diff --git a/Dockerfile b/Dockerfile index 0cb9e30..1b19854 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,4 +3,4 @@ FROM python:3.9 COPY *whl /opt/ RUN pip install --no-cache-dir /opt/*whl -ENTRYPOINT ["python", "-m", "rpfbagr"] +ENTRYPOINT ["python", "-m", "straindesign"] diff --git a/README.md b/README.md index cddaf39..4663cc4 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,25 @@ -# rpfbagr +# StrainDesign -[![Github Version](https://img.shields.io/github/v/release/brsynth/rpfbagr?display_name=tag&sort=semver)](version) [![Conda Version](https://img.shields.io/conda/vn/bioconda/rpfbagr.svg)](https://anaconda.org/bioconda/rpfbagr) -[![GitHub Super-Linter](https://github.com/brsynth/rpfbagr/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter) [![Coverage](https://img.shields.io/coveralls/github/brsynth/rpfbagr)](coveralls) -[![License](https://img.shields.io/github/license/brsynth/rpfbagr)](license) [![DOI](https://zenodo.org/badge/436924636.svg)](https://zenodo.org/badge/latestdoi/436924636) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Gitter](https://badges.gitter.im/BioRetroSynth/SynBioCAD.svg)](https://gitter.im/BioRetroSynth/SynBioCAD?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) +[![Github Version](https://img.shields.io/github/v/release/brsynth/straindesign?display_name=tag&sort=semver)](version) [![Conda Version](https://img.shields.io/conda/vn/bioconda/straindesign.svg)](https://anaconda.org/bioconda/straindesign) +[![GitHub Super-Linter](https://github.com/brsynth/straindesign/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter) [![Coverage](https://img.shields.io/coveralls/github/brsynth/straindesign)](coveralls) +[![License](https://img.shields.io/github/license/brsynth/straindesign)](license) [![DOI](https://zenodo.org/badge/436924636.svg)](https://zenodo.org/badge/latestdoi/436924636) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Gitter](https://badges.gitter.im/BioRetroSynth/SynBioCAD.svg)](https://gitter.im/BioRetroSynth/SynBioCAD?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) ## Description -*rpfbagr* provides a cli interface to predict gene knockout targets with an heterologous pathway +*straindesign* provides a cli interface to predict gene knockout targets with an heterologous pathway ## Installation ### Conda ```sh -conda install -c bioconda rpfbagr +conda install -c bioconda straindesign ``` ### Docker ```sh -docker pull ghcr.io/brsynth/rpfbagr: +docker pull ghcr.io/brsynth/straindesign: ``` ### Pip @@ -43,7 +43,7 @@ pip install .whl Example: Define the best combination of genes deletion to optimize a target. ```sh -python -m rpfbagr \ +python -m straindesign \ [input files] --input-model-file --input-pathway-file @@ -63,7 +63,7 @@ docker run \ -it \ --rm \ -v $PWD:/data \ - rpfbagr:latest \ + straindesign:latest \ --input-model /data/ \ --input-pathway-file /data/ \ --input-medium-file /data/ \ diff --git a/environment.yml b/environment.yml index 0ac1764..6ef779a 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: rpfbagr +name: straindesign channels: - bioconda - conda-forge diff --git a/setup.py b/setup.py index 2c4f4fd..e083655 100644 --- a/setup.py +++ b/setup.py @@ -32,7 +32,7 @@ author_email=["guipagui@gmail.com"], description=description, long_description_content_type="text/markdown", - url="https://github.com/brsynth/rpfbagr", + url="https://github.com/brsynth/straindesign", package_dir={"": "src"}, packages=setuptools.find_packages(where="src"), include_package_data=True, diff --git a/src/rpfbagr/_version.py b/src/rpfbagr/_version.py deleted file mode 100644 index 8d3f443..0000000 --- a/src/rpfbagr/_version.py +++ /dev/null @@ -1,2 +0,0 @@ -__app_name__ = "rpfbagr" -__version__ = "2.2.2" diff --git a/src/rpfbagr/__init__.py b/src/straindesign/__init__.py similarity index 100% rename from src/rpfbagr/__init__.py rename to src/straindesign/__init__.py diff --git a/src/rpfbagr/__main__.py b/src/straindesign/__main__.py similarity index 93% rename from src/rpfbagr/__main__.py rename to src/straindesign/__main__.py index 9316bc9..9de087f 100644 --- a/src/rpfbagr/__main__.py +++ b/src/straindesign/__main__.py @@ -3,19 +3,20 @@ import os import sys -from rpfbagr.medium import associate_flux_env, load_medium -from rpfbagr.metabolic import gene_ko, gene_ou -from rpfbagr.preprocess import build_model, genes_annotate, save_results +from straindesign._version import __app_name__ +from straindesign.medium import associate_flux_env, load_medium +from straindesign.metabolic import gene_ko, gene_ou +from straindesign.preprocess import build_model, genes_annotate, save_results def main(): - """CLI for rpfbagr""" + """CLI for StrainDesign""" desc = ( - "rpfbagr provides a cli interface to run OptGene with an heterologous pathway." + __app_name__ + + " provides a cli interface to run OptGene with an heterologous pathway." ) - - parser = argparse.ArgumentParser(description=desc, prog="python -m rpfbagr") + parser = argparse.ArgumentParser(description=desc, prog="python -m " + __app_name__) # Input parser_input = parser.add_argument_group("Input") parser_input.add_argument( diff --git a/src/straindesign/_version.py b/src/straindesign/_version.py new file mode 100644 index 0000000..0c07118 --- /dev/null +++ b/src/straindesign/_version.py @@ -0,0 +1,2 @@ +__app_name__ = "straindesign" +__version__ = "2.2.2" diff --git a/src/rpfbagr/medium.py b/src/straindesign/medium.py similarity index 100% rename from src/rpfbagr/medium.py rename to src/straindesign/medium.py diff --git a/src/rpfbagr/metabolic.py b/src/straindesign/metabolic.py similarity index 100% rename from src/rpfbagr/metabolic.py rename to src/straindesign/metabolic.py diff --git a/src/rpfbagr/preprocess.py b/src/straindesign/preprocess.py similarity index 100% rename from src/rpfbagr/preprocess.py rename to src/straindesign/preprocess.py diff --git a/tests/test_medium.py b/tests/test_medium.py index eef38f7..22d421f 100644 --- a/tests/test_medium.py +++ b/tests/test_medium.py @@ -3,7 +3,7 @@ from cameo import load_model from main_test import Main_test -from rpfbagr.medium import associate_flux_env, load_medium +from straindesign.medium import associate_flux_env, load_medium class Test_functional(Main_test): diff --git a/tests/test_preprocess.py b/tests/test_preprocess.py index 9c829ab..1ac6fa6 100644 --- a/tests/test_preprocess.py +++ b/tests/test_preprocess.py @@ -1,7 +1,7 @@ import logging from main_test import Main_test -from rpfbagr.preprocess import build_model +from straindesign.preprocess import build_model class Test_functional(Main_test): diff --git a/tests/test_software.py b/tests/test_software.py index cf68942..c056cf2 100644 --- a/tests/test_software.py +++ b/tests/test_software.py @@ -5,7 +5,7 @@ import tempfile from main_test import Main_test -from rpfbagr._version import __app_name__ +from straindesign._version import __app_name__ class Test_software(Main_test):