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443c7c7
added splitter in parameters, image_split and test of strange list ac…
alexlib Jun 27, 2025
f6098f7
plugins now has to have 'default' if plugin text files exist and spli…
alexlib Jun 27, 2025
6b20f8c
much more reasonable plugins.json treatment
alexlib Jun 27, 2025
3f37a2d
move plugins into test_cavity where it should appear in the working f…
alexlib Jun 27, 2025
ec835be
first part cal_splitter works
alexlib Jun 28, 2025
66d0d84
working version with the calibration and splitter
alexlib Jun 28, 2025
75f9dd4
removed debuging plot, changed highpass behaivor for calibration
alexlib Jun 28, 2025
a73f376
Select Split TWICE: in main gui and in calibration gui, added test_sp…
alexlib Jun 28, 2025
88eb749
also detect and show trajectories work
alexlib Jun 28, 2025
38bb702
slight update of user_manual, it's not what's needed really
alexlib Jun 28, 2025
3c231d8
fixed tests, added test of plugins
alexlib Jun 28, 2025
11cfc3d
bumped version to 0.3.8, ready for pull request
alexlib Jun 28, 2025
640224c
default low pass filter size is 25 - to remove uneven illumination
alexlib Jun 28, 2025
625d349
moved to tests/
alexlib Jun 28, 2025
96af78f
proper error
alexlib Jun 28, 2025
8f87dbd
ruff
alexlib Jun 28, 2025
6951a1a
Fix: Update parameter handling to match optv API changes
alexlib Jun 29, 2025
bb96e31
work in progress
alexlib Jul 1, 2025
96a7eee
copy test cavity should not be tracked
alexlib Jul 1, 2025
0004a78
work in progress
alexlib Jul 1, 2025
c2fbd79
working on tests
alexlib Jul 1, 2025
b68cd80
we do not need small yaml files
alexlib Jul 2, 2025
0277cf3
experiment.py
alexlib Jul 2, 2025
9117bf2
higphass works and masking doesn't fail
alexlib Jul 2, 2025
ebea2d3
we do not need yaml except for parameters.yaml
alexlib Jul 2, 2025
738e542
before change in parameters_manager
alexlib Jul 2, 2025
81eff41
fixed volume params
alexlib Jul 2, 2025
c944228
parameters are managed by manager, which is under Experiment
alexlib Jul 2, 2025
dbd0fc5
from directories to yaml files
alexlib Jul 2, 2025
1b2cc92
n_cams top level
alexlib Jul 2, 2025
d68753a
updated n_cams to top level
alexlib Jul 2, 2025
9a87e6b
man_ori inside
alexlib Jul 2, 2025
a925e23
more yaml stuff
alexlib Jul 3, 2025
93345f9
why do we have another folder /parameters in pyptv?
alexlib Jul 3, 2025
4847027
removed /parameters
alexlib Jul 3, 2025
319fbb3
testing parameters - translation to Cython is not good
alexlib Jul 3, 2025
7bb5c2d
parameters tests pass
alexlib Jul 4, 2025
ff28513
fixed parameters. tests pass.
alexlib Jul 4, 2025
68a76cd
pyptv_gui also works. need to test more stuff, including splitter
alexlib Jul 4, 2025
6ac1f8e
moved docs to docs tests to tests
alexlib Jul 4, 2025
fa14f45
more tests, parameters and gui
alexlib Jul 5, 2025
c5a90ea
tests the closer version
alexlib Jul 6, 2025
fe285e9
tests pass
alexlib Jul 6, 2025
0d4254b
obsolete
alexlib Jul 6, 2025
1c5f379
experiment is clean python, no traits
alexlib Jul 6, 2025
c6950d0
hastraits needed for gui
alexlib Jul 6, 2025
7817717
fixed gui bugs
alexlib Jul 6, 2025
2d59fd2
parameters
alexlib Jul 6, 2025
6b31499
there should be no n_img in the yaml file
alexlib Jul 6, 2025
13704ee
docs
alexlib Jul 6, 2025
774a999
cleaning up the docs
alexlib Jul 6, 2025
c34f0a3
working on detection gui
alexlib Jul 7, 2025
457883e
detection_gui almost there
alexlib Jul 8, 2025
723ca6b
a bit messy option to change the range sliders
alexlib Jul 9, 2025
18e531f
added paramter_gui work to pyptv_gui
alexlib Jul 12, 2025
c4dafe0
fixed bug in the first processing
alexlib Jul 12, 2025
ed95d1f
print is now in the local message window - don't need to look it up
alexlib Jul 12, 2025
203c2c4
fixed test detection
alexlib Jul 12, 2025
2883154
fixed bug as we should call detect_plate and not targ_rec.
alexlib Jul 12, 2025
7bdbcb6
solved detection in calibration
alexlib Jul 12, 2025
b4b4490
fixed manual orientation
alexlib Jul 12, 2025
77f656b
DetectionGUI expects Path to the working folder. glass is 1.46, water…
alexlib Jul 13, 2025
5138043
plugins
alexlib Jul 13, 2025
95536c8
fixed detect_plate bug. todo: check splitter and calibration, bump ve…
alexlib Jul 14, 2025
a632beb
splitter
alexlib Jul 14, 2025
6071f55
tests updated with batch plugins and splitter
alexlib Jul 14, 2025
98a9b8b
some tests that play with the tracking parameters. we need a ground t…
alexlib Jul 14, 2025
29ee7d2
more tests of ptv.py
alexlib Jul 15, 2025
a328a4c
tests partially fixed
alexlib Jul 15, 2025
c5e789d
previous tests with plugins
alexlib Jul 16, 2025
4ee31e4
plugins.json are obsolete
alexlib Jul 16, 2025
0ecdfea
test_cavity with larger tracking distances
alexlib Jul 16, 2025
0bef149
batch parallel test
alexlib Jul 16, 2025
a6f5f88
tracker
alexlib Jul 16, 2025
084a2b9
bumped version for future tag, rmeove message window which didn't hel…
alexlib Jul 16, 2025
4cc2b8a
fixed calibration_gui bug
alexlib Jul 16, 2025
6b2ff27
fixed calibration of test-splitter
alexlib Jul 16, 2025
ac7b952
updated tests
alexlib Jul 16, 2025
f8b2e9f
Update python-package.yml
alexlib Jul 16, 2025
7f65de5
fixed one test
alexlib Jul 16, 2025
102e6ba
Merge branch 'simple_yaml_with_tests' of https://github.com/alexlib/p…
alexlib Jul 16, 2025
62560e2
one test as pytest
alexlib Jul 16, 2025
431a353
one more pytest
alexlib Jul 16, 2025
06e488c
File->Open works
alexlib Jul 16, 2025
3cb6046
added subprocess
alexlib Jul 16, 2025
766583a
Squashed commit of the following:
alexlib Jul 26, 2025
847db8c
updated one more test
alexlib Jul 26, 2025
d44a195
target_filenames created once under mainGui and kept through. also up…
alexlib Jul 27, 2025
aa738d4
added the new target_filenames
alexlib Jul 27, 2025
e1462dc
tests pass but obviously one of the last tests of tests/track prints …
alexlib Jul 27, 2025
869bb63
Create check.yml
alexlib Jul 27, 2025
a286b4e
added test code editor for coverage
alexlib Jul 27, 2025
f9df971
marked two qt tests
alexlib Jul 27, 2025
5a2357e
some tests are difficult due to the change in pyptv_gui use of target…
alexlib Jul 27, 2025
17c8fac
dockerfile qt in __init__
alexlib Jul 27, 2025
ce4664b
Squashed commit of the following:
alexlib Jul 28, 2025
023b240
copied from pbi dumbbell calibration module
alexlib Aug 1, 2025
d568954
removed py_rclick_delete obsolete
alexlib Aug 1, 2025
12da049
cleaning up
alexlib Aug 2, 2025
a2c6664
copied some version from pbi - but maybe it's wiser just to use pbi s…
alexlib Aug 2, 2025
600480f
moved all to Python
alexlib Aug 2, 2025
e8543e3
fixed the dumbbell
alexlib Aug 2, 2025
e1a012d
separated gui tests, added batch to run, new github actions, and upda…
alexlib Aug 3, 2025
4e8ede0
Update check.yml
alexlib Aug 3, 2025
40a4150
removed old github workflows
alexlib Aug 3, 2025
ddfb57a
Merge branch 'simple_yaml_with_tests' of https://github.com/alexlib/p…
alexlib Aug 3, 2025
980b6a3
remove check.yml
alexlib Aug 3, 2025
59667de
should possibly pass
alexlib Aug 3, 2025
de6854a
Update requirements-dev.txt
alexlib Aug 3, 2025
7e248f5
try better
alexlib Aug 3, 2025
2e037de
all gui in a separate folder
alexlib Aug 3, 2025
5d4c6ac
also this one
alexlib Aug 3, 2025
543dfbe
added img_orig
alexlib Aug 3, 2025
02082a8
fixed the tests
alexlib Aug 3, 2025
e24396d
we do not use uv right now, so we can remove it from the requirements…
alexlib Aug 3, 2025
250e15f
Update tests/test_parameter_manager_prints.py
alexlib Aug 3, 2025
5248dbe
Update tests/test_parameter_manager.py
alexlib Aug 3, 2025
69ccb6a
Merge branch 'simple_yaml_with_tests' of https://github.com/alexlib/p…
alexlib Aug 3, 2025
f9bbe06
updated some markdown documents
alexlib Aug 3, 2025
24866f1
organized readme
alexlib Aug 3, 2025
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24 changes: 24 additions & 0 deletions .github/workflows/python-app.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
name: Python application

