markdownlint checks

.github/workflows/md.yml

@@ -0,0 +1,11 @@
+---
+name: Lint markdown files
+on: [pull_request]  # yamllint disable-line rule:truthy
+jobs:
+  run-markdownlint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: DavidAnson/markdownlint-cli2-action@v20
+        with:
+          globs: "**/*.md"

.markdownlint.yaml

@@ -0,0 +1,17 @@
+default: true
+line-length: false
+#  line_length: 88
+#  tables: false
+no-trailing-punctuation: true
+heading-style:
+  style: atx
+no-missing-space-atx: true
+single-title: false
+fenced-code-language: true
+code-block-style:
+  style: fenced
+no-duplicate-heading:
+  siblings_only: true
+# todo reenable this
+no-inline-html: false
+first-line-heading: false

README.md

@@ -7,19 +7,25 @@ The website is based on jekyll.
 For local compilation, you will first need to install ruby and bundler. Next install the
 required gems:
 
-    bundler install
+```sh
+bundler install
+```
 
 And serve the website:
 
-    bundle exec jekyll serve
+```sh
+bundle exec jekyll serve
+```
 
 Access the website at [http://localhost:4000](http://localhost:4000).
 
 ## Building with docker
 
 You can also run jekyll in a docker container
 
-    docker compose up -d
+```sh
+docker compose up -d
+```
 
 This is equivalent running `jekyll serve`.
 

_includes/button_row.html

@@ -0,0 +1,9 @@
+{% comment %}
+  Wraps multiple buttons in a horizontal row.
+
+  Arguments:
+  - contents:
+{% endcomment -%}
+<div class="button-container">
+    {{- include.content | markdownify | remove: "<p>" | remove: "</p>" -}}
+</div>

_includes/fa.html

@@ -0,0 +1,8 @@
+{% comment %}
+Font Awesome icons
+
+Arguments:
+- icon: Icon name, e.g. "caret-right"
+- family: Icon family, e.g. "fas"
+{% endcomment %}
+<i class="{{ include.family | default: "fas" }} fa-{{include.icon}}" aria-hidden="true"></i>

_includes/facility_table.md

@@ -2,6 +2,7 @@
 Infobox for a facility.
 
 Arguments:
+
 - facility: JSON with facility info; see facilities.yml for contents
 
 {% endcomment %}
@@ -25,4 +26,4 @@ Arguments:
 {%- endfor %}|
 {% endif -%}
 | Storage Location | {{ f.storageLocation | default: PSI }} |
-| Ingestor URL | [{{ f.facilityBackend }}](https://discovery.development.psi.ch/ingestor?backendUrl={{ f.facilityBackend | url_encode }}) |
+| Ingestor URL | [{{ f.facilityBackend }}](https://discovery.development.psi.ch/ingestor?backendUrl={{f.facilityBackend|url_encode}}) |

_includes/gallery.html

@@ -0,0 +1,29 @@
+{% comment %}
+Gallery of images
+
+Arguments:
+- images: List of image URLs
+- image: Single image URL (conflicts with 'images')
+- caption: Optional caption for the gallery
+- width: Optional total width (default: 100%)
+{% endcomment -%}
+{% if include.images %}
+    {%- assign images = include.images -%}
+{%- else -%}
+    {%- assign images = "" | split: "," -%}
+    {%- if include.image -%}
+        {%- assign images = images | push: include.image -%}
+    {%- endif -%}
+{%- endif -%}
+<div class="image-box" style="width: {{ include.width | default: '100%' }};">
+    <div class="flex-box">
+    {%- for img in images %}
+        <a href="{{ img }}">
+            <img src="{{ img }}" />
+        </a>
+    {%- endfor %}
+    </div>
+{%- if include.caption -%}
+    <div class="caption">{{ include.caption }}</div>
+{%- endif -%}
+</div>

_includes/news_timeline.html

@@ -0,0 +1,15 @@
+{% comment %}
+Make a timeline of news posts
+
+Arguments:
+- posts: List of posts to show
+{% endcomment %}
+<ul class="timeline">
+  {% for post in include.posts -%}
+  <li class="timeline-item right">
+    <div class="timeline-content">
+      {% include news_item.html post=post %}
+    </div>
+  </li>
+{%- endfor %}
+</ul>

