A Python toolbox for COPASI

CiaranWelsh, updated 🕥 2022-12-08 06:34:36

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Pycotools3

Pycotools3 is a set of tools for interacting with COPASI simulation software from Python 3. The old repository supports Python 2 only, can be found here and is the version that is described in detail in the bioinformatics publication.

Since publication, the pycotools project has moved to this pycotools3 repository, which is maintained separetly from pycotools. Since moving, the interface to COPASI's parameter estimation task has been significantly improved including inherent multi-model configuration and profile likelihood support - please refer to the pycotools3 documentation for more detail. Despite these improvements, there still a few things left to implement, namely full support for visualisation facilities. For now, users are advised to checkout matplotlib and seaborn.

Documentation

pycotools3 documentation

Support

I'm happy to help if you post questions, bugs, feature ideas etc. as an issue.

Contributions

Contributions, ideas, suggestions, feature requests or anything generally geared towards improving the package are welcome.

Citations

  • Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP. PyCoTools: a Python toolbox for COPASI. Bioinformatics. 2018 May 22;34(21):3702-10.

Since this package relies heavily on COPASI and tellurium please also cite

  • Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P. and Kummer, U., 2006. COPASI—a complex pathway simulator. Bioinformatics, 22(24), pp.3067-3074.

  • Medley, J.K., Choi, K., König, M., Smith, L., Gu, S., Hellerstein, J., Sealfon, S.C. and Sauro, H.M., 2018. Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology. PLoS computational biology, 14(6), p.e1006220.

Issues

Bump certifi from 2019.9.11 to 2022.12.7

opened on 2022-12-08 06:34:35 by dependabot[bot]

Bumps certifi from 2019.9.11 to 2022.12.7.

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Bump joblib from 0.14.0 to 1.2.0

opened on 2022-09-30 19:52:59 by dependabot[bot]

Bumps joblib from 0.14.0 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 lxml from 4.4.1 to 4.9.1

opened on 2022-07-06 19:57:38 by dependabot[bot]

Bumps lxml from 4.4.1 to 4.9.1.

Changelog

Sourced from lxml's changelog.

4.9.1 (2022-07-01)

Bugs fixed

  • A crash was resolved when using iterwalk() (or canonicalize()) after parsing certain incorrect input. Note that iterwalk() can crash on valid input parsed with the same parser after failing to parse the incorrect input.

4.9.0 (2022-06-01)

Bugs fixed

  • GH#341: The mixin inheritance order in lxml.html was corrected. Patch by xmo-odoo.

Other changes

  • Built with Cython 0.29.30 to adapt to changes in Python 3.11 and 3.12.

  • Wheels include zlib 1.2.12, libxml2 2.9.14 and libxslt 1.1.35 (libxml2 2.9.12+ and libxslt 1.1.34 on Windows).

  • GH#343: Windows-AArch64 build support in Visual Studio. Patch by Steve Dower.

4.8.0 (2022-02-17)

Features added

  • GH#337: Path-like objects are now supported throughout the API instead of just strings. Patch by Henning Janssen.

  • The ElementMaker now supports QName values as tags, which always override the default namespace of the factory.

Bugs fixed

  • GH#338: In lxml.objectify, the XSI float annotation "nan" and "inf" were spelled in lower case, whereas XML Schema datatypes define them as "NaN" and "INF" respectively.

... (truncated)

Commits
  • d01872c Prevent parse failure in new test from leaking into later test runs.
  • d65e632 Prepare release of lxml 4.9.1.
  • 86368e9 Fix a crash when incorrect parser input occurs together with usages of iterwa...
  • 50c2764 Delete unused Travis CI config and reference in docs (GH-345)
  • 8f0bf2d Try to speed up the musllinux AArch64 build by splitting the different CPytho...
  • b9f7074 Remove debug print from test.
  • b224e0f Try to install 'xz' in wheel builds, if available, since it's now needed to e...
  • 897ebfa Update macOS deployment target version from 10.14 to 10.15 since 10.14 starts...
  • 853c9e9 Prepare release of 4.9.0.
  • d3f77e6 Add a test for https://bugs.launchpad.net/lxml/+bug/1965070 leaving out the a...
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Bump numpy from 1.17.3 to 1.22.0

opened on 2022-06-21 21:37:55 by dependabot[bot]

Bumps numpy from 1.17.3 to 1.22.0.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

  • Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
  • A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
  • NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
  • New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.
  • A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

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Bump ipython from 7.8.0 to 7.16.3

opened on 2022-01-21 19:45:07 by dependabot[bot]

Bumps ipython from 7.8.0 to 7.16.3.

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Bump urllib3 from 1.25.6 to 1.26.5

opened on 2021-06-01 23:15:22 by dependabot[bot]

Bumps urllib3 from 1.25.6 to 1.26.5.

Release notes

Sourced from urllib3's releases.

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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Releases

v2.1.2 2019-03-21 21:30:15

Second release after making revisions to the way pycotools handles parameter estimation configuration

v1.0.13 2019-02-19 16:48:22

This release corresponds very similarly to the published pycotools package. This is the last published version before major revisions in the way parameter estimation configurations are handled.

Ciaran Welsh

Software Engineer at Biosoftware Development

GitHub Repository

copasi python profile-likelihood parameter-estimation ode-models