Taxonomy addition for complete trees

Related tags

Miscellaneouspython
Overview

TACT: Taxonomic Addition for Complete Trees

PyPI Build status Docker Hub

TACT is a Python app for stochastic polytomy resolution. It uses birth-death-sampling estimators across an ultrametric phylogeny to generate branching times for unsampled taxa, using taxonomic information to compatibly place new taxa onto a backbone phylogeny.

Getting started with TACT

Citation

TACT is described more fully in its manuscript. If you use TACT, please cite:

  • Chang, J., Rabosky, D. L., & Alfaro, M. E. (2019). Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology. doi:10.1093/sysbio/syz081

TACT owes its existence to much foundational work in the area of stochastic polytomy resolution, namely PASTIS and CorSiM.

  • Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. O. (2013). PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011–1017. doi:10.1111/2041-210x.12117

  • Cusimano, N., Stadler, T., & Renner, S. S. (2012). A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies. Systematic Biology, 61(5), 785–792. doi:10.1093/sysbio/sys031

Sponsorship

Please consider sponsoring the ongoing maintenance of TACT via GitHub Sponsors.

Initial development was supported by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB-1601830).

Comments
  • dendropy.utility.error.UltrametricityError when using TACT

    dendropy.utility.error.UltrametricityError when using TACT

    Hi @jonchang ,

    I'm trying to use TACT adding some species to GBMB.tre from Smith and Brown (2018). The backbone is fine, which was confirmed by phyx.

    [cactus]$ pxlstr -t GBMB_bi-rmbadtip.tre [some tips are cleaned]
tree #: 0
rooted: true
binary: true
nterminal: 78929
ninternal: 78928
branch lengths: true
rttipvar: 2.23112e-10
treelength: 490017
ultrametric: true
rootheight: 325.05

    When I run TACT with tact_add_taxa function, it gives error as below:

    Traceback (most recent call last): File "/home/cactus/.local/bin/tact_add_taxa", line 8, in sys.exit(main()) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(*args, **kwargs) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/tact/cli_add_taxa.py", line 392, in main tree.calc_node_ages() File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 5666, in calc_node_ages subtree=subtree, dendropy.utility.error.UltrametricityError: Tree is not ultrametric within threshold of 1e-05: 1.0000000017384991e-05. Encountered in subtree of node <Node object at 0x7fc312709470: 'None' (None)> (edge length of 1.291905):

    ####huge newick tree skipped ...####

    Age of children:

    • <Node object at 0x7fc3127094e0: 'None' (None)>: has age of 88.17562399999998 and edge length of 5.093615, resulting in parent node age of 93.26923899999998
    • <Node object at 0x7fc3126849b0: 'None' (None)>: has age of 25.721769000000002 and edge length of 67.54748, resulting in parent node age of 93.269249

    I suspect it could be issues from dendropy, not really TACT, but would like to hear from your advice first. Thank you!

    Happy to mail you my tree file and taxonomy data if you have time to check it.

    Cheers,

    Miao

    opened by Cactusolo 14
  • Bump scipy from 1.4.1 to 1.5.0

    Bump scipy from 1.4.1 to 1.5.0

    Bumps scipy from 1.4.1 to 1.5.0.

    Release notes

    Sourced from scipy's releases.

    SciPy 1.5.0 Release Notes

    SciPy 1.5.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.5.x branch, and on adding new features on the master branch.

    This release requires Python 3.6+ and NumPy 1.14.5 or greater.

    For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required.

    Highlights of this release

    • wrappers for more than a dozen new LAPACK routines are now available in scipy.linalg.lapack
    • Improved support for leveraging 64-bit integer size from linear algebra backends
    • addition of the probability distribution for two-sided one-sample Kolmogorov-Smirnov tests

    New features

    scipy.cluster improvements

    Initialization of scipy.cluster.vq.kmeans2 using minit="++" had a quadratic complexity in the number of samples. It has been improved, resulting in a much faster initialization with quasi-linear complexity.

    scipy.cluster.hierarchy.dendrogram now respects the matplotlib color palette

    scipy.fft improvements

    A new keyword-only argument plan is added to all FFT functions in this module. It is reserved for passing in a precomputed plan from libraries providing a FFT backend (such as PyFFTW and mkl-fft), and it is currently not used in SciPy.