_includes/toc_table.md

@@ -3,6 +3,7 @@ Table-of-contents styled as a table.
 Used in overview pages
 
 Arguments:
+
 - docs: list of documents
 {% endcomment %}
 

_includes/wpbar.html

@@ -0,0 +1,22 @@
+{% comment %}
+Table for workpackage tasks
+
+Arguments:
+
+- items: List of workpackage items (from site.data.deliverables-*)
+
+{% endcomment %}
+<div class="wp-bar">
+    <div class="wp-header-row">
+        <div class="wp-header-col">ID</div>
+        <div class="wp-header-col">Description</div>
+        <div class="wp-header-col">Status</div>
+    </div>
+    {% for item in include.items %}
+        <div class="wp-row">
+            <div class="wp-col">{{ item.id }}</div>
+            <div class="wp-col">{{ item.description }}</div>
+            <div class="wp-col wp-status {{ item.status | downcase | replace: ' ', '-' }}">{{ item.status }}</div>
+        </div>
+    {% endfor %}
+</div>

_includes/wptasks.md

@@ -0,0 +1,24 @@
+{% comment %}
+List all workpackage tasks. Tasks are grouped by category (organizational and technical).
+
+Arguments:
+
+- tasks: List of workpackage tasks (from site.data.deliverables-*)
+
+{% endcomment %}
+{%- assign org_items = include.tasks | where: "table", "org" %}
+{%- assign tec_items = include.tasks | where: "table", "tec" %}
+{% if org_items.size > 0 %}
+
+#### Organisational tasks
+
+{% include wpbar.html items=org_items %}
+
+{% endif %}
+{%- if tec_items.size > 0 %}
+
+#### Technical tasks
+
+{% include wpbar.html items=tec_items %}
+
+{% endif %}

_posts/2023-01-16-psi-highlight.md

@@ -7,4 +7,4 @@ categories: media
 
 OpenEM has been featured in a recent article entitled ["Making the most of our
 data"](https://www.psi.ch/en/science/scientific-highlights/making-the-most-of-our-data).
-The article highlights Open Research Data projects at the Paul Scherrer Institute.
+The article highlights Open Research Data projects at the Paul Scherrer Institute.

_posts/2023-04-21-ccpem.md

@@ -12,16 +12,3 @@ April 25-27. Please give us your thoughts on OpenEM!
 
 The conference poster about OpenEM can be viewed on
 [Zenodo](https://zenodo.org/record/7845286).
----
-layout: post
-title:  "Visit OpenEM at the CCP-EM 2023 Spring Symposium"
-date:   2023-04-21
-categories: news
----
-
-Spencer Bliven and Alun Ashton will be at the
-[CCP-EM Symposium](https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php)
-April 25-27. Please give us your thoughts on OpenEM!
-
-The conference poster about OpenEM can be viewed on
-[Zenodo](https://zenodo.org/record/7845286).

_posts/2023-06-15-logo.md

@@ -19,8 +19,9 @@ up of two proteins, VipA and VipB, which form a helical structure with six spira
 strands. The logo shows the electron density from a short segment of the sheath.
 
 Data for this image is available from three sources:
+
 - micrographs from EMPAIR: [EMPIAR-10019](https://www.ebi.ac.uk/empiar/entry/10019)
-- reconstructed 3D electron density from EMDB: [EMD-2699](https://www.ebi.ac.uk/emdb/EMD-2699); and a 
+- reconstructed 3D electron density from EMDB: [EMD-2699](https://www.ebi.ac.uk/emdb/EMD-2699); and a
 - molecular model from PDB: [3j9g](https://www.ebi.ac.uk/pdbe/entry/pdb/3j9g)
 The logo was created from this data using [ChimeraX](https://www.cgl.ucsf.edu/chimerax/).
 
@@ -45,4 +46,4 @@ Proceedings MC 2013:
 > K. Kunze, A. Sologubenko, H. Ma, and R. Spolenak. (2013)
 > Orientation contrast imaging and crystallographic orientation mapping using transmission Kikuchi diffraction in the SEM.
 > *Proceedings MC 2013*. Regensburg, August 25 – 30, 2013. Part 1, pages 744-​745.
-> DOI: [10.5283/epub.28734](http://doi.org/10.5283/epub.28734)
+> DOI: [10.5283/epub.28734](http://doi.org/10.5283/epub.28734)

_posts/2023-07-17-unige-dci-jobs.md

@@ -13,4 +13,4 @@ Additionally, DCI-Lausanne (UNIL/EPFL) is looking for a software engineer.
 
