widdowquinn/pyani issues and pull requests

#435 - How to produce a clustered plot?

Issue - State: open - Opened by abrianmc 4 days ago

#434 - Fix percentage identity in Comparison str

Pull Request - State: closed - Opened by peterjc about 1 month ago - 2 comments

#433 - Use pytest markers for slurm tests

Issue - State: closed - Opened by peterjc about 2 months ago - 1 comment

#432 - Update docs - CI now GitHub Actions

Pull Request - State: closed - Opened by peterjc about 2 months ago

#431 - AttributeError: module 'matplotlib.pyplot' has no attribute 'register_cmap'

Issue - State: closed - Opened by despathe about 2 months ago - 2 comments
Labels: bug

#430 - segment fault

Issue - State: open - Opened by lingc31415 3 months ago - 1 comment

#429 - Installation issues

Issue - State: open - Opened by TommyH-Tran 5 months ago - 3 comments

#428 - ZeroDivisionError: float division by zero

Issue - State: open - Opened by ivaneskos 5 months ago - 3 comments
Labels: question

#427 - Running --graphics after analysis

Issue - State: open - Opened by artfet 5 months ago - 1 comment

#426 - docs: add kiepczi as a contributor for code, design, and test

Pull Request - State: closed - Opened by allcontributors[bot] 6 months ago

#425 - Issue 421: Fix alignment coverage >1.0 and aniM symmetrical behaviour

Pull Request - State: closed - Opened by kiepczi 6 months ago - 1 comment
Labels: bug, enhancement, performance, method, VERSION_3, HIGH PRIORITY

#424 - add `pyani dnadiff` subcommand

Issue - State: open - Opened by kiepczi 7 months ago - 5 comments
Labels: enhancement

#423 - numpy: No module named 'version'

Issue - State: closed - Opened by ireneortega 7 months ago - 4 comments
Labels: bug, unable to reproduce

#422 - Add separate columns for subject and query alignment lengths in `--run_results`

Issue - State: open - Opened by kiepczi 7 months ago - 23 comments

#421 - Fix alignment coverage >1.0 and aniM symmetrical behaviour

Issue - State: closed - Opened by kiepczi 8 months ago - 8 comments
Labels: bug, HIGH PRIORITY

#420 - Inquiry on Analysis Duration with ANIb and ANIm for Streptomyces Genomes

Issue - State: closed - Opened by ZiliaMR 8 months ago - 4 comments

#419 - Pyani not installing through conda

Issue - State: closed - Opened by conmeehan 12 months ago - 5 comments
Labels: duplicate, documentation, VERSION_2

#418 - ValueError in pyani plot using pyani 0.3.0-alpha

Issue - State: open - Opened by jmoltzau over 1 year ago

#417 - Type strain vs X of genomes

Issue - State: open - Opened by nikolomics over 1 year ago - 1 comment
Labels: enhancement, question

#416 - ERROR: This has possibly been a NUCmer run failure, please investigate ERROR: NoneType: None

Issue - State: open - Opened by Yuanzhou-W over 1 year ago - 3 comments

#415 - sending some love for this script: " genbank_get_genomes_by_taxon.py"

Issue - State: closed - Opened by peterthorpe5 over 1 year ago - 2 comments

#414 - Error "Cannot update because the update target is missing these hooks" when trying to use autoupdate on my repo

Issue - State: closed - Opened by dmentock almost 2 years ago - 1 comment

#413 - Cannot run anim in pyani 0.3.0-alpha using provided data, on macosx 12.6, nucmer fails.

Issue - State: closed - Opened by joneson almost 2 years ago - 4 comments

#412 - `pyani` command not found

Issue - State: closed - Opened by friedsh2 almost 2 years ago - 1 comment
Labels: duplicate

#411 - pyani command not found

Issue - State: closed - Opened by chjp about 2 years ago - 1 comment

#410 - Update `get_version()` tests based on discussion surrounding Issue #405

Pull Request - State: open - Opened by baileythegreen about 2 years ago - 1 comment
Labels: tests

#409 - Issue# 405: New test case for previously missed code in fastani

Pull Request - State: open - Opened by baileythegreen about 2 years ago
Labels: tests

#408 - Use of `unittest.TestCase` assertion methods provides more informative error messages than `assert`

Issue - State: closed - Opened by baileythegreen about 2 years ago - 1 comment
Labels: tests

#407 - Issue# 405: New test case for previously missed code in `fastani`

Pull Request - State: closed - Opened by baileythegreen about 2 years ago - 1 comment

#406 - pyani: command not found

Issue - State: closed - Opened by Gahyeon-K about 2 years ago - 1 comment

#405 - Untested code in `fastani.py`

Issue - State: open - Opened by baileythegreen over 2 years ago - 1 comment
Labels: VERSION_3

