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Recent Releases of NCBImeta

NCBImeta - v0.8.3 - Update Dependencies

v0.8.3

Notes

  1. Drop support for Python 3.7.
  2. Test support for Python 3.10 (conda numpy isn't ready).
  3. Implement str enconding changes that accomdate all versions of biopython (>=1.74).
  4. Consolidate pytest and pycov command to test/test.py.
  5. Build and Example workflow include more comprehensive tests for conda.
  6. Create a fallback conda environment for installation (environment.yaml).
  7. Applied a hotfix for problematic packaging of lxml in conda.

Commits

  • 1abe4542 update CHANGELOG for v0.8.3
  • a3bb443c update pre-commit dependencies
  • e5d6420b change v0.8.3dev to v0.8.3
  • 1d45f5bb update recent projects in README
  • b0fab147 update paths to docs
  • 22d7f0f7 update notes for v0.8.3
  • 30bc84e3 add lxml hotfix to build
  • 3d1e7040 restore gcc to environment
  • 6f4b3f9c update install documentation
  • 560b8175 add auto yes to pip uninstall
  • 9087056e remove python 3.10, try lxml hotfix
  • f892e9b9 fix missing activate
  • c003f02a update development docs
  • 9b5c819e create named conda environment
  • de731fef fix missing conda activate
  • 6d3e91fc try to run example from conda using different python versions
  • 636931dd try to install from conda using different python versions
  • 2c9e2c62 restrict workflows py 3.10 version to 3.10.1
  • b970d73a simplify calls to pytest and pycov
  • ececd98c implement functionality for different biopython versions
  • See CHANGELOG.md for additional commits.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

NCBImeta - v0.8.2 - Annotate Simplicity

v0.8.2

Notes

  1. Add quiet mode with --quiet.
  2. Create NCBImetaAnnotate that consolidates NCBImetaAnnotateReplace and NCBImetaAnnotateConcatenate.
  3. Add configs yersinia_pestis, mammuthus, hmp_oral, ncov_canada.
  4. Remove sphinx related dev dependencies.

Commits

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 4 years ago

NCBImeta - v0.8.1 - Add Python 3.9 Support

v0.8.1

Notes

  1. Add Python 3.9 Support.
  2. Bugfix the test export workflow.
  3. Update dependncies: lxml, PyYAML, NumPy
  4. Disable example workflow.

Pull Requests

Commits

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] about 5 years ago

NCBImeta - v0.8.0 - lxml Bump and Plain Executables

v0.8.0

Notes

  1. Start new dev branch for v0.7.1.
  2. Update miniconda actions and use mamba.
  3. Update lxml for security vulnerability.
  4. Add autologs as a submodule.
  5. Create CHANGELOG with autologs.
  6. Simplify test config with less fields to check.
  7. Remove .py extension from executable scripts.

Pull Requests

  • pull/19 Security fix for lxml, autologs, and workflow overhaul

Commits

  • 3b3d630 update autologs for branch and tag link
  • b5ee965 update submodules for release
  • 2290cfc restrict testing workflows to master and dev
  • 3efed45 Merge pull request #19 from ktmeaton/dev
  • b325be9 disable fail fast and restrict codecov upload
  • 5cb358e workflow overhaul
  • cc99998 restrict python versions to >=3.6,<3.9
  • 4eaa9bc overhaul test workflow
  • c174036 overhaul build workflow
  • cb0ba1f add execute permissions to the newly renamed files
  • 0a519e0 replace .py extensions for Utilities script
  • bf4f608 update autologs
  • db06fd2 update to v0.8.0
  • 6b85877 Remove .py extension from executable scripts
  • c73cb41 Update dev changelog
  • 7c22198 simplify database columns for export
  • 9aacd23 add autolog notes for v0.7.0
  • 34ba549 update lxml for security fixes
  • 2e203c1 update miniconda action and use mamba for macos
  • 78b4229 lint new mammuthus config
  • See CHANGELOG.md for additional commits.

Scientific Software - Peer-reviewed - Python
Published by github-actions[bot] over 5 years ago

NCBImeta - v0.7.0 - Strict Version Control

  • Remove Python 3.5 support.
  • Restrict biopython to >=1.74,<1.77. (Issue #13)
  • Restrict all user and dev dependencies to verified versions.
  • Allow the following config parameters to be specified at run-time (--email, --api, --force-pause-seconds). (Issue #15)
  • Do not print API and EMAIL to stdout.

~Lock it down!~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton almost 6 years ago

NCBImeta -

  • GH-Actions deploy server needed a setuptools update.
  • README should upload correctly to PyPI now.
  • Use a post-release tag compatible with PyPI.

