diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 0000000..d93c422 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,32 @@ +# CHANGES + +## 1.3.0 + +* Fixes `valid_q` value of `seq-valid` json report. Always returned false previously. +* Correct command line help text for `seq-valid` input option. +* Extends the `seq-valid` json report to include the ascii range detected and which types of +phred score these align to. +* Additional command line options for `seq-valid` + * `-o | --output` - Generates an interleaved gzip compressed fastq file when input is paired fastq + * `-q | --qc` - Specify the number of pairs to be used when assessing the phred quality range + * Added for performance reasons + +## 1.2.1 + +* More informative exceptions for low-level issues + +## 1.2.0 + +* Changes to command line, using sub commands now +* Changed test framework +* Add travis and codeclimate checks + +## 1.1.0 + +* Fixed issue of `json.loads()` in py<3.5 being unable to decode resource string to utf-8 automatically. +* Adds a UUID to the header of a processed manifest if incoming not set +* Improve documentation + +## 1.0.0 + +Early functional release diff --git a/README.md b/README.md index d79aeb1..acde45a 100644 --- a/README.md +++ b/README.md @@ -81,6 +81,8 @@ Installation is via `pip`. Simply execute with the path to the packaged distrib ```bash pip install --find-links=~/wheels cgp_seq_input_val +# or +pip install https://github.com/cancerit/cgp_seq_input_val/archive/master.tar.gz ``` ### Package Dependancies @@ -133,10 +135,7 @@ For testing/coverage (`./run_tests.sh`) ``` source env/bin/activate # if not already in env -pip install pytest -pip install pytest-cov -pip install pep8 -pip install radon +pip install -r requirements.txt gem install --user-install mdl ``` diff --git a/setup.py b/setup.py index 94f99fd..96be014 100755 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ 'url': 'https://github.com/cancerit/cgp_seq_input_val', 'download_url': '', 'author_email': 'cgphelp@sanger.ac.uk', - 'version': '1.2.1', + 'version': '1.3.0', 'python_requires': '>= 3.4', 'setup_requires': ['pytest'], 'install_requires': ['progressbar2', 'xlrd', 'xopen'],