nomad-parser-plugins-workflow 1.1.7__tar.gz → 1.1.9__tar.gz

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/.github/workflows/python-actions.yaml

@@ -1,29 +1,53 @@
 name: install-and-test-workflow
+
 on: [push]
+
+env:
+  REGISTRY: ghcr.io
+  UV_VERSION: 0.7
+  PYTHON_VERSION: 3.12
+
+permissions:
+  contents: write
+  packages: write
+  attestations: write
+  id-token: write
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+
+    - uses: docker/login-action@v3
       with:
-        python-version: 3.9
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Start containers
+      run: |
+        docker compose up -d --quiet-pull
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        version: ${{ env.UV_VERSION }}
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
     - name: Install dependencies
       run: |
-        pip install --upgrade pip
-        pip install '.[tests]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-        # we need the latest nomad version for testing
-        # pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
-        pip install coverage coveralls
-        pip install types-PyYAML
+        uv sync --all-extras
+
     - name: mypy
       run: |
-        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional *parsers tests
+        uv run python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional *parsers tests
     - name: Test with pytest
-      if: success() || failure()
       run: |
-        python -m coverage run -m pytest -sv tests
+        uv run python -m coverage run -m pytest -sv tests
     - name: Submit to coveralls
       continue-on-error: true
       env:

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-parser-plugins-workflow
-Version: 1.1.7
+Version: 1.1.9
 Summary: Collection of NOMAD parsers for workflow engines.
 Author: The NOMAD Authors
 License: 
@@ -209,13 +209,13 @@ License:
 Project-URL: homepage, https://github.com/nomad-coe/workflow-parsers
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: nomad-lab>=1.3.13
+Requires-Dist: nomad-lab[infrastructure]>=1.3.13
 Requires-Dist: nomad-schema-plugin-simulation-workflow>=1.0.1
 Requires-Dist: nomad-schema-plugin-run>=1.0.1
 Requires-Dist: lxml>=5.2
 Requires-Dist: asr==0.4.1
 Requires-Dist: xarray>=0.20.1
-Requires-Dist: phonopy>=2.35
+Requires-Dist: phonopy<=2.38,>=2.35
 Requires-Dist: h5py>=3.11.0
 Requires-Dist: pydantic>=1.10.8
 Provides-Extra: tests
@@ -226,6 +226,9 @@ Requires-Dist: pytest-timeout>=1.4.2; extra == "tests"
 Requires-Dist: pytest-cov>=2.7.1; extra == "tests"
 Requires-Dist: ruff>=0.6; extra == "tests"
 Requires-Dist: typing-extensions>=4.12; extra == "tests"
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: coveralls; extra == "tests"
+Requires-Dist: types-PyYAML; extra == "tests"
 Dynamic: license-file
 
 [![DOI](https://zenodo.org/badge/461070260.svg)](https://zenodo.org/badge/latestdoi/461070260)

nomad_parser_plugins_workflow-1.1.9/docker-compose.yml

@@ -0,0 +1,107 @@
+name: workflow-parsers-test
+services:
+  # broker for celery
+  rabbitmq:
+    restart: unless-stopped
+    image: rabbitmq:3.11.5
+    container_name: rabbitmq
+    environment:
+      - RABBITMQ_ERLANG_COOKIE=SWQOKODSQALRPCLNMEQG
+      - RABBITMQ_DEFAULT_USER=rabbitmq
+      - RABBITMQ_DEFAULT_PASS=rabbitmq
+      - RABBITMQ_DEFAULT_VHOST=/
+    ports:
+      - "5672:5672"
+    volumes:
+      - rabbitmq:/var/lib/rabbitmq
+    healthcheck:
+      test: ["CMD", "rabbitmq-diagnostics", "--silent", "--quiet", "ping"]
+      interval: 10s
+      timeout: 10s
+      retries: 30
+      start_period: 10s
+
+  # the search engine
+  elastic:
+    restart: unless-stopped
+    image: docker.elastic.co/elasticsearch/elasticsearch:7.17.24
+    container_name: elastic
+    environment:
+      - ES_JAVA_OPTS=-Xms512m -Xmx512m
+      - discovery.type=single-node
+    ports:
+      - "9200:9200"
+    volumes:
+      - elastic:/usr/share/elasticsearch/data
+    healthcheck:
+      test:
+        - "CMD"
+        - "curl"
+        - "--fail"
+        - "--silent"
+        - "http://elastic:9200/_cat/health"
+      interval: 10s
+      timeout: 10s
+      retries: 30
+      start_period: 60s
+
+  # the user data db
+  mongo:
+    restart: unless-stopped
+    image: mongo:5.0.6
+    container_name: mongo
+    environment:
+      - MONGO_DATA_DIR=/data/db
+      - MONGO_LOG_DIR=/dev/null
+    ports:
+      - "27017:27017"
+    volumes:
+      - mongo:/data/db
+      - ./.volumes/mongo:/backup
+    command: mongod --logpath=/dev/null # --quiet
+    healthcheck:
+      test:
+        - "CMD"
+        - "mongo"
+        - "mongo:27017/test"
+        - "--quiet"
+        - "--eval"
+        - "'db.runCommand({ping:1}).ok'"
+      interval: 10s
+      timeout: 10s
+      retries: 30
+      start_period: 10s
+
+  keycloak:
+    image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-test-keycloak:v1.0
+    platform: linux/amd64
+    container_name: keycloak
+    environment:
+      # clashes with imported admin user in master realm
+      # - KC_BOOTSTRAP_ADMIN_USERNAME=admin
+      # - KC_BOOTSTRAP_ADMIN_PASSWORD=password
+      - KC_LOG_LEVEL=info
+      - KC_HOSTNAME_DEBUG=true
+      - KC_METRICS_ENABLED=true
+      - KC_HEALTH_ENABLED=true
+    command:
+      - start-dev
+      - --import-realm
+      - --verbose
+    ports:
+      - 8080:8080
+      - 9000:9000
+    healthcheck:
+      interval: 10s
+      timeout: 10s
+      retries: 5
+      start_period: 30s
+      test: bash /opt/keycloak/bin/healthcheck_keycloak.sh || exit 1
+
+volumes:
+  mongo:
+    name: "mongo"
+  elastic:
+    name: "elastic"
+  rabbitmq:
+    name: "rabbitmq"