    scipy.integrate improvements

    Commits
    • 4c0fd79 REL: set version to 1.5.0 "final"
    • ce8c972 Merge pull request #12391 from tylerjereddy/prep_scipy_150_final
    • d60c1b3 MAINT: prepare for SciPy 1.5.0 "final"
    • a7131fa REL: set version to 1.5.0rc2 released
    • 896480b Merge pull request #12345 from tylerjereddy/treddy_150rc2_backports
    • 1e5c8d9 DOC: 1.5.0rc2 release notes update
    • e468042 CI: don't install pydata/sparse when running on Numpy prerelease
    • 3d96899 CI: split travis arm64 run into two
    • a3795e9 DOC: update SciPy 1.5.0rc2 release notes
    • 9803615 MAINT: Work around Sphinx bug (#12335)
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot will merge this PR once CI passes on it, as requested by @jonchang.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies 
    opened by dependabot[bot] 7
  • Bump pytest from 5.3.5 to 5.4.0

    Bump pytest from 5.3.5 to 5.4.0

    Bumps pytest from 5.3.5 to 5.4.0.

    Changelog

    Sourced from pytest's changelog.

    Commits
    • c9fd1bd Preparing release version 5.4.0
    • 93aa988 Merge pull request #6901 from RonnyPfannschmidt/regendoc-fix-simple
    • 7996724 Merge pull request #6902 from RoyalTS/filterwarnings-docfix
    • 90ee8a7 docfix
    • 378a75d run and fix tox -e regen to prepare 5.4
    • e1b3a68 Merge pull request #6896 from nicoddemus/release-trigger
    • fb7dbc9 Merge pull request #6893 from RonnyPfannschmidt/url-fixes
    • a0ea300 Fix bot trigger event
    • 09b289e fix mozilla qa project link
    • 694dbe5 fix pydanny.com url to the one with ssl set up
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot will merge this PR once it's up-to-date and CI passes on it, as requested by @jonchang.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    • @dependabot use these labels will set the current labels as the default for future PRs for this repo and language
    • @dependabot use these reviewers will set the current reviewers as the default for future PRs for this repo and language
    • @dependabot use these assignees will set the current assignees as the default for future PRs for this repo and language
    • @dependabot use this milestone will set the current milestone as the default for future PRs for this repo and language
    • @dependabot badge me will comment on this PR with code to add a "Dependabot enabled" badge to your readme

    Additionally, you can set the following in your Dependabot dashboard:

    • Update frequency (including time of day and day of week)
    • Pull request limits (per update run and/or open at any time)
    • Automerge options (never/patch/minor, and dev/runtime dependencies)
    • Out-of-range updates (receive only lockfile updates, if desired)
    • Security updates (receive only security updates, if desired)
    dependencies 
    opened by dependabot-preview[bot] 6
  • Assumptions made by TACT?

    Assumptions made by TACT?

    Hi,

    I was curious what assumptions TACT means with regards to input files. Occasionally I have noticed that some taxonomically added clades are not monophyletic; for instance, I have a subgenera column, and while this column retains its monophyly, the genera to which subgenera below do not always retain their monophyly when added to the backbone tree.

    opened by jsoghigian 4
  • Bump scipy from 1.8.1 to 1.9.2

    Bump scipy from 1.8.1 to 1.9.2

    Bumps scipy from 1.8.1 to 1.9.2.

    Release notes

    Sourced from scipy's releases.

    SciPy 1.9.2 Release Notes

    SciPy 1.9.2 is a bug-fix release with no new features compared to 1.9.1. It also provides wheels for Python 3.11 on several platforms.

    Authors

    • Hood Chatham (1)
    • Thomas J. Fan (1)
    • Ralf Gommers (22)
    • Matt Haberland (5)
    • Julien Jerphanion (1)
    • Loïc Estève (1)
    • Nicholas McKibben (2)
    • Naoto Mizuno (1)
    • Andrew Nelson (3)
    • Tyler Reddy (28)
    • Pamphile Roy (1)
    • Ewout ter Hoeven (2)
    • Warren Weckesser (1)
    • Meekail Zain (1) +

    A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

    SciPy 1.9.1 Release Notes

    SciPy 1.9.1 is a bug-fix release with no new features compared to 1.9.0. Notably, some important meson build fixes are included.