#404 - Issue #402: Fix tests that fail as a result of running `pytest` with no flags

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 2 comments
Labels: bug, tests

#403 - Problem with EASY-INSTALL-ENTRY-SCRIPT for miniconda

Issue - State: closed - Opened by baileythegreen over 2 years ago - 1 comment

#402 - `test_cli_parsing()` tests fail when `pytest` is run with no flags

Issue - State: open - Opened by baileythegreen over 2 years ago - 1 comment
Labels: bug, interface, tests

#401 - Add contributors

Pull Request - State: closed - Opened by baileythegreen over 2 years ago - 1 comment

#400 - Updating `Contributors.md`

Issue - State: closed - Opened by baileythegreen over 2 years ago - 3 comments
Labels: documentation

#399 - docs: add zakisaati as a contributor for bug

Pull Request - State: closed - Opened by allcontributors[bot] over 2 years ago

#398 - Relocate info about `fastANI` + Python ≥3.9 + macOS

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 1 comment
Labels: documentation

#397 - Bug in CircleCI tests for python 3.6: caching issue

Issue - State: closed - Opened by baileythegreen over 2 years ago - 4 comments
Labels: bug, tests

#396 - Update v2 distribution on PyPI (and bioconda)

Issue - State: closed - Opened by baileythegreen over 2 years ago - 8 comments
Labels: VERSION_2

#394 - How do I provide a labels.txt or classes.txt file?

Issue - State: closed - Opened by widdowquinn over 2 years ago - 3 comments
Labels: question, Marked for closure

#393 - ERROR: This has possibly been a NUCmer run failure, please investigate > ERROR: NoneType: None

Issue - State: closed - Opened by neelam19051 over 2 years ago - 4 comments
Labels: question

#392 - Rationalise documentation

Issue - State: open - Opened by widdowquinn over 2 years ago - 2 comments
Labels: documentation

#391 - Update CircleCI config and related files

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#390 - Issue 389

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 2 comments
Labels: bug

#389 - `pyani createdb` fails is databse is not present

Issue - State: closed - Opened by widdowquinn over 2 years ago - 1 comment
Labels: bug

#388 - Can't reference `run_id` if the run fails

Pull Request - State: closed - Opened by baileythegreen over 2 years ago

#387 - Issue #378: Add `alembic` support for database migrations

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 3 comments
Labels: enhancement

#386 - Which coordinate in the percentage heat map drawn by pyaini is used as a reference

Issue - State: closed - Opened by Reynababy over 2 years ago - 5 comments

#385 - Add `try/except` around extraction to accommodate failing uncompression in `pyani download`

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 3 comments

#384 - Move `fastANI` to a separate `requirements`

Pull Request - State: closed - Opened by baileythegreen over 2 years ago - 2 comments

#383 - `pyani download` is blocked if downloaded file cannot be uncompressed.

Issue - State: closed - Opened by widdowquinn over 2 years ago - 6 comments
Labels: bug

#380 - Report `fastANI` version in `pyani listdeps` output

Pull Request - State: closed - Opened by baileythegreen over 2 years ago - 1 comment

#379 - `fastANI` is not listed in the output of `listdeps`

Issue - State: closed - Opened by baileythegreen over 2 years ago

#378 - Use `alembic` to manage SQLite schema changes?

Issue - State: open - Opened by widdowquinn over 2 years ago - 41 comments
Labels: enhancement

#377 - `fastani` is not installed under Python 3.9

Issue - State: closed - Opened by widdowquinn over 2 years ago - 3 comments
Labels: bug

#376 - Issue #373: ANIm should not be symmetric

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 3 comments

#375 - Issue 373

Pull Request - State: closed - Opened by widdowquinn over 2 years ago - 1 comment

#374 - `pyani report` is not consistent with `pyani plot` in terms of arguments

Issue - State: closed - Opened by widdowquinn over 2 years ago - 2 comments
Labels: interface

#373 - ANIm should not be symmetric

Issue - State: closed - Opened by donovan-h-parks over 2 years ago - 8 comments
Labels: bug, Marked for closure, HIGH PRIORITY

#372 - PyANI not on path after installation

Issue - State: closed - Opened by donovan-h-parks over 2 years ago - 2 comments

#371 - ValueError: zero-size array to reduction operation minimum which has no identity

Issue - State: open - Opened by neelam19051 over 2 years ago - 9 comments
Labels: bug

#370 - Tree 186

Pull Request - State: open - Opened by baileythegreen over 2 years ago - 1 comment
Labels: enhancement, visualisation

#369 - `PyQt` (an `ete3` dependency) seems to need different specifications for `pip` and `conda`

Issue - State: closed - Opened by baileythegreen over 2 years ago - 1 comment
Labels: bug, tests

#368 - why the clustering results are different in the two directions

Issue - State: closed - Opened by magksi over 2 years ago - 2 comments
Labels: question

