Merge branch 'main' into blog/querying-curated-database

.github/workflows/ci.yml

@@ -15,13 +15,13 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.8
+    - name: Set up Python 3.11
       uses: actions/setup-python@v2
       with:
-        python-version: '3.8'
+        python-version: '3.11'
     - name: Install python dependencies
       run: |
         pip install --upgrade pip
         pip install -rrequirements.txt
     - name: Run linkcheck
-      run: sphinx-build -b linkcheck docs/ docs/_build/linkcheck
+      run: sphinx-build -b linkcheck docs/ docs/_build/linkcheck --color -q

create_post.py

@@ -13,6 +13,7 @@
     "event": "Events",
     "report": "Reports",
     "release": "Releases",
+    "blog": "Blog",
 }
 
 

docs/conf.py

@@ -17,6 +17,7 @@
     "legacy_redirects",
     "check_events",
     "selective_css",
+    "sphinx_favicon",
 ]
 
 # see https://myst-parser.readthedocs.io
@@ -29,25 +30,19 @@
 templates_path = ["_templates"]
 html_show_sourcelink = False
 
+# sphinx_favicon
+favicons = [
+    "favicon-16x16.png",
+    "favicon-32x32.png",
+]
+
 # see https://pydata-sphinx-theme.readthedocs.io
 html_theme_options = {
     # "announcement": "Welcome to the new AiiDA site!",
     "logo": {
         "image_light": "logo-light.svg",
         "image_dark": "logo-dark.svg",
     },
-    "favicons": [
-        {
-            "rel": "icon",
-            "sizes": "16x16",
-            "href": "favicon-16x16.png",
-        },
-        {
-            "rel": "icon",
-            "sizes": "32x32",
-            "href": "favicon-32x32.png",
-        },
-    ],
     "icon_links": [
         {
             "name": "Discourse",
@@ -64,7 +59,7 @@
         {
             "name": "Twitter",
             "url": "https://twitter.com/aiidateam",
-            "icon": "fa-brands fa-square-twitter",
+            "icon": "fa-brands fa-square-x-twitter",
             "type": "fontawesome",
         },
     ],
@@ -74,7 +69,7 @@
         "theme-switcher",
         "navbar-icon-links",
     ],
-    "footer_items": ["copyright"],
+    "footer_start": ["copyright"],
     "use_edit_page_button": True,
     "search_bar_text": "Search ...",
 }
@@ -148,6 +143,8 @@
     r"https://aip.scitation.org/doi/.*",
     r"https://pubs.acs.org/doi/.*",
     r"https://www.sciencedirect.com/science/.*",
+    r"http://dx.doi.org/10.5075/epfl-thesis-7179",  # EPFL blocks repeating requests
+    r"http://qe2019.ijs.si/index.html",  # event page does not exist anymore
 ]
 
 aiida_ignore_event_checks = [

docs/events.yaml

@@ -133,7 +133,6 @@
   start: 2019-09-23
   duration: 4 days
   location: SINTEF Oslo (NO)
-  url: https://www.sigma2.no/vasp-and-aiida-workshop-0
 
 - name: AiiDA tutorial within the summer school on Advanced Materials and Molecular Modelling with Quantum ESPRESSO
   start: 2019-09-16

docs/news/posts/2020-05-27-new-mc-archive.md

@@ -11,7 +11,7 @@ We would like to announce the launch of a newly engineered [Materials Cloud Arch
 
 The [Materials Cloud Archive](https://archive.materialscloud.org/), active since March 2017, is a public, free, open-access repository for research data and tools in computational materials science and in related experimental efforts, inspired by the archive initiatives for preprints. It provides the capability to upload and persist arbitrary data records from anyone in the community with a minimum guaranteed 10-year retention time per record. Currently, 0.5 petabytes are already allocated; the  limits for standard submissions are of 5 GB for data sets in any format, and of 50 GB for AiiDA databases; moderators can approve larger data sets upon request. Each entry is assigned a globally unique and persistent digital object identifier (DOI) and harvestable metadata. The new Invenio platform makes it easier for authors to submit and later update data records, provides full-text searches, and powers streamlined workflows for content moderation.
 
