astir | Automated cell identity from single-cell multiplexed imaging and proteomics ūüĖ•ūüĒ¨‚ú®

camlab-bioml, updated ūüē• 2023-02-10 23:17:13

=================================================================================== astir - Automated cell identity from single-cell multiplexed imaging and proteomics ===================================================================================

|Build Status| |PyPI| |Code Style|

.. |Build Status| image:: https://travis-ci.com/camlab-bioml/astir.svg?branch=master :target: https://travis-ci.org/camlab-bioml/astir .. |Code Style| image:: https://img.shields.io/badge/code%20style-black-black :target: https://github.com/python/black .. |PyPI| image:: https://img.shields.io/badge/pypi-v2.1-orange :target: https://pypi.org/project/pypi/

astir is a modelling framework for the assignment of cell type across a range of single-cell technologies such as Imaging Mass Cytometry (IMC). astir is built using pytorch <https://pytorch.org/>_ and uses recognition networks for fast minibatch stochastic variational inference.

Key applications:

  • Automated assignment of cell type and state from highly multiplexed imaging and proteomic data
  • Diagnostic measures to check quality of resulting type and state inferences
  • Ability to map new data to cell types and states trained on existing data using recognition neural networks
  • A range of plotting and data loading utilities

.. image:: https://www.camlab.ca/img/astir.png :align: center :alt: automated single-cell pathology

Getting started

Launch the interactive tutorial: |in collab| |on github|

.. |in collab| image:: https://camo.githubusercontent.com/52feade06f2fecbf006889a904d221e6a730c194/68747470733a2f2f636f6c61622e72657365617263682e676f6f676c652e636f6d2f6173736574732f636f6c61622d62616467652e737667 :target: https://colab.research.google.com/github/camlab-bioml/Astir-Vignette/blob/main/astir_tutorial.ipynb .. |on github| image:: https://img.shields.io/badge/on-github-black :target: https://github.com/camlab-bioml/Astir-Vignette

See the full documentation <https://astir.readthedocs.io/en/latest> and check out the tutorials <https://astir.readthedocs.io/en/latest/tutorials/index.html>.

Authors

| Jinyu Hou, Sunyun Lee, Michael Geuenich, Kieran Campbell | Lunenfeld-Tanenbaum Research Institute & University of Toronto

Issues

Bump ipython from 7.17.0 to 8.10.0

opened on 2023-02-10 23:17:08 by dependabot[bot]

Bumps ipython from 7.17.0 to 8.10.0.

Release notes

Sourced from ipython's releases.

See https://pypi.org/project/ipython/

We do not use GitHub release anymore. Please see PyPI https://pypi.org/project/ipython/

Commits
  • 15ea1ed release 8.10.0
  • 560ad10 DOC: Update what's new for 8.10 (#13939)
  • 7557ade DOC: Update what's new for 8.10
  • 385d693 Merge pull request from GHSA-29gw-9793-fvw7
  • e548ee2 Swallow potential exceptions from showtraceback() (#13934)
  • 0694b08 MAINT: mock slowest test. (#13885)
  • 8655912 MAINT: mock slowest test.
  • a011765 Isolate the attack tests with setUp and tearDown methods
  • c7a9470 Add some regression tests for this change
  • fd34cf5 Swallow potential exceptions from showtraceback()
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Bump certifi from 2020.6.20 to 2022.12.7

opened on 2022-12-08 11:29:58 by dependabot[bot]

Bumps certifi from 2020.6.20 to 2022.12.7.

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Bump pillow from 7.2.0 to 9.3.0

opened on 2022-11-22 06:42:43 by dependabot[bot]

Bumps pillow from 7.2.0 to 9.3.0.

