Ncbimeta

Notes

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

Commits

* [a3bb443c](https://github.com/ktmeaton/NCBImeta/commit/a3bb443c) update pre-commit dependencies
* [e5d6420b](https://github.com/ktmeaton/NCBImeta/commit/e5d6420b) change v0.8.3dev to v0.8.3
* [1d45f5bb](https://github.com/ktmeaton/NCBImeta/commit/1d45f5bb) update recent projects in README
* [b0fab147](https://github.com/ktmeaton/NCBImeta/commit/b0fab147) update paths to docs
* [22d7f0f7](https://github.com/ktmeaton/NCBImeta/commit/22d7f0f7) update notes for v0.8.3
* [30bc84e3](https://github.com/ktmeaton/NCBImeta/commit/30bc84e3) add lxml hotfix to build
* [3d1e7040](https://github.com/ktmeaton/NCBImeta/commit/3d1e7040) restore gcc to environment
* [6f4b3f9c](https://github.com/ktmeaton/NCBImeta/commit/6f4b3f9c) update install documentation
* [560b8175](https://github.com/ktmeaton/NCBImeta/commit/560b8175) add auto yes to pip uninstall
* [9087056e](https://github.com/ktmeaton/NCBImeta/commit/9087056e) remove python 3.10, try lxml hotfix
* [f892e9b9](https://github.com/ktmeaton/NCBImeta/commit/f892e9b9) fix missing activate
* [c003f02a](https://github.com/ktmeaton/NCBImeta/commit/c003f02a) update development docs
* [9b5c819e](https://github.com/ktmeaton/NCBImeta/commit/9b5c819e) create named conda environment
* [de731fef](https://github.com/ktmeaton/NCBImeta/commit/de731fef) fix missing conda activate
* [6d3e91fc](https://github.com/ktmeaton/NCBImeta/commit/6d3e91fc) try to run example from conda using different python versions
* [636931dd](https://github.com/ktmeaton/NCBImeta/commit/636931dd) try to install from conda using different python versions
* [2c9e2c62](https://github.com/ktmeaton/NCBImeta/commit/2c9e2c62) restrict workflows py 3.10 version to 3.10.1
* [b970d73a](https://github.com/ktmeaton/NCBImeta/commit/b970d73a) simplify calls to pytest and pycov
* [ececd98c](https://github.com/ktmeaton/NCBImeta/commit/ececd98c) implement functionality for different biopython versions
* [88061b34](https://github.com/ktmeaton/NCBImeta/commit/88061b34) specify python 3.10.1 is supported
* [0acf7a5f](https://github.com/ktmeaton/NCBImeta/commit/0acf7a5f) relax biopython dependencies to allow most recent package
* [1abff891](https://github.com/ktmeaton/NCBImeta/commit/1abff891) delete old annotate replace file
* [42907aa9](https://github.com/ktmeaton/NCBImeta/commit/42907aa9) lint test files
* [801614df](https://github.com/ktmeaton/NCBImeta/commit/801614df) try putting 3.10 in quotes
* [709a8817](https://github.com/ktmeaton/NCBImeta/commit/709a8817) add a full environment for conda install
* [11024c4c](https://github.com/ktmeaton/NCBImeta/commit/11024c4c) drop 3.6 add 3.10 in CI
* [47dd5849](https://github.com/ktmeaton/NCBImeta/commit/47dd5849) add a stock environment for dev
* [0828d35e](https://github.com/ktmeaton/NCBImeta/commit/0828d35e) relax dependencies
* [d93afb2b](https://github.com/ktmeaton/NCBImeta/commit/d93afb2b) enable debugging mode
* [b9f0afdb](https://github.com/ktmeaton/NCBImeta/commit/b9f0afdb) update sars-cov-2 search term
* [8ff08d70](https://github.com/ktmeaton/NCBImeta/commit/8ff08d70) update README with v0.8.2 project as released
* [f81e8184](https://github.com/ktmeaton/NCBImeta/commit/f81e8184) note conda install issue

