Merge branch 'release/0.8.0'

Author: simonvh

.gitignore

@@ -2,22 +2,22 @@
 *.pyc
 *.so
 *.swp
-*egg-info
 *egg
 .cache
-.pytest_cache
 .coverage
 coverage.xml
 cc-test-reporter
 Log.out
 genomepy/cfg/default.yaml
-tests/data/small_genome.fa.gz
 
 # Directories
+.pytest_cache
 build
+docs/_build
+genomepy.egg-info
+tests/data
 dist
 eggs
 tmp
-docs/_build
 .vscode
 .idea

.travis.yml

@@ -10,8 +10,6 @@ env:
     - CC_TEST_REPORTER_ID=951f438ac8a0fa93801ff0bf69922df59fe03800bf7ea8ab77a3c26cda444979
   jobs:
     - PYTHON_VERSION: "3.6"
-#    - PYTHON_VERSION: "3.7"
-#    - PYTHON_VERSION: "3.8"
 
 before_install:
   # install miniconda
@@ -26,7 +24,6 @@ before_install:
   - conda config --set always_yes yes
 
 install:
-  # python version is specified in environment.yml
   - conda env create -n genomepy python=$PYTHON_VERSION -f environment.yml
   - source activate genomepy
   - python setup.py develop
@@ -35,19 +32,18 @@ install:
 before_script:
   # install codeclimate test coverage
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-        wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64;
-    else
-        wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-darwin-amd64;
+      wget -O cc-test-reporter https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64;
+      chmod +x ./cc-test-reporter;
+      ./cc-test-reporter before-build;
     fi
-  - chmod +x ./cc-test-reporter
-  - ./cc-test-reporter before-build
 
 script:
   - black --check setup.py genomepy/ tests/
   - flake8 setup.py genomepy/ tests/
-  - pytest -v --disable-pytest-warnings --cov=genomepy --cov-report=xml tests/
-  - genomepy providers
+  - pytest -vv --disable-pytest-warnings --cov=genomepy --cov-config=tests/.coveragerc --cov-report=xml tests/*
 
-# Pipe the coverage data to Code Climate
 after_script:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT; fi
+  # send the coverage data to Code Climate
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      ./cc-test-reporter after-build -t coverage.py --exit-code $TRAVIS_TEST_RESULT;
+    fi

CHANGELOG.md

@@ -6,15 +6,73 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [0.8.0] - 2020-05-11
+
+### Added
+- Now using the UCSC rest API
+- `genomepy search` now accepts taxonomy IDs
+- `genomepy search` will now return taxonomy IDs and Accession numbers
+- The README.txt will now store taxonomy IDs and Accession numbers
+- Gene annotations:
+    - Downloading of annotation file (BED/GTF/GFF3) from URL
+    - Automatic search for annotation file (GTF/GFF3) in genome directory when downloading from URL
+    - Option for URL provider to link to annotation file (to process is similarly to other providers)
+    - Automatic annotation sanitizing (and skip sanitizing flag `-s` for `genomepy install`)
+    - Option to only download annotation with `genomepy install -o`
+- Plugins:
+    - Blacklists are automatically unzipped.
+    - Multithreading support for plugins, thanks to alienzj!
+    - STAR now uses the annotation file for a (one-pass) splice-aware index
+
+### Changed
+- sizes no longer a plugin, but always gets executed
+- `genomepy FUNCTION --help` texts expanded
+- all genomepy classes exported when imported into Python
+- all providers now let you know when they are downloading assembly information.
+- more descriptive feedback to installing & many errors
+
+### Removed
+- Sizes plugin
+- Old tests
+- Removed outdated dependency `xmltodict`
+
+### Fixed
+- `genomepy config` options made more robust
+- README.txt will no longer:
+  - update 3x for each command
+  - drop regex info
+  - have duplicate lines
+
+### Refactoring
+- Genome class moved to `genome.py`
+- Many functions moved to `utils.py`
+- Many other functions made static methods of a class
+- `Genome.track2fasta` and `Genome.get_random_sequence` optimized
+- All Provider classes now store their genomes as a dict-in-dict, with the assembly name as key.
+- Many Provider class functions now standardized. Many functions moved to from the daughter classes to the ProviderBase class.
+- README.txt file generation and updating standardized
+- Unit tests! all functions now have an individual test. Almost all test use functions already tested prior to them.
+- Old tests incorporated in several extra tests (e01, e02, e03).
+- Raise statements now use more fitting errors
+- All instances of `os.remove` exchanged for `os.unlink`
+- Almost all warnings fixed
+- Extensive, COVID19-enabled, and somewhat pointless alphabetizing, optimizing and/or organizing changes to
+    - imports everywhere
+    - `.gitignore`
+    - `.travis.yml`
+    - `release_checklist.md`
+    - `cli.py`
+    - strings (many strings with .format() replaced with f-strings)
+
 ## [0.7.2] - 2019-03-31
 
-### Fixes
+### Fixed
 - Fix minor issue with hg19 wrong blacklist url
 - Ensembl downloads over http instead of https (release 99 no longer has https)
 
 ## [0.7.1] - 2019-11-20
 
-### Fixes
+### Fixed
 - STAR is not longer enabled by default
 
 ## [0.7.0] - 2019-11-18
@@ -89,7 +147,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Fixed
 
-- Fixed genome_dir argument to `genomepy install`
+- Fixed genomes_dir argument to `genomepy install`
 - Fixed msgpack dependency
 - Fixed issue with `config generate` where config directory does note exist.