    Authors

    • Anirudh Dagar (1)
    • Ralf Gommers (12)
    • Matt Haberland (2)
    • Andrew Nelson (1)
    • Tyler Reddy (14)
    • Atsushi Sakai (1)
    • Eli Schwartz (1)
    • Warren Weckesser (2)

    A total of 8 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

    ... (truncated)

    Commits
    • 656076c MAINT: wheel push 1.9.2 [wheel build]
    • ad0d0f9 REL: set 1.9.2 released [wheel build]
    • d9ad980 Merge pull request #17150 from tylerjereddy/treddy_scipy_192_more_backports
    • 6b098c2 TST: optimize.milp: remove problematic timeout/iteration test
    • 24dce97 DOC: stats.pearsonr: typo in coefficient (#17153)
    • a6ba7ca MAINT: misc 1.9.2 updates
    • ed9760e MAINT: stats.pearson3: fix ppf for negative skew (#17055)
    • 6fb6700 FIX: optimize.milp: return feasible solution if available on timeout/node lim...
    • bcfce27 Merge pull request #17132 from tylerjereddy/treddy_192_backports
    • 2bc973a BLD: set version to 1.9.2.dev0 (and trigger wheel build CI)
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies python 
    opened by dependabot[bot] 3
  • Bump scipy from 1.8.1 to 1.9.0

    Bump scipy from 1.8.1 to 1.9.0

    Bumps scipy from 1.8.1 to 1.9.0.

    Release notes

    Sourced from scipy's releases.

    SciPy 1.9.0 Release Notes

    SciPy 1.9.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.9.x branch, and on adding new features on the main branch.

    This release requires Python 3.8-3.11 and NumPy 1.18.5 or greater.

    For running on PyPy, PyPy3 6.0+ is required.

    Highlights of this release

    • We have modernized our build system to use meson, substantially improving our build performance, and providing better build-time configuration and cross-compilation support,
    • Added scipy.optimize.milp, new function for mixed-integer linear programming,
    • Added scipy.stats.fit for fitting discrete and continuous distributions to data,
    • Tensor-product spline interpolation modes were added to scipy.interpolate.RegularGridInterpolator,
    • A new global optimizer (DIviding RECTangles algorithm) scipy.optimize.direct.

    New features

    scipy.interpolate improvements

    • Speed up the RBFInterpolator evaluation with high dimensional interpolants.
    • Added new spline based interpolation methods for scipy.interpolate.RegularGridInterpolator and its tutorial.
    • scipy.interpolate.RegularGridInterpolator and scipy.interpolate.interpn now accept descending ordered points.
    • RegularGridInterpolator now handles length-1 grid axes.
    • The BivariateSpline subclasses have a new method partial_derivative

    ... (truncated)

    Commits
    • 651a9b7 REL: set 1.9.0 released.
    • 253f894 Merge pull request #16727 from tylerjereddy/treddy_final_190_backports
    • 4e9ed02 REL: 1.9.0 final unreleased.
    • b83feac DOC: update 1.9.0 relnotes
    • ee9b834 MAINT: stats.monte_carlo_test: used biased estimate of p-value (#16721)
    • 7ecca8d MAINT: stats: Work around Cython bug. (#16719)
    • 87945b3 DOC: a few mailmap updates
    • 8cefead MAINT: optimize.linprog: ensure integrality can be an array (#16684)
    • 15e96a0 DOC: pin pydata-sphinx-theme to prevent incoming breaking changes.
    • c4c9348 REL: set 1.9.0rc3 released.
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies python 
    opened by dependabot[bot] 3
  • duplicate taxa and error for parenthesis

    duplicate taxa and error for parenthesis

    Hello Jon,

    I am using the most recent Docker version of TACT on MacOS and I am trying to add a lot of taxa (16,000) to a relatively sparse (~200) backbone. Maybe this is a bad idea in the first place, which would make sense as to why I'm encountering difficulty. TACT runs fine, but there are a few issues that I am having with the output tree.

