Adapt to latest standards

.bumpversion.toml

@@ -0,0 +1,64 @@
+[tool.bumpversion]
+current_version = "1.3.2-dev0"
+parse = """(?x)
+    (?P<major>0|[1-9]\\d*)\\.
+    (?P<minor>0|[1-9]\\d*)\\.
+    (?P<patch>0|[1-9]\\d*)
+    (?:
+        -                             # dash separator for pre-release section
+        (?P<pre_l>[a-zA-Z-]+)         # pre_l: pre-release label
+        (?P<pre_n>0|[1-9]\\d*)        # pre_n: pre-release version number
+    )?                                # pre-release section is optional
+"""
+serialize = [
+    "{major}.{minor}.{patch}-{pre_l}{pre_n}",
+    "{major}.{minor}.{patch}",
+]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[tool.bumpversion.parts.pre_l]
+# 'final' is just a dummy, but required to have the versioning compatible with the reusable alphashared workflow
+values = ["dev", "final"]
+optional_value = "final"
+
+[[tool.bumpversion.files]]
+filename = "./peptdeep/__init__.py"
+
+[[tool.bumpversion.files]]
+filename = "./docs/conf.py"
+
+[[tool.bumpversion.files]]
+filename = "./README.md"
+
+[[tool.bumpversion.files]]
+filename = "./release/linux/control"
+
+[[tool.bumpversion.files]]
+filename = "./release/linux/build_package_linux.sh"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/distribution.xml"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/Info.plist"
+
+[[tool.bumpversion.files]]
+filename = "./release/macos/build_package_macos.sh"
+
+[[tool.bumpversion.files]]
+filename = "./release/windows/peptdeep_innoinstaller.iss"

.github/workflows/branch-checks.yaml

@@ -14,12 +14,13 @@ jobs:
     - uses: pre-commit/action@v3.0.1
   # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
   run-tests-loose:
-    name: Test loose pip installation on ubuntu-latest
+    name: Test stable pip installation on ubuntu-latest
     strategy:
       matrix:
         os: [ubuntu-latest]
+        python-version: [3.9]
     uses: ./.github/workflows/_run_tests.yml
     with:
       python-version: ${{ matrix.python-version }}
       os: ${{ matrix.os }}
-      install-script: "loose_pip_install.sh"
+      install-script: pip_install.sh stable,tests

.github/workflows/bump_version.yml

@@ -0,0 +1,24 @@
+# Bump the version for releases
+# Requires a .bumpversion.toml file in the root of the repository
+name: Bump version
+
+on:
+  workflow_dispatch:
+    inputs:
+      bump_type:
+        description: 'Bump type'
+        required: true
+        default: 'patch'
+        type: choice
+        options:
+        - prerelease
+        - patch
+        - minor
+        - major
+
+jobs:
+  bump-version:
+    uses: MannLabs/alphashared/.github/workflows/bump_version.yml@v1
+    secrets: inherit
+    with:
+     bump_type: ${{inputs.bump_type}}

.github/workflows/code_review.yml

@@ -0,0 +1,24 @@
+# Create an automated AI code review that runs when a PR is labeled with 'code-review'
+name: code-review
+
+on:
+  pull_request:
+    types: [ labeled ]
+
+jobs:
+  get-code-review:
+    runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.labels.*.name, 'code-review') # || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
+    permissions:
+      contents: read
+      pull-requests: write
+    steps:
+      - uses: MannLabs/alphashared/actions/code-review@v1
+        continue-on-error: true
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+          CODE_REVIEW_PROMPT: ${{ secrets.CODE_REVIEW_PROMPT }}
+          CODE_REVIEW_SYSTEM_MESSAGE: ${{ secrets.CODE_REVIEW_SYSTEM_MESSAGE }}
+          GITHUB_EVENT_NUMBER: ${{ github.event.number }}
+          EXCLUDED_EXTENSIONS: "ipynb;js"

.github/workflows/pip_installation.yml

@@ -20,23 +20,25 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
+        python-version : [3.9]
         # macOS-latest and macos-latest-xlarge use Arm64, resulting in MPS OOM error in peptdeep
         # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: "stable_pip_install.sh"
+      install-script: pip_install.sh stable,tests
 
   loose_installation:
     name: Test loose pip installation on ${{ matrix.os }}
     # runs-on: ${{ matrix.os }} # See https://github.com/orgs/community/discussions/62320
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, windows-latest]
+        python-version : [3.9]
         # os: [ubuntu-latest, macos-13, macos-latest, windows-latest, macos-latest-xlarge]
     uses: ./.github/workflows/_run_tests.yml
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      install-script: "loose_pip_install.sh"
+      install-script: pip_install.sh loose,tests

.pre-commit-config.yaml

@@ -12,5 +12,3 @@ repos:
   hooks:
     - id: ruff-format
 #     - id: ruff
-
-exclude: .bumpversion.cfg

.readthedocs.yaml

@@ -22,4 +22,6 @@ sphinx:
 # # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements/requirements_development.txt
+    - method: pip
+      path: .
+    - requirements: requirements/requirements_docs.txt

README.md

@@ -112,10 +112,10 @@ The GUI of peptdeep is a completely stand-alone tool that requires no
 knowledge of Python or CLI tools. Click on one of the links below to
 download the latest release for:
 
-- [**Windows**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-windows-amd64.exe)
-- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-macos-darwin-x64.pkg)
-- [**macOS ARM**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-macos-darwin-arm64.pkg )
-- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.1-linux-x64.deb)
+- [**Windows**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.2-dev0-windows-amd64.exe)
+- [**macOS**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.2-dev0-macos-darwin-x64.pkg)
+- [**macOS ARM**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.2-dev0-macos-darwin-arm64.pkg )
+- [**Linux**](https://github.com/MannLabs/alphapeptdeep/releases/latest/download/peptdeep-1.3.2-dev0-linux-x64.deb)
 
 Older releases remain available on the [release
 page](https://github.com/MannLabs/alphapeptdeep/releases), but no

docs/conf.py

@@ -24,7 +24,7 @@
 copyright = "2022, Mann Labs, MPIB"
 author = "Mann Labs, MPIB"
 
-release = "1.3.1"
+release = "1.3.2-dev0"
 
 # -- General configuration ---------------------------------------------------
 

misc/pip_install.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+### Install the package with a given type in a defined conda environment with a define python version,
+### and call it to check if it works
+### example usage:
+### ./pip_install.sh stable my_env 3.9
+set -e -u
+
+INSTALL_TYPE=$1 # stable, loose, etc..
+ENV_NAME=${2:-peptdeep}
+PYTHON_VERSION=${3:-3.9}
+
+conda create -n $ENV_NAME python=$PYTHON_VERSION -y
+
+if [ "$INSTALL_TYPE" = "loose" ]; then
+  INSTALL_STRING=""
+else
+  INSTALL_STRING="[${INSTALL_TYPE}]"
+fi
+
+# print pip environment for reproducibility
+conda run -n $ENV_NAME --no-capture-output pip freeze
+
+# conda 'run' vs. 'activate', cf. https://stackoverflow.com/a/72395091
+conda run -n $ENV_NAME --no-capture-output pip install -e "../.$INSTALL_STRING"
+conda run -n $ENV_NAME --no-capture-output peptdeep -v

peptdeep/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.3.1"
+__version__ = "1.3.2-dev0"
 # This information is duplicated in pyproject.toml:
 __author_email__ = "jalew.zwf@qq.com"
 __github__ = "https://github.com/MannLabs/peptdeep"