-The Archive is an integral part of the [Materials Cloud](https://www.materialscloud.org/) FAIR data infrastructure, in partnership with several European and national centres - these include the [MaX](http://www.max-centre.eu/) Centre of Excellence, the  [MARVEL](https://nccr-marvel.ch/) NCCR, the H2020 [MarketPlace](https://www.the-marketplace-project.eu/), [NFFA](http://www.nffa.eu/), and [Intersect](http://intersect-project.eu/) projects, [EMMC](https://emmc.eu/), [swissuniversities](https://www.materialscloud.org/swissuniversities), [PASC](https://www.pasc-ch.org/), and [OSSCAR](https://www.osscar.org/). It is a [recommended repository for Nature’s Scientific Data](https://www.nature.com/sdata/policies/repositories#materials), it is indexed by [FAIRsharing](https://fairsharing.org/biodbcore-001089/), [Google Dataset Search](https://datasetsearch.research.google.com/search?query=Materials%20Cloud) and [EOSC-hub](https://www.eosc-hub.eu/)/[EUDAT](https://www.eudat.eu/)’s service [B2FIND](http://b2find.eudat.eu/organization/materialscloud), and it is registered on [re3data](https://www.re3data.org/repository/r3d100012611). Finally, it is an official [implementation network](https://www.go-fair.org/implementation-networks/overview/materials-cloud/) of the [GO FAIR initiative](https://www.go-fair.org/).
+The Archive is an integral part of the [Materials Cloud](https://www.materialscloud.org/) FAIR data infrastructure, in partnership with several European and national centres - these include the [MaX](http://www.max-centre.eu/) Centre of Excellence, the  [MARVEL](https://nccr-marvel.ch/) NCCR, the H2020 [MarketPlace](https://www.the-marketplace-project.eu/), [NFFA](http://www.nffa.eu/), and [Intersect](http://intersect-project.eu/) projects, [EMMC](https://emmc.eu/), [swissuniversities](https://www.materialscloud.org/swissuniversities), [PASC](https://www.pasc-ch.org/), and [OSSCAR](https://www.osscar.org/). It is a [recommended repository for Nature’s Scientific Data](https://www.nature.com/sdata/policies/repositories#materials), it is indexed by [FAIRsharing](https://fairsharing.org/biodbcore-001089/), [Google Dataset Search](https://datasetsearch.research.google.com/search?query=Materials%20Cloud) and [EOSC-hub](https://www.eosc-hub.eu/)/[EUDAT](https://www.eudat.eu/)’s service [B2FIND](http://b2find.eudat.eu/organization/materialscloud), and it is registered on [re3data](https://www.re3data.org/repository/r3d100012611).
 
 More information on the Materials Cloud integration of data, workflows and codes can be found in [L. Talirz et al., Materials Cloud, a platform for open computational science, arXiv:2003.12510 (2020)](https://arxiv.org/abs/2003.12510) and in [S. Huber et al., AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance, arXiv:2003.12476 (2020)](https://arxiv.org/abs/2003.12476).
 

docs/news/posts/2021-03-28-aiida-160-release.md

@@ -42,7 +42,7 @@ See the [Transferring data how-to](https://aiida.readthedocs.io/projects/aiida-
 
 The way the global/profile configuration is accessed has undergone a number of improvements:
 
-* When loaded, the `config.json` (found in the `.aiida` folder) is now validated against a JSON Schema that can be found in [aiida/manage/configuration/schema](https://github.com/aiidateam/aiida-core/tree/develop/aiida/manage/configuration/schema).
+* When loaded, the `config.json` (found in the `.aiida` folder) is now validated against a JSON Schema that can be found in [aiida/manage/configuration/schema](https://github.com/aiidateam/aiida-core/tree/v1.6.0/aiida/manage/configuration/schema).
 * The schema includes a number of new global/profile options, including: `transport.task_retry_initial_interval`, `transport.task_maximum_attempts`, `rmq.task_timeout` and `logging.aiopika_loglevel`.
 * The `cache_config.yml` has now also been **deprecated** and merged into the `config.json`, as part of the profile options. This merge will be handled automatically, upon first load of the `config.json` using the new AiiDA version.
 