    1. There are duplicate taxon names, usually all clustered together away from their taxonomic ranks. Some programs won't open the tree with duplicate taxon names (e.g. FigTree), but others will (e.g. TreeGraph/iTOL).
    2. When I attempt to load the tree into ape/ete3 (with any format option in ete3), I get an error about parenthesis not matching. This is curious since the GUIs seem to open it fine. It doesn't matter which newick format code I use in ete3, I continue to get the error.
    3. It looks like the output tree is not ultrametric, at least how it is displayed in iTOL or TreeGraph. If I export from iTOL it seems to fix the issue with the parentheses, but it is then no longer ultrametric.

    Do you have any ideas for these issues? I am happy to send my input files to you via email if that would help.

    Many thanks, Paul

    opened by pbfrandsen 3
  • Don't emit rooting annotations for Newick-format trees

    Don't emit rooting annotations for Newick-format trees

    The newick tree produced by tact_add_taxa (i.e., *.tacted.newick.tre) has a rooting annotation:

    [&R] (newick tree string);

    AFAIK such an annotation is not strictly newick-compliant. Regardless, it is giving me trouble with another tool. This PR makes it so that this annotation is not written.

    opened by josephwb 3
  • Bump scipy from 1.8.1 to 1.9.1

    Bump scipy from 1.8.1 to 1.9.1

    Bumps scipy from 1.8.1 to 1.9.1.

    Release notes

    Sourced from scipy's releases.

    SciPy 1.9.1 Release Notes

    SciPy 1.9.1 is a bug-fix release with no new features compared to 1.9.0. Notably, some important meson build fixes are included.

    Authors

    • Anirudh Dagar (1)
    • Ralf Gommers (12)
    • Matt Haberland (2)
    • Andrew Nelson (1)
    • Tyler Reddy (14)
    • Atsushi Sakai (1)
    • Eli Schwartz (1)
    • Warren Weckesser (2)

    A total of 8 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

    SciPy 1.9.0 Release Notes

    SciPy 1.9.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.9.x branch, and on adding new features on the main branch.

    This release requires Python 3.8-3.11 and NumPy 1.18.5 or greater.

    For running on PyPy, PyPy3 6.0+ is required.

    Highlights of this release

    • We have modernized our build system to use meson, substantially improving our build performance, and providing better build-time configuration and cross-compilation support,
    • Added scipy.optimize.milp, new function for mixed-integer linear

    ... (truncated)

    Commits
    • 2e5883e REL: set 1.9.1 released
    • fdd33ae Merge pull request #16908 from tylerjereddy/treddy_191_relnotes_update
    • 55e4f9f Update doc/release/1.9.1-notes.rst
    • 04945c5 DOC: 1.9.1 relnotes update
    • 5f06ddd Merge pull request #16904 from rgommers/update-191-pins
    • 987c698 Merge pull request #16901 from tylerjereddy/treddy_191_backports
    • 8e494e1 BLD: update dependency ranges for meson-python and pybind11 for 1.9.1
    • 8b97528 BLD: make the way we count commits for version numbering more robust
    • cc0a2bf TST: sparse.linalg: Loosen tolerance for the lobpcg test 'test_tolerance_floa...
    • c055c31 BLD: cp310 needs numpy==1.22.3
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies python 
    opened by dependabot[bot] 2
  • Bump ubuntu from 21.04 to 21.10

    Bump ubuntu from 21.04 to 21.10

    Bumps ubuntu from 21.04 to 21.10.

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies docker 
    opened by dependabot[bot] 2
  • When installing with Linuxbrew: Failed to download resource

    When installing with Linuxbrew: Failed to download resource "tact"

    Hi there,

    Thanks again for the awesome software!

    I've got a working Docker version of TACT on another machine, but I wanted to install TACT on my home WSL machine. But I ran into a problem when trying to install with brew:

    myusrname:~$ brew install jonchang/biology/tact
==> Installing tact from jonchang/biology
... (other preqs downloading here) ...
==> Downloading https://dl.bintray.com/jonchang/bottles-biology/tact-0.3.4.x86_64_linux.bottle.tar.gz

curl: (22) The requested URL returned error: 403 Forbidden
Error: Failed to download resource "tact"
Download failed: https://dl.bintray.com/jonchang/bottles-biology/tact-0.3.4.x86_64_linux.bottle.tar.gz

    I've truncated the full install messages, because there's just a lot of downloading of other files successfully. I can add them in if you think they might be a problem, but no errors were indicated before attempting to download TACT

    opened by jsoghigian 2
  • Bump scipy from 1.8.1 to 1.9.3

    Bump scipy from 1.8.1 to 1.9.3

    Bumps scipy from 1.8.1 to 1.9.3.

