Merge pull request #224 from pachterlab/devel

Release version 0.27.3 → 0.28.0

Author: Yenaled

.github/workflows/ci.yml

@@ -5,7 +5,7 @@ on: [push]
 jobs:
   check-code:
     name: Check code quality
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout branch
         uses: actions/checkout@master
@@ -19,10 +19,10 @@ jobs:
       - name: Check code quality
         run: make check
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9 ]
+        python: [3.7, 3.8, 3.9 ]
         os: [ubuntu-20.04]
     name: Test on Python ${{ matrix.python }}
     steps:

.github/workflows/release.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   release-to-pypi:
     name: Release to Pypi
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout branch
         uses: actions/checkout@master

.gitignore

@@ -63,6 +63,9 @@ instance/
 # Scrapy stuff:
 .scrapy
 
+# Mac stuff:
+.DS_Store
+
 # Sphinx documentation
 docs/_build/
 docs/api/
@@ -104,4 +107,5 @@ venv.bak/
 # mypy
 .mypy_cache/
 .DS_Store
-.vscode/
+.vscode/
+.Rhistory

README.md

@@ -1,6 +1,6 @@
 # kb-python
-![github version](https://img.shields.io/badge/Version-0.27.3-informational)
-[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.27.3/)
+![github version](https://img.shields.io/badge/Version-0.28.0-informational)
+[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.28.0/)
 ![python versions](https://img.shields.io/pypi/pyversions/kb_python)
 ![status](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/pachterlab/kb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/pachterlab/kb_python)
@@ -59,10 +59,14 @@ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa <GENOME> <GENOME_ANNOTATION>
 	- For example, the zebrafish genome annotation file is hosted by [ensembl](https://uswest.ensembl.org/Danio_rerio/Info/Index) and can be downloaded [here](http://ftp.ensembl.org/pub/release-107/gtf/danio_rerio/Danio_rerio.GRCz11.107.gtf.gz)
 - **Note:** The latest genome annotation and genome file for every species on ensembl can be found with the [`gget`](https://github.com/pachterlab/gget) command-line tool.
 
+Prebuilt indices are available at https://github.com/pachterlab/kallisto-transcriptome-indices
+
 #### Examples
 ```bash
-# Index the zebrafish transcriptome genome.fa.gz annotation.gtf.gz
+# Index the transcriptome from genome FASTA (genome.fa.gz) and GTF (annotation.gtf.gz)
 $ kb ref -i index.idx -g t2g.txt -f1 transcriptome.fa genome.fa.gz annotation.gtf.gz
+# An example for downloading a prebuilt reference for mouse
+$ kb ref -d mouse -i index.idx -g t2g.txt
 ```
 ---
 ### `kb count`: pseudoalign and count reads
@@ -93,9 +97,9 @@ The `kb info` command prints out package information including the version of `k
 
 ```bash
 $ kb info
-kb_python 0.27.3 ...
-kallisto: 0.48.0 ...
-bustools: 0.41.0 ...
+kb_python 0.28.0 ...
+kallisto: 0.50.1 ...
+bustools: 0.43.1 ...
 ...
 ```
 ---

dev-requirements.txt

@@ -7,5 +7,5 @@ sphinx>=3.3.1
 sphinx-autoapi>=1.5.1
 sphinx_rtd_theme>=0.5.0
 twine>=2.0.0
-wheel==0.34.2
+wheel==0.38.1
 yapf==0.30.0

docs/conf.py

@@ -24,7 +24,7 @@
 author = 'Kyung Hoi (Joseph) Min'
 
 # The full version, including alpha/beta/rc tags
-release = '0.27.3'
+release = '0.28.0'
 master_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -6,7 +6,7 @@
 Welcome to kb-python's documentation!
 =====================================
 
-This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.27.3``.
+This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.28.0``.
 For user documentation and tutorials, please go to `kallisto | bustools <https://www.kallistobus.tools/>`_.
 
 Development Prerequisites

kb_python/__init__.py

@@ -1 +1 @@
-__version__ = '0.27.3'
+__version__ = '0.28.0'