nomad_parser_plugins_workflow-1.1.9/nomad.yaml

@@ -0,0 +1,12 @@
+keycloak:
+  server_url: 'http://localhost:8080/'
+  public_server_url: 'http://localhost:8080/'
+  realm_name: 'fairdi_nomad_test'
+  username: 'admin'
+  password: 'password'
+client:
+  url: 'http://localhost:8000/fairdi/nomad/latest/api'
+  user: 'admin'
+  password: 'password'
+fs:
+  staging: '/tmp/volumes/fs/staging'

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/nomad_parser_plugins_workflow.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nomad-parser-plugins-workflow
-Version: 1.1.7
+Version: 1.1.9
 Summary: Collection of NOMAD parsers for workflow engines.
 Author: The NOMAD Authors
 License: 
@@ -209,13 +209,13 @@ License:
 Project-URL: homepage, https://github.com/nomad-coe/workflow-parsers
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: nomad-lab>=1.3.13
+Requires-Dist: nomad-lab[infrastructure]>=1.3.13
 Requires-Dist: nomad-schema-plugin-simulation-workflow>=1.0.1
 Requires-Dist: nomad-schema-plugin-run>=1.0.1
 Requires-Dist: lxml>=5.2
 Requires-Dist: asr==0.4.1
 Requires-Dist: xarray>=0.20.1
-Requires-Dist: phonopy>=2.35
+Requires-Dist: phonopy<=2.38,>=2.35
 Requires-Dist: h5py>=3.11.0
 Requires-Dist: pydantic>=1.10.8
 Provides-Extra: tests
@@ -226,6 +226,9 @@ Requires-Dist: pytest-timeout>=1.4.2; extra == "tests"
 Requires-Dist: pytest-cov>=2.7.1; extra == "tests"
 Requires-Dist: ruff>=0.6; extra == "tests"
 Requires-Dist: typing-extensions>=4.12; extra == "tests"
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: coveralls; extra == "tests"
+Requires-Dist: types-PyYAML; extra == "tests"
 Dynamic: license-file
 
 [![DOI](https://zenodo.org/badge/461070260.svg)](https://zenodo.org/badge/latestdoi/461070260)

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/nomad_parser_plugins_workflow.egg-info/SOURCES.txt

@@ -3,6 +3,8 @@ CITATION.cff
 LICENSE
 MANIFEST.in
 README.md
+docker-compose.yml
+nomad.yaml
 pyproject.toml
 .github/workflows/publish.yml
 .github/workflows/python-actions.yaml
@@ -19,6 +21,7 @@ tests/test_asrparser.py
 tests/test_atomateparser.py
 tests/test_elasticparser.py
 tests/test_fhivibesparser.py
+tests/test_files.py
 tests/test_lobsterparser.py
 tests/test_phonopyparser.py
 tests/test_quantum_espresso_epw.py
@@ -883,6 +886,7 @@ tests/data/lobster/Fe/RMSp.lobster
 tests/data/lobster/Fe/bandOverlaps.lobster
 tests/data/lobster/Fe/lobsterin
 tests/data/lobster/Fe/lobsterout
+tests/data/lobster/Fe/vasprun.archive.json
 tests/data/lobster/Fe/vasprun.xml
 tests/data/lobster/HfV2/DOSCAR.lobster
 tests/data/lobster/HfV2/ICOHPLIST.lobster

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/nomad_parser_plugins_workflow.egg-info/requires.txt