docs/news/posts/2021-10-06-coding-week-event.md

@@ -178,7 +178,7 @@ We are very grateful to our sponsors for helping to make this event possible:
 - [EPFL](http://epfl.ch) for for providing administrative support
 - The [MARVEL National Centre of Competence in Research](http://nccr-marvel.ch/) “OSP” for funding
 - The [MaX European Centre of Excellence](http://www.max-centre.eu/) for funding
-- The [swissuniversities P-5 project](https://www.swissuniversities.ch/en/organisation/projects-and-programmes/) “Materials Cloud” and [Empa](https://www.empa.ch/) for funding
+- The [swissuniversities P-5 project](https://www.swissuniversities.ch/en/topics/digitalisation/p-5-scientific-information) “Materials Cloud” and [Empa](https://www.empa.ch/) for funding
 - The [MarketPlace](https://www.the-marketplace-project.eu/) project for funding
 - The [DOME](https://dome40.eu/) project for funding
 - The [Open-Model project](https://www.open-model.eu/) funding

docs/news/posts/2022-11-24-ord-project-premise.md

@@ -10,7 +10,7 @@ date: 2022-11-24
 A consortium led by Dr. Giovanni Pizzi (project leader of [NCCR MARVEL's Pillar 3, "Digital Infrastructure of Open Simulations and Data,"](https://nccr-marvel.ch/research/iii/projects/open-digital-infrastructure) and Group leader of the ["Materials Software and Data" group](https://www.psi.ch/en/lms/msd-group) at the Paul Scherrer Institute PSI), including also researchers from Empa and ETH Zurich, has won funding of almost CHF1.3 million for a 3-year project funded under the ["ORD-R Establish" initiative of the ETH Board](https://ethrat.ch/en/measure-1-calls-for-field-specific-actions/).
 
 ## About the project
-The project, dubbed PREMISE, aims to establish, promote and facilitate the adoption of Open Research Data (ORD) practices that adhere to FAIR data principles in the field of materials science. It will provide missing critical components to enable open and reproducible research, focusing in particular on the interoperability of data from simulations and experiments.
+The project, dubbed [PREMISE](https://ord-premise.org/), aims to establish, promote and facilitate the adoption of Open Research Data (ORD) practices that adhere to FAIR data principles in the field of materials science. It will provide missing critical components to enable open and reproducible research, focusing in particular on the interoperability of data from simulations and experiments.
 During their project, the researchers will draw on the existing platforms [openBIS](https://openbis.ch/), an open-source data management platform developed at ETH Zurich, and [AiiDA](https://www.aiida.net), an open-source workflow management system mainly developed at PSI and EPFL. The two platforms focus on different parts of the data life cycle—experiments and simulations, respectively.
 You can read the [full press release here](https://nccr-marvel.ch/news/communication/11-PREMISE).
 

docs/news/posts/2023-06-22-aiida-tightly-integr.md

@@ -9,6 +9,6 @@ date: 2023-06-22
 
 Microsoft recently launched their new [Azure Quantum Elements](https://quantum.microsoft.com/en-us/our-story/quantum-elements-overview) platform. We are happy to share that AiiDA is tightly integrated in it!
 
-You can check out for instance the [launch video](https://news.microsoft.com/azure-quantum-june-event/#watch-now) introduced by Microsoft's CEO Satya Nadella (check e.g. from minute 13:00, where AiiDA workflows are used to drive workflows).
+You can check out for instance the [launch video](https://news.microsoft.com/azure-quantum-june-event) introduced by Microsoft's CEO Satya Nadella (check e.g. from minute 13:00, where AiiDA workflows are used to drive workflows).
 
 If you are interested, you can also check out the [Microsoft webinar](https://connect.discoveracs.org/CENWebinar_Microsoft_6_22_23?partnerref=Microsoft) today at 5PM CEST, where they discuss their Azure Quantum platform to accelerate scientific discovery, and the interaction with AiiDA is also highlighted.