Notes

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

Commits

* [089858ee](https://github.com/ktmeaton/NCBImeta/commit/089858ee) include notes in CHANGELOG
* [c1a4b2a1](https://github.com/ktmeaton/NCBImeta/commit/c1a4b2a1) update notes
* [aed461b8](https://github.com/ktmeaton/NCBImeta/commit/aed461b8) update CHANGELOG
* [d040d1ce](https://github.com/ktmeaton/NCBImeta/commit/d040d1ce) update README and CHANGELOG
* [79a35353](https://github.com/ktmeaton/NCBImeta/commit/79a35353) re add autolots as submodule
* [e1712b86](https://github.com/ktmeaton/NCBImeta/commit/e1712b86) remove autologs
* [372589b2](https://github.com/ktmeaton/NCBImeta/commit/372589b2) change config outputs to database dir
* [38869cbc](https://github.com/ktmeaton/NCBImeta/commit/38869cbc) add bioproject and sra to ncov_canada
* [c29cab00](https://github.com/ktmeaton/NCBImeta/commit/c29cab00) update help documentation
* [653fe168](https://github.com/ktmeaton/NCBImeta/commit/653fe168) add quiet mode
* [b11ed919](https://github.com/ktmeaton/NCBImeta/commit/b11ed919) add execute permissions to new annotate script
* [72d4b870](https://github.com/ktmeaton/NCBImeta/commit/72d4b870) add ncov canada config
* [f2b54b21](https://github.com/ktmeaton/NCBImeta/commit/f2b54b21) adjust test workflow for renamed annotate
* [f4a9bd65](https://github.com/ktmeaton/NCBImeta/commit/f4a9bd65) fix code block in README
* [741185b1](https://github.com/ktmeaton/NCBImeta/commit/741185b1) new configs for hmp_oral and yersinia_pestis
* [e4efa58f](https://github.com/ktmeaton/NCBImeta/commit/e4efa58f) remove wheel and sphinx related from setup
* [bdd193f3](https://github.com/ktmeaton/NCBImeta/commit/bdd193f3) remove wheel and sphinx related dependencies
* [58c162b5](https://github.com/ktmeaton/NCBImeta/commit/58c162b5) adjust wheel pos in requirements
* [14fedacd](https://github.com/ktmeaton/NCBImeta/commit/14fedacd) try adding wheel to requirements
* [07f4bb2c](https://github.com/ktmeaton/NCBImeta/commit/07f4bb2c) adjust workflows for new example and annotation
* [2e24ec28](https://github.com/ktmeaton/NCBImeta/commit/2e24ec28) consolidate the annotation tool to a single file
* [be0d6036](https://github.com/ktmeaton/NCBImeta/commit/be0d6036) update install channels in build
* [31ce01ac](https://github.com/ktmeaton/NCBImeta/commit/31ce01ac) update install instructions
* [ae039b34](https://github.com/ktmeaton/NCBImeta/commit/ae039b34) add png versions of paper figures
* [2706b1a8](https://github.com/ktmeaton/NCBImeta/commit/2706b1a8) relax dependencies
* [07bde416](https://github.com/ktmeaton/NCBImeta/commit/07bde416) try to limit codecov to os and python
* [55ec78d0](https://github.com/ktmeaton/NCBImeta/commit/55ec78d0) remove the executable suffix in pypi testing

Notes

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

Pull Requests

* [pull/22](https://github.com/ktmeaton/NCBImeta/pull/22) Add Python 3.9 Support

Commits

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

Notes

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

Pull Requests

* [pull/19](https://github.com/ktmeaton/NCBImeta/pull/19) Security fix for lxml, autologs, and workflow overhaul

