Merge pull request #70 from RIVM-bioinformatics/dev

Use conda for all dependencies + conda-build compatibility

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/

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 = []

env.yml

@@ -18,6 +18,4 @@ dependencies:
   - fpdf2==2.5.1
   - python-magic==0.4.27
   - rich=13
-  - pip
-  - pip:
-    - AminoExtract==0.2.1
+  - aminoextract==0.2.1