Merge branch 'v1.3.16' into 'main'

v1.3.16

See merge request nomad-lab/nomad-FAIR!2439

Author: Lauri Himanen

.gitlab-ci.yml

@@ -52,13 +52,13 @@ stages:
   - release
 
 # JOBS
-
 update changelog:
   stage: build
+  when: manual
   script:
-    - curl -X POST "https://gitlab.mpcdf.mpg.de/api/v4/projects/$CI_PROJECT_ID/repository/changelog?version=${CI_COMMIT_TAG:1}&access_token=$CI_ACCESS_TOKEN&message=Add%20changelog%20for%20version%20$CI_COMMIT_TAG%20%5Bskip-ci%5D"
+    - curl -X POST "https://gitlab.mpcdf.mpg.de/api/v4/projects/$CI_PROJECT_ID/repository/changelog?branch=${CI_COMMIT_REF_NAME}&version=${CI_COMMIT_REF_NAME:1}&access_token=$CI_ACCESS_TOKEN&message=Add%20changelog%20for%20version%20$CI_COMMIT_REF_NAME%20%5Bskip-ci%5D"
   rules:
-    - if: $CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/
+    - if: $CI_COMMIT_REF_NAME =~ /^v\d+\.\d+\.\d+$/
 
 .build_image:
   image:
@@ -335,11 +335,11 @@ python package install tests:
     - |
       for PYTHON_VERSION in 3.10 3.11 3.12; do
         echo "Running for Python $PYTHON_VERSION"
-        
+
         uv venv -p $PYTHON_VERSION
-        
+
         uv pip install dist/nomad_*.whl
-        
+
         ./.venv/bin/python -c 'import nomad.cli'
         ./.venv/bin/python -c 'from nomad.client import ArchiveQuery'
         ./.venv/bin/python -m nomad.cli parse --skip-normalizers archive.json

CHANGELOG.md

@@ -1,3 +1,28 @@
+## 1.3.16 (2025-05-15)
+
+### Changed (4 changes)
+
+- [Added more context to the ConfigBaseModel validation logger warning](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/96b76947d6fc01c1d42defcd868bfe2b333334f9) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2429))
+- [Removed direct infrastructure dependency from mkdocs macros](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/075653f2b839539e90a07e729d2304268b8f2527) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2366))
+- [Use newer version of setuptools](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/112dc2b9a08103da228c12333ae3fd93c870dfc5) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2426))
+
+### Fixed (5 changes)
+
+- [Fixed issue with undefined spectra data](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/c2e6601ba5ca611e308ed35adeac9d4f130aca25) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2436))
+- [Fixed performance issues with API response for entries with large amounts of search quantities](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/cc3f32a034f57f07aab14ddfd94184106ad09758) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2409))
+- [Fixed issue with unit conversion from/to delta units](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/fa071c5df9255c1489ef61a44667cf1105c07289) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2380))
+- [Fixed issue with histograms that contain negative numbers](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/5d8438f86461da28e20c62eb72187f85a7ec5442) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2367))
+- [Fixed ForwardRef related pydantic error in annotation models](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/d324719cf5f0d006dfa51ae452e9685484c802b3) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2403))
+
+### Added (6 changes)
+
+- [Added option for setting the query mode for terms widget and terms menu item](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/f744bea733616076ab72bdfba0aa450a4194edb9) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2428))
+- [Added experimental API endpoint for bulk entries metadata export](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/072952d29940df4d16e010f870af1d5fdb1eb584) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2315))
+- [Added new action for launching remote tools from the results table](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/e7343bd0de909b3f9a8ae57b48044455a2adfa2d) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2279))
+- [Added support for negative parser levels](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/203b6e11308bca7f18d7cb7580116c87b0e92bdd) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2362))
+- [Added mkdocs function to add schema section and package reference](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/bd2d5c84824cc1a4bbd2c40e1d9c1871c1a41aa6) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2116))
+- [Added wheel to the Python package](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/commit/aa13798e378ca1d78d576820eee0f1be0f360aba) ([merge request](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/2433))
+
 ## 1.3.15 (2025-03-05)
 
 ### Fixed (1 change)

README.md

@@ -46,11 +46,16 @@ Scheidgen et al., (2023). NOMAD: A distributed web-based platform for managing m
 
 For citation in academic works, you can use this [BibTeX file](docs/assets/joss_paper.bib).
 
