Sync upstream

.circleci/config.yml

@@ -79,8 +79,12 @@ jobs:
           name: Execute mutagene fetch
           command: |
             pipenv run mutagene -v fetch cohorts MSKCC --cohort paac_jhu_2014
-            FETCH_MD5SUM=$(md5sum paac_jhu_2014.tar.gz | awk '{print $1}')
-            [ $FETCH_MD5SUM = 'b7709f55eaeade1b1c6102d134b16c18' ]
+
+            # Removed due to inconsistent md5 sums across repeated downloads, affecting both this test and pytest
+            #FETCH_MD5SUM=$(md5sum paac_jhu_2014.tar.gz | awk '{print $1}')
+            #[ $FETCH_MD5SUM = 'acbf8c569c2b8f5684ccfb1e036743f0' ]
+            FETCH_SIZE=$(stat -c %s paac_jhu_2014.tar.gz)
+            [ $FETCH_SIZE = '271932' ]
 
       - run:
           name: Execute mutagene motif

.github/dependabot.yaml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.readthedocs.yml

@@ -2,19 +2,12 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: html
 
 # Optionally set the version of Python and requirements required to build your docs
 python:

CHANGELOG.md

@@ -1,7 +1,20 @@
 ## Changelog
 
+0.9.2.0 Release
+---------------
+* Support for ranking of silent mutations given MAF file (e.g. L20=)
+* Fixed pyvcf installation by replacing with pyvcf3
+
+0.9.1.0 Release
+---------------
+* Rank is able to calculate cohort on the fly from MAF files, no need to rely on precalculated cohorts
+* Rank documentation overhauled
+* Fixed bugs and issues [#50] [#44] [#51] [#54] [#56] [#38] [#64]
+* Test framework updates
+* More informative error messages (with genome selection)
+
 0.9.0.2 Release
------------------------
+---------------
 * Genome is set to hg19 by default [#2]
 * Two bootstrap strategies for confidence intervals: t-distribution-based and percentile-based
 * Bootstrap options can be fine-tuned in a separate menu section
@@ -22,20 +35,20 @@
 * Fixed typos in documentation [#31]
 
 0.9.0 Release
------------------------
+-------------
 * Changed --save-motif-matches output to BED format, now includes sample and motif
 * Fixed tests according to new motif API
 
 0.9.0dev2 Testing release
------------------------
+-------------------------
 * Fixed incorrect parsing of mutations on '-' transcribed strand
 * Avoiding double-thresholding on motif significance. Now only qvalue threshold matters
 * Added an option --save-motif-matches to save all mutations that match motif in a separate file 
 * Not showing progress bar in motif search in debug mode
 * Now using T for transcribed, N for non-transcribed and A for any strand to avoid confusion with the reference strand + - and =
 
 0.9.0dev1 Testing release
------------------------
+-------------------------
 * Simplified command-line interface in all subpackages, e.g. 'mutagene motif search' is now simply 'mutagene motif'
 * Retained backward compatibility of command-line interface with 0.8.6
 * Added aliases for subpackages, e.g. fetch = download
@@ -55,33 +68,27 @@
 * MAF file loading improved for GDC and MSKCC data sources. More meaningfull error messages
 
 0.8.6.4 Release
------------------------
+---------------
 * testing and development releases are not available in pip mirrors, bumping version
 
 0.8.6.4dev1 Testing release
------------------------
-
+---------------------------
 * added handling of VCF files to motif analysis
 * Signatures from COSMIC v3 available as signature set "49"
 
 0.8.6.3dev1  Development release
 ------------------------
-
 * Fixed issue with counting matches in asymmetric motifs on reverse complementary strand
 * Changed calculation of enrichment, it is now calculated as Risk Ratio
 * Pvalue reports one-sided Fisher test by default with a 0.05 threshold
 * Formatting of floating point numbers in the output is more tidy
 
 0.8.5.1 Bug-Fix Release
 -----------------------
-
 * several error messages downgraded in log level
 * correct handling of missing parameters
 
 0.8.5 Release
 -------------
-
 * Functionality available 'fetch_genomes', 'fetch_cohorts', and 'rank'
 * Uploaded to PyPi as mutagene
-
-