Ecosyste.ms: Issues

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GitHub / lumicks/pylake issues and pull requests

#604 - release: release pylake v1.3.0

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#603 - release prep: merge `1.2` back into `main`

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#602 - zenodo: fix `download_from_doi`

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#601 - calibration: add model for salt water

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#599 - export_movie: force showing the figure

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#597 - Small test improvements and bugfix on `Slice`.

Pull Request - State: closed - Opened by JoepVanlier 12 months ago

#596 - Hidden Markov models

Pull Request - State: closed - Opened by rpauszek 12 months ago - 1 comment

#595 - Migrate plot export tests

Pull Request - State: closed - Opened by rpauszek almost 1 year ago

#594 - Migrate scan slicing/cropping

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#593 - Migrate basic scan tests

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#592 - Migrate test point scan

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#591 - Migrate tests for `_kymo_from_array`

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#590 - calibration: add private api for motion blur model

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#589 - Fix scan aspect ratio

Pull Request - State: closed - Opened by rpauszek about 1 year ago - 2 comments

#587 - tracking: add `min_duration` argument to `lk.filter_tracks`

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#586 - Fix fetching files from zenodo

Pull Request - State: closed - Opened by agom about 1 year ago

#585 - force_calibration: coupling model for active calibration

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago - 8 comments

#584 - merge `v1.2.1` back into `main`

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#583 - Prerelease v1.2.1

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#582 - Fixup zenodo

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#581 - Add zenodo link to index.rst

Pull Request - State: closed - Opened by aafkevandenberg about 1 year ago - 1 comment

#580 - Update update instructions install.rst

Pull Request - State: closed - Opened by aafkevandenberg about 1 year ago

#579 - Fix tracks csv export

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#578 - Rework more tests

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#577 - Rework plotting tests

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#576 - kymo: make single line scan return a valid `line_time_seconds`

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#575 - tracking widget: fix width of kymograph part of the widget layout

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#574 - Consolidate plotting documentation

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#573 - Rework confocal downsampling tests

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#572 - Rework confocal tests: kymo basics

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#571 - More options of image plotting `channel` argument

Pull Request - State: closed - Opened by rpauszek about 1 year ago

#570 - Add custom mapping of photon counter channels to RGB colors

Pull Request - State: closed - Opened by agom about 1 year ago - 1 comment

#569 - Velocity estimation by piecewise linear regression

Pull Request - State: open - Opened by rpauszek about 1 year ago

#568 - force calibration: new lower bound for f-diode

Pull Request - State: closed - Opened by rjmoerland about 1 year ago - 2 comments

#567 - ci: convert convertible list of lists to `ndarray`

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#566 - ci: small improvements to freezing test output

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#565 - caching: backward compatibility for `cachetools<5`

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#564 - Reorganize the docs sidebar

Pull Request - State: closed - Opened by rpauszek about 1 year ago - 1 comment

#563 - merge `1.2` into main

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#562 - touchdown: use nonzero initial guess for decay

Pull Request - State: closed - Opened by JoepVanlier about 1 year ago

#561 - Docs diffusion intro

Pull Request - State: closed - Opened by aafkevandenberg about 1 year ago

#560 - docs: update install instruction with latest conda

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#559 - kymotrackgroup: test round trip from old csv

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#558 - fdfitter: Improve inversion performance (Friday afternoon)

Pull Request - State: open - Opened by JoepVanlier over 1 year ago

#557 - Release v1.2.0

Pull Request - State: closed - Opened by rpauszek over 1 year ago

#556 - docs: apply review suggestions to robust fitting tutorial

Pull Request - State: closed - Opened by rjmoerland over 1 year ago

#555 - deps: update `pylake` dependencies

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#554 - Update China faq install.rst

Pull Request - State: closed - Opened by aafkevandenberg over 1 year ago

#553 - Further speed up `import lumicks.pylake` and add regression test

Pull Request - State: closed - Opened by dean0x7d over 1 year ago

#552 - black: enable `black` formatting for tests

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#551 - docs: add section on robust fitting in force calibration tutorial