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9.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/9.3.0.html

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... (truncated)

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9.3.0 (2022-10-29)

  • Limit SAMPLESPERPIXEL to avoid runtime DOS #6700 [wiredfool]

  • Initialize libtiff buffer when saving #6699 [radarhere]

  • Inline fname2char to fix memory leak #6329 [nulano]

  • Fix memory leaks related to text features #6330 [nulano]

  • Use double quotes for version check on old CPython on Windows #6695 [hugovk]

  • Remove backup implementation of Round for Windows platforms #6693 [cgohlke]

  • Fixed set_variation_by_name offset #6445 [radarhere]

  • Fix malloc in _imagingft.c:font_setvaraxes #6690 [cgohlke]

  • Release Python GIL when converting images using matrix operations #6418 [hmaarrfk]

  • Added ExifTags enums #6630 [radarhere]

  • Do not modify previous frame when calculating delta in PNG #6683 [radarhere]

  • Added support for reading BMP images with RLE4 compression #6674 [npjg, radarhere]

  • Decode JPEG compressed BLP1 data in original mode #6678 [radarhere]

  • Added GPS TIFF tag info #6661 [radarhere]

  • Added conversion between RGB/RGBA/RGBX and LAB #6647 [radarhere]

  • Do not attempt normalization if mode is already normal #6644 [radarhere]

... (truncated)

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Bump py from 1.9.0 to 1.10.0

opened on 2022-10-18 20:31:33 by dependabot[bot]

Bumps py from 1.9.0 to 1.10.0.

Changelog

Sourced from py's changelog.

1.10.0 (2020-12-12)

  • Fix a regular expression DoS vulnerability in the py.path.svnwc SVN blame functionality (CVE-2020-29651)
  • Update vendored apipkg: 1.4 => 1.5
  • Update vendored iniconfig: 1.0.0 => 1.1.1
Commits
  • e5ff378 Update CHANGELOG for 1.10.0
  • 94cf44f Update vendored libs
  • 5e8ded5 testing: comment out an assert which fails on Python 3.9 for now
  • afdffcc Rename HOWTORELEASE.rst to RELEASING.rst
  • 2de53a6 Merge pull request #266 from nicoddemus/gh-actions
  • fa1b32e Merge pull request #264 from hugovk/patch-2
  • 887d6b8 Skip test_samefile_symlink on pypy3 on Windows
  • e94e670 Fix test_comments() in test_source
  • fef9a32 Adapt test
  • 4a694b0 Add GitHub Actions badge to README
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Bump joblib from 0.16.0 to 1.2.0

opened on 2022-09-30 19:11:43 by dependabot[bot]

Bumps joblib from 0.16.0 to 1.2.0.

Changelog

Sourced from joblib's changelog.

Release 1.2.0

  • Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported. joblib/joblib#1327

  • Make sure that joblib works even when multiprocessing is not available, for instance with Pyodide joblib/joblib#1256

  • Avoid unnecessary warnings when workers and main process delete the temporary memmap folder contents concurrently. joblib/joblib#1263

  • Fix memory alignment bug for pickles containing numpy arrays. This is especially important when loading the pickle with mmap_mode != None as the resulting numpy.memmap object would not be able to correct the misalignment without performing a memory copy. This bug would cause invalid computation and segmentation faults with native code that would directly access the underlying data buffer of a numpy array, for instance C/C++/Cython code compiled with older GCC versions or some old OpenBLAS written in platform specific assembly. joblib/joblib#1254

  • Vendor cloudpickle 2.2.0 which adds support for PyPy 3.8+.

  • Vendor loky 3.3.0 which fixes several bugs including:

    • robustly forcibly terminating worker processes in case of a crash (joblib/joblib#1269);

    • avoiding leaking worker processes in case of nested loky parallel calls;

    • reliability spawn the correct number of reusable workers.

Release 1.1.0

  • Fix byte order inconsistency issue during deserialization using joblib.load in cross-endian environment: the numpy arrays are now always loaded to use the system byte order, independently of the byte order of the system that serialized the pickle. joblib/joblib#1181

  • Fix joblib.Memory bug with the ignore parameter when the cached function is a decorated function.

