Merge pull request #102 from refgenie/dev

v0.10.0

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

.github/workflows/run-pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
         os: [ubuntu-latest, macos-latest]
 
     steps:

.gitignore

@@ -26,7 +26,6 @@ tests/test/*
 # git has its own built in compression methods
 *.7z
 *.dmg
-*.gz
 *.iso
 *.jar
 *.rar

MANIFEST.in

@@ -1,3 +1,4 @@
+include refgenconf/schemas/*
 include requirements/*
 include README.md
 include LICENSE.txt

codecov.yml

@@ -0,0 +1,2 @@
+ignore:
+  - "refgenconf/refgenconf_v03.py"

docs/changelog.md

@@ -1,6 +1,29 @@
 # Changelog
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
+## [0.10.0] - 2021-03-11
+**After updating to this version your configuration file and genome assets will not be compatible with the software. Please refer to the [upgrade tutorial](config_upgrade_03_to_04.md) for instructions on how to migrate the config between versions.**
+
+## Changed
+
+- instead of using human-readable names as genome identifiers refgenie uses sequence-derived digests in the config
+- asset data moved to `data` directory
+- asset files are now named after genome digests
+- refgenieserver APIv3 is now used for remote assets retrieval
+- `RefGenConf.genomes` becomes an `AliasedYacAttMap` object
+
+### Removed
+- `as_string` and `order` option from `listr` method
+
+### Added
+- `upgrade_config` function for genome configuration file migrating between versions
+- `RefGenConf.compare` method for genome compatibility level determination
+- `as_digests` option in `RefGenConf.listr` method
+- genome config validation on `RefGenConf` object instantiation stage and on every write
+- new progress bar in `RefGenConf.pull`  
+- `RefGenConf.get_ta`
+- numerous `RefGenConf` object properties and methods related to genome aliases handling: `genome_aliases`, `genome_aliases_table`, `alias_dir`, `data_dir`, `get_genome_alias`, `get_genome_alias_digest`, `remove_genome_aliases`, `set_genome_alias`, `initialize_genome`. Refer to [API documentation](http://refgenie.databio.org/en/latest/autodoc_build/refgenconf/) for more specific information.
+- `get_asset_table` method, which displays a concise assets table 
 
 ## [0.9.3] - 2020-09-02
 

refgenconf/__init__.py

@@ -1,12 +1,5 @@
 from ._version import __version__
-
+from .refgenconf import RefGenConf, upgrade_config
+from .helpers import select_genome_config, get_dir_digest
 from .const import *
 from .exceptions import *
-from .helpers import *
-from .refgenconf import *
-
-__all__ = ["RefGenConf", "select_genome_config", "get_dir_digest",
-           "GenomeConfigFormatError", "MissingAssetError",
-           "MissingConfigDataError", "MissingGenomeError", "RefgenconfError",
-           "UnboundEnvironmentVariablesError"] + ["DEFAULT_SERVER"] + \
-          CFG_KEY_NAMES

refgenconf/_version.py

@@ -1 +1 @@
-__version__ = "0.9.3"
+__version__ = "0.10.0"