Merge branch 'aiidateam:master' into mlip

.github/workflows/dev-ci.yml

@@ -0,0 +1,53 @@
+name: CI
+
+# For development, use the following instead:
+on: [pull_request]
+
+
+# https://docs.github.com/en/actions/using-jobs/using-concurrency
+concurrency:
+    # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+  test-utils:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Repo ⚡️
+      uses: actions/checkout@v4
+    - name: Create dev environment
+      uses: ./.github/actions/create-dev-env
+    - name: Run tests
+      run: pytest tests/
+
+  test-webpage-build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    timeout-minutes: 30
+    steps:
+    # This is a CI job that checks if the webpage can be built
+    # We use the plugins metadata from caching since we don't want to
+    # fetch it twice and it is not essential for this job to have
+    # the latest generated metadata
+    - name: Checkout Repo ⚡️
+      uses: actions/checkout@v4
+
+    - name: Create dev environment
+      uses: ./.github/actions/create-dev-env
+
+    - name: Generate metadata
+      uses: ./.github/actions/generate-metadata
+      with:
+        gh_token: ${{ secrets.GITHUB_TOKEN }}
+        cache: true
+
+    - uses: actions/setup-node@v3
+      with:
+        node-version: '18.x'
+    - name: Install npm dependencies and build
+      run: |
+        npm install
+        npm run build
+      working-directory: ./aiida-registry-app

.github/workflows/ci.yml → .github/workflows/plugin-ci.yml

@@ -32,21 +32,6 @@ jobs:
       - uses: suzuki-shunsuke/[email protected]
         id: pr
 
-  pre-commit:
-    runs-on: ubuntu-latest
-    needs:
-      - get-pr
-    steps:
-    - name: Checkout Repo ⚡️
-      uses: actions/checkout@v4
-      with:
-        ref: ${{needs.get-pr.outputs.merge_commit_sha}}
-    - name: Create dev environment
-      uses: ./.github/actions/create-dev-env
-    - name: Run pre-commit
-      run:
-        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
-
   test-utils:
     runs-on: ubuntu-latest
     needs:

.pre-commit-config.yaml

@@ -3,29 +3,18 @@
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
     - id: end-of-file-fixer
     - id: fix-encoding-pragma
     - id: mixed-line-ending
     - id: trailing-whitespace
     - id: check-json
 
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.3.3
   hooks:
-  - id: isort
-    args: ["--profile", "black", "--filter-files"]
-
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-    - id: black
-
-- repo: local
-  hooks:
-    - id: pylint
-      name: pylint
-      entry: pylint
-      types: [python]
-      language: system
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+      - id: ruff-format

aiida_registry/__init__.py

@@ -2,9 +2,9 @@
 # -*- coding: utf-8 -*-
 """Configuration of plugin registry.
 
- * paths to files & folders
- * info on entry points
- * info on development status
+* paths to files & folders
+* info on entry points
+* info on development status
 """
 
 import os
@@ -134,7 +134,7 @@
     "Development Status :: 7 - Inactive": "inactive",
 }
 
-status_no_pip_url_allowed = {"planning", "pre-alpha", "alpha"}
+status_no_pip_url_required = {"planning", "pre-alpha", "alpha"}
 
 ## dictionary of human-readable entrypointtypes
 entrypointtypes = {k: v["longname"] for k, v in entrypoint_metainfo.items()}

aiida_registry/cli.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """CLI for AiiDA registry."""
+
 import click
 
 from aiida_registry.make_pages import make_pages

aiida_registry/fetch_metadata.py

@@ -4,6 +4,7 @@
 Data is primarily sourced from PyPI,
 with a fallback to the repository build file (setup.json, setup.cfg, pyproject.toml).
 """
+
 import json
 
 # pylint: disable=consider-using-f-string
@@ -134,9 +135,7 @@ def get_git_commits_count(repo_name):
     return int(commits_count)
 
 
-def complete_plugin_data(
-    plugin_data: dict, fetch_pypi=True, fetch_pypi_wheel=True
-):  # pylint: disable=too-many-branches,too-many-statements
+def complete_plugin_data(plugin_data: dict, fetch_pypi=True, fetch_pypi_wheel=True):  # pylint: disable=too-many-branches,too-many-statements
     """Update plugin data dictionary.
 