-## Changelog
+## Changelog highlights
 
-Omitted versions are plain bugfix releases with only minor changes and fixes. The
-file [`CHANGELOG.md`](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/blob/develop/CHANGELOG.md)
-contains much more detailed information about changes and fixes in the released versions.
+The following list contains highlights from different versions, the file [`CHANGELOG.md`](https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/blob/develop/CHANGELOG.md) contains much more detailed information about changes and fixes in the released versions. Omitted versions are plain bugfix releases with only minor changes and fixes.
+
+### v1.3.16
+
+- Added option for setting the query mode for terms widget and terms menu item
+- Added new action for launching remote tools from the results table
+- Fixed performance issues with API response for entries with large amounts of search quantities
+- Fixed issue with unit conversion from/to delta units
 
 ### v1.3.15
 

examples/data/rdm_tutorial/tutorial.ipynb

@@ -6814,7 +6814,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {
     "tags": []
    },
@@ -6908,7 +6908,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "tags": []
    },
@@ -6961,7 +6961,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {
     "tags": []
    },
@@ -6989,7 +6989,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {
     "tags": []
    },
@@ -7093,7 +7093,7 @@
     "        # Add hydrogens, store molecule formula and mass\n",
     "        rdkit_mol = Chem.AddHs(rdkit_mol)\n",
     "        self.molecular_formula = Chem.rdMolDescriptors.CalcMolFormula(rdkit_mol)\n",
-    "        self.molecular_mass = Chem.rdMolDescriptors.CalcExactMolWt(rdkit_mol)\n"
+    "        self.molecular_mass = Chem.rdMolDescriptors.CalcExactMolWt(rdkit_mol)"
    ]
   },
   {
@@ -7411,9 +7411,9 @@
     "class TADFMoleculesParser(MatchingParser):\n",
     "    def __init__(self):\n",
     "        super().__init__(\n",
-    "            mainfile_name_re='\\.*molecule{\\d*}.json',\n",
-    "            mainfile_mime_re='\\.*',\n",
-    "            mainfile_contents_re='\\.*',\n",
+    "            mainfile_name_re=r'\\.*molecule{\\d*}.json',\n",
+    "            mainfile_mime_re=r'\\.*',\n",
+    "            mainfile_contents_re=r'\\.*',\n",
     "        )\n",
     "\n",
     "    def parse(\n",
@@ -7423,7 +7423,7 @@
     "        logger,\n",
     "    ) -> None:\n",
     "        pass\n",
-    "        # TODO: You parsing logic here\n"
+    "        # TODO: You parsing logic here"
    ]
   },
   {
@@ -7448,16 +7448,15 @@
    "outputs": [],
    "source": [
     "import json\n",
-    "import re\n",
     "from nomad.units import ureg\n",
     "\n",
     "\n",
     "class TADFMoleculesParser(MatchingParser):\n",
     "    def __init__(self):\n",
     "        super().__init__(\n",
-    "            mainfile_name_re='\\.*molecule{\\d*}.json',\n",
-    "            mainfile_mime_re='\\.*',\n",
-    "            mainfile_contents_re='\\.*',\n",
+    "            mainfile_name_re=r'\\.*molecule{\\d*}.json',\n",
+    "            mainfile_mime_re=r'\\.*',\n",
+    "            mainfile_contents_re=r'\\.*',\n",
     "        )\n",
     "\n",
     "    def parse(\n",
@@ -7605,7 +7604,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 19,
    "metadata": {
     "tags": []
    },
@@ -7615,7 +7614,6 @@
     "    App,\n",
     "    Axis,\n",
     "    Column,\n",
-    "    Columns,\n",
     "    Dashboard,\n",
     "    Format,\n",
     "    Layout,\n",
@@ -7744,8 +7742,7 @@
     "            ),\n",
     "        ]\n",
     "    ),\n",
-    ")\n",
-    "\n"
+    ")"
    ]
   },
   {
@@ -7800,7 +7797,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.11.0rc1"
   }
  },
  "nbformat": 4,

gui/src/components/search/SearchResults.js

@@ -56,20 +56,26 @@ export const extractPathContent = ({action, data, key}) => {
  */
 export const ActionURL = React.memo(({action, data}) => {
   const {raiseError} = useErrors()
-  const href = extractPathContent({action, data, key: 'path'})
+  let href = extractPathContent({action, data, key: 'path'})
 
   if (isArray(href)) {
-    raiseError(`
-    Encountered and array in ${action.path}. Expected a string.
-    Update the path in you app to target only one item in the array.`
-    )
-    return
+    if (href.length > 1) {
+      raiseError(`
+        The data for a row action as returned by the path "${action.path}"
+        contains an array with more than one item. Update the path in your app
+        to target only one item in the array.`
+      )
+      return null
+    } else {
+      href = href[0]
+    }
   }
   const disabled = !href
   const size = 'medium'
   const svgIcon = {
     'github': <GitHubIcon fontSize={size}/>
   }[action.icon]
+
   return <Tooltip title={disabled ? 'Not available' : (action.description || '')}>
     <div>
       <IconButton size={size} href={href} target="_blank" disabled={disabled}>
@@ -120,19 +126,18 @@ export const NorthURL = React.memo(({ action, data }) => {
 
