Merge pull request #94 from refgenie/dev

v0.8.0

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.travis.yml

@@ -1,15 +1,18 @@
 language: python
 python:
-  - "2.7"
   - "3.5"
   - "3.6"
+  - "3.7"
+  - "3.8"
 os:
   - linux
 install:
   - pip install .
   - pip install -r requirements/requirements-dev.txt
   - pip install -r requirements/requirements-test.txt
 script: pytest --remote-data --cov=refgenconf
+after_success:
+  - coveralls
 branches:
   only:
     - dev

README.md

@@ -1,7 +1,7 @@
 # refgenconf
 
 [![Build Status](https://travis-ci.org/databio/refgenconf.svg?branch=master)](https://travis-ci.org/databio/refgenconf)
-[![Coverage Status](https://coveralls.io/repos/github/vreuter/refgenconf/badge.svg?branch=master)](https://coveralls.io/github/vreuter/refgenconf?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/refgenie/refgenconf/badge.svg?branch=master)](https://coveralls.io/github/refgenie/refgenconf?branch=master)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/refgenconf/README.html)
 
 Configuration object for refgenie *et al.*

docs/changelog.md

@@ -2,6 +2,17 @@
 
 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. 
 
+## [0.8.0] - 2020-06-25
+
+### Added
+- plugins functionality
+
+### Changed
+- dropped Python 2 support
+
+### Removed
+- preciously deprecated `get_asset` method. Use `seek` instead
+
 ## [0.7.0] - 2020-03-17
 
 ### Added

refgenconf/_version.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.8.0"

refgenconf/const.py

@@ -54,6 +54,7 @@
 CFG_ARCHIVE_KEY = "genome_archive_folder"
 CFG_ARCHIVE_KEY_OLD = "genome_archive"
 CFG_ARCHIVE_CONFIG_KEY = "genome_archive_config"
+CFG_REMOTE_URL_BASE_KEY = "remote_url_base"
 CFG_VERSION_KEY = "config_version"
 CFG_GENOMES_KEY = "genomes"
 
@@ -78,7 +79,7 @@
 
 CFG_TOP_LEVEL_KEYS = [
     CFG_FOLDER_KEY, CFG_SERVER_KEY, CFG_SERVERS_KEY, CFG_ARCHIVE_KEY, CFG_GENOMES_KEY,
-    CFG_VERSION_KEY, CFG_ARCHIVE_CONFIG_KEY, CFG_ARCHIVE_KEY_OLD]
+    CFG_VERSION_KEY, CFG_ARCHIVE_CONFIG_KEY, CFG_ARCHIVE_KEY_OLD, CFG_REMOTE_URL_BASE_KEY]
 CFG_GENOME_KEYS = [
     CFG_GENOME_DESC_KEY, CFG_ASSETS_KEY, CFG_CHECKSUM_KEY]
 CFG_GENOME_ATTRS_KEYS = [CFG_GENOME_DESC_KEY, CFG_CHECKSUM_KEY]
@@ -92,8 +93,22 @@
     "CFG_ASSET_PATH_KEY", "CFG_ASSET_DESC_KEY", "CFG_ARCHIVE_KEY", "CFG_ARCHIVE_SIZE_KEY", "CFG_SEEK_KEYS_KEY",
     "CFG_ASSET_SIZE_KEY", "CFG_CHECKSUM_KEY", "CFG_ARCHIVE_CHECKSUM_KEY", "CFG_VERSION_KEY", "CFG_ASSET_PARENTS_KEY",
     "CFG_ASSET_CHILDREN_KEY", "CFG_TAG_DESC_KEY", "CFG_ASSET_CHECKSUM_KEY", "CFG_ASSET_TAGS_KEY",
-    "CFG_ASSET_RELATIVES_KEYS", "CFG_ARCHIVE_CONFIG_KEY", "CFG_ARCHIVE_KEY_OLD"]
-
+    "CFG_ASSET_RELATIVES_KEYS", "CFG_ARCHIVE_CONFIG_KEY", "CFG_ARCHIVE_KEY_OLD", "CFG_REMOTE_URL_BASE_KEY"]
+
+# hook identifiers
+PRE_UPDATE_HOOK = "pre_update"
+POST_UPDATE_HOOK = "post_update"
+PRE_PULL_HOOK = "pre_pull"
+POST_PULL_HOOK = "post_pull"
+PRE_TAG_HOOK = "pre_tag"
+POST_TAG_HOOK = "post_tag"
+PRE_LIST_HOOK = "pre_list"
+POST_LIST_HOOK = "post_list"
+# HOOKS is a list of all available plugin entry points
+HOOK_NAMES = [
+    "PRE_LIST_HOOK", "PRE_PULL_HOOK", "PRE_TAG_HOOK", "PRE_UPDATE_HOOK",
+    "POST_TAG_HOOK", "POST_LIST_HOOK", "POST_PULL_HOOK", "POST_UPDATE_HOOK"]
+HOOKS = [eval(x) for x in HOOK_NAMES]
 
 # other consts
 REQ_CFG_VERSION = 0.3
@@ -106,7 +121,7 @@
 __all__ = ["DEFAULT_SERVER", "CFG_ASSET_DEFAULT_TAG_KEY", "CFG_KEY_NAMES", "CFG_GENOME_DESC_KEY", "REQ_CFG_VERSION",
            "CFG_ASSETS_KEY", "CFG_GENOME_ATTRS_KEYS", "REFGENIE_BY_CFG", "DEFAULT_TAG", "ATTRS_COPY_PULL",
            "RGC_REQ_KEYS", "REQ_TAG_ATTRS", "CUSTOM_BAR_FMT", "API_VERSION", "CONF_STRUCTURE", "OPERATION_IDS",
-           "CUSTOM_PFX"] + FILE_DIR_NAMES + CFG_CONST + CFG_KEY_NAMES + API_IDS
+           "CUSTOM_PFX", "HOOKS"] + FILE_DIR_NAMES + CFG_CONST + CFG_KEY_NAMES + API_IDS + HOOK_NAMES
 
 CONF_STRUCTURE = """
 # example genome configuration structure

refgenconf/exceptions.py

@@ -5,7 +5,7 @@
 __all__ = ["DownloadJsonError", "GenomeConfigFormatError", "MissingAssetError", "MissingRecipeError",
            "MissingConfigDataError", "MissingGenomeError", "MissingSeekKeyError", "MissingTagError",
            "RefgenconfError", "UnboundEnvironmentVariablesError", "ConfigNotCompliantError",
-           "RemoteDigestMismatchError"]
+           "RemoteDigestMismatchError", "UndefinedAliasError"]
 
 DOC_URL = "http://refgenie.databio.org/en/latest/genome_config/"
 
@@ -80,3 +80,8 @@ def __init__(self, asset, local_digest, remote_digest):
               "because the remote version was not built from the same parent asset you have locally." \
             .format(asset, local_digest, remote_digest)
         super(RemoteDigestMismatchError, self).__init__(msg)
+
+
+class UndefinedAliasError(RefgenconfError):
+    """ Alias is is not defined. """
+    pass