Pull Request - State: closed - Opened by rjmoerland over 1 year ago

#550 - Speed up `import lumicks.pylake` by streamlining `scipy` imports

Pull Request - State: closed - Opened by dean0x7d over 1 year ago

#549 - dwelltime: enforce minimum time

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#548 - Mark file APIs with `os.PathLike` type hint

Pull Request - State: closed - Opened by dean0x7d over 1 year ago - 1 comment

#546 - deps: enforce upper limit `jupyter_client` and `pyzmq`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#545 - Fun with css

Pull Request - State: closed - Opened by rpauszek over 1 year ago - 1 comment

#544 - confocal: faster pixel and line times.

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#543 - save_as: suppress `FutureWarning`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#542 - Format (almost) all tests with black

Pull Request - State: closed - Opened by rpauszek over 1 year ago

#540 - dwelltime analysis: correctly handle minimum observable time

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#539 - ci: add option to freeze reference data

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#538 - Update install.rst: update installation instructions for China in faq

Pull Request - State: closed - Opened by aafkevandenberg over 1 year ago - 2 comments

#537 - msvst: stabilized wavelets

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#536 - file: add ability to crop to time interval when using `save_as`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#535 - file: allow `str` for `omit_data` in `save_as`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#534 - ci: close figures before issuing another plot

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment

#533 - peakfinding: split peak finding from `track_greedy`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#532 - Generate colormaps from wavelengths

Pull Request - State: closed - Opened by rpauszek over 1 year ago

#531 - docs: add logical mask example

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#530 - ci: fix deprecation warning in latest `numpy`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#529 - pylake: Replace $math$ unit labels with Unicode variants

Pull Request - State: closed - Opened by mikhas over 1 year ago

#528 - Force calibration: add robust fitting to fit_power_spectrum()

Pull Request - State: closed - Opened by rjmoerland over 1 year ago - 3 comments

#527 - merge v1.1.1 back into main

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#526 - release: release pylake v1.1.1

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#525 - deps: import rarely used dependencies on demand

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment

#524 - widgets: Add display_unit to KymotrackerParameter

Pull Request - State: closed - Opened by mikhas over 1 year ago

#523 - widgets: Fix parameter description for minimum length

Pull Request - State: closed - Opened by mikhas over 1 year ago - 1 comment

#521 - dwelltimes: take into account maximum possible dwelltime

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#520 - Pytest: fix check whether a test is marked to be skipped

Pull Request - State: closed - Opened by tobiasjj over 1 year ago

#519 - docs: swap order for consistency with changelog

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#518 - merge `v1.1.0` back into `main`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#517 - release: release Pylake v1.1

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#516 - docs: prepare release

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago
Labels: blocks release

#515 - Remove `KymoTrackGroup._kymo`

Pull Request - State: closed - Opened by rpauszek over 1 year ago

#514 - `KymoTrackGroup._kymo` only valid for single source kymo

Pull Request - State: closed - Opened by rpauszek over 1 year ago - 2 comments
Labels: blocks release

#513 - sample_from_image: ensure backward compatibility

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment
Labels: blocks release

#512 - Bugfix release v1.0.1

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment

#511 - fitting: fix incorrect model being used for `dsdna`

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#510 - diffusion: include gaussian refinement in warning

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment
Labels: bug

#509 - kymotrack/kymotrackgroup: allow plotting the localization fit

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 2 comments
Labels: enhancement

#508 - Finalize global binding profile

Pull Request - State: closed - Opened by rpauszek over 1 year ago

#507 - flake8: B028 got renamed to B907. See link in the description

Pull Request - State: open - Opened by tobiasjj over 1 year ago - 1 comment
Labels: enhancement

#506 - Gaussian refinement: Don't allow track swaps

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago

#505 - kymotrack: add photon counts as an attribute

Pull Request - State: closed - Opened by JoepVanlier over 1 year ago - 1 comment
Labels: enhancement