Commits

* [3b3d630f](https://github.com/ktmeaton/NCBImeta/commit/3b3d630f) update autologs for branch and tag link
* [b5ee965a](https://github.com/ktmeaton/NCBImeta/commit/b5ee965a) update submodules for release
* [2290cfce](https://github.com/ktmeaton/NCBImeta/commit/2290cfce) restrict testing workflows to master and dev
* [3efed457](https://github.com/ktmeaton/NCBImeta/commit/3efed457) Merge pull request #19 from ktmeaton/dev
* [b325be9e](https://github.com/ktmeaton/NCBImeta/commit/b325be9e) disable fail fast and restrict codecov upload
* [5cb358eb](https://github.com/ktmeaton/NCBImeta/commit/5cb358eb) workflow overhaul
* [cc99998e](https://github.com/ktmeaton/NCBImeta/commit/cc99998e) restrict python versions to >=3.6,<3.9
* [4eaa9bc6](https://github.com/ktmeaton/NCBImeta/commit/4eaa9bc6) overhaul test workflow
* [c174036f](https://github.com/ktmeaton/NCBImeta/commit/c174036f) overhaul build workflow
* [cb0ba1f5](https://github.com/ktmeaton/NCBImeta/commit/cb0ba1f5) add execute permissions to the newly renamed files
* [0a519e0b](https://github.com/ktmeaton/NCBImeta/commit/0a519e0b) replace .py extensions for Utilities script
* [bf4f608b](https://github.com/ktmeaton/NCBImeta/commit/bf4f608b) update autologs
* [db06fd2f](https://github.com/ktmeaton/NCBImeta/commit/db06fd2f) update to v0.8.0
* [6b858776](https://github.com/ktmeaton/NCBImeta/commit/6b858776) Remove .py extension from executable scripts
* [c73cb41b](https://github.com/ktmeaton/NCBImeta/commit/c73cb41b) Update dev changelog
* [7c221988](https://github.com/ktmeaton/NCBImeta/commit/7c221988) simplify database columns for export
* [9aacd232](https://github.com/ktmeaton/NCBImeta/commit/9aacd232) add autolog notes for v0.7.0
* [34ba5495](https://github.com/ktmeaton/NCBImeta/commit/34ba5495) update lxml for security fixes
* [2e203c12](https://github.com/ktmeaton/NCBImeta/commit/2e203c12) update miniconda action and use mamba for macos
* [78b42297](https://github.com/ktmeaton/NCBImeta/commit/78b42297) lint new mammuthus config
* [6dd43d81](https://github.com/ktmeaton/NCBImeta/commit/6dd43d81) update miniconda action and use mamba
* [d275545b](https://github.com/ktmeaton/NCBImeta/commit/d275545b) start new dev branch for v0.7.1
* [c96c186f](https://github.com/ktmeaton/NCBImeta/commit/c96c186f) resolve merges before v0.7.1
* [42239bc3](https://github.com/ktmeaton/NCBImeta/commit/42239bc3) add mammuthus config
* [97fcd956](https://github.com/ktmeaton/NCBImeta/commit/97fcd956) add new logo to README
* [e466196f](https://github.com/ktmeaton/NCBImeta/commit/e466196f) add new logo

Notes

1. Allow config parameters to be specified at run-time.
1. Restrict biopython to >=1.74,<1.77 because of Issue 13
1. Specify versions for all user and dev dependencies.
1. Updated and moved PR template.
1. Updated Contributor's Guideline
1. Remove Python 3.5 support because of incompatibility with black.
1. Remove user email and API key from stdout.

Pull Requests

* [pull/16](https://github.com/ktmeaton/NCBImeta/pull/16) Cli Params
* [pull/14](https://github.com/ktmeaton/NCBImeta/pull/14) Typeerror