   const handleLaunch = async () => {
     if (!tool) return
-    const {state: currentState, uploadid_is_mounted} = await getToolStatus()
+    const { state: currentState, uploadid_is_mounted } = await getToolStatus()
     if (currentState === "stopped") {
-      const { toolUrl } = await launch()
-      setToolUrl(toolUrl)
-      if (toolUrl) window.open(toolUrl, tool.name)
+      const { toolUrl: newUrl } = await launch()
+      setToolUrl(newUrl)
+      if (newUrl) window.open(newUrl, tool.name)
     } else if (uploadid_is_mounted === false) {
       setDialogMessage(
         `The upload ${data?.upload_id} is not mounted. You need to stop the tool before relaunching it.
         Stopping the tool may cause loss of unsaved data.`)
       setShowStopOnly(true)
       setOpenDialog(true)
     } else {
-      setToolUrl(toolUrl)
       setDialogMessage("The tool is already running. Stopping it will delete any unsaved data.")
       setShowStopOnly(false)
       setOpenDialog(true)
@@ -150,14 +155,23 @@ export const NorthURL = React.memo(({ action, data }) => {
     setOpenDialog(false)
   }
 
-  const handleOpenTool = () => {
-    setOpenDialog(false)
-    window.open(
-      toolUrl || `${northBase}/user/${keycloak.tokenParsed?.preferred_username}/${tool.name}`,
-      "_blank"
-    )
+  const handleOpenTool = async () => {
+  setOpenDialog(false)
+  let url = toolUrl
+
+  if (!url) {
+    const { state, uploadid_is_mounted } = await getToolStatus()
+    if (state === "running" && uploadid_is_mounted) {
+      const { toolUrl: fetchedUrl } = await launch()
+      url = fetchedUrl || `${northBase}/user/${keycloak.tokenParsed?.preferred_username}/${tool.name}`
+    } else {
+      url = `${northBase}/user/${keycloak.tokenParsed?.preferred_username}/${tool.name}`
+    }
   }
 
+  window.open(url, "_blank")
+}
+
   const disabled = !filepath || !isAuthenticated
   const tooltipMessage = !isAuthenticated
     ? "You must be logged in to use this tool."

nomad/cli/admin/run.py

@@ -71,7 +71,9 @@ def run_app(
 ):
     config.meta.service = 'app'
     host = host or config.services.api_host or '0.0.0.0'
-    port = int(port or config.services.api_port or 8000)
+    # TODO: respect `config.services.api_port` instead of defaulting to 8000
+    # port = int(port or config.services.api_port or 8000)
+    port = int(port or 8000)
 
     if with_gui:
         import glob

nomad/config/models/config.py

@@ -202,7 +202,7 @@ class Services(ConfigBaseModel):
     """,
     )
     upload_members_group_search_enabled: bool = Field(
-        False,
+        True,
         description='If true, the GUI will show a search for groups as upload members.',
     )
     log_api_queries: bool = Field(

nomad/jupyterhub_config.py

@@ -121,7 +121,7 @@ def pre_spawn(spawner):
 c.GenericOAuthenticator.scope = ['openid', 'profile']
 c.Authenticator.auto_login = True
 c.Authenticator.enable_auth_state = True
-c.Ahtenticator.allow_all = True
+c.Authenticator.allow_all = True
 
 
 # configure docker spawner

pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.md"
 authors = [
     { name = "NOMAD Laboratory", email = '[email protected]' },
 ]
-dynamic = ["version"]
+version = "1.3.16"
 license = { text = "Apache-2.0" }
 requires-python = ">=3.10"
 
@@ -64,9 +64,9 @@ infrastructure = [
     'fastapi',
     'gunicorn',
     'h5grove[fastapi]',
-    'jupyterhub',
+    'jupyterhub<5.0.0', # Connection issues with newer versions
     'mongoengine',
-    'oauthenticator',
+    'oauthenticator<16.0.0', # Connection issues with newer versions
     'optimade[mongo]',
     'pyjwt[crypto]',
     'python-logstash',
@@ -191,4 +191,4 @@ testpaths = ["tests"]
 filterwarnings = [
     "ignore::DeprecationWarning",
     "ignore::SyntaxWarning",
-]
+]