Modernize packaging

.github/workflows/codeql-analysis.yml

@@ -39,11 +39,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v5
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v4
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -54,7 +54,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
+      uses: github/codeql-action/autobuild@v4
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -68,4 +68,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v4

.github/workflows/testing.yml

@@ -34,9 +34,10 @@ jobs:
       - name: Install dependencies
         run: |
           python${{ matrix.python-version }} -m pip install --upgrade "pip<25.3" build pip-tools pre-commit
-          python${{ matrix.python-version }} -m piptools compile --extra dev -o requirements.txt mpcontribs-client/setup.py mpcontribs-api/setup.py
+          python${{ matrix.python-version }} -m piptools compile --extra dev -o requirements.txt mpcontribs-client/pyproject.toml mpcontribs-api/pyproject.toml
           python${{ matrix.python-version }} -m pip install -r requirements.txt
-          cd mpcontribs-api && python${{ matrix.python-version }} -m pip install --no-deps .
+          cd mpcontribs-api
+          python${{ matrix.python-version }} -m pip install --no-deps .
       - name: Set SSL_CERT_FILE (Linux)
         if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
         run: |
@@ -50,7 +51,6 @@ jobs:
 
       - name: Run pre-commit
         run: |
-          python${{ matrix.python-version }} -m pip install pre-commit
           pre-commit install
           pre-commit run --all-files
 
@@ -61,9 +61,10 @@ jobs:
         shell: bash
         run: |
           cd mpcontribs-client
+          python${{ matrix.python-version }} -m pip install --no-deps .
           python${{ matrix.python-version }} -m flake8 --max-line-length 100
           python${{ matrix.python-version }} -m pycodestyle --max-line-length 100 .
-          python${{ matrix.python-version }} -m pytest -v -s --cov=mpcontribs/client --cov-report=term-missing --cov-report=xml --ignore=bravado
+          python${{ matrix.python-version }} -m pytest -n auto -v -s --cov=mpcontribs/client --cov-report=term-missing --cov-report=xml --ignore=bravado
           python${{ matrix.python-version }} -m build --outdir ../dist
 
       - name: Install lux and test with pytest

.pre-commit-config.yaml

@@ -28,12 +28,6 @@ repos:
         files: cloudformation/.*\.(json|yml|yaml)$
         args: ["--ignore-checks=E3030,E3001,E3002,E3012"]
 
-  #- repo: https://gitlab.com/pycqa/flake8
-  #  rev: 3.7.9
-  #  hooks:
-  #      - id: flake8
-  #        args: [--max-line-length=99]
-
   - repo: https://github.com/psf/black
     rev: 25.9.0
     hooks:
@@ -47,3 +41,8 @@ repos:
           - --drop-empty-cells
           - --strip-init-cells
           - --extra-keys=metadata.kernelspec
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.1
+    hooks:
+      - id: pyupgrade

mpcontribs-api/Dockerfile

@@ -7,7 +7,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends gcc git g++ lib
 ENV PIP_FLAGS "--no-cache-dir --compile"
 COPY requirements/deployment.txt ./requirements.txt
 RUN pip install $PIP_FLAGS -r requirements.txt
-COPY setup.py .
+COPY pyproject.toml .
 COPY mpcontribs mpcontribs
 RUN pip install $PIP_FLAGS --no-deps .
 #ENV SETUPTOOLS_SCM_PRETEND_VERSION 0.0.0

mpcontribs-api/mpcontribs/api/__init__.py

@@ -8,6 +8,7 @@
 
 from email.message import EmailMessage
 from importlib import import_module
+from importlib.metadata import version
 from websocket import create_connection
 from flask import Flask, current_app, request, jsonify
 from flask_marshmallow import Marshmallow
@@ -26,6 +27,11 @@
 from notebook.gateway.managers import GatewayClient
 from requests.exceptions import ConnectionError, Timeout
 
