Merge pull request #11 from ressy/release-0.0.5

Release 0.0.5

.circleci/config.yml

@@ -14,6 +14,9 @@ jobs:
       - run:
           command: python -m unittest
           name: Test
+      - run:
+          command: python -m vquest -h
+          name: Try CLI
 
 workflows:
   main:

.gitignore

@@ -1 +1,4 @@
 __pycache__/
+build/
+dist/
+vquest.egg-info/

CHANGELOG.md

@@ -0,0 +1,28 @@
+# Changelog
+
+## 0.0.5 - 2021-03-10
+
+### Added
+
+ * `--align` argument (via `airr_to_fasta` function) for exraction of sequence
+   alignment FASTA from AIRR results ([#1])
+ * Error messages sent by the server are now raised as an exception containing
+   the server-provided message(s) ([#7])
+
+### Changed
+
+ * Reorganized and expanded test code as its own package ([#6])
+ * Added basic test of command-line usage ([#10])
+ * Clarified wording on required options ([#8])
+
+### Fixed
+
+ * Parse command-line options that should be integers from a finite list of
+   options as integers instead of strings ([#5])
+
+[#10]: https://github.com/ressy/vquest/pull/10
+[#8]: https://github.com/ressy/vquest/pull/8
+[#7]: https://github.com/ressy/vquest/pull/7
+[#6]: https://github.com/ressy/vquest/pull/6
+[#5]: https://github.com/ressy/vquest/pull/5
+[#1]: https://github.com/ressy/vquest/pull/1

README.md

@@ -1,5 +1,7 @@
 # Automate IMGT V-QUEST usage on imgt.org
 
+[![vquest](https://circleci.com/gh/ressy/vquest.svg?style=shield)](https://circleci.com/gh/ressy/vquest)
+
 [IMGT](http://imgt.org)'s [V-QUEST](http://www.imgt.org/IMGT_vquest/analysis)
 is only available via a web interface.  This Python package automates V-QUEST
 usage by submitting request data like the web form does.  Curently only the
@@ -13,6 +15,12 @@ Example command-line usage, with rhesus sequences in seqs.fasta:
 The output is saved to `Parameters.txt` and `vquest_airr.tsv` (the files
 V-QUEST provides in a zip archive) in the working directory.
 
+Or with `--align` to automatically extract the alignment as FASTA:
+
+    vquest --align --species rhesus-monkey --receptorOrLocusType IG --fileSequences seqs.fasta
+
+Here the aligned FASTA text is printed directly to standard output.
+
 Example Python usage:
 
     >>> from vquest import *

requirements.txt

@@ -1,3 +1,4 @@
 biopython
 requests
+requests-html
 PyYAML

setup.py

@@ -27,6 +27,6 @@
         "License :: OSI Approved :: GNU Affero General Public License v3",
         "Operating System :: OS Independent",
     ],
-    install_requires=["biopython", "PyYAML", "requests"],
+    install_requires=["biopython", "PyYAML", "requests", "requests-html"],
     python_requires='>=3.6',
 )

test_vquest/data/test_vquest/TestVquestCustom/config.yml

@@ -0,0 +1,9 @@
+species: rhesus-monkey
+receptorOrLocusType: IG
+v_regionsearchindel: true
+sequences: |
+  >IGKV2-ACR*02
+  GACATTGTGATGACCCAGACTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCAGCCTCCATCTCCTGCAGGTCTAGTCA
+  GAGCCTCTTGGATAGTGACGGGTACACCTGTTTGGACTGGTACCTGCAGAAGCCAGGCCAGTCTCCACAGCTCCTGATCT
+  ATGAGGTTTCCAACCGGGTCTCTGGAGTCCCTGACAGGTTCAGTGGCAGTGGGTCAGNCACTGATTTCACACTGAAAATC
+  AGCCGGGTGGAAGCTGAGGATGTTGGGGTGTATTACTGTATGCAAAGTATAGAGTTTCCTCC

test_vquest/data/test_vquest/TestVquestInvalid/headers.txt

@@ -0,0 +1 @@
+Content-Type text/html