Merge branch 'main' into stable

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"]

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:<release version>
+docker pull ghcr.io/brsynth/straindesign:<release version>
 ```
 
 ### Pip
@@ -43,7 +43,7 @@ pip install <unzipped file>.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 <SBML file>
     --input-pathway-file <SBML file>
@@ -63,7 +63,7 @@ docker run \
     -it \
     --rm \
     -v $PWD:/data \
-    rpfbagr:latest \
+    straindesign:latest \
     --input-model /data/<SBML file> \
     --input-pathway-file /data/<SBML file> \
     --input-medium-file /data/<CSV file> \

environment.yml

@@ -1,4 +1,4 @@
-name: rpfbagr
+name: straindesign
 channels:
   - bioconda
   - conda-forge

setup.py

@@ -32,7 +32,7 @@
     author_email=["[email protected]"],
     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,

src/rpfbagr/__main__.py → 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(

src/straindesign/_version.py

@@ -0,0 +1,2 @@
+__app_name__ = "straindesign"
+__version__ = "2.2.2"

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):

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):

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):