refactor: Merge in 1.1.0rc2

.gitattributes

@@ -0,0 +1,17 @@
+.gitattributes export-ignore
+.gitignore export-ignore
+
+3diphy/ export-ignore
+A-pro/ export-ignore
+CATH_data/ export-ignore
+Protein-comparison-tool/ export-ignore
+docs/ export-ignore
+docsource/ export-ignore
+examples/ export-ignore
+figures/ export-ignore
+foldseek/ export-ignore
+madroot/ export-ignore
+mafftmat/ export-ignore
+notebooks/ export-ignore
+slurmsimple/ export-ignore
+test-example/ export-ignore

.github/workflows/main.yml

@@ -19,36 +19,3 @@ jobs:
           DEFAULT_BRANCH: main
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VALIDATE_SNAKEMAKE_SNAKEFMT: true
-
-  Linting:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .
-        snakefile: workflow/Snakefile
-        args: "--lint"
-
-  Testing:
-    runs-on: ubuntu-latest
-    needs: 
-      - Linting
-      - Formatting
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
-
-    - name: Test report
-      uses: snakemake/snakemake-github-action@v1.24.0
-      with:
-        directory: .test
-        snakefile: workflow/Snakefile
-        args: "--report report.zip"

.gitignore

@@ -46,4 +46,6 @@ src/dataprep/**
 !src/dataprep/*.py
 !src/dataprep/*.sh
 
-notebooks/**.pkl
+notebooks/**.pkl
+
+.ipynb_checkpoints/