Added Poetry support

README.md

@@ -3,7 +3,7 @@
 <img src="https://github.com/hillerlab/TOGA/blob/master/supply/logo.png" width="500">
 
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-![version](https://img.shields.io/badge/version-1.1.7.dev-blue)
+![version](https://img.shields.io/badge/version-1.1.7-blue)
 [![DOI](https://zenodo.org/badge/277817661.svg)](https://zenodo.org/badge/latestdoi/277817661)
 [![License](https://img.shields.io/github/license/hillerlab/TOGA.svg)](https://github.com/hillerlab/TOGA/blob/master/LICENSE)
 [![made-with-Nextflow](https://img.shields.io/badge/Made%20with-Nextflow-23aa62.svg)](https://www.nextflow.io/)
@@ -59,17 +59,24 @@ To get TOGA do the following:
 # clone the repository
 git clone https://github.com/hillerlab/TOGA.git
 cd TOGA
-# install necessary python packages:
+```
+
+Install necessary python packages using pip:
+
+```shell
 python3 -m pip install -r requirements.txt --user
-# call configure to:
-# 1) train xgboost models
-# 2) download CESAR2.0
-# 3) compile C code
-./configure.sh
-# run a test, it will take a couple of minutes
-./run_test.sh micro
 ```
 
+Alternatively, if you use poetry, just do `poetry install`
+
+Call `configure.sh` to:
+1) train xgboost models
+2) download CESAR2.0
+3) compile C code
+
+
+Run a test, it will take a couple of minutes: `./run_test.sh micro`
+
 If you see something like this at the very end, then TOGA is almost ready to go:
 
 ```txt

VersionHistory.md

@@ -77,15 +77,15 @@ Documentation improvements.
 * (started): better code organisation - constants class
 * Replaced CESAR2.0 submodule with Kirilenko's lightweight fork (without Kent, etc.)
 
-# TOGA 1.1.6 (current release) #
+# TOGA 1.1.6 #
 
 * Removed obsolete optimised CESAR path.
 * Fixed a minor bug with re-running CESAR jobs memory parameter if no buckets were specified.
 * (by shjenkins94) added gene_prefix argument
 * (by shjenkins94) fixed U12 argument check bug
 * minor code style improvements
 
-# TOGA 1.1.7 (planned) #
+# TOGA 1.1.7 (current release) #
 
 * Drafted sanity checker to ensure no temporary directories match necessary directories, see `modules.toga_sanity_checks.TogaSanityChecker.check_dir_args_safety` and issue [132](https://github.com/hillerlab/TOGA/issues/132)
 * Added logging for filtered out reference transcripts
@@ -95,8 +95,9 @@ Documentation improvements.
 * Utility class for TOGA sanity checks
 * Added argument to control cluster queue name (before, it was just `batch`).
 * `GLP_values.py` content merged with `constants.py`
+* Added support for the Poetry package manager through the inclusion of a `pyproject.toml` file.
 
-# TOGA 1.1.8
+# TOGA 1.1.8 (planned)
 
 * (planned) Step management - now user can rerun TOGA from any desired step.
 * (planned) Using CESAR in the single exon mode for most of the exons to solve the RAM bottleneck (maybe TOGA 1.2.x?)

toga.py

@@ -45,7 +45,7 @@
 
 
 __author__ = "Bogdan M. Kirilenko"
-__email__ = "kirilenkobm [at] google mail"
+__github__ = "https://github.com/kirilenkobm"
 __credits__ = ["Michael Hiller", "Virag Sharma", "David Jebb"]
 
 LOCATION = os.path.dirname(__file__)

version.py

@@ -37,7 +37,7 @@ def to_string(self):
         return self.version_repr
 
 
-__version__ = Version(1, 1, 7, metadata="dev")
+__version__ = Version(1, 1, 7)
 
 if __name__ == "__main__":
     print(f"TOGA version: {__version__}")