... (truncated)

Commits
  • 5991350 Release 1.2.0
  • 3fa2188 MAINT cleanup numpy warnings related to np.matrix in tests (#1340)
  • cea26ff CI test the future loky-3.3.0 branch (#1338)
  • 8aca6f4 MAINT: remove pytest.warns(None) warnings in pytest 7 (#1264)
  • 067ed4f XFAIL test_child_raises_parent_exits_cleanly with multiprocessing (#1339)
  • ac4ebd5 MAINT add back pytest warnings plugin (#1337)
  • a23427d Test child raises parent exits cleanly more reliable on macos (#1335)
  • ac09691 [MAINT] various test updates (#1334)
  • 4a314b1 Vendor loky 3.2.0 (#1333)
  • bdf47e9 Make test_parallel_with_interactively_defined_functions_default_backend timeo...
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Bump urllib3 from 1.25.10 to 1.26.5

opened on 2022-09-20 22:17:31 by dependabot[bot]

Bumps urllib3 from 1.25.10 to 1.26.5.

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1.26.5

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Fixed deprecation warnings emitted in Python 3.10.
  • Updated vendored six library to 1.16.0.
  • Improved performance of URL parser when splitting the authority component.

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.4

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Changed behavior of the default SSLContext when connecting to HTTPS proxy during HTTPS requests. The default SSLContext now sets check_hostname=True.

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.3

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Fixed bytes and string comparison issue with headers (Pull #2141)

  • Changed ProxySchemeUnknown error message to be more actionable if the user supplies a proxy URL without a scheme (Pull #2107)

If you or your organization rely on urllib3 consider supporting us via GitHub Sponsors

1.26.2

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

1.26.1

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Fixed an issue where two User-Agent headers would be sent if a User-Agent header key is passed as bytes (Pull #2047)

1.26.0

:warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap

  • Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

  • Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning should opt-in explicitly by setting ssl_version=ssl.PROTOCOL_TLSv1_1 (Pull #2002) Starting in urllib3 v2.0: Connections that receive a DeprecationWarning will fail

  • Deprecated Retry options Retry.DEFAULT_METHOD_WHITELIST, Retry.DEFAULT_REDIRECT_HEADERS_BLACKLIST and Retry(method_whitelist=...) in favor of Retry.DEFAULT_ALLOWED_METHODS, Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT, and Retry(allowed_methods=...) (Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed

... (truncated)

Changelog

Sourced from urllib3's changelog.

1.26.5 (2021-05-26)

  • Fixed deprecation warnings emitted in Python 3.10.
  • Updated vendored six library to 1.16.0.
  • Improved performance of URL parser when splitting the authority component.

1.26.4 (2021-03-15)

  • Changed behavior of the default SSLContext when connecting to HTTPS proxy during HTTPS requests. The default SSLContext now sets check_hostname=True.

1.26.3 (2021-01-26)

  • Fixed bytes and string comparison issue with headers (Pull #2141)

  • Changed ProxySchemeUnknown error message to be more actionable if the user supplies a proxy URL without a scheme. (Pull #2107)

1.26.2 (2020-11-12)

  • Fixed an issue where wrap_socket and CERT_REQUIRED wouldn't be imported properly on Python 2.7.8 and earlier (Pull #2052)

1.26.1 (2020-11-11)

  • Fixed an issue where two User-Agent headers would be sent if a User-Agent header key is passed as bytes (Pull #2047)

1.26.0 (2020-11-10)

  • NOTE: urllib3 v2.0 will drop support for Python 2. Read more in the v2.0 Roadmap <https://urllib3.readthedocs.io/en/latest/v2-roadmap.html>_.

  • Added support for HTTPS proxies contacting HTTPS servers (Pull #1923, Pull #1806)

  • Deprecated negotiating TLSv1 and TLSv1.1 by default. Users that still wish to use TLS earlier than 1.2 without a deprecation warning

... (truncated)

Commits
  • d161647 Release 1.26.5
  • 2d4a3fe Improve performance of sub-authority splitting in URL
  • 2698537 Update vendored six to 1.16.0
  • 07bed79 Fix deprecation warnings for Python 3.10 ssl module
  • d725a9b Add Python 3.10 to GitHub Actions
  • 339ad34 Use pytest==6.2.4 on Python 3.10+
  • f271c9c Apply latest Black formatting
  • 1884878 [1.26] Properly proxy EOF on the SSLTransport test suite
  • a891304 Release 1.26.4
  • 8d65ea1 Merge pull request from GHSA-5phf-pp7p-vc2r
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machine-learning imaging-mass-cytometry multiplexed-imaging