Merge pull request #183 from refgenie/dev

v0.9.2

.github/workflows/build-package.yml

@@ -0,0 +1,41 @@
+name: Build package
+
+on:
+  push:
+    branches: [master, dev]
+  pull_request:
+    branches: [master, dev]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dev dependancies
+      run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
+
+    # - name: Install test dependancies
+    #   run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+    - name: Install package
+      run: python -m pip install .
+
+    # - name: Run pytest tests
+    #   run: pytest tests --remote-data --cov=./ --cov-report=xml
+
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v1
+    #   with:
+    #     file: ./coverage.xml
+    #     name: py-${{ matrix.python-version }}-${{ matrix.os }}

.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/*

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/databio/refgenie.svg?branch=master)](https://travis-ci.org/databio/refgenie)
+![Build package](https://github.com/refgenie/refgenie/workflows/Build%20package/badge.svg)
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/refgenie/README.html)
 
 <img src="https://raw.githubusercontent.com/databio/refgenie/master/docs/img/refgenie_logo.svg?sanitize=true" alt="Refgenie" height="70"/><br>

docs/README.md

@@ -4,6 +4,8 @@
 [![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)
 [![PyPi](https://img.shields.io/pypi/v/refgenie.svg)](https://pypi.org/project/refgenie/)
 
+<iframe src="https://ghbtns.com/github-btn.html?user=refgenie&repo=refgenie&type=star&count=true" frameborder="0" scrolling="0" width="150" height="20" title="GitHub"></iframe>
+
 ## What is refgenie?
 
 Refgenie manages storage, access, and transfer of reference genome resources. It provides command-line and Python interfaces to *download* pre-built reference genome "assets", like indexes used by bioinformatics tools. It can also *build* assets for custom genome assemblies. Refgenie provides programmatic access to a standard genome folder structure, so software can swap from one genome to another.

docs/autodoc_build/refgenconf.md

@@ -65,7 +65,7 @@ Create a block of text representing genome-to-asset mapping.
 - `asset_sep` (`str`):  the delimiter between names of types of assets,within each genome line
 - `genome_assets_delim` (`str`):  the delimiter to place betweenreference genome assembly name and its list of asset names
 - `genome` (`list[str] | str`):  genomes that the assets should be found for
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 
 
 #### Returns:
@@ -209,7 +209,7 @@ def genomes_str(self, order=None)
 Get as single string this configuration's reference genome assembly IDs.
 #### Parameters:
 
-- `order` (``):  function(str) -> object how to key genome IDs for sort
+- `order` (`function(str) -> object`):  how to key genome IDs for sort
 
 
 #### Returns:
@@ -219,36 +219,6 @@ Get as single string this configuration's reference genome assembly IDs.
 
 
 
-```python
-def get_asset(self, genome_name, asset_name, tag_name=None, seek_key=None, strict_exists=True, check_exist=<function RefGenConf.<lambda> at 0x7f3f69ae2d40>, enclosing_dir=False)
-```
-
-Get a path to the a specified genome-asset-tag. Note: enforces file existence checks by default
-#### Parameters:
-
-- `genome_name` (`str`):  name of a reference genome assembly of interest
-- `asset_name` (`str`):  name of the particular asset to fetch
-- `tag_name` (`str`):  name of the particular asset tag to fetch
-- `seek_key` (`str`):  name of the particular subasset to fetch
-- `strict_exists` (`bool | NoneType`):  how to handle case in whichpath doesn't exist; True to raise IOError, False to raise RuntimeWarning, and None to do nothing at all
-- `check_exist` (`function(callable) -> bool`):  how to check forasset/path existence
-- `enclosing_dir` (`bool`):  whether a path to the entire enclosing directory should be returned, e.g.for a fasta asset that has 3 seek_keys pointing to 3 files in an asset dir, that asset dir is returned
-
-
-#### Returns:
-
-- `str`:  path to the asset
-
-
-#### Raises:
-
-- `TypeError`:  if the existence check is not a one-arg function
-- `refgenconf.MissingGenomeError`:  if the named assembly isn't knownto this configuration instance
-- `refgenconf.MissingAssetError`:  if the names assembly is known tothis configuration instance, but the requested asset is unknown
-
-
-
-
 ```python
 def get_default_tag(self, genome, asset, use_existing=True)
 ```
@@ -293,7 +263,7 @@ List locally available reference genome IDs and assets by ID.
 #### Parameters:
 
 - `genome` (`list[str] | str`):  genomes that the assets should be found for
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 
 
 #### Returns:
@@ -304,15 +274,15 @@ List locally available reference genome IDs and assets by ID.
 
 
 ```python
-def get_remote_data_str(self, genome=None, order=None, get_url=<function RefGenConf.<lambda> at 0x7f3f69ae6170>)
+def get_remote_data_str(self, genome=None, order=None, get_url=<function RefGenConf.<lambda> at 0x1051476a8>)
 ```
 
 List genomes and assets available remotely.
 #### Parameters:
 
 - `get_url` (`function(refgenconf.RefGenConf) -> str`):  how to determineURL request, given RefGenConf instance
 - `genome` (`list[str] | str`):  genomes that the assets should be found for
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 
 
 #### Returns:
@@ -403,7 +373,7 @@ def list(self, genome=None, order=None, include_tags=False)
 List local assets; map each namespace to a list of available asset names
 #### Parameters:
 