on:
push:
branches: [ main, simple_yaml_with_tests ]
pull_request:
branches: [ main, simple_yaml_with_tests ]

jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.11'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install -r requirements-dev.txt
python -m pip install -e .
- name: Run headless tests only
run: bash run_headless_tests.sh
70 changes: 0 additions & 70 deletions .github/workflows/python-package.yml

This file was deleted.

6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -74,3 +74,9 @@ pyptv/.vscode/launch.json
# Wheels
**/wheels/
.vscode/*.json
tests/test_splitter/parametersRun1/*
tests/test_splitter/res/*
test_output/*
tests/test_cavity/parameters__test_new.yaml
pyptv_session_log_*.txt
tests/track/res/*
32 changes: 32 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
# Slim Dockerfile for local testing of pyptv (mimics GitHub Actions)
FROM python:3.11-slim

# Install system dependencies for Qt, traitsui, and scientific stack
RUN apt-get update && apt-get install -y \
build-essential \
libgl1-mesa-glx \
libglib2.0-0 \
libxkbcommon-x11-0 \
libxcb-xinerama0 \
git \
xvfb \
&& rm -rf /var/lib/apt/lists/*

# Set workdir
WORKDIR /workspace

# Copy repo
COPY . /workspace

# Install pip, wheel, and setuptools
RUN pip install --upgrade pip wheel setuptools

# Install pyptv and dependencies
RUN pip install .
RUN pip install -r requirements-dev.txt || true

# Optionally install test dependencies for Qt
RUN pip install PySide6 traits traitsui pytest

# Run all tests
CMD ["xvfb-run", "pytest", "-v", "-x", "--tb=short"]
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