 [Apply for the DCI-Lausanne position](https://recruiting.epfl.ch/Vacancies/2973/Description/2)
 
-Additional jobs may be posted soon at other [participating institutions](/members).
+Additional jobs may be posted soon at other [participating institutions](/members).

_posts/2024-02-23-oscem.md

@@ -31,4 +31,4 @@ publishing in public repositories.
 If you are interested in joining the community, please contact [Jose Maria
 Carazo](http://i2pc.es/carazo/) or [Spencer
 Bliven](https://www.psi.ch/en/lsm/people/spencer-edward-bliven), or see the [workshop
-event page](https://indico.psi.ch/e/em-standards-2024).
+event page](https://indico.psi.ch/e/em-standards-2024).

_posts/2024-06-10-establish-updates.md

@@ -11,14 +11,15 @@ Join us for updates on OpenEM and our sister project, PREMISE! This follows the
 ---
 
 On 13 June 2024, the two establish projects financed by the ETH Domain ORD programme will be presented:
+
 - 9.00-9.30: Open and Reproducible Materials Science Research led by Giovanni Pizzi
 - 9.30-10.00: Open EM Data Network led by Henning Stahlberg
 - 10.00-10.30: Discussion – “open science in these two projects”, best practices, exchanges, etc.
 
 The establish projects aim at establishing ORD practices that are already existing, with a research agenda and a common understanding about ORD practices. The goal is that they become the de facto standards in a community and raise the quality level.
 
-Anyone is welcome to attend this event online. You can register for free [here](https://lnkd.in/gAQSeQgd).
+Anyone is welcome to attend this event online. You can [register for free](https://lnkd.in/gAQSeQgd).
 
 Slides from the presentation are available from [zenodo](https://zenodo.org/doi/10.5281/zenodo.11632469).
 
-*Edit*: A recording of the presentations can be viewed [here](https://epfl.zoom.us/rec/play/rWpJ4kYbs9Y5tCWx7HSKAjtJ88DpSprhpgrChGQ6MXSq4awDtVU7csV6MUYrfnCSiVuIdQfVoBRel01O.Ck4LyAPReXgo7fm4?canPlayFromShare=true&from=my_recording&continueMode=true&componentName=rec-play&originRequestUrl=https%3A%2F%2Fepfl.zoom.us%2Frec%2Fshare%2FxzKmvOza1unpe_fI7fycddZwltVoXbDDB4sZAITIM76xYg5wx1caRPxedjOKhi3P.jzbj-h0fjspgWxrE). The OpenEM portion starts at 41:03 in the recording.
+*Edit*: A [recording of the presentations](https://epfl.zoom.us/rec/play/rWpJ4kYbs9Y5tCWx7HSKAjtJ88DpSprhpgrChGQ6MXSq4awDtVU7csV6MUYrfnCSiVuIdQfVoBRel01O.Ck4LyAPReXgo7fm4?canPlayFromShare=true&from=my_recording&continueMode=true&componentName=rec-play&originRequestUrl=https%3A%2F%2Fepfl.zoom.us%2Frec%2Fshare%2FxzKmvOza1unpe_fI7fycddZwltVoXbDDB4sZAITIM76xYg5wx1caRPxedjOKhi3P.jzbj-h0fjspgWxrE) is now available. The OpenEM portion starts at 41:03 in the recording.

_posts/2024-07-29-updated-project-page.md

@@ -6,4 +6,4 @@ categories: news
 
 ---
 
-We have worked on our project page and added the most important project information. You can now find everything about the project and the members on the page. Technical documentation and instructions will be added over time.
+We have worked on our project page and added the most important project information. You can now find everything about the project and the members on the page. Technical documentation and instructions will be added over time.

_posts/2024-11-14-documentation-started.md

@@ -6,4 +6,4 @@ categories: news
 
 ---
 
-We have completed our website and filled the documentation with initial life. Some components are still under development and their call-up and appearance have not yet been finalised. The documentation for these components will be added at a later date.
+We have completed our website and filled the documentation with initial life. Some components are still under development and their call-up and appearance have not yet been finalised. The documentation for these components will be added at a later date.

_posts/2024-12-13-christmas-newsletter.md

@@ -31,7 +31,6 @@ We are happy to announce that the website can now be reached at [https://www.ope
 
 In order to keep you continuously informed about the project status, we will be sending out regular newsletters in future. Please invite any colleagues who you think might be interested to [subscribe](https://psilists.ethz.ch/sympa/subscribe/openem-members?previous_action=info) to the mailing list.
 
