diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index bb05eab..0c9c742 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,6 +6,7 @@ on: - main tags: - '*' + jobs: test: runs-on: ubuntu-latest diff --git a/.readthedocs.yml b/.readthedocs.yml deleted file mode 100644 index 3008296..0000000 --- a/.readthedocs.yml +++ /dev/null @@ -1,24 +0,0 @@ -# .readthedocs.yml -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -# Required -version: 2 - -# Build documentation in the docs/ directory with Sphinx -sphinx: - configuration: docs/source/conf.py - -# Build documentation with MkDocs -#mkdocs: -# configuration: mkdocs.yml - -# Optionally build your docs in additional formats such as PDF and ePub -formats: - - pdf - -# Optionally set the version of Python and requirements required to build your docs -python: - version: 3.7 - install: - - requirements: docs/requirements.txt \ No newline at end of file diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..4d7c4c3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,34 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +authors: +- family-names: "Oarga" + given-names: "Alexandru" +- family-names: "Bannerman" + given-names: "Bridget P" +- family-names: "Júlvez" + given-names: "Jorge" +title: "CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities" +version: 0.2.1 +doi: 10.1093/bioinformatics/btad053 +date-released: 2023-02-02 +url: "https://doi.org/10.1093/bioinformatics/btad053" +preferred-citation: + type: article + authors: + - family-names: "Oarga" + given-names: "Alexandru" + - family-names: "Bannerman" + given-names: "Bridget P" + - family-names: "Júlvez" + given-names: "Jorge" + doi: "10.1093/bioinformatics/btad053" + journal: "Bioinformatics" + month: 2 + start: "btad053" + end: "btad053" + title: "CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities" + issue: 2 + volume: 39 + year: 2023 + publisher: "Oxford University Press" + diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index f958a8a..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -sphinx_rtd_theme -sphinx>=1.4 -nbsphinx -ipykernel -myst-parser diff --git a/requirements.txt b/requirements.txt index e1f1bee..99fb62f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -8,6 +8,7 @@ mpmath numpy>=1.16.5 optlang>=1.4.2 pandas>=0.17.0 +pipdeptree==0.13.1 python-dateutil python-libsbml python-libsbml-experimental==5.18.0 diff --git a/test/requirements.txt b/test/requirements.txt index e40a357..3a85744 100644 --- a/test/requirements.txt +++ b/test/requirements.txt @@ -8,7 +8,7 @@ mpmath numpy>=1.16.5 optlang>=1.4.2 pandas>=0.17.0 -pipdeptree +pipdeptree==0.13.1 python-dateutil python-libsbml python-libsbml-experimental==5.18.0