Fix datasets

.githooks/compress_files.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+# File:             zip_files.sh
+# Description:      This bash file compresses the .cpp core code of prospr
+#                       multiple times into archives with different extensions.
+#                       It also compresses the provided datasets into archives
+#                       with different extensions. All archives are moved into
+#                       the archives folder.
+
+set -e
+
+ARCHIVEDIR=archives
+COREDIR=prospr/core/src
+DATADIR=prospr/data
+
+
+# Create .zip core archive.
+zip -jrq prospr_core.zip "${COREDIR}/"
+mv prospr_core.zip "${ARCHIVEDIR}/prospr_core.zip"
+
+# Create .tar.gz core archive.
+cd "${COREDIR}"
+tar -czf prospr_core.tar.gz *.cpp *.hpp
+cd ../../../
+mv "${COREDIR}"/prospr_core.tar.gz "${ARCHIVEDIR}"/prospr_core.tar.gz
+
+# Create .zip data archive.
+cd "${DATADIR}"
+zip -rq prospr_data.zip .
+cd ../../
+mv "${DATADIR}"/prospr_data.zip "${ARCHIVEDIR}"/prospr_data.zip
+
+# Create .tar.gz data archive.
+cd "${DATADIR}"
+tar -czf prospr_data.tar.gz */*.csv
+cd ../../
+mv "${DATADIR}"/prospr_data.tar.gz "${ARCHIVEDIR}"/prospr_data.tar.gz
+
+# Add archives to git stage.
+git add "${ARCHIVEDIR}"/prospr_core.zip "${ARCHIVEDIR}"/prospr_core.tar.gz \
+    "${ARCHIVEDIR}"/prospr_data.zip "${ARCHIVEDIR}"/prospr_data.tar.gz

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
         language_version: python3.8
   - repo: local
     hooks:
-      - id: zip-core
-        name: zip-core
-        entry: ./.githooks/zip_core.sh
+      - id: compress-files
+        name: compress-files
+        entry: ./.githooks/compress_files.sh
         language: script

README.md

@@ -19,10 +19,19 @@ This package can simply be installed via pip by running:
 pip install prospr
 ```
 
-## C++ core archives
+## Archives
+All the C++ core files and datasets are also available as compressed archives.
+See the subsections below for direct links.
+
+### C++ core
 All the core code which prospr runs on, is available as a compressed archive.
-The folder `core_archives` contains a [.zip](core_archives/prospr_core.zip) and
-a [.tar.gz](core_archives/prospr_core.tar.gz) archive.
+The folder `archives` contains a [.zip](archives/prospr_core.zip) and
+a [.tar.gz](archives/prospr_core.tar.gz) archive.
+
+### Datasets
+The complete collection of datasets is available as a compressed archive in the
+`archives` folder. It is available as a [.zip](archives/prospr_data.zip) and a
+[.tar.tz](archives/prospr_data.tar.gz) archive.
 
 ## Example usage
 *Work in progress*

prospr/core/src/depth_first.hpp

@@ -1,6 +1,7 @@
 /* File:            depth_first.h
  * Description:     Header file for a depth-first search function.
  */
+
 #ifndef DEPTH_FIRST_H
 #define DEPTH_FIRST_H
 

prospr/core/src/depth_first_bnb.hpp

@@ -2,6 +2,7 @@
  * Description:     Header file for a depth-first branch-and-bound search
  *                      function.
  */
+
 #ifndef DEPTH_FIRST_BNB_H
 #define DEPTH_FIRST_BNB_H
 

prospr/core/src/protein.hpp

@@ -1,6 +1,7 @@
 /* File:            protein.h
  * Description:     Header file for a protein object within the HP-model.
  */
+
 #ifndef PROTEIN_H
 #define PROTEIN_H