,7 @@ class ADC_Result(MeasurementData, Resultable, Drawable, DamarisFFT, Signalpath):
expectedrows=len(self.index))
index_table.flavor="numpy"
# save channel data
new_row=index_table.row
new_row = cast(Any, index_table.row)
for i in range(len(self.index)):
new_row["start"]=self.index[i][0]
new_row["dwelltime"]=1.0/self.sampling_rate
@@ -436,27 +440,14 @@ class ADC_Result(MeasurementData, Resultable, Drawable, DamarisFFT, Signalpath):
# save data
time_slice_data=None
if filter is not None:
chunkshape = numpy.shape(timedata)
if len(chunkshape) <= 1:
chunkshape = (min(chunkshape[0],1024*8),)
else:
chunkshape = (min(chunkshape[0],1024*8), chunkshape[1])
if tables.__version__[0]=="1":
time_slice_data=hdffile.create_carray(accu_group,
name="adc_data",
shape=timedata.shape,
atom=tables.Int16Atom(shape=chunkshape,
flavor="numpy"),
filters=filter,
title="adc data")
else:
time_slice_data=hdffile.create_carray(accu_group,
name="adc_data",
shape=timedata.shape,
chunkshape=chunkshape,
atom=tables.Int16Atom(),
filters=filter,
title="adc data")
chunkshape = (min(timedata.shape[0], 1024 * 8), timedata.shape[1])
time_slice_data=hdffile.create_carray(accu_group,
name="adc_data",
shape=timedata.shape,
chunkshape=chunkshape,
atom=tables.Int16Atom(),
filters=filter,
title="adc data")
time_slice_data[:]=timedata
else:
time_slice_data=hdffile.create_array(accu_group,
@@ -684,7 +675,8 @@ def read_from_hdf(hdf_node: object) -> ADC_Result | None:
if not isinstance(hdf_node, tables.Group):
return None
if hdf_node._v_attrs.damaris_type!="ADC_Result":
attrs = cast(Any, hdf_node._v_attrs)
if attrs.damaris_type!="ADC_Result":
return None
if not (hdf_node.__contains__("indices") and hdf_node.__contains__("adc_data")):
@@ -696,12 +688,12 @@ def read_from_hdf(hdf_node: object) -> ADC_Result | None:
adc.set_title(hdf_node._v_title)
# populate description dictionary
adc.description={}
for attrname in hdf_node._v_attrs._v_attrnamesuser:
for attrname in attrs._v_attrnamesuser:
if attrname.startswith("description_"):
adc.description[attrname[12:]]=hdf_node._v_attrs.__getattr__(attrname)
adc.description[attrname[12:]]=attrs.__getattr__(attrname)
if "time" in dir(hdf_node._v_attrs):
timestring=hdf_node._v_attrs.__getattr__("time")
if "time" in dir(attrs):
timestring=attrs.__getattr__("time")
adc.job_date=datetime.datetime(int(timestring[:4]), # year
int(timestring[4:6]), # month
int(timestring[6:8]), # day
src/damaris/data/Accumulation.py
+47 -47
View File
@@ -26,12 +26,13 @@ import datetime # added by Oleg Petrov
import ctypes # added by Oleg Petrov
import struct # added by Oleg Petrov
import os # added by Oleg Petrov
from typing import IO
from typing import IO, Any, Literal, cast
_XArray = numpy.ndarray | list
_YChannels = list[numpy.ndarray]
_IndexList = list[tuple[int, int]]
_Description = dict[str, str]
_CompressionLibrary = Literal["blosc", "blosc2", "bzip2", "lzo", "zlib"]
class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath):
@@ -307,7 +308,7 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
for i in range(len(xdata)):
dest.write("%e"%xdata[i])
for j in range(ch_no):
if self.use_error:
if self.use_error and yerr is not None:
dest.write("%s%e%s%e"%(delimiter, ydata[j][i], delimiter, yerr[j][i]))
else:
dest.write("%s%e"%(delimiter,ydata[j][i]))
@@ -358,7 +359,7 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
self.lock.release()
# ------------- added by Oleg Petrov, 10 Sep 2013 -----------------------
def write_to_tecmag(self, destination = sys.stdout, nrecords: int = 1,\
def write_to_tecmag(self, destination: str | IO[bytes] = sys.stdout.buffer, nrecords: int = 1,\
frequency: float = 100.,\
last_delay: float = 1.,\
receiver_phase: float = 0.,\
@@ -388,8 +389,8 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
else:
record = (self.job_id/self.n)%nrecords + 1
the_destination=destination
if type(destination) in (str,):
the_destination: IO[bytes] | None = None
if isinstance(destination, str):
if record == 1 and os.path.exists(destination):
os.rename(destination, os.path.dirname(destination)+'/~'+os.path.basename(destination))
@@ -420,7 +421,10 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
data = data.flatten()
if record == 1:
the_destination=open(destination, "wb")
if isinstance(destination, str):
the_destination = open(destination, "wb")
else:
the_destination = destination
# allocate space for all records in advance:
buff = ctypes.create_string_buffer(1056+data_offset+2068)
@@ -481,20 +485,24 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
struct.pack_into('4s', buff, 1056+data_offset+2060, 'PSEQ') # 'PSEQ' tag 658476
struct.pack_into('?', buff, 1056+data_offset+2064, False) # BOOLean 658480
the_destination.write(buff)
the_destination.write(buff.raw)
else:
the_destination=open(destination, "rb+")
if isinstance(destination, str):
the_destination = open(destination, "rb+")
else:
the_destination = destination
buff = ctypes.create_string_buffer(4*2*npts[0])
struct.pack_into('%sf' % (2*npts[0]), buff, 0, *data)
the_destination.seek(1056+4*2*npts[0]*(record-1))
the_destination.write(buff)
the_destination.write(buff.raw)
the_destination = None
ydata=None
finally:
if isinstance(destination, str) and the_destination is not None:
the_destination.close()
self.lock.release()
# -----------------------------------------------------------------------
@@ -518,25 +526,28 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
:param complevel: compression level.