docs/news/posts/2023-11-20-open-postdoc-position-marvel-2023.md

@@ -0,0 +1,24 @@
+---
+blogpost: true
+category: News
+tags: positions
+date: 2023-11-20
+---
+
+# 1 post-doc positions at PSI (Switzerland) on high-throughput materials discovery
+
+One new post-doc opportunity is open in the [Materials Software and Data Group](https://www.psi.ch/en/lms/msd-group) led by Dr. Giovanni Pizzi, part of the Laboratory for Materials Simulations, at the [Paul Scherrer Institute (PSI)](https://www.psi.ch/en), Switzerland.
+
+**The successful candidate will be in charge of setting up and maintaining large scale materials discovery projects based on the fully automated and robust computational infrastructure [AiiDA](https://www.aiida.net).**
+Tasks will involve the management and coordination of scientific research projects (setting up the projects, writing the workflows, running the simulations, writing scientific papers), maintaining and documenting existing computational pipelines for generating the databases published on [Materials Cloud](https://www.materialscloud.org) (e.g., [MC3D](https://www.materialscloud.org/mc3d) and [MC2D](https://www.materialscloud.org/mc2d)), supporting the research community by maintaining and developing relevant plugins (e.g. AiiDA-Quantum ESPRESSO), and supporting the development of GUIs to new simulations via [AiiDAlab](https://www.aiidalab.net/).
+
+This positions is funded by the [NCCR MARVEL](https://nccr-marvel.ch/), offering close collaboration with project partners such as the Swiss Supercomputer Center CSCS, EPFL, and Empa, among others. Additionally, you will have the opportunity to network with current and former members of the well-established MARVEL community, with colleagues in the group and in the laboratory funded by other projects with strong synergies with MARVEL, and to engage in collaborative projects across Switzerland and Europe, expanding your network of international collaborations.
+
+We are seeking candidates with a PhD degree in the physical sciences (e.g., physics, chemistry, or materials science/engineering), strong organization skills, and a passion for writing open-source tools that can be used by a broad audience of researchers.
+Essential qualifications include experience in running simulations on HPC and proficient software development and programming skills in Python. Desirable skills include experience in managing software projects in a team, handling large amounts of data, and developing complex automated computational tools for running simulations at scale.
+
+**More details and information, requirements for the positions, and instructions on how to apply can be found at <https://www.psi.ch/en/pa/job-opportunities/60368-postdoctoral-fellow>**
+
+**The application deadline is on December 10th, 2023.**
+
+If you know someone who might be interested in this opportunity, please feel free to forward this announcement to them.

docs/news/posts/2023-12-20-release-2.5.0.md

@@ -0,0 +1,29 @@
+---
+blogpost: true
+category: Releases
+tags: aiida-core
+date: 2023-12-20
+---
+
+# AiiDA v2.5.0 released
+
+We are pleased to announce that AiiDA v2.5 was just released [^1].
+It can be installed as always from PyPI using pip:
+
+    pip install aiida-core==2.5
+
+or using Conda instead:
+
+    conda install aiida-core=2.5
+
+This release includes a number of interesting features and bug fixes.
+For example, new storage backends are added that make it easy to setup profiles without a PostgreSQL server; ideal for testing and demonstration purposes.
+For a complete overview, please refer to the change log [^2].
+
+Happy computing!
+
+The AiiDA team
+
+
+[^1]: https://pypi.org/project/aiida-core/2.5.0/
+[^2]: https://github.com/aiidateam/aiida-core/blob/v2.5.0/CHANGELOG.md

docs/news/posts/2024-07-01-release-2.6.0.md

@@ -0,0 +1,18 @@
+---
+blogpost: true
+category: Releases
+tags: aiida-core
+date: 2024-07-01
+---
+
+# AiiDA v2.6.0 released
+
+We just released the latest version of AiiDA. This minor release comes with a number of features that are focused on user friendliness of the CLI and the API. The [changelog](https://aiida.readthedocs.io/projects/aiida-core/en/stable/reference/_changelog.html#v2-6-0-2024-07-01) contains a list of all changes including a nice overview of some of the new features.
+
+A lot of work has especially gone in making it easier to install AiiDA and try it out without having to install services like PostgreSQL and RabbitMQ. It is now possible to operate AiiDA without RabbitMQ, at the cost of losing daemon functionality. The new command `verdi presto` allows setting up a complete and ready-to-go profile with a single command without any configuration. The installation [documentation](https://aiida.readthedocs.io/projects/aiida-core/en/stable/installation/index.html) has seen a complete overhaul.
+
+The caching mechanism has received a number of improvements guaranteeing even greater savings of computational time. For existing calculations to be valid cache sources in the new version, their hash has to be regenerated (see [Improvements and changes to caching](https://aiida.readthedocs.io/projects/aiida-core/en/stable/reference/_changelog.html#improved-test-fixtures-without-services) for details).
+
+Happy computing!
+
+The AiiDA team

docs/news/posts/2024-08-07-release-2.6.2.md

@@ -0,0 +1,14 @@
+---
+blogpost: true
+category: Releases
+tags: aiida-core
+date: 2024-08-07
+---
+
+# AiiDA v2.6.2 released
+
+We just released the latest version of AiiDA, v2.6.2. This patch release comes with a number of bug fixes and additions to the documentation. You can find a list of all changes in the [changelog](https://github.com/aiidateam/aiida-core/blob/fb3686271fcdeb5506838a5a3069955546b05460/CHANGELOG.md).
+
+Happy computing!
+
+The AiiDA team