Merge branch 'v0.5.3' into 'master'

v0.5.3

See merge request !56

README.md

@@ -76,6 +76,7 @@ Open [http://localhost:8888/html/setup.html](http://localhost:8888/html/setup.ht
 your browser.
 
 ## Change log
+Omitted versions are plain bugfix releases with only minor changes and fixes.
 
 ### v0.5.2
 - allows to download large files over longer time period

crystal @ 7863212e

-Subproject commit a824f0f72303bb8e39c8ae7ee710210edc287331
+Subproject commit 7863212e4bde3443fae8fbb57caf3b0d95fb28f3

nomad/cli/admin/uploads.py

@@ -77,16 +77,47 @@ def query_uploads(ctx, uploads):
 
 @uploads.command(help='List selected uploads')
 @click.argument('UPLOADS', nargs=-1)
+@click.option('-c', '--calculations', is_flag=True, help='Show details about calculations.')
+@click.option('--ids', is_flag=True, help='Only show a list of ids.')
+@click.option('--json', is_flag=True, help='Output a JSON array of ids.')
 @click.pass_context
-def ls(ctx, uploads):
+def ls(ctx, uploads, calculations, ids, json):
     _, uploads = query_uploads(ctx, uploads)
 
+    def row(upload):
+        row = [
+            upload.upload_id,
+            upload.name,
+            upload.user_id,
+            upload.process_status,
+            upload.tasks_status,
+            upload.published]
+
+        if calculations:
+            row += [
+                upload.total_calcs,
+                upload.failed_calcs,
+                upload.total_calcs - upload.processed_calcs]
+
+        return row
+
+    headers = ['id', 'name', 'user', 'process', 'tasks', 'published']
+    if calculations:
+        headers += ['calcs', 'failed', 'processing']
+
+    if ids:
+        for upload in uploads:
+            print(upload.upload_id)
+        return
+
+    if json:
+        print('[%s]' % ','.join(['"%s"' % upload.upload_id for upload in uploads]))
+        return
+
     print('%d uploads selected, showing no more than first 10' % uploads.count())
     print(tabulate(
-        [
-            [upload.upload_id, upload.name, upload.user_id, upload.process_status, upload.published]
-            for upload in uploads[:10]],
-        headers=['id', 'name', 'user', 'status', 'published']))
+        [row(upload) for upload in uploads[:10]],
+        headers=headers))
 
 
 @uploads.command(help='Change the owner of the upload and all its calcs.')

nomad/cli/client/statistics.py

@@ -200,7 +200,7 @@ def bar_plot(client, retrieve, metric1, metric2=None, title=None):
 @client.command(help='Generate various matplotlib charts')
 @click.option('--errors', is_flag=True, help='Two charts with relative and absolute parser/normalizer errors per code.')
 @click.option('--x-axis', type=str, help='Aggregation used for x-axis, values are "code" and "time".')
-@click.option('--y-axis', multiple=True, type=str, help='Metrics used for y-axis, values are "entries", "energies", "users".')
+@click.option('--y-axis', multiple=True, type=str, help='Metrics used for y-axis, values are "entries", "energies", "calculations", "users".')
 @click.option('--cumulate', is_flag=True, help='Cumulate over x-axis.')
 @click.option('--title', type=str, help='Override chart title with given value.')
 @click.option('--total', is_flag=True, help='Provide total sums of key metrics.')
@@ -258,6 +258,11 @@ def statistics(errors, title, x_axis, y_axis, cumulate, total):
             'total_energies',
             label='total energy calculations',
             cumulate=cumulate,
+            power=0.25 if not cumulate else 1, multiplier=1e-6, format='{x:,.1f}M'),
+        'calculations': Metric(
+            'calculations',
+            label='single configuration calculations',
+            cumulate=cumulate,
             power=0.25 if not cumulate else 1, multiplier=1e-6, format='{x:,.1f}M')
     }
 
@@ -279,5 +284,5 @@ def statistics(errors, title, x_axis, y_axis, cumulate, total):
         bar_plot(client, x_axis, *y_axis, title=title)
 
     if total:
-        data = client.repo.search(per_page=1, owner='admin', metrics=['total_energies', 'users', 'datasets']).response().result
+        data = client.repo.search(per_page=1, owner='admin', metrics=['total_energies', 'calculations', 'users', 'datasets']).response().result
         print(data.quantities['total'])

nomad/cli/parse.py

@@ -30,7 +30,7 @@ def parse(
         else:
             parser_name = parser.__class__.__name__
 
-    assert parser is not None, 'there is not parser matching %s' % mainfile
+    assert parser is not None, 'there is no parser matching %s' % mainfile
     logger = logger.bind(parser=parser.name)  # type: ignore
     logger.info('identified parser')
 

nomad/config.py

@@ -193,7 +193,7 @@ client = NomadConfig(
     url='http://localhost:8000/fairdi/nomad/latest/api'
 )
 
-version = '0.5.2'
+version = '0.5.3'
 commit = gitinfo.commit
 release = 'devel'
 domain = 'DFT'

nomad/parsing/__init__.py

@@ -263,13 +263,10 @@ parsers = [
     LegacyParser(
         name='parsers/gaussian', code_name='Gaussian',
         parser_class_name='gaussianparser.GaussianParser',
-        # This previous file matching string was too far down the line.
-        # r'\s*Cite this work as:'
-        # r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9.]*,'
-        # r'\s\*\*\*\*\*\*\*\*\*\*\*\**'
-        # r'\s*Gaussian\s*([0-9]+):\s*([A-Za-z0-9-.]+)\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)'
-        # r'\s*([0-9][0-9]?\-[A-Z][a-z][a-z]\-[0-9]+)')
-        mainfile_contents_re=r'Gaussian, Inc'),
+        mainfile_contents_re=(
+            r'\s*Cite this work as:'
+            r'\s*Gaussian [0-9]+, Revision [A-Za-z0-9\.]*,')
+    ),
     LegacyParser(
         name='parsers/quantumespresso', code_name='Quantum Espresso',
         parser_class_name='quantumespressoparser.QuantumEspressoParserPWSCF',

ops/deployments/nomad.reprocess.values.yaml

@@ -6,6 +6,7 @@ proxy:
 
 api:
   disableReset: true
+  adminPasswordSecret: 'nomad-production-repository-password'
 
 gui:
   debug: true

ops/helm/nomad/Chart.yaml

 apiVersion: v1
-appVersion: "0.5.2"
+appVersion: "0.5.3"
 description: A Helm chart for Kubernetes that only runs nomad services and uses externally hosted databases.
 name: nomad
-version: 0.5.2
+version: 0.5.3

setup.py

@@ -12,7 +12,7 @@ reqs = [str(ir.req) for ir in install_reqs if 'sphinxcontrib.httpdomain' not in
 
 setup(
     name='nomad',
-    version='0.5.2',
+    version='0.5.3',
     description='The nomad@FAIRDI infrastructure python package',
     py_modules=['nomad'],
     install_requires=reqs,