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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.
I'm happy to help if you post questions, bugs, feature ideas etc. as an issue.
Contributions, ideas, suggestions, feature requests or anything generally geared towards improving the package are welcome.
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.
Bumps certifi from 2019.9.11 to 2022.12.7.
9e9e840
2022.12.07b81bdb2
2022.09.24939a28f
2022.09.14aca828a
2022.06.15.2de0eae1
Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ...b8eb5e9
2022.06.15.147fb7ab
Fix deprecation warning on Python 3.11 (#199)b0b48e0
fixes #198 -- update link in license9d514b4
2022.06.154151e88
Add py.typed to MANIFEST.in to package in sdist (#196)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Bumps joblib from 0.14.0 to 1.2.0.
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#1327Make 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 resultingnumpy.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#1254Vendor 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.
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Release 1.2.03fa2188
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...Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Bumps lxml from 4.4.1 to 4.9.1.
Sourced from lxml's changelog.
4.9.1 (2022-07-01)
Bugs fixed
- A crash was resolved when using
iterwalk()
(orcanonicalize()
) after parsing certain incorrect input. Note thatiterwalk()
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 supportsQName
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.
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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...Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Bumps numpy from 1.17.3 to 1.22.0.
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 aTypeError
.(gh-19539)
Expired deprecations for
loads
,ndfromtxt
, andmafromtxt
in npyio
numpy.loads
was deprecated in v1.15, with the recommendation that users usepickle.loads
instead.ndfromtxt
andmafromtxt
were both deprecated in v1.17 - users should usenumpy.genfromtxt
instead with the appropriate value for theusemask
parameter.(gh-19615)
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Merge pull request #20685 from charris/prepare-for-1.22.0-releasefd66547
REL: Prepare for the NumPy 1.22.0 release.125304b
wipc283859
Merge pull request #20682 from charris/backport-204165399c03
Merge pull request #20681 from charris/backport-20954f9c45f8
Merge pull request #20680 from charris/backport-20663794b36f
Update armccompiler.pyd93b14e
Update test_public_api.py7662c07
Update init.py311ab52
Update armccompiler.pyDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Bumps ipython from 7.8.0 to 7.16.3.
d43c7c7
release 7.16.35fa1e40
Merge pull request from GHSA-pq7m-3gw7-gq5x8df8971
back to dev9f477b7
release 7.16.2138f266
bring back release helper from master branch5aa3634
Merge pull request #13341 from meeseeksmachine/auto-backport-of-pr-13335-on-7...bcae8e0
Backport PR #13335: What's new 7.16.28fcdcd3
Pin Jedi to <0.17.2.2486838
release 7.16.120bdc6f
fix conda buildDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Bumps urllib3 from 1.25.6 to 1.26.5.
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 defaultSSLContext
now setscheck_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
andCERT_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 aUser-Agent
header key is passed asbytes
(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 aDeprecationWarning
will failDeprecated
Retry
optionsRetry.DEFAULT_METHOD_WHITELIST
,Retry.DEFAULT_REDIRECT_HEADERS_BLACKLIST
andRetry(method_whitelist=...)
in favor ofRetry.DEFAULT_ALLOWED_METHODS
,Retry.DEFAULT_REMOVE_HEADERS_ON_REDIRECT
, andRetry(allowed_methods=...)
(Pull #2000) Starting in urllib3 v2.0: Deprecated options will be removed
... (truncated)
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 defaultSSLContext
now setscheck_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
andCERT_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 aUser-Agent
header key is passed asbytes
(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
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d161647
Release 1.26.52d4a3fe
Improve performance of sub-authority splitting in URL2698537
Update vendored six to 1.16.007bed79
Fix deprecation warnings for Python 3.10 ssl moduled725a9b
Add Python 3.10 to GitHub Actions339ad34
Use pytest==6.2.4 on Python 3.10+f271c9c
Apply latest Black formatting1884878
[1.26] Properly proxy EOF on the SSLTransport test suitea891304
Release 1.26.48d65ea1
Merge pull request from GHSA-5phf-pp7p-vc2rDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase
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Second release after making revisions to the way pycotools handles parameter estimation configuration
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.
copasi python profile-likelihood parameter-estimation ode-models