    Release notes

    Sourced from scipy's releases.

    SciPy 1.9.3 Release Notes

    SciPy 1.9.3 is a bug-fix release with no new features compared to 1.9.2.

    Authors

    • Jelle Aalbers (1)
    • Peter Bell (1)
    • Jake Bowhay (3)
    • Matthew Brett (3)
    • Evgeni Burovski (5)
    • drpeteb (1) +
    • Sebastian Ehlert (1) +
    • GavinZhang (1) +
    • Ralf Gommers (2)
    • Matt Haberland (15)
    • Lakshaya Inani (1) +
    • Joseph T. Iosue (1)
    • Nathan Jacobi (1) +
    • jmkuebler (1) +
    • Nikita Karetnikov (1) +
    • Lechnio (1) +
    • Nicholas McKibben (1)
    • Andrew Nelson (1)
    • o-alexandre-felipe (1) +
    • Tirth Patel (1)
    • Tyler Reddy (51)
    • Martin Reinecke (1)
    • Marie Roald (1) +
    • Pamphile Roy (2)
    • Eli Schwartz (1)
    • serge-sans-paille (1)
    • ehsan shirvanian (1) +
    • Mamoru TASAKA (1) +
    • Samuel Wallan (1)
    • Warren Weckesser (7)
    • Gavin Zhang (1) +

    A total of 31 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

    SciPy 1.9.2 Release Notes

    SciPy 1.9.2 is a bug-fix release with no new features compared to 1.9.1. It also provides wheels for Python 3.11

    ... (truncated)

    Commits
    • de80faf REL: set 1.9.3 released [wheel build]
    • 25e6b90 Merge pull request #17239 from tylerjereddy/treddy_backport_193
    • ba33e43 DOC: update 1.9.3 relnotes
    • 92d892e MAINT: Handle numpy's deprecation of accepting out-of-bound integers.
    • ba5f6da MAINT: PR 17239 revisions
    • 381089e DOC: update 1.9.3 relnotes
    • 2db3440 BLD: fix invalid shebang for build helper script
    • a9a6582 DOC: stats.mode: add versionadded tag and correct order of keepdims descripti...
    • f473888 BLD: fix issue with incomplete threads dependency handling (#17200)
    • 5370f15 MAINT: update meson.build to make it work on IBM i system (#17193)
    • Additional commits viewable in compare view

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies python 
    opened by dependabot[bot] 0
  • Bump peaceiris/actions-gh-pages from 3.8.0 to 3.9.0

    Bump peaceiris/actions-gh-pages from 3.8.0 to 3.9.0

    Bumps peaceiris/actions-gh-pages from 3.8.0 to 3.9.0.

    Release notes

    Sourced from peaceiris/actions-gh-pages's releases.

    actions-github-pages v3.9.0

    • deps: bump node12 to node16
    • deps: bump @​actions/core from 1.6.0 to 1.10.0

    See CHANGELOG.md for more details.

    Changelog

    Sourced from peaceiris/actions-gh-pages's changelog.

    3.9.0 (2022-10-23)

    chore

    ci

    ... (truncated)

    Commits

    Dependabot compatibility score

    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.

    Dependabot commands and options

    You can trigger Dependabot actions by commenting on this PR:

    • @dependabot rebase will rebase this PR
    • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
    • @dependabot merge will merge this PR after your CI passes on it
    • @dependabot squash and merge will squash and merge this PR after your CI passes on it
    • @dependabot cancel merge will cancel a previously requested merge and block automerging
    • @dependabot reopen will reopen this PR if it is closed
    • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
    • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
    • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
    dependencies github_actions 
    opened by dependabot[bot] 0
Releases(v0.4.1)
Owner
Jonathan Chang
I am an evolutionary biologist whose research involves understanding the origin and maintenance of biological diversity.
Jonathan Chang
GitHub Repository https://tact.jonathanchang.org
The Great Autoencoder Bake Off

The Great Autoencoder Bake Off The companion repository to a post on my blog. It contains all you need to reproduce the results. Features Currently fe