#367 - Issue #130: Add `try/except` to catch `ModuleNotFoundError` when no `openpyxl`

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 1 comment

#366 - White space error in absence of white spaces

Issue - State: closed - Opened by rmostowy almost 3 years ago - 2 comments

#365 - Explicitly list parser choices in `help` output

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 1 comment
Labels: interface, VERSION_3

#364 - Add `pyani compare`

Pull Request - State: open - Opened by baileythegreen almost 3 years ago - 3 comments
Labels: enhancement

#363 - ANI identity values missing on pyani plots

Issue - State: closed - Opened by papicbojan almost 3 years ago - 2 comments
Labels: question, interface

#362 - Add tests for `--recovery` mode

Issue - State: open - Opened by baileythegreen almost 3 years ago
Labels: tests

#361 - Issue #357: Fix genome labels in matrix output

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 2 comments

#360 - Revert "Parser choices"

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago

#359 - Parser choices

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 2 comments

#355 - Sort genomes (for stable anim recovery mode)

Pull Request - State: closed - Opened by peterjc almost 3 years ago - 7 comments
Labels: bug, performance

#353 - anim nested tree recovery mode follow up

Issue - State: closed - Opened by peterjc almost 3 years ago - 15 comments

#350 - Sparse distance matrix

Issue - State: closed - Opened by snayfach almost 3 years ago - 2 comments
Labels: question, Marked for closure

#346 - Issue 292: Parallelise plot creation using `multiprocessing`

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 9 comments
Labels: performance, visualisation

#345 - Correct `pyani.py` in usage examples to `pyani`

Pull Request - State: closed - Opened by baileythegreen almost 3 years ago - 1 comment
Labels: documentation

#343 - Add a `--dry-run` flag, generally

Issue - State: open - Opened by baileythegreen almost 3 years ago - 8 comments
Labels: enhancement, interface

#342 - Use `--noextend` in NUCmer as a rule

Issue - State: open - Opened by baileythegreen about 3 years ago - 28 comments
Labels: bug, method, VERSION_3

#341 - docs: add dparks1134 as a contributor for bug

Pull Request - State: closed - Opened by allcontributors[bot] about 3 years ago

#340 - Alignment coverage >1.0

Issue - State: closed - Opened by donovan-h-parks about 3 years ago - 26 comments
Labels: bug, HIGH PRIORITY

#338 - Issue #123: Add `anib`

Pull Request - State: open - Opened by baileythegreen about 3 years ago - 8 comments
Labels: enhancement, method, VERSION_3, PR of Supreme Importance

#337 - Issue #336: Update CLI to not use positional arguments

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 2 comments
Labels: documentation, interface

#335 - Issue #326: Add new regex to catch MUMmer v4 version information

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 2 comments
Labels: bug

#326 - MUMmer 4 reports version differently to MUMmer 3

Issue - State: closed - Opened by baileythegreen about 3 years ago - 14 comments

#321 - Issues #241, #242: Add a logger warning to flag comparisons that fail

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 1 comment
Labels: enhancement, interface

#320 - Issue #289: Check for the existence of a database file that is passed

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 4 comments
Labels: interface

#319 - Issue 175: Plot identity vs coverage scatter plot

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 2 comments
Labels: enhancement, interface, visualisation

#315 - Issue 286: Update deprecated plotting functions

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 1 comment
Labels: visualisation

#313 - Similarity error count discrepancy with other aligners

Issue - State: closed - Opened by cssulliv about 3 years ago - 3 comments

#310 - Issue 128 (again): Test for `create_hash` when the 'file' given does not exist

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 1 comment

#309 - Issue 149: Filling in missing documentation on ReadTheDocs

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 2 comments
Labels: documentation

#307 - Issue 300: Update `.md5` file names in docs

Pull Request - State: closed - Opened by baileythegreen about 3 years ago - 1 comment
Labels: documentation

#306 - NUCmer job generation for large jobs slows down rapidly.

Issue - State: open - Opened by widdowquinn about 3 years ago - 6 comments
Labels: bug, enhancement

#299 - fastANI

Pull Request - State: closed - Opened by baileythegreen over 3 years ago - 2 comments
Labels: enhancement, VERSION_3, PR of Supreme Importance

#289 - SQLalchemy (or maybe SQLite3) errors for a missing database are unclear

Issue - State: closed - Opened by baileythegreen over 3 years ago - 3 comments
Labels: interface

#242 - Add more detail to reporting so users can tell which comparison jobs fail

Issue - State: closed - Opened by widdowquinn over 3 years ago - 1 comment
Labels: enhancement

#241 - Find genomes causing Blast to fail

Issue - State: closed - Opened by nclaesnacw over 3 years ago - 6 comments
Labels: enhancement

GitHub / widdowquinn/pyani issues and pull requests