Scientific Software - Peer-reviewed - Python
Published by ktmeaton about 6 years ago

NCBImeta - v0.6.6 - PyPI Fix and Contributor's Guide

  • Fix PyPI deployment bug (Issue #10) to properly handle dependencies on install.
  • Wrote a Contributor's Guide and Pull Request Template
  • Bug fixes to the NCBImetaAnnotate scripts to improve inserting/updating values.
  • Retroactively linted the entire project (*.py, *.yaml, *.md)

Thanks to @hmontenegro for catching the PyPI packaging bug and submitting Issue #10!

image

Source: Perforce

Scientific Software - Peer-reviewed - Python
Published by ktmeaton about 6 years ago

NCBImeta - v0.6.5 - XPath Advanced

  • Advanced users now have the option to use XPath queries directly in the configuration files.
  • This can enhance precision and is hugely beneficial in scaling to new databases and challenging records.
  • Bugfixes for multiple record matches in SRA, BioSample, and Nucleotide.

Thank you to @hellothisisMatt for submitting PR #9, the implementation of advanced xml search with user XPath, and all design discussions!

~Multiple (X)Paths to the Same Destination~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.6.4 - Bobby Tables

  • SQL security update: project-wide value parameterization, sanitize table and column names
  • Bugfixes for issues #7 and #8
  • Removal of unnecessary use of encode/decode/UTF-8

~Always Sanitize Your Inputs~ image https://xkcd.com/327/

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.6.3 - Automating the Chain

  • Development Chain Automation:
    • Github Release, Travis-CI, CodeCov, Zenodo, PyPI, PiWheel, Bioconda, Biocontainers

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.6.2 - Conda and Initial Peer-Review

  • Bioconda packaging. Credits and thanks to @druvus for creating the recipe (PR #5)
  • An error is no longer raised when the output directory does not exist (Issue #4)
  • Automated PyPI Deployment on new release (tags) through Travis-CI.

~Biological Packages~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.6.1 - JOSS Submission and Zenodo

  • JOSS Submission Files: paper, bibliography, figures, and P. aeruginosa database.
  • Zenodo Integration
  • Start using asciinema and ShareX to record the video for the README
  • Fixed executable versions and CHANGELOG links.

~Archive It!~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.6.0 - XML Overhaul XPath

  • XML parsing now done with lxml rather than minidom, explicit use of XPATH
  • All tables except assembly now use efetch rather than esummary
  • Multi-match nodes are concatenated by semi-colon
  • Sevearl field changes and removal (see CHANGELOG)

~The Power of XPath~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.5.0 - pytest and Codecov

  • pytest integration, Codecov integration
  • project-wide code documentation and clean-up
  • no longer test Python 3.4 builds (only Python 3.5+ for pytest 5.x.y)
  • bugfixes: columnindex position, flattendict function
  • general fix: typo in example config (Nucleotidet)
  • method migration: HTTPErrorCatch
  • reupload truncated gif files

~Rigorous Testing Arrives!~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.4.2 - Pip Installation

  • Pip is now the preferred installation method.
  • setup.py for installation from PyPI and source
  • Rename all files containing "NCBImeta_" to "NCBImeta", correct all references
  • Change src/ directory to ncbimeta/ directory

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.4.1 - Travis CI Integration

  • Travis CI Integration (Linux, macOSX)
  • Bugfix for execute permissions
  • Bugfix for esearch
  • More HTTP Error catching

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.4.0 - YAML Configuration Files

  • All configuration and schema files switched to yaml format (Issue #3)
  • The PyYAML module is now a required dependency.
  • Implemented fix for Runtime Errors appearing at the start of a new table (Issue #2)
  • Removed extra config files and deprecated scripts.
  • Main README file reorganized with simpler commands.

~Happy Halloween!~ image

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.3.4 - HTTP Error Catching

  • NCBImeta is more likely to run to completion without interruption or need for restarting.
  • HTTP Error 429 (Too Many Requests) error handling bug fix.
  • General HTTP Error catching with 3 retries before exiting.

Scientific Software - Peer-reviewed - Python
Published by ktmeaton over 6 years ago

NCBImeta - v0.3.3 - Pubmed Table Support

  • This release provides support for the Pubmed database, introducing the Pubmed table to the database.

Scientific Software - Peer-reviewed - Python
Published by ktmeaton almost 7 years ago

NCBImeta - v0.3.2 - Genome Annotation Capture

  • This release improves genome annotation metadata parsing (CDS, Pseudogenes, tRNAs, etc.)
  • This release also marks the definitive end of attempts at Python2 support.
  • A master join of all tables is now included as part of the example.
  • For a list of all the changes, please consult CHANGELOG.md

Scientific Software - Peer-reviewed - Python
Published by ktmeaton almost 7 years ago

NCBImeta - v0.3.1 - Alpha release for user testing.

  • v0.3.1 Alpha release for user testing.

  • Currently, no identified bugs, although I suspect there will be additional problems in unicode encoding.

Scientific Software - Peer-reviewed - Python
Published by ktmeaton almost 8 years ago