"""
accu_group=hdffile.create_group(where=where,name=name,title=title)
accu_group._v_attrs.damaris_type="Accumulation"
attrs = cast(Any, accu_group._v_attrs)
attrs.damaris_type="Accumulation"
if self.contains_data():
self.lock.acquire()
try:
# save time stamps
if self.time_period is not None and len(self.time_period)>0:
accu_group._v_attrs.earliest_time = self.time_period[0].isoformat(sep=' ', timespec='milliseconds')
accu_group._v_attrs.oldest_time = self.time_period[1].isoformat(sep=' ', timespec='milliseconds')
attrs.earliest_time = self.time_period[0].isoformat(sep=' ', timespec='milliseconds')
attrs.oldest_time = self.time_period[1].isoformat(sep=' ', timespec='milliseconds')
if self.common_descriptions is not None:
for (key,value) in self.common_descriptions.items():
accu_group._v_attrs.__setattr__("description_"+key,str(value))
accu_group._v_attrs.__setattr__("sampling_rate",self.sampling_rate)
attrs.__setattr__("description_"+key,str(value))
attrs.__setattr__("sampling_rate",self.sampling_rate)
filter=None
if complib is not None:
if complevel is None:
complevel=3
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
filter=tables.Filters(complevel=complevel,
complib=cast(_CompressionLibrary, complib),
shuffle=True)
# save interval information
# start save index_table
@@ -553,7 +564,7 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
expectedrows=len(self.index))
index_table.flavor="numpy"
# save interval data
new_row=index_table.row
new_row = cast(Any, index_table.row)
for i in range(len(self.index)):
new_row["start"]=self.index[i][0]
new_row["dwelltime"]=1.0/self.sampling_rate
@@ -574,7 +585,7 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
title="job_ids used for accumulation",
filters=filter,
expectedrows=len(self.job_ids))
new_row=jobid_table.row
new_row = cast(Any, jobid_table.row)
for i,job_id in enumerate(self.job_ids):
new_row["job_date"] = self.job_ids[job_id].isoformat(timespec='milliseconds')
new_row["job_id"]=job_id
@@ -595,27 +606,14 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
# save data
time_slice_data=None
if filter is not None:
chunkshape=timedata.shape
if len(chunkshape) <= 1:
chunkshape = (min(chunkshape[0],1024*8),)
else:
chunkshape = (min(chunkshape[0],1024*8), chunkshape[1])
if tables.__version__[0]=="1":
time_slice_data=hdffile.create_carray(accu_group,
name="accu_data",
shape=timedata.shape,
atom=tables.Float32Atom(shape=chunkshape,
flavor="numpy"),
filters=filter,
title="accu data")
else:
time_slice_data=hdffile.create_carray(accu_group,
name="accu_data",
shape=timedata.shape,
chunkshape=chunkshape,
atom=tables.Float32Atom(),
filters=filter,
title="accu data")
chunkshape = (min(timedata.shape[0], 1024 * 8), timedata.shape[1])
time_slice_data=hdffile.create_carray(accu_group,
name="accu_data",
shape=timedata.shape,
chunkshape=chunkshape,
atom=tables.Float32Atom(),
filters=filter,
title="accu data")
time_slice_data[:]=timedata
else:
@@ -1111,7 +1109,8 @@ class Accumulation(MeasurementData, Errorable, Drawable, DamarisFFT, Signalpath)
self.set_title(self.__title_pattern % self.n)
if hasattr(other, "is_clipped"):
self.is_clipped = other.is_clipped
self.common_descriptions=other.common_descriptions.copy()
self.common_descriptions = (other.common_descriptions.copy()
if other.common_descriptions is not None else None)
self.time_period=other.time_period[:] if other.time_period is not None else None
self.job_id = other.job_id # added by Oleg Petrov
self.job_ids.update(other.job_ids)
@@ -1213,7 +1212,8 @@ def read_from_hdf(hdf_node: object) -> "Accumulation | None":
if not isinstance(hdf_node, tables.Group):
return None
if hdf_node._v_attrs.damaris_type!="Accumulation":
attrs = cast(Any, hdf_node._v_attrs)
if attrs.damaris_type!="Accumulation":
return None
if not (hdf_node.__contains__("indices") and hdf_node.__contains__("accu_data")):