Commits

* [18bf0c8d](https://github.com/ktmeaton/NCBImeta/commit/18bf0c8d) remove dev suffix from version number
* [fc0a25d4](https://github.com/ktmeaton/NCBImeta/commit/fc0a25d4) Merge pull request #16 from ktmeaton/cli-params
* [1592e45e](https://github.com/ktmeaton/NCBImeta/commit/1592e45e) update help output
* [28233181](https://github.com/ktmeaton/NCBImeta/commit/28233181) add tests for cli param and bad api key
* [2710af1c](https://github.com/ktmeaton/NCBImeta/commit/2710af1c) cli parameters for NCBI api
* [b5d48112](https://github.com/ktmeaton/NCBImeta/commit/b5d48112) reorganize community and additional contributors
* [34cf2259](https://github.com/ktmeaton/NCBImeta/commit/34cf2259) update docs with final changes from typeerror
* [adb51d7f](https://github.com/ktmeaton/NCBImeta/commit/adb51d7f) Merge pull request #14 from ktmeaton/typeerror
* [2baf5ba0](https://github.com/ktmeaton/NCBImeta/commit/2baf5ba0) update the PR checklist
* [1faf1bc6](https://github.com/ktmeaton/NCBImeta/commit/1faf1bc6) change ver to 0.7.0dev and restrict all ver
* [894f428f](https://github.com/ktmeaton/NCBImeta/commit/894f428f) restrict pytest and cov ver
* [8c490bcd](https://github.com/ktmeaton/NCBImeta/commit/8c490bcd) fix lint workflow desc
* [6dd00337](https://github.com/ktmeaton/NCBImeta/commit/6dd00337) remove python 3.5 support
* [d3a5a060](https://github.com/ktmeaton/NCBImeta/commit/d3a5a060) update changelog for v0.6.7dev
* [e9ce2d09](https://github.com/ktmeaton/NCBImeta/commit/e9ce2d09) fix build ver broken link
* [ffe033b4](https://github.com/ktmeaton/NCBImeta/commit/ffe033b4) merge pr changes for lint workflow
* [4146f54f](https://github.com/ktmeaton/NCBImeta/commit/4146f54f) Merge branch 'dev' into typeerror
* [5e69d662](https://github.com/ktmeaton/NCBImeta/commit/5e69d662) change PR template
* [bf2e903c](https://github.com/ktmeaton/NCBImeta/commit/bf2e903c) restrict pre-commit to <= 2.6.0
* [6da67ac9](https://github.com/ktmeaton/NCBImeta/commit/6da67ac9) reformat workflows and use pip dev install
* [fa35c1e7](https://github.com/ktmeaton/NCBImeta/commit/fa35c1e7) restrict biopython ver to <1.77
* [b6379306](https://github.com/ktmeaton/NCBImeta/commit/b6379306) update to 0.6.7dev
* [dca6bb2d](https://github.com/ktmeaton/NCBImeta/commit/dca6bb2d) remove outdated project ver number
* [f7d748fc](https://github.com/ktmeaton/NCBImeta/commit/f7d748fc) add python support and black linting
* [aa1f84c1](https://github.com/ktmeaton/NCBImeta/commit/aa1f84c1) update test table assembly values
* [b7094501](https://github.com/ktmeaton/NCBImeta/commit/b7094501) add black and flake8 to dev dependencies
* [41290068](https://github.com/ktmeaton/NCBImeta/commit/41290068) fix list numbering indentation
* [f302cce8](https://github.com/ktmeaton/NCBImeta/commit/f302cce8) add logo asset attribution
* [5acd4b78](https://github.com/ktmeaton/NCBImeta/commit/5acd4b78) add draft logo
* [d9ce0451](https://github.com/ktmeaton/NCBImeta/commit/d9ce0451) add logo draft
* [2723e189](https://github.com/ktmeaton/NCBImeta/commit/2723e189) add url link for ncbi ref
* [86776275](https://github.com/ktmeaton/NCBImeta/commit/86776275) note add contributors
* [d9b47239](https://github.com/ktmeaton/NCBImeta/commit/d9b47239) conda link

Commits

* [e931c8be](https://github.com/ktmeaton/NCBImeta/commit/e931c8be) test post suffix again
* [c4b682b5](https://github.com/ktmeaton/NCBImeta/commit/c4b682b5) update to a1 ver
* [5aafdbc0](https://github.com/ktmeaton/NCBImeta/commit/5aafdbc0) run example workflow when src py is changed
* [ffe86dd9](https://github.com/ktmeaton/NCBImeta/commit/ffe86dd9) just increment the minor ver for bug fix
* [d4e906b2](https://github.com/ktmeaton/NCBImeta/commit/d4e906b2) commit to post suffix after test
* [5be6eb63](https://github.com/ktmeaton/NCBImeta/commit/5be6eb63) update ver use the post suffix
* [7103b41b](https://github.com/ktmeaton/NCBImeta/commit/7103b41b) remove tag hook causes problems for pypi dup
* [32dcb8ad](https://github.com/ktmeaton/NCBImeta/commit/32dcb8ad) update ver
* [cb2997e4](https://github.com/ktmeaton/NCBImeta/commit/cb2997e4) delete bad position tags
* [047e96b6](https://github.com/ktmeaton/NCBImeta/commit/047e96b6) move tag hook under push action
* [93d6b819](https://github.com/ktmeaton/NCBImeta/commit/93d6b819) also run workflows on tags
* [72c05853](https://github.com/ktmeaton/NCBImeta/commit/72c05853) update to ver v0.6.7a
* [43747be1](https://github.com/ktmeaton/NCBImeta/commit/43747be1) update pip and setuptools
* [6116cdb1](https://github.com/ktmeaton/NCBImeta/commit/6116cdb1) remove mention of setuptools install
* [792e28c5](https://github.com/ktmeaton/NCBImeta/commit/792e28c5) mark project v0.6.6 as RELEASED
* [9582d78c](https://github.com/ktmeaton/NCBImeta/commit/9582d78c) make pypi install plain no ver