rename & add comments

README.md

@@ -121,14 +121,14 @@ Older releases remain available on the [release
 page](https://github.com/MannLabs/alphapeptdeep/releases), but no
 backwards compatibility is guaranteed.
 
-
-TODO
 Note that, as GitHub does not allow large release files, these installers do not have GPU support.
-To create GPU version installers, clone the source code and install GPU-version pytorch [see here](#use-gpu),
-and then use `release/[macos, linux, windows]/create_installer_*.sh` to build an installer locally.
+To create GPU version installers: clone the source code, install the GPU-version of pytorch [see here](#use-gpu),
+and then use the `build_installer_*.sh` and `build_package_*.sh`
+script in the respective `release/[macos, linux, windows]` folder to build the installer locally.
 For Linux you need to additionally pass the "GPU" flag, i.e. run
 ```bash
-release/linux/XXXX.sh GPU
+release/linux/build_installer_linux.sh GPU
+release/linux/build_package_linux.sh
 ```
 
 ### Pip

release/linux/build_installer_linux.sh

@@ -1,27 +1,22 @@
 #!/bin/bash
 
+# Build the installer for Linux.
+# This script is intended to be run from the root of the repository.
 
-PACKAGE_NAME="peptdeep"
-PACKAGE_VERSION="1.2.1"
+rm -rf dist
+rm -rf build
 
-ARCH=$(uname -m)
-if [ "$ARCH" == "x86_64" ]; then
-  ARCH="x64"
-fi
-echo "ARCH=${ARCH}" >> $GITHUB_ENV
-
-KERNEL=$(uname -s | tr '[:upper:]' '[:lower:]')
+# Creating the wheel
+python setup.py sdist bdist_wheel
 
-BUILD_NAME="${PACKAGE_NAME}-${PACKAGE_VERSION}-${KERNEL}-${ARCH}"
+# Setting up the local package
+# Make sure you include the required extra packages and always use the stable or very-stable options!
+pip install "dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 
-# If needed, include additional source such as e.g.:
-# cp ../../peptdeep/data/*.fasta dist/peptdeep/data
-# WARNING: this probably does not work!!!!
+if [ "$1" != "GPU" ]; then
+    pip install torch -U --extra-index-url https://download.pytorch.org/whl/cpu
+fi
 
-# Wrapping the pyinstaller folder in a .deb package
-mv dist/peptdeep dist/peptdeep.tmp
-mkdir -p dist/$BUILD_NAME/usr/local/bin
-mv dist/peptdeep.tmp dist/$BUILD_NAME/usr/local/bin/peptdeep
-mkdir dist/$BUILD_NAME/DEBIAN
-cp release/linux/control dist/$BUILD_NAME/DEBIAN
-dpkg-deb --build --root-owner-group dist/$BUILD_NAME/
+# Creating the stand-alone pyinstaller folder
+pip install pyinstaller
+pyinstaller release/pyinstaller/peptdeep.spec -y

release/linux/build_package_linux.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# Build the install package for Linux.
+# This script is intended to be run from the root of the repository after running build_installer_linux.sh
+
+PACKAGE_NAME="peptdeep"
+PACKAGE_VERSION="1.2.1"
+
+ARCH=$(uname -m)
+if [ "$ARCH" == "x86_64" ]; then
+  ARCH="x64"
+fi
+echo "ARCH=${ARCH}" >> $GITHUB_ENV
+
+KERNEL=$(uname -s | tr '[:upper:]' '[:lower:]')
+
+BUILD_NAME="${PACKAGE_NAME}-${PACKAGE_VERSION}-${KERNEL}-${ARCH}"
+
+# If needed, include additional source such as e.g.:
+# cp ../../peptdeep/data/*.fasta dist/peptdeep/data
+# WARNING: this probably does not work!!!!
+
+# Wrapping the pyinstaller folder in a .deb package
+mv dist/peptdeep dist/peptdeep.tmp
+mkdir -p dist/$BUILD_NAME/usr/local/bin
+mv dist/peptdeep.tmp dist/$BUILD_NAME/usr/local/bin/peptdeep
+mkdir dist/$BUILD_NAME/DEBIAN
+cp release/linux/control dist/$BUILD_NAME/DEBIAN
+dpkg-deb --build --root-owner-group dist/$BUILD_NAME/

release/macos/build_backend_macos.sh → release/macos/build_installer_macos.sh

@@ -1,6 +1,11 @@
 #!/bin/bash
 
-# OUT OF SCOPE: moving to pyproject.toml / unifying these scripts
+# Build the installer for MacOS.
+# This script is intended to be run from the root of the repository.
+
+
+rm -rf dist
+rm -rf build
 
 # Creating the wheel
 python setup.py sdist bdist_wheel

release/macos/build_pkg_macos.sh → release/macos/build_package_macos.sh

@@ -1,8 +1,13 @@
 #!/bin/bash
 
+# Build the install package for MacOS.
+# This script is intended to be run from the root of the repository after running build_installer_macos.sh
+
 PACKAGE_NAME="peptdeep"
 PACKAGE_VERSION="1.2.1"
 
+rm -rf ${PACKAGE_NAME}.pkg
+
 ARCH=$(uname -m)
 if [ "$ARCH" == "x86_64" ]; then
   ARCH="x64"
@@ -27,5 +32,5 @@ cp LICENSE.txt dist/peptdeep/Contents/Resources/LICENSE.txt
 cp release/logos/alpha_logo.png dist/peptdeep/Contents/Resources/alpha_logo.png
 chmod 777 release/macos/scripts/*
 
-pkgbuild --root dist/${PACKAGE_NAME} --identifier de.mpg.biochem.${PACKAGE_NAME}.app --version 1.2.1 --install-location /Applications/${PACKAGE_NAME}.app --scripts release/macos/scripts peptdeep.pkg
-productbuild --distribution release/macos/distribution.xml --resources Resources --package-path peptdeep.pkg dist/${BUILD_NAME}.pkg
+pkgbuild --root dist/${PACKAGE_NAME} --identifier de.mpg.biochem.${PACKAGE_NAME}.app --version 1.2.1 --install-location /Applications/${PACKAGE_NAME}.app --scripts release/macos/scripts ${PACKAGE_NAME}.pkg
+productbuild --distribution release/macos/distribution.xml --resources Resources --package-path ${PACKAGE_NAME}.pkg dist/${BUILD_NAME}.pkg

release/windows/build_backend.ps1 → release/windows/build_installer_windows.ps1

@@ -1,3 +1,6 @@
+# Build the installer for Windows.
+# This script is intended to be run from the root of the repository.
+
 Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./build
 Remove-Item -Recurse -Force -ErrorAction SilentlyContinue ./dist
 
@@ -10,11 +13,6 @@ pip install "dist/peptdeep-1.2.1-py3-none-any.whl[stable]"
 pip install pyinstaller
 pyinstaller release/pyinstaller/peptdeep.spec -y
 
-
-echo ls dist:
-ls dist
-
-set +e
 # for some reason, the installer builder expects the files here
 mv dist/* release/windows/dist
 mkdir release/windows/dist/peptdeep