      * add metadata, aiida_version and entrypoints from plugin_info

aiida_registry/make_pages.py

@@ -18,7 +18,7 @@
     entrypointtypes,
     main_entrypoints,
     status_dict,
-    status_no_pip_url_allowed,
+    status_no_pip_url_required,
 )
 
 entrypoints_count = defaultdict(list)
@@ -120,11 +120,10 @@ def global_summary():
 
 
 def get_pip_install_cmd(plugin_data):
-    if (
-        "pip_url" not in plugin_data
-        and plugin_data["development_status"] in status_no_pip_url_allowed
-    ):
-        return "See source code repository."
+    if "pip_url" not in plugin_data:
+        if plugin_data["development_status"] in status_no_pip_url_required:
+            return "See source code repository."
+        return "Missing, see source code repository"
 
     pip_url = plugin_data["pip_url"]
 
@@ -159,9 +158,9 @@ def make_pages(package=None):
     all_data["plugins"] = plugins_metadata
     all_data["globalsummary"] = global_summary()
     all_data["status_dict"] = status_dict
-    all_data[
-        "entrypointtypes"
-    ] = entrypointtypes  # add a static entrypointtypes dictionary
+    all_data["entrypointtypes"] = (
+        entrypointtypes  # add a static entrypointtypes dictionary
+    )
 
     with open(PLUGINS_METADATA, "w", encoding="utf8") as handle:
         json.dump(all_data, handle, indent=2)

aiida_registry/parse_build_file.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Module for parsing package build files."""
+
 import ast
 import json
 from configparser import ConfigParser
@@ -261,9 +262,9 @@ def parse_setup_cfg(content: str, ep_only=False) -> SourceData:
     }
     if config.has_option("metadata", "classifiers"):
         infos["metadata"]["classifiers"] = [
-            l.strip()
-            for l in config.get("metadata", "classifiers").splitlines()
-            if l.strip() and not l.strip().startswith("#")
+            line.strip()
+            for line in config.get("metadata", "classifiers").splitlines()
+            if line.strip() and not line.strip().startswith("#")
         ]
 
     return SourceData(**infos)

aiida_registry/parse_pypi.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Parse metadata from PyPI."""
+
 # pylint: disable=too-many-ancestors,too-many-locals,too-many-branches
 import configparser
 import json

aiida_registry/test_install.py

@@ -241,9 +241,9 @@ def test_install_all(container_image):
                     for key, _ in data["plugins"][plugin_name]["entry_points"][
                         ep_group
                     ].items():
-                        data["plugins"][plugin_name]["entry_points"][ep_group][
-                            key
-                        ] = process_metadata[ep_group][key]
+                        data["plugins"][plugin_name]["entry_points"][ep_group][key] = (
+                            process_metadata[ep_group][key]
+                        )
             except KeyError:
                 continue
 

aiida_registry/utils.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Utility functions."""
+
 import os
 import traceback
 

bin/analyze_entrypoints.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-""""
+"""
 Fetch information about plugins and print it in a human-readable format.
 
 Adapted from `aiida.cmdline.commands.cmd_plugin`.
 
 Note: This script should run inside the aiida-core docker container without requiring additional dependencies.
 """
+
 # pylint: disable=missing-class-docstring,import-outside-toplevel
 import inspect
 import json

plugins.yaml

@@ -16,10 +16,10 @@ aiida-alloy:
   pip_url: git+https://github.com/DanielMarchand/aiida-alloy
   plugin_info: https://raw.githubusercontent.com/DanielMarchand/aiida-alloy/master/setup.json
 aiida-amber:
-  code_home: https://github.com/PSDI-Biomolecular-team/aiida-amber
+  code_home: https://github.com/PSDI-UK/aiida-amber
   entry_point_prefix: amber
-  pip_url: git+https://github.com/PSDI-Biomolecular-team/aiida-amber
-  plugin_info: https://raw.githubusercontent.com/PSDI-Biomolecular-team/aiida-amber/main/pyproject.toml
+  pip_url: git+https://github.com/PSDI-UK/aiida-amber
+  plugin_info: https://raw.githubusercontent.com/PSDI-UK/aiida-amber/main/pyproject.toml
 aiida-ase:
   code_home: https://github.com/aiidateam/aiida-ase
   documentation_url: https://aiida-ase.readthedocs.io/
@@ -188,11 +188,11 @@ aiida-graphql:
   pip_url: aiida-graphql
   plugin_info: https://raw.github.com/dev-zero/aiida-graphql/develop/pyproject.toml
 aiida-gromacs:
-  code_home: https://github.com/PSDI-Biomolecular-team/aiida-gromacs
+  code_home: https://github.com/PSDI-UK/aiida-gromacs
   documentation_url: https://aiida-gromacs.readthedocs.io/
   entry_point_prefix: gromacs
   pip_url: aiida-gromacs
-  plugin_info: https://raw.githubusercontent.com/PSDI-Biomolecular-team/aiida-gromacs/master/pyproject.toml
+  plugin_info: https://raw.githubusercontent.com/PSDI-UK/aiida-gromacs/master/pyproject.toml
 aiida-gudhi:
   code_home: https://github.com/ltalirz/aiida-gudhi
   development_status: beta

pyproject.toml

@@ -37,7 +37,6 @@ dependencies = [
     "markupsafe~=2.0.1",
     # dev dependencies
     "pre-commit~=2.2",
-    "pylint~=2.16.1",
     "pytest~=6.2.2",
     "pytest-regressions~=2.5.0",
 ]

tests/test_basic.py

@@ -11,6 +11,7 @@
  * poetry: pyproject.toml
  * flit: pyproject.toml
 """
+
 from pathlib import Path
 
 import yaml