From 712983d6f86f813ae5c09c63c93e565f318d012c Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker Date: Wed, 1 Mar 2023 12:18:35 +0100 Subject: [PATCH 1/3] chore: add DOI as main citation url --- CITATION.cff | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 46767a5..e5f45e3 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -23,10 +23,11 @@ authors: Environment (RIVM) - name: "The RIVM-IDS Bioinformatics team" version: 1.2.3 #x-release-please-version -# identifiers: -# - type: doi -# value: none -# description: This is the collection of archived snapshots of all versions of ViroConstrictor +doi: 10.5281/zenodo.7688035 +identifiers: + - type: doi + value: 10.5281/zenodo.7688035 + description: This is the collection of archived snapshots of all versions of ViroConstrictor repository-code: 'https://github.com/RIVM-bioinformatics/ViroConstrictor' url: >- https://rivm-bioinformatics.github.io/ViroConstrictor/latest/ From 2266afee0b8a5f6e2e7735927187bf210a7f124b Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker Date: Thu, 2 Mar 2023 13:26:22 +0100 Subject: [PATCH 2/3] refactor: swap argument parser and configuration reader for compatibility with conda-build recipe --- ViroConstrictor/ViroConstrictor.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/ViroConstrictor/ViroConstrictor.py b/ViroConstrictor/ViroConstrictor.py index 85d39e0..7fa47c4 100644 --- a/ViroConstrictor/ViroConstrictor.py +++ b/ViroConstrictor/ViroConstrictor.py @@ -58,12 +58,16 @@ def main(): --> Run snakemake with appropriate settings """ - ##> Check the default userprofile, make it if it doesn't exist - conf = ReadConfig(os.path.expanduser("~/.ViroConstrictor_defaultprofile.ini")) - flags, sampleinfo, samples_df = ValidArgs(sys.argv[1:]) samples_df = samples_df.reset_index(drop=False).rename(columns={"index": "SAMPLE"}) - sampleinfo_df = pd.DataFrame.from_dict(sampleinfo, orient="index").reset_index(drop=False).rename(columns={"index": "SAMPLE"}) + sampleinfo_df = ( + pd.DataFrame.from_dict(sampleinfo, orient="index") + .reset_index(drop=False) + .rename(columns={"index": "SAMPLE"}) + ) + + ##> Check the default userprofile, make it if it doesn't exist + conf = ReadConfig(os.path.expanduser("~/.ViroConstrictor_defaultprofile.ini")) preset_fallback_warnings = [] preset_score_warnings = [] From 1855470c2ead4510e785ec0f81526259281fe73a Mon Sep 17 00:00:00 2001 From: Florian Zwagemaker Date: Thu, 2 Mar 2023 13:35:45 +0100 Subject: [PATCH 3/3] deps: use conda for installing aminoextract instead of pip --- env.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/env.yml b/env.yml index 9206b3a..f84e45b 100644 --- a/env.yml +++ b/env.yml @@ -18,6 +18,4 @@ dependencies: - fpdf2==2.5.1 - python-magic==0.4.27 - rich=13 - - pip - - pip: - - AminoExtract==0.2.1 \ No newline at end of file + - aminoextract==0.2.1 \ No newline at end of file