Merged.

ops/docker-compose/matomo/reverse-proxy.apach2

 RewriteRule "^/fairdi/stat/stat.js$" "http://<the ip address>:8001/piwik.js" [p]
-RewriteRule "^/fairdi/stat/stat.php$" "http://<the ip address>:8001/piwik.php" [p]
+RewriteRule "^/fairdi/stat/stat$" "http://<the ip address>:8001/piwik.php" [p]
 ProxyPass /fairdi/stat http://<the ip address>:8001
 ProxyPassReverse /fairdi/stat http://<the ip address>:8001
 <Proxy http://<the ip address>:8001/app>

ops/docker-compose/matomo/reverse-proxy.nginx

 location /fairdi/stat {
     rewrite ^(.*)/stat.js$ $1/piwik.js;
-    rewrite ^(.*)/stat.php$ $1/piwik.php;
+    rewrite ^(.*)/stat$ $1/piwik.php;
     rewrite ^/fairdi/stat/(.*)$ /$1 break;
     proxy_set_header X-Forwarded-Uri /fairdi/stat;
     proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;

ops/helm/nomad/templates/api-deployment.yaml

@@ -92,8 +92,14 @@ data:
       "keycloakClientId": "{{ .Values.keycloak.guiClientId }}",
       "matomoSiteId": {{ .Values.gui.matomoSiteId }},
       "matomoUrl": "{{ .Values.gui.matomoUrl }}",
-      "sendTrackingData": {{ .Values.gui.sendTrackingData }},
-      "debug": {{ .Values.gui.debug }}
+      "matomoEnabled": {{ .Values.gui.matomoEnabled }},
+      "debug": {{ .Values.gui.debug }},
+      "version": {
+        "label": "{{ .Values.version.label }}",
+        "isBeta": {{ .Values.version.isBeta }},
+        "usesBetaData": {{ .Values.version.usesBetaData }},
+        "officialUrl": "{{ .Values.version.officialUrl }}"
+      }
     };
 ---
 apiVersion: v1

ops/helm/nomad/templates/nomad-configmap.yml

@@ -9,6 +9,7 @@ metadata:
     app.kubernetes.io/managed-by: {{ .Release.Service }}
 data:
   nomad.yaml: |
+    meta:
       release: "{{ .Release.Name }}"
     reprocess_unmatched: {{ .Values.reprocess_unmatched }}
     fs:

ops/helm/nomad/values.yaml

 ## Default values for nomad@FAIRDI
+version:
+  label: "0.8.1"
+  isBeta: false
+  usesBetaData: false
+  officialUrl: "https://repository.nomad-coe.eu/app/gui"
 
 ## Everything concerning the container images to be used
 image:
@@ -68,11 +73,11 @@ gui:
   ## This variable is used in the GUI to show or hide additional information
   debug: false
   ## URL for matomo(piwik) user tracking
-  matomoUrl: 'http://nowhere.no'
+  matomoUrl: 'https://repository.nomad-coe.eu/fairdi/stat'
   ## site id for matomo(piwik) user tracking
   matomoSiteId: 1
   ## send matomo(piwik) user tracking data
-  sendTrackingData: false
+  matomoEnabled: false
 
 ## Everything concerning the nginx that serves the gui, proxies the api
 #  It is run via NodePort service

requirements.txt

@@ -35,6 +35,7 @@ parmed==3.0.0
 mdtraj
 mdanalysis
 nomadcore
+nomadDOSfingerprints
 
 # [infrastructure]
 optimade

setup.py

@@ -25,7 +25,7 @@ import fastentrypoints  # pylint: disable=unused-import
 '''
 This setup.py works differently for creating a distribution than installing for
 development. The idea is that for distributions, we compile the requirements, packages, and
-data files from all dependencies and install everything under one package called 'nomad'.
+data files from all dependencies and install everything under one package called 'nomad-lab'.
 For development we install each dependency as its own project. This is mainly due to
 pip's limitation of not being able to install from multiple source folders in develop
 mode.
@@ -43,6 +43,7 @@ requirements.txt where specific comments are used to assign an extra to requirem
 ignore_extra_requires = ['optimade']
 ''' Dependencies where the extra_requires should not be added '''
 
+
 def parse_requirements():
     '''
     Parses the requirements.txt file to extras install and extra requirements.
@@ -179,7 +180,7 @@ def compile_dependency_setup_kwargs(paths, **kwargs):
 
