Merge branch 'release/0.14.0'

.gitignore

@@ -11,14 +11,15 @@ Log.out
 genomepy/config/default.yaml
 
 # Directories
-docs/_autosummary
-docs/_build
-tests/data
-.pytest_cache
-build
-genomepy.egg-info
-dist
-eggs
-tmp
-.vscode
-.idea
+__pychache__/
+.idea/
+.pytest_cache/
+.vscode/
+build/
+dist/
+docs/_autosummary/
+docs/_build/
+eggs/
+genomepy.egg-info/
+tests/data/
+tmp/

.travis.yml

@@ -7,7 +7,7 @@ branches:
 # use the minimal travis environment since we test in conda
 language: minimal
 
-#dist
+# dist
 dist: focal
 
 os:
@@ -18,7 +18,7 @@ env:
   global:
     - CC_TEST_REPORTER_ID=951f438ac8a0fa93801ff0bf69922df59fe03800bf7ea8ab77a3c26cda444979
   jobs:
-    - PYTHON_VERSION=3.6
+    - PYTHON_VERSION=3.7
 
 cache:
   directories:
@@ -43,14 +43,14 @@ before_install:
 
       export PATH=$HOME/miniconda/bin:$PATH;
       conda config --set always_yes yes;
-      conda install conda-forge::mamba;
+      conda update -c defaults conda;
+      conda install -c conda-forge mamba;
       mamba env create -n genomepy python=$PYTHON_VERSION -f environment.yml;
     fi
 
 install:
   - source activate genomepy
-  - python setup.py develop
-  - python setup.py build
+  - pip install -e .
 
 before_script:
   # install codeclimate test coverage

CHANGELOG.md

@@ -6,6 +6,21 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.14.0] - 2022-08-01
+
+### Added
+- now using `filelock` for improved thread safety
+- now checking if every API/FTP/HTTP(S) is accessible before proceeding
+- genomepy search improvements:
+  - text search now accepts regex, and multiple substrings (space separated) are unordered.
+  - taxonomy search now returns all hits that start with the given number.
+
+### Changed
+- switched to `pyproject.toml` + `hatchling` for packaging
+
+### Fixed
+- updated the README and CLI documentation to mention the `Local` provider
+
 ## [0.13.1] - 2022-06-21
 
 ### Changed
@@ -416,6 +431,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Added `-r` and `--match/--no-match` option to select sequences by regex.
 
 [Unreleased]: https://github.com/vanheeringen-lab/genomepy/compare/master...develop
+[0.14.0]: https://github.com/vanheeringen-lab/genomepy/compare/0.13.1...0.14.0
 [0.13.1]: https://github.com/vanheeringen-lab/genomepy/compare/0.13.0...0.13.1
 [0.13.0]: https://github.com/vanheeringen-lab/genomepy/compare/0.12.0...0.13.0
 [0.12.0]: https://github.com/vanheeringen-lab/genomepy/compare/0.11.1...0.12.0

LICENSE

@@ -1,3 +1,5 @@
+MIT License
+
 Copyright (c) 2016 Simon van Heeringen <[email protected]>
 
 Permission is hereby granted, free of charge, to any person