@@ -1,10 +1,10 @@
-nomad-lab>=1.3.13
+nomad-lab[infrastructure]>=1.3.13
 nomad-schema-plugin-simulation-workflow>=1.0.1
 nomad-schema-plugin-run>=1.0.1
 lxml>=5.2
 asr==0.4.1
 xarray>=0.20.1
-phonopy>=2.35
+phonopy<=2.38,>=2.35
 h5py>=3.11.0
 pydantic>=1.10.8
 
@@ -16,3 +16,6 @@ pytest-timeout>=1.4.2
 pytest-cov>=2.7.1
 ruff>=0.6
 typing-extensions>=4.12
+coverage
+coveralls
+types-PyYAML

{nomad_parser_plugins_workflow-1.1.7 → nomad_parser_plugins_workflow-1.1.9}/pyproject.toml

@@ -10,13 +10,13 @@ readme = "README.md"
 authors = [{ name = "The NOMAD Authors" }]
 license = { file = "LICENSE" }
 dependencies = [
-    "nomad-lab>=1.3.13",
+    "nomad-lab[infrastructure]>=1.3.13",
     "nomad-schema-plugin-simulation-workflow>=1.0.1",
     "nomad-schema-plugin-run>=1.0.1",
     "lxml>=5.2",
     "asr==0.4.1",
     "xarray>=0.20.1",
-    "phonopy>=2.35",
+    "phonopy>=2.35,<=2.38",
     "h5py>=3.11.0",
     "pydantic>=1.10.8",
 ]
@@ -24,6 +24,11 @@ dependencies = [
 [project.urls]
 homepage = "https://github.com/nomad-coe/workflow-parsers"
 
+[tool.uv]
+extra-index-url = [
+  "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple",
+]
+
 [project.optional-dependencies]
 tests = [
     "astroid==2.11.7",
@@ -33,6 +38,9 @@ tests = [
     'pytest-cov>=2.7.1',
     'ruff>=0.6',
     'typing-extensions>=4.12',
+    'coverage',
+    'coveralls',
+    'types-PyYAML',
 ]
 
 [tool.ruff]

nomad_parser_plugins_workflow-1.1.9/tests/conftest.py

@@ -0,0 +1,109 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD.
+# See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+import os
+import pytest
+import json
+
+from nomad.datamodel import EntryArchive, EntryMetadata
+
+from nomad.utils.exampledata import ExampleData
+from nomad import infrastructure
+from nomad.datamodel.context import ServerContext
+from nomad.utils import create_uuid
+
+
+# Set up pytest to pass control to the debugger on an exception.
+if os.getenv('_PYTEST_RAISE', '0') != '0':
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_exception_interact(call):
+        raise call.excinfo.value
+
+    @pytest.hookimpl(tryfirst=True)
+    def pytest_internalerror(excinfo):
+        raise excinfo.value
+
+
+@pytest.fixture(scope='session')
+def upload_id():
+    return 'test_upload'
+
+
+@pytest.fixture(scope='session')
+def main_author():
+    from nomad.config import config  # noqa
+
+    return infrastructure.user_management.get_user(username=config.client.user)
+
+
+@pytest.fixture(scope='session')
+def auth():
+    from nomad.client import Auth  # noqa
+    from nomad.config import config  # noqa
+
+    return Auth(user=config.client.user, password=config.client.password, from_api=True)
+
+
+@pytest.fixture(scope='session')
+def upload_files():
+    # add pre-parsed json achive files only to avoid loading parsers
+    return {'tests/data/lobster/Fe/vasprun.archive.json': 'parsers/vasp'}
+
+
+@pytest.fixture(scope='session')
+def upload_archives(upload_files, main_author, upload_id):
+    archives = []
+    for mainfile, parser in upload_files.items():
+        entry_id = create_uuid()
+        archive = EntryArchive(metadata=EntryMetadata())
+        with open(mainfile) as f:
+            archive.m_update_from_dict(json.load(f))
+        archive.metadata.main_author = main_author
+        archive.metadata.parser_name = parser
+        archive.metadata.upload_id = upload_id
+        archive.metadata.entry_id = entry_id
+        archive.metadata.mainfile = mainfile
+        archives.append(archive)
+    return archives
+
+
+@pytest.fixture(scope='session')
+def upload_data(upload_id, main_author, upload_archives):
+
+    infrastructure.setup_mongo()
+    infrastructure.setup_elastic()
+
+    data = ExampleData(main_author=main_author)
+    data.create_upload(upload_id=upload_id)
+    for archive in upload_archives:
+        archive = data.create_entry(
+            entry_archive=archive,
+            entry_id=archive.metadata.entry_id,
+            upload_id=upload_id,
+            mainfile=archive.metadata.mainfile,
+        )
+    data.save()
+
+
+@pytest.fixture(scope='session')
+def context(upload_data, upload_id, main_author):
+    from nomad.app.v1.routers.uploads import get_upload_with_read_access  # noqa
+
+    upload = get_upload_with_read_access(upload_id, main_author)
+    return ServerContext(upload)