Resolve pylint errors

Dockerfile

@@ -1,43 +1,51 @@
-FROM vanallenlab/almanac:base
+FROM vanallenlab/miniconda:3.12
 
 WORKDIR /
 
+RUN apt-get update && apt-get install -y
+
 COPY requirements.txt /
+RUN pip install --upgrade pip
 RUN pip install -r requirements.txt
 
 COPY example_data/ /example_data/
 COPY example_output/ /example_output/
-COPY test/ /test/
 
 RUN mkdir /moalmanac/
-RUN mkdir /moalmanac/datasources/
-
-COPY moalmanac/datasources/acmg/ /moalmanac/datasources/acmg/
-COPY moalmanac/datasources/almanac/ /moalmanac/datasources/almanac/
-COPY moalmanac/datasources/cancergenecensus/ /moalmanac/datasources/cancergenecensus/
-COPY moalmanac/datasources/cancerhotspots/ /moalmanac/datasources/cancerhotspots/
-COPY moalmanac/datasources/clinvar/ /moalmanac/datasources/clinvar/
-COPY moalmanac/datasources/cosmic/ /moalmanac/datasources/cosmic/
-COPY moalmanac/datasources/exac/ /moalmanac/datasources/exac/
-COPY moalmanac/datasources/gsea_gene_sets/ /moalmanac/datasources/gsea_gene_sets/
-COPY moalmanac/datasources/hereditary/ /moalmanac/datasources/hereditary/
-COPY moalmanac/datasources/lawrence/ /moalmanac/datasources/lawrence/
-COPY moalmanac/datasources/oncotree/ /moalmanac/datasources/oncotree/
-
-COPY moalmanac/datasources/preclinical/almanac-gdsc-mappings.json /moalmanac/datasources/preclinical/almanac-gdsc-mappings.json
-COPY moalmanac/datasources/preclinical/cell-lines.summary.txt /moalmanac/datasources/preclinical/cell-lines.summary.txt
-COPY moalmanac/datasources/preclinical/ccle.variants.evaluated.txt /moalmanac/datasources/preclinical/ccle.variants.evaluated.txt
-COPY moalmanac/datasources/preclinical/ccle.copy-numbers.evaluated.txt /moalmanac/datasources/preclinical/ccle.copy-numbers.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.gene1.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.gene1.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.fusions.gene2.evaluated.txt /moalmanac/datasources/preclinical/sanger.fusions.gene2.evaluated.txt
-COPY moalmanac/datasources/preclinical/sanger.gdsc.txt /moalmanac/datasources/preclinical/sanger.gdsc.txt
-COPY moalmanac/datasources/preclinical/cell-lines.pkl /moalmanac/datasources/preclinical/cell-lines.pkl
+RUN mkdir /datasources
+RUN mkdir /docs/
+
+COPY moalmanac/test/ moalmanac/test/
+
+COPY datasources/acmg/ /datasources/acmg/
+COPY datasources/cancergenecensus/ /datasources/cancergenecensus/
+COPY datasources/cancerhotspots/ /datasources/cancerhotspots/
+COPY datasources/clinvar/ /datasources/clinvar/
+COPY datasources/cosmic/ /datasources/cosmic/
+COPY datasources/exac/ /datasources/exac/
+COPY datasources/gsea_gene_sets/ /datasources/gsea_gene_sets/
+COPY datasources/hereditary/ /datasources/hereditary/
+COPY datasources/lawrence/ /datasources/lawrence/
+COPY datasources/oncotree/ /datasources/oncotree/
 
 COPY moalmanac/templates/ /moalmanac/templates/
-COPY moalmanac/wrapper_deconstructsigs.sh moalmanac/run_deconstructsigs.R /moalmanac/
 COPY moalmanac/*.py moalmanac/*.ini /moalmanac/
 
+COPY datasources/moalmanac/ /datasources/moalmanac/
+
+COPY datasources/preclinical/README.md /datasources/preclinical/README.md
+COPY datasources/preclinical/generate-dictionary.ipynb /datasources/preclinical/generate-dictionary.ipynb
+COPY datasources/preclinical/cell-lines.pkl /datasources/preclinical/cell-lines.pkl
+COPY datasources/preclinical/formatted/almanac-gdsc-mappings.json /datasources/preclinical/formatted/almanac-gdsc-mappings.json
+COPY datasources/preclinical/formatted/cell-lines.summary.txt /datasources/preclinical/formatted/cell-lines.summary.txt
+COPY datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt /datasources/preclinical/annotated/cell-lines.somatic-variants.annotated.txt
+COPY datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt  /datasources/preclinical/annotated/cell-lines.copy-numbers.annotated.txt
+COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.txt  /datasources/preclinical/annotated/cell-lines.fusions.annotated.txt
+COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt /datasources/preclinical/annotated/cell-lines.fusions.annotated.gene1.txt
+COPY datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt /datasources/preclinical/annotated/cell-lines.fusions.annotated.gene2.txt
+COPY datasources/preclinical/formatted/sanger.gdsc.txt /datasources/preclinical/formatted/sanger.gdsc.txt
+
+COPY docs/* /docs/
 COPY README.md /
 COPY LICENSE /
 COPY Dockerfile /