@@ -1224,13 +1224,13 @@ def read_from_hdf(hdf_node: object) -> "Accumulation | None":
# populate description dictionary
accu.common_descriptions={}
for attrname in hdf_node._v_attrs._v_attrnamesuser:
for attrname in attrs._v_attrnamesuser:
if attrname.startswith("description_"):
accu.common_descriptions[attrname[12:]]=hdf_node._v_attrs.__getattr__(attrname)
accu.common_descriptions[attrname[12:]]=attrs.__getattr__(attrname)
earliest_time=None
if "earliest_time" in dir(hdf_node._v_attrs):
timestring=hdf_node._v_attrs.__getattr__("earliest_time")
if "earliest_time" in dir(attrs):
timestring=attrs.__getattr__("earliest_time")
# Handle both formats: "20260705 19:13:59.162" and "2026-07-05 19:13:59.162"
if '-' in timestring:
# New format: "2026-07-05 19:13:59.162"
@@ -1261,8 +1261,8 @@ def read_from_hdf(hdf_node: object) -> "Accumulation | None":
)
oldest_time=None
if "oldest_time" in dir(hdf_node._v_attrs):
timestring=hdf_node._v_attrs.__getattr__("oldest_time")
if "oldest_time" in dir(attrs):
timestring=attrs.__getattr__("oldest_time")
# Handle both formats: "20260705 19:13:59.162" and "2026-07-05 19:13:59.162"
if '-' in timestring:
# New format: "2026-07-05 19:13:59.162"
src/damaris/data/MeasurementResult.py
+15 -8
View File
@@ -4,7 +4,7 @@ import sys
import tables
import numpy
import collections
from typing import IO
from typing import IO, Any, Literal, cast
from . import Drawable
## provide gaussian statistics for a series of measured data points
@@ -31,7 +31,10 @@ class AccumulatedValue:
self.y2=self.y**2
self.n=1
elif mean_err is None:
self.n=max(1, int(n))
if n is None:
self.n=1
else:
self.n=max(1, n)
self.y=float(mean)*self.n
self.y2=(float(mean)**2)*self.n
elif n is None:
@@ -240,7 +243,9 @@ class MeasurementResult(Drawable.Drawable, collections.UserDict):
if complib is not None:
if complevel is None:
complevel=9
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
filter=tables.Filters(complevel=complevel,
complib=cast(Literal["blosc", "blosc2", "bzip2", "lzo", "zlib"], complib),
shuffle=True)
mr_table=hdffile.create_table(where=where,name=name,
description=h5_table_format,
@@ -248,11 +253,12 @@ class MeasurementResult(Drawable.Drawable, collections.UserDict):
filters=filter,
expectedrows=len(self))
mr_table.flavor="numpy"
mr_table.attrs.damaris_type="MeasurementResult"
attrs = cast(Any, mr_table.attrs)
attrs.damaris_type="MeasurementResult"
self.lock.acquire()
try:
mr_table.attrs.quantity_name=self.quantity_name
row=mr_table.row
attrs.quantity_name=self.quantity_name
row = cast(Any, mr_table.row)
xdata=self.get_xdata()
if xdata.shape[0]!=0:
for x in xdata:
@@ -276,10 +282,11 @@ def read_from_hdf(hdf_node: object) -> "MeasurementResult | None":
if not isinstance(hdf_node, tables.Table):
return None
if hdf_node._v_attrs.damaris_type!="MeasurementResult":
attrs = cast(Any, hdf_node._v_attrs)
if attrs.damaris_type!="MeasurementResult":
return None
mr=MeasurementResult(hdf_node._v_attrs.quantity_name)
mr=MeasurementResult(attrs.quantity_name)
for r in hdf_node.iterrows():
mr[r["x"]]=AccumulatedValue(r["y"],r["y_err"],r["n"])
tests/test_Accumulation.py
+14
View File
@@ -360,6 +360,20 @@ class TestAccumulation(unittest.TestCase):
r *= 2
np.testing.assert_array_equal(accu.y[0], np.array([10, 20, 30], dtype="float32"))
def test_empty_iadd_accumulation_without_common_descriptions(self):
"""An accumulation without common descriptions can be copied in-place."""
other = Accumulation(x=np.array([0.0, 1.0]),
y=[np.array([10.0, 20.0])],
n=1,
index=[(0, 1)],
sampl_freq=1000.0)
accu = Accumulation()
accu += other
self.assertIsNone(accu.common_descriptions)
np.testing.assert_array_equal(accu.y[0], other.y[0])
def test_accumulation_plus_accumulation_keeps_both_job_ids(self):
"""accu1 + accu2 must keep the provenance of both operands."""
adc1 = self.create_adc_result()