Fix compressing core and installed pre-commit (#15)

* Pre-commit test * Added local hook for zipping core * Added .zip and .tar.gz autozips into core_archives folder * Zip test * tar.gz test * Compressing works, only really ugly workaround for moving files * Refered to the archives in the README
okkevaneck · okkevaneck · Feb 6, 2023 · Mar 19, 2021 · Mar 22, 2021 · Mar 22, 2021
commit 4b3cb6e40578fbf8dd4e4d64321d9e40baa53b99
diff --git a/.githooks/zip_core.sh b/.githooks/zip_core.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+# File:             zip_core.sh
+# Description:      This bash file compresses the .cpp core code of prospr
+#                       multiple times into archives with different extensions.
+
+set -e
+
+COREDIR=prospr/core/src
+ARCHIVEDIR=core_archives
+
+# Create .zip archive.
+zip -jrq prospr_core.zip "${COREDIR}/"
+mv prospr_core.zip "${ARCHIVEDIR}/prospr_core.zip"
+
+# Create .tar.gz archive.
+cd "${COREDIR}"
+tar -czf prospr_core.tar.gz *.cpp *.hpp
+cd ../../../
+mv "${COREDIR}"/prospr_core.tar.gz "${ARCHIVEDIR}"/prospr_core.tar.gz
+
+# Add archives to git stage.
+git add "${ARCHIVEDIR}"/prospr_core.zip "${ARCHIVEDIR}"/prospr_core.tar.gz
diff --git a/.github/hooks/pre-commit b/.github/hooks/pre-commit
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,35 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+exclude: >
+  (?x)^(
+      .idea/.*|
+  )$
+default_stages: [commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+      - id: flake8
+        additional_dependencies: ["flake8-bugbear==20.1.4"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.812
+    hooks:
+        - id: mypy
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+        language_version: python3.8
+  - repo: local
+    hooks:
+      - id: zip-core
+        name: zip-core
+        entry: ./.githooks/zip_core.sh
+        language: script
diff --git a/README.md b/README.md
@@ -1,8 +1,9 @@
-## Prospr: The Protein Structure Prediction Toolbox  
+## Prospr: The Protein Structure Prediction Toolbox
 ![GitHub](https://img.shields.io/github/license/OkkeVanEck/prospr)
 ![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/OkkeVanEck/prospr?include_prereleases)
-![GitHub Workflow Status (branch)](https://img.shields.io/github/workflow/status/OkkeVanEck/prospr/CI-CD/master)  
-**Creator:** Okke van Eck  
+![GitHub Workflow Status (branch)](https://img.shields.io/github/workflow/status/OkkeVanEck/prospr/CI-CD/master)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+**Creator:** Okke van Eck
 
 This project is a universal toolbox for protein structure prediction within the HP-model.
 It will contain a datastructure for creating own algorithms, pre-created algorithms, datasets and visualization functions.
@@ -18,12 +19,17 @@ This package can simply be installed via pip by running:
 pip install prospr
 ```
 
+## C++ core archives
+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.
+
 ## Example usage
 *Work in progress*
 
 ## Future work
 This toolbox could be used for other protein folding problems within discrete models.
-It would be a great extension to support different models by creating a modular amino acid. 
+It would be a great extension to support different models by creating a modular amino acid.
 
 ## Changelog
 *Work in progress*

diff --git a/core_archives/prospr_core.tar.gz b/core_archives/prospr_core.tar.gz
diff --git a/prospr_core.zip → core_archives/prospr_core.zip b/prospr_core.zip → core_archives/prospr_core.zip
diff --git a/input.txt b/input.txt
diff --git a/manage.sh b/manage.sh
@@ -3,12 +3,10 @@
 # Description:      This bash file supports the commands:
 #                       - "init"        for setting up a developing environment.
 #                       - "echo_debug"  for printing the used global variables.
-#                       - "zip_core"    for zipping all core .cpp files.
 #						- "build"	    for building the Python interfaces for
 #										    the core .cpp files.
 #						- "clean"	    for removing all Python interfaces,
 #	                    					.cxx files, and Python caches.
-#						- "deploy"	    for updating the live version on PyPI.
 
 set -e
 
@@ -22,8 +20,8 @@ PYCACHES=$(find prospr/ -type d -name "__pycache__")
 case "$1" in
     # Setup a developing environment.
     "init")
-        git config core.hooksPath .github/hooks
         pip install -r requirements.txt
+        pre-commit install
     ;;
     # Echo all global variables.
     "echo_debug")
@@ -33,11 +31,6 @@ case "$1" in
         echo -e "PY files:\n${PY_FILES}\n"
         echo -e "PyCaches:\n${PYCACHES}\n"
         ;;
-    # Zip all .cpp files from core to 'prospr_core.zip'.
-    "zip_core")
-        echo "Compressing all C++ files into 'prospr_core.zip'.."
-        zip -jrq prospr_core.zip "${COREDIR}/src/"
-    ;;
     # Build all python interfaces for the core .cpp files.
     "build")
         echo "~ Creating the .py interface for the core.."
@@ -54,16 +47,6 @@ case "$1" in
         rm -rf ${PYCACHES}
         echo -e "\n~ Done cleaning!"
         ;;
-    # Update the live version on PyPI.
-    "deploy")
-        echo "~ Removing old files.."
-        rm -rf build dist prospr.egg-info
-        echo -e "\n~ Creating new package.."
-        python3 setup.py sdist bdist_wheel
-        echo -e "\n~ Uploading package.."
-        twine upload dist/*
-        echo -e "\n~ Done deploying!"
-        ;;
     *)
         echo "No command detected from first argument.."
         ;;

diff --git a/requirements.txt b/requirements.txt
@@ -2,6 +2,7 @@ matplotlib==3.3.0
 numpy==1.19.0
 pandas==1.0.5
 pybind11==2.6.2
+pre-commit==2.11.1
 seaborn==0.10.1
 setuptools>=49.2.0
 twine>=3.2.0