-- `order` (`function(str) -> object`):  how to key genome IDs for sort
+- `order` (`callable(str) -> object`):  how to key genome IDs for sort
 - `genome` (`list[str] | str`):  genomes that the assets should be found for
 - `include_tags` (`bool`):  whether asset tags should be included in the returned dict
 
@@ -423,7 +393,7 @@ List types/names of assets that are available for one--or all--genomes.
 #### Parameters:
 
 - `genome` (`str | NoneType`):  reference genome assembly ID, optional;if omitted, the full mapping from genome to asset names
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 - `include_tags` (`bool`):  whether asset tags should be included in the returned dict
 
 
@@ -442,7 +412,7 @@ List assemblies for which a particular asset is available.
 #### Parameters:
 
 - `asset` (`str | NoneType`):  name of type of asset of interest, optional
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 
 
 #### Returns:
@@ -453,15 +423,15 @@ List assemblies for which a particular asset is available.
 
 
 ```python
-def listr(self, genome=None, order=None, get_url=<function RefGenConf.<lambda> at 0x7f3f69ae6290>)
+def listr(self, genome=None, order=None, get_url=<function RefGenConf.<lambda> at 0x1051477b8>)
 ```
 
 List genomes and assets available remotely.
 #### Parameters:
 
 - `get_url` (`function(refgenconf.RefGenConf) -> str`):  how to determineURL request, given RefGenConf instance
 - `genome` (`list[str] | str`):  genomes that the assets should be found for
-- `order` (``):  function(str) -> object how to key genome IDs and assetnames for sort
+- `order` (`function(str) -> object`):  how to key genome IDs and assetnames for sort
 
 
 #### Returns:
@@ -472,7 +442,19 @@ List genomes and assets available remotely.
 
 
 ```python
-def pull(self, genome, asset, tag, unpack=True, force=None, get_json_url=<function RefGenConf.<lambda> at 0x7f3f69ae6560>, build_signal_handler=<function _handle_sigint at 0x7f3f69ba07a0>)
+def plugins(self)
+```
+
+Plugins registered by entry points in the current Python env
+#### Returns:
+
+- `dict[dict[function(refgenconf.RefGenConf)]]`:  dict which keysare names of all possible hooks and values are dicts mapping registered functions names to their values
+
+
+
+
+```python
+def pull(self, genome, asset, tag, unpack=True, force=None, get_json_url=<function RefGenConf.<lambda> at 0x105147a60>, build_signal_handler=<function _handle_sigint at 0x1050a8ea0>)
 ```
 
 Download and possibly unpack one or more assets for a given ref gen.
@@ -547,7 +529,19 @@ Remove any relationship links associated with the selected asset
 
 
 ```python
-def seek(self, genome_name, asset_name, tag_name=None, seek_key=None, strict_exists=None, enclosing_dir=False, check_exist=<function RefGenConf.<lambda> at 0x7f3f69ae2c20>)
+def run_plugins(self, hook)
+```
+
+Runs all installed plugins for the specified hook.
+#### Parameters:
+
+- `hook` (`str`):  hook identifier
+
+
+
+
+```python
+def seek(self, genome_name, asset_name, tag_name=None, seek_key=None, strict_exists=None, enclosing_dir=False, check_exist=<function RefGenConf.<lambda> at 0x1051472f0>)
 ```
 
 Seek path to a specified genome-asset-tag
@@ -714,7 +708,7 @@ A convenience method which wraps the update assets and uses it to update the ass
 def update_seek_keys(self, genome, asset, tag=None, keys=None)
 ```
 
-A convenience method which wraps the update assets and uses it to update the seek keys for a tagged asset.
+A convenience method which wraps the updated assets and uses it to update the seek keys for a tagged asset.
 #### Parameters:
 
 - `genome` (`str`):  genome to be added/updated
@@ -762,6 +756,30 @@ Return writability flag or None if not set
 
 
 
+```python
+def write(self, filepath=None)
+```
+
+Write the contents to a file. If pre- and post-update plugins are defined, they will be executed automatically
+#### Parameters:
+
+- `filepath` (`str`):  a file path to write to
+
+
+#### Returns:
+
+- `str`:  the path to the created files
+
+
+#### Raises:
+
+- `OSError`:  when the object has been created in a read only mode or other process has locked the file
+- `TypeError`:  when the filepath cannot be determined.This takes place only if YacAttMap initialized with a Mapping as an input, not read from file.
+- `OSError`:  when the write is called on an object with no write capabilitiesor when writing to a file that is locked by a different object
+
+
+
+
 ## <a name="GenomeConfigFormatError"></a> Class `GenomeConfigFormatError`
 Exception for invalid genome config file format.
 
@@ -815,4 +833,4 @@ Get path to genome configuration file.
 
 
 
-*Version Information: `refgenconf` v0.7.0-dev, generated by `lucidoc` v0.4.2*
+*Version Information: `refgenconf` v0.7.1-dev, generated by `lucidoc` v0.4.3*

docs/changelog.md

@@ -2,6 +2,15 @@
 
 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. 
 
+## [0.9.2] - 2020-07-01
+
+## Changed 
+- in `refgenie build` reduced the config file locking time to prevent problems in multi-build context
+- dropped Python 2 support
+## Added
+- parametrized `kmer` in salmon recipes 
+- support for all genome configuration file parameter values initialization in `refgenie init`
+
 ## [0.9.1] - 2020-05-01 
 
 ### Added

refgenie/_version.py

@@ -1 +1 @@
-__version__ = "0.9.1"
+__version__ = "0.9.2"