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.

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

• 089858ee include notes in CHANGELOG
• c1a4b2a1 update notes
• aed461b8 update CHANGELOG
• d040d1ce update README and CHANGELOG
• 79a35353 re add autolots as submodule
• e1712b86 remove autologs
• 372589b2 change config outputs to database dir
• 38869cbc add bioproject and sra to ncov_canada
• c29cab00 update help documentation
• 653fe168 add quiet mode
• b11ed919 add execute permissions to new annotate script
• 72d4b870 add ncov canada config
• f2b54b21 adjust test workflow for renamed annotate
• f4a9bd65 fix code block in README
• 741185b1 new configs for hmp_oral and yersinia_pestis
• e4efa58f remove wheel and sphinx related from setup
• bdd193f3 remove wheel and sphinx related dependencies
• 58c162b5 adjust wheel pos in requirements
• 14fedacd try adding wheel to requirements
• 07f4bb2c adjust workflows for new example and annotation
• See CHANGELOG.md for additional commits.

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

• pull/22 Add Python 3.9 Support

Commits

• f0ebe0a0 remove dev suffix from version
• 8a7e17f7 update docs
• 45baf436 update autologs with standardized hash
• dab96e71 Merge pull request #22 from ktmeaton/dev
• dcaca613 add python 3.9 to the install job of build
• 038d4f3b document example workflow disabled
• 6d491ac5 relocate codecov config
• 2c798bca add config file for codecov
• e0d7920f update docs before PR
• 3d79271c test numpy-1.19.5
• 3bbbe596 bugfix in example workflow trigger
• 05d19602 remove print statement
• d3028113 update dependencies lxml pyaml and numpy
• d5eaf85b fix bug in test_export biosample date
• 4a1d4a7b add python 3.9 to the testing matrix
• 31bfcafe update ver number to v0.8.1
• 4272d9ed update changelog for v0.8.0

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.

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!~

v0.6.6.post1

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

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!

Source: Perforce

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~

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~

https://xkcd.com/327/

v0.6.3 - Automating the Chain

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