Tilman Krokotsch 61 Jan 06, 2023
Viewer for NFO files

NFO Viewer NFO Viewer is a simple viewer for NFO files, which are "ASCII" art in the CP437 codepage. The advantages of using NFO Viewer instead of a t

Osmo Salomaa 114 Dec 29, 2022
Multi View Stereo on Internet Images

Evaluating MVS in a CPC Scenario This repository contains the set of artficats used for the ENGN8601/8602 research project. The thesis emphasizes on t

Namas Bhandari 1 Nov 10, 2021
tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure.

tetrados tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure. Currently, only VASP calculatio

Alex Ganose 1 Dec 21, 2021
Arcpy Tool developed for ArcMap 10.x that checks DVOF points against TDS data and creates an output feature class as well as a check database.

DVOF_check_tool Arcpy Tool developed for ArcMap 10.x that checks DVOF points against TDS data and creates an output feature class as well as a check d

3 Apr 18, 2022
Just a simple python script to generate graphs of salt state requisites.

saltstatevis Just a simple python script to generate graphs of salt state requisites. Installation Requirements You will need to install graphviz to r

Dwayn Matthies 3 May 04, 2022
Python Project Template

A low dependency and really simple to start project template for Python Projects.

Bruno Rocha 651 Dec 29, 2022
A python mathematics module

A python mathematics module

Fayas Noushad 4 Nov 28, 2021
An After Effects render queue for ShotGrid Toolkit.

AEQueue An After Effects render queue for ShotGrid Toolkit. Features Render multiple comps to locations defined by templates in your Toolkit config. C

Brand New School 5 Nov 20, 2022
This tool helps you to reverse any regex and gives you the opposite/allowed Letters,numerics and symbols.

Regex-Reverser This tool helps you to reverse any regex and gives you the opposite/allowed Letters,numerics and symbols. Screenshots Usage/Examples py

x19 0 Jun 02, 2022
Python code for YouTube videos.

#This is a open source project. Python 3 These files are mainly intended to accompany my series of YouTube tutorial videos here, https://www.youtube.c

Joe James 1.3k Dec 26, 2022
Snakemake worflow to process and filter long read data from Oxford Nanopore Technologies.

Nanopore-Workflow Snakemake workflow to process and filter long read data from Oxford Nanopore Technologies. It is designed to compare whole human gen

5 May 13, 2022
Mute your mic while you're typing. An app for Ubuntu.

Hushboard Mute your microphone while typing, for Ubuntu. Install from kryogenix.org/code/hushboard/. Installation We recommend you install Hushboard t

Stuart Langridge 142 Jan 05, 2023
Class and mathematical functions for quaternion numbers.

Quaternions Class and mathematical functions for quaternion numbers. Installation Python This is a Python 3 module. If you don't have Python installed

3 Nov 08, 2022
Gives criticality score for an open source project

Open Source Project Criticality Score (Beta) This project is maintained by members of the Securing Critical Projects WG. Goals Generate a criticality

Open Source Security Foundation (OpenSSF) 1.1k Dec 23, 2022
Python implementation of the Learning Time-Series Shapelets method, that learns a shapelet-based time-series classifier with gradient descent.

shaplets Python implementation of the Learning Time-Series Shapelets method by Josif Grabocka et al., that learns a shapelet-based time-series classif

Mohamed Haseeb 187 Dec 14, 2022
GitHub saver for stargazers, forks, repos

GitHub backup repositories Save your repos and list of stargazers & list of forks for them. Pure python3 and git with no dependencies to install. GitH

Alexander Kapitanov 23 Aug 21, 2022
Simple Python API for the Ergo Platform Explorer

Ergo is a "Resilient Platform for Contractual Money." It is designed to be a platform for applications with the main focus to provide an efficient, se

7 Jul 06, 2021
HSPyLib is a Python library that will elevate your experience to another level.

HomeSetup Python Library - HSPyLib Your mature python application HSPyLib is a Python library that will elevate your experience to another level. It r

Hugo Saporetti Junior 4 Dec 14, 2022
Simple python bot, that notifies about new manga chapters through Telegram.

Simple python bot, that notifies about new manga chapters through Telegram.

Dmitry Kopturov 1 Dec 05, 2021