[DOCS] Adding fair software badge and GA

.github/workflows/fair-software.yml

@@ -0,0 +1,15 @@
+name: fair-software
+
+on: push
+
+jobs:
+  verify:
+    name: "fair-software"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: fair-software/[email protected]
+        name: Measure compliance with fair-software.eu recommendations
+        env:
+          PYCHARM_HOSTED: "Trick colorama into displaying colored output" 
+        with:
+          MY_REPO_URL: "https://github.com/${{ github.repository }}"

.github/workflows/linting_and_testing.yaml

@@ -10,6 +10,7 @@ on:
       - 'LICENSE'
       - 'setup.py'
       - 'README.md'
+      - 'CITATION.cff'
       - 'references.jsonld'
       - '**/docs/**'
       - '**/json_schemas/**'

.gitignore

@@ -112,3 +112,11 @@ traj_comp.xtc
 
 # pycharm
 .idea
+
+# vscode
+.vscode
+
+# Pytest cache
+__pycache__/
+.pytest_cache/
+

CITATION.cff

@@ -0,0 +1,84 @@
+# YAML 1.2
+---
+abstract: "BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
+authors:
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Andrio"
+    given-names: "Pau"
+    orcid: "https://orcid.org/0000-0003-2116-3880"
+  -
+    affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
+    family-names: "Hospital"
+    given-names: "Adam"
+    orcid: "https://orcid.org/0000-0002-8291-8071"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Conejero"
+    given-names:  "Javier"
+    orcid: "https://orcid.org/0000-0001-6401-6229"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Jordà"
+    given-names: "Luis"
+    orcid: "https://orcid.org/0000-0002-9407-9703"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Del Pino"
+    given-names: "Marc"
+    orcid: "https://orcid.org/0000-0001-5565-7577"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Laia"
+    given-names: "Codó"
+    orcid: "https://orcid.org/0000-0002-6797-8746"
+  -
+    affiliation: "School of computer Science, the University of Manchester"
+    family-names: Werkhoven
+    given-names: Ben
+    name-particle: van
+    orcid: "https://orcid.org/0000-0002-7508-3272"
+  -
+    affiliation: "University of Manchester (UOM)"
+    family-names: "Soiland-Reyes"
+    given-names: "Stian"
+    orcid: "https://orcid.org/0000-0001-9842-9718"
+  -
+    affiliation: "University of Manchester (UOM)"
+    family-names: "Goble"
+    given-names: "Carole"
+    orcid: "https://orcid.org/0000-0003-1219-2137"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Lezzi"
+    given-names: "Daniele"
+    orcid: "https://orcid.org/0000-0001-5081-7244"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC)"
+    family-names: "Rosa M"
+    given-names: "Badia"
+    orcid: "https://orcid.org/0000-0003-2941-5499"
+  -
+    affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
+    family-names: "Orozco"
+    given-names: "Modesto"
+    orcid: "https://orcid.org/0000-0002-8608-3278"
+  -
+    affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
+    family-names: "Gelpí"
+    given-names: "Josep Ll."
+    orcid: "https://orcid.org/0000-0002-0566-7723"
+    email: "[email protected]"
+
+cff-version: "1.2.0"
+date-released: "2019-09-10"
+keywords:
+  - "BioExcel"
+  - "BioBB"
+  - "Bioinformatics"
+  - "Computational Biology"
+  - "Biomolecular Workflows"
+license: "Apache-2.0"
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/bioexcel/biobb"
+title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"

README.md

@@ -22,6 +22,13 @@
 [![](https://img.shields.io/github/last-commit/bioexcel/biobb_pmx?label=Last%20Commit)](https://github.com/bioexcel/biobb_pmx/commits/master)
 [![](https://img.shields.io/github/issues/bioexcel/biobb_pmx.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_pmx/issues/)
 
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
+
+[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
+
+[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
+
 
 # biobb_pmx
 

biobb_pmx/__init__.py

@@ -1,3 +1,5 @@
+from . import pmxbiobb
+
 name = "biobb_pmx"
 __all__ = ["pmxbiobb"]
 __version__ = "4.1.0"

biobb_pmx/pmxbiobb/__init__.py

@@ -1,2 +1,10 @@
+from . import pmxanalyse
+from . import pmxgentop
+from . import pmxmutate
+from . import pmxatom_mapping
+from . import pmxligand_hybrid
+from . import pmxmerge_ff
+from . import pmxcreate_top
+
 name = "pmxbiobb"
 __all__ = ["pmxanalyse", "pmxgentop", "pmxmutate", "pmxatom_mapping", "pmxligand_hybrid", "pmxmerge_ff", "pmxcreate_top"]