Ecosyste.ms: Issues

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GitHub / widdowquinn/pyani issues and pull requests

#449 - ZeroDivisionError: float division by zero

Issue - State: open - Opened by f12345zxcvbnm2 7 days ago - 3 comments

#447 - Spaces in input filenames/paths cause cryptic failures

Issue - State: open - Opened by peterjc about 1 month ago
Labels: bug, enhancement, VERSION_3

#446 - Drop pinning on mummer=3.23=h6de7cb9_11 for macOS

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

#445 - At least one NUCmer comparison failed. Please investigate (exiting)

Issue - State: closed - Opened by ChristophKnapp about 1 month ago - 24 comments

#444 - Download does not work

Issue - State: open - Opened by ChristophKnapp about 1 month ago - 9 comments

#443 - Fix error message for missing <inputdir>/<genome>.md5 file

Pull Request - State: open - Opened by peterjc 3 months ago

#442 - anim analysis and classes object issue

Issue - State: closed - Opened by luigallucci 3 months ago - 13 comments

#441 - Average-Nucleotide-Identity-ANI-analysis

Issue - State: closed - Opened by ispa24 3 months ago - 2 comments

#440 - Passing a string to pd.read_json is deprecated

Pull Request - State: open - Opened by peterjc 4 months ago

#439 - Default diagonal for sim-errors should be zero

Pull Request - State: closed - Opened by peterjc 4 months ago

#438 - Self-vs-self sim-error values of 1 rather than 0

Issue - State: open - Opened by peterjc 4 months ago

#437 - Passing a string to pd.read_json is deprecated

Pull Request - State: closed - Opened by peterjc 5 months ago - 2 comments

#435 - How to produce a clustered plot?

Issue - State: closed - Opened by abrianmc 5 months ago

#434 - Fix percentage identity in Comparison __str__

Pull Request - State: closed - Opened by peterjc 6 months ago - 2 comments

#433 - Use pytest markers for slurm tests

Issue - State: closed - Opened by peterjc 6 months ago - 1 comment

#432 - Update docs - CI now GitHub Actions

Pull Request - State: closed - Opened by peterjc 7 months ago

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

Issue - State: closed - Opened by despathe 7 months ago - 2 comments
Labels: bug

#430 - segment fault

Issue - State: open - Opened by lingc31415 7 months ago - 1 comment

#429 - Installation issues

Issue - State: open - Opened by TommyH-Tran 10 months ago - 3 comments

#428 - ZeroDivisionError: float division by zero

Issue - State: open - Opened by ivaneskos 10 months ago - 3 comments
Labels: question

#427 - Running --graphics after analysis

Issue - State: open - Opened by artfet 10 months ago - 1 comment

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

Pull Request - State: closed - Opened by kiepczi 11 months ago - 1 comment
Labels: bug, enhancement, performance, method, VERSION_3, HIGH PRIORITY

#424 - add `pyani dnadiff` subcommand

Issue - State: open - Opened by kiepczi 11 months ago - 5 comments
Labels: enhancement

#423 - numpy: No module named 'version'

Issue - State: closed - Opened by ireneortega 11 months ago - 4 comments
Labels: bug, unable to reproduce

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

Issue - State: closed - Opened by kiepczi about 1 year 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 about 1 year ago - 4 comments

#419 - Pyani not installing through conda

Issue - State: closed - Opened by conmeehan over 1 year 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

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

Issue - State: closed - Opened by peterthorpe5 about 2 years ago - 2 comments

#412 - `pyani` command not found

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

#411 - pyani command not found

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

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

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

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

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

#406 - pyani: command not found

Issue - State: closed - Opened by Gahyeon-K over 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 almost 3 years ago - 3 comments
Labels: documentation

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

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

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

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

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

Issue - State: closed - Opened by baileythegreen almost 3 years ago - 4 comments
Labels: bug, tests

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

Issue - State: closed - Opened by baileythegreen almost 3 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 almost 3 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 almost 3 years ago - 4 comments
Labels: question

#392 - Rationalise documentation

Issue - State: open - Opened by widdowquinn almost 3 years ago - 2 comments
Labels: documentation

#391 - Update CircleCI config and related files

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

#390 - Issue 389

Pull Request - State: closed - Opened by widdowquinn almost 3 years ago - 2 comments
Labels: bug

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

Issue - State: closed - Opened by widdowquinn almost 3 years ago - 1 comment
Labels: bug

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

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

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

Pull Request - State: open - Opened by baileythegreen almost 3 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 almost 3 years ago - 5 comments

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

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

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

Issue - State: closed - Opened by widdowquinn almost 3 years ago - 6 comments
Labels: bug

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

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

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

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

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

Issue - State: open - Opened by widdowquinn about 3 years ago - 41 comments
Labels: enhancement

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

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

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

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

#375 - Issue 373

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

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

Issue - State: closed - Opened by widdowquinn about 3 years ago - 2 comments
Labels: interface

#373 - ANIm should not be symmetric

Issue - State: closed - Opened by donovan-h-parks about 3 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 about 3 years ago - 2 comments

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

Issue - State: open - Opened by neelam19051 about 3 years ago - 9 comments
Labels: bug

#370 - Tree 186

Pull Request - State: open - Opened by baileythegreen about 3 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 about 3 years ago - 1 comment
Labels: bug, tests

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

Issue - State: closed - Opened by magksi about 3 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 about 3 years ago - 1 comment

#366 - White space error in absence of white spaces

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

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

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

#364 - Add `pyani compare`

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

#363 - ANI identity values missing on pyani plots

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

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

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

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

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

#360 - Revert "Parser choices"

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

#359 - Parser choices

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

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

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

#353 - anim nested tree recovery mode follow up

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

#350 - Sparse distance matrix

Issue - State: closed - Opened by snayfach over 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 over 3 years ago - 9 comments
Labels: performance, visualisation

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

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

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

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

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

Issue - State: open - Opened by baileythegreen over 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] over 3 years ago

#340 - Alignment coverage >1.0

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

#338 - Issue #123: Add `anib`

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

#326 - MUMmer 4 reports version differently to MUMmer 3

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