         # 3. requires
         local_install_requires = set()
-        if not name in ignore_extra_requires:
+        if name not in ignore_extra_requires:
             for extra_require in local_kwargs.get('extras_require', {}).values():
                 for require in extra_require:
                     local_install_requires.add(require)
@@ -234,17 +235,26 @@ def setup_kwargs():
     from nomad import config
 
     install_requires, extras_require = parse_requirements()
+    with open("README.md", "r") as fh:
+        long_description = fh.read()
 
     return dict(
         name='nomad-lab',
+        author='NOMAD Laboratory',
+        author_email='markus.scheidgen@physik.hu-berlin.de',
+        url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR',
         version=config.meta.version,
+        license='APACHE 2.0',
         description='The NOvel MAterials Discovery (NOMAD) Python package',
+        long_description=long_description,
+        long_description_content_type="text/markdown",
         package_dir={'': './'},
         packages=['nomad.%s' % pkg for pkg in find_packages('./nomad')] + ['nomad'],
         setup_requires=['pip', 'setuptools', 'wheel', 'fastentrypoints', 'numpy', 'pyyaml'],
         install_requires=install_requires,
         extras_require=extras_require,
         include_package_data=True,
+        python_requires='>=3.6',
         entry_points='''
             [console_scripts]
             nomad=nomad.cli:run_cli

setup.sh

@@ -3,7 +3,6 @@
 set -e
 
 git submodule sync
-git submodule update --init
-pip install -r requirements.txt
+git submodule update --init --jobs=4
 ./dependencies.sh -e
-pip install -e .
\ No newline at end of file
+pip install -e .[all]
\ No newline at end of file

tests/app/test_optimade.py

@@ -224,13 +224,17 @@ def test_base_info_endpoint(api):
     assert data['data']['id'] == '/'
 
 
-def test_calculation_info_endpoint(api):
-    rv = api.get('/info/calculations')
+@pytest.mark.parametrize('entry_type', ['calculations', 'structures'])
+def test_entry_info_endpoint(api, entry_type):
+    rv = api.get('/info/%s' % entry_type)
     assert rv.status_code == 200
     data = json.loads(rv.data)
     for key in ['description', 'properties', 'formats', 'output_fields_by_format']:
         assert key in data['data']
 
+    assert '_nmd_atoms' in data['data']['properties']
+    assert '_nmd_dft_system' in data['data']['properties']
+
 
 # TODO the implementation should be fixed to return actual references first
 # def test_references_endpoint(api, example_structures):
@@ -277,3 +281,15 @@ def test_structure_endpoint(api, example_structures):
     assert attr is not None
     assert attr.get('elements') == ['H', 'O']
     assert len(attr.get('dimension_types')) == 3
+
+
+def test_nmd_properties(api, example_structures):
+    rv = api.get('/structures/%s' % 'test_calc_id_1?request_fields=_nmd_atoms,_nmd_dft_system,_nmd_doesnotexist')
+    assert rv.status_code == 200
+    data = json.loads(rv.data)
+    assert data.get('data') is not None
+    attr = data['data'].get('attributes')
+    assert attr is not None
+    assert attr.get('_nmd_atoms') == ['H', 'O']
+    assert '_nmd_dft_system' in attr
+    assert '_nmd_doesnotexist' not in attr

tests/normalizing/test_dos.py

@@ -17,6 +17,8 @@ import numpy as np
 from tests.test_parsing import parse_file
 from tests.normalizing.conftest import run_normalize
 
+from nomad_dos_fingerprints import DOSFingerprint, tanimoto_similarity
+
 
 vasp_parser_dos = (
     'parsers/vasp', 'tests/data/parsers/vasp/vasp_dos.xml')
@@ -36,3 +38,14 @@ def test_dos_normalizer():
     expected = 1.7362195274239454e+47
     # Compare floats properly with numpy (delta tolerance involved)
     assert np.allclose(last_value, expected)
+
+    # Check if DOS fingerprint was created
+    backend_dos_fingerprint = backend['section_dos_fingerprint'][0]
+    dos_fingerprint = DOSFingerprint().from_dict(dict(
+        bins=backend_dos_fingerprint.bins,
+        indices=backend_dos_fingerprint.indices,
+        grid_id=backend_dos_fingerprint.grid_id,
+        stepsize=backend_dos_fingerprint.stepsize,
+        filling_factor=backend_dos_fingerprint.filling_factor))
+
+    assert tanimoto_similarity(dos_fingerprint, dos_fingerprint) == 1