From 82f8f2f913c60c6f3f78cea3c4ddd3e62e1cfd0c Mon Sep 17 00:00:00 2001 From: Bogdan Kirilenko Date: Thu, 18 Jan 2024 00:30:47 +0100 Subject: [PATCH] Added Poetry support --- README.md | 25 ++++++++++++++++--------- VersionHistory.md | 7 ++++--- toga.py | 2 +- version.py | 2 +- 4 files changed, 22 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index dbf1ba8..604ee76 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![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 diff --git a/VersionHistory.md b/VersionHistory.md index 1d48927..3e4102d 100644 --- a/VersionHistory.md +++ b/VersionHistory.md @@ -77,7 +77,7 @@ 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. @@ -85,7 +85,7 @@ Documentation improvements. * (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?) diff --git a/toga.py b/toga.py index 0438d59..40357b3 100755 --- a/toga.py +++ b/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__) diff --git a/version.py b/version.py index 47cd690..1282349 100755 --- a/version.py +++ b/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__}")