+try:
+    __version__ = version("mpcontribs-api")
+except Exception:
+    # package is not installed
+    pass
 
 delimiter, max_depth = ".", 7  # = MAX_NESTING + 2 from client
 invalidChars = set(punctuation.replace("*", "").replace("|", "") + whitespace)

mpcontribs-api/mpcontribs/api/config.py

@@ -2,11 +2,10 @@
 """configuration module for MPContribs Flask API"""
 
 import os
-import datetime
 import json
 import gzip
 
-from semantic_version import Version
+from mpcontribs.api import __version__
 
 formulae_path = os.path.join(
     os.path.dirname(__file__), "contributions", "formulae.json.gz"
@@ -15,12 +14,6 @@
 with gzip.open(formulae_path) as f:
     FORMULAE = json.load(f)
 
-now = datetime.datetime.now()
-VERSION = str(Version(
-    major=now.year, minor=now.month, patch=now.day,
-    prerelease=(str(now.hour), str(now.minute))
-))
-
 JSON_ADD_STATUS = False
 SECRET_KEY = "super-secret"  # TODO in local prod config
 
@@ -65,7 +58,7 @@
         "title": "MPContribs API",
         "description": "Operations to contribute, update and retrieve materials data on Materials Project",
         "termsOfService": "https://materialsproject.org/terms",
-        "version": VERSION,
+        "version": __version__,
         "contact": {
             "name": "MPContribs",
             "email": "[email protected]",

mpcontribs-api/pyproject.toml

@@ -0,0 +1,103 @@
+[build-system]
+requires = ["setuptools>=80.0.0","setuptools-scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+root = ".."
+relative_to = "__file__"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["scripts","supervisord"]
+include = ["mpcontribs.api"]
+
+[project]
+name = "mpcontribs-api"
+dynamic = ["version"]
+requires-python = ">=3.11"
+description="API for community-contributed Materials Project data"
+license = {text = "MIT"}
+authors = [
+    {name = "Patrick Huck", email = "[email protected]"},
+    {name = "The Materials Project", email="[email protected]"},
+]
+dependencies = [
+    "numpy",
+    "apispec<6",
+    "asn1crypto",
+    "blinker",
+    "boltons",
+    "css-html-js-minify",
+    "dateparser",
+    "ddtrace",
+    "dnspython",
+    "filetype",
+    "flasgger-tschaume>=0.9.7",
+    "flask-compress",
+    "flask-marshmallow",
+    "flask-mongorest-mpcontribs>=3.2.1",
+    "Flask-RQ2",
+    "gunicorn[gevent]",
+    "jinja2",
+    "json2html",
+    "marshmallow<4",
+    "more-itertools",
+    "nbformat",
+    "notebook<7",
+    "pint>=0.24",
+    "psycopg2-binary",
+    "pymatgen",
+    "pyopenssl",
+    "python-snappy",
+    "rq<=2.3.2",  # see https://github.com/rq/Flask-RQ2/issues/620
+    "supervisor",
+    "setproctitle",
+    "uncertainties",
+    "websocket_client",
+    "zstandard",
+]
+
+[project.urls]
+Homepage = "https://github.com/materialsproject/MPContribs"
+Documentation = "https://docs.materialsproject.org/services/mpcontribs"
+
+[project.optional-dependencies]
+dev = [
+    "flake8",
+    "pytest",
+    "pytest-flake8",
+    "pytest-pycodestyle",
+    "pytest-xdist",
+]
+all = [
+    "mpcontribs-api[dev]"
+]
+
+[tool.pytest]
+markers = [
+    "base: basic resource testing",
+    "extra: all extra views",
+]
+
+[tool.pycodestyle]
+count = true
+ignore = ["E121","E123","E126","E133","E226","E241","E242","E704","W503","W504","W505","E741","W605"]
+max-line-length = 120
+statistics = true
+exclude = ["flasgger","flask-mongorest"]
+
+[tool.flake8]
+exclude = [".git","__pycache__","tests","flasgger","flask-mongorest"]
+extend-ignore = ["E741",]
+max-line-length = 120
+
+[tool.pydocstyle]
+ignore = ["D105","D2","D4"]
+
+[tool.mypy]
+ignore_missing_imports = true
+namespace_packages = true
+python_version = 3.11