-
 ### Completed Milestones
 
 We have now completed four of our seven [milestones](/timeline/), with major deliverables achieved from all [workpackages](/deliverables/). We published the first [dataset](https://doi.psi.ch/detail/10.16907%2Fa2ab7849-5de7-4e7f-8286-72ec73089ca8) in September as part of *MS-III: Proof of Concept*, and with the recently completed *MS-IV: Alpha Release* the service is running at Uni Basel for initial testing.

_posts/2025-01-13-oscem-newsletter.md

@@ -23,7 +23,7 @@ Dear OSC-EM members,
 
 Happy 2025! It has now been nearly a year since the EM standards workshop established the _Open Science Community for Electron Microscopy_ (OSC-EM). This mailing list has been fairly quiet in that year, but the technical group has been hard at work. One of my new year’s resolutions is to provide more regular updates to all of you on our progress, as well as invite more people to review and contribute to the burgeoning standard.
 
-As a first step, the technical group will hold regular monthly meetings. These are currently planned for the first Monday of the month online, and are open to everyone. The next meeting will be Monday, 3 Feb 2025, at 16:00 CET/15:00 GMT/10:00 EST. More information is available [here](https://indico.psi.ch/e/oscem-2025).
+As a first step, the technical group will hold regular monthly meetings. These are currently planned for the first Monday of the month online, and are open to everyone. The next meeting will be Monday, 3 Feb 2025, at 16:00 CET/15:00 GMT/10:00 EST. More information is available [on indico](https://indico.psi.ch/e/oscem-2025).
 
 Work on the project is organized through our [osc-em github organization](https://github.com/osc-em). Yves Tittes, Lola Sánchez de Lara, Sofya Laskina, and others have contributed to [schemas](https://github.com/osc-em/OSCEM_Schemas) for a number of methods, including single particle cryoEM, tomography, and processing. The schemas are authored using the [LinkML](https://linkml.io) schema language, from which we automatically generate JSON Schema, JSON-LD contexts, OWL, and other formats required for validation and semantic reasoning.
 

_posts/2025-03-05-depositor-newsletter.md

@@ -21,7 +21,6 @@ Dear OpenEM members,
 the coming months, we’ll keep you updated on the project’s status and introduce key
 components in more detail. This month’s focus: the Depositor Service!
 
-
 ## The project status
 
 We're in the [Milestone V](https://www.openem.ch/timeline/), which means OpenEM is now
@@ -35,8 +34,7 @@ Scipionusers, as we expect full integration with OpenEM. Stay tuned!
 
 Our recent All-Hands Workshop took place on February 13, 2025, at the University of
 Bern. The hybrid format allowed us to record the session for those who couldn’t attend.
-You can watch the recording
-[here](https://psich.zoom.us/rec/share/0ouVFIZnhm547bav5PuN71-MrHDYkTyvs-RVb43YM73YMcKdZzt4571JgEpnn8qN.1gROCU2I5PlhniB8)
+You can watch the [recording](https://psich.zoom.us/rec/share/0ouVFIZnhm547bav5PuN71-MrHDYkTyvs-RVb43YM73YMcKdZzt4571JgEpnn8qN.1gROCU2I5PlhniB8)
 (Password: .cPK005m) or read the slides on
 [zenodo](https://doi.org/10.5281/zenodo.14937442). During the workshop, we:
 
@@ -96,4 +94,4 @@ Unlike biological research, where OneDep is the standard repository, the best de
 
 Best regards,
 
-OpenEM Team
+OpenEM Team

_posts/2025-04-15-ord-workshop.md

@@ -11,11 +11,11 @@ Join us for updates on OpenEM and other open research data projects:
 
 ---
 
-**"Advancing Open Research Data (ORD) Practices: collaboration and innovation in the ETH Domain"**<br/>
-12 June 2025 - 9am to 6pm (including an aperitif at the end)<br/>
+**"Advancing Open Research Data (ORD) Practices: collaboration and innovation in the ETH Domain"** \
+12 June 2025 - 9am to 6pm (including an aperitif at the end) \
 In Casino Bern, Casinoplatz 1, 3011 Bern
 
-Please register [here](https://bookwhen.com/fr/epflopenscience/e/ev-s3ef-20250612000000).<br/>
+Please [register](https://bookwhen.com/fr/epflopenscience/e/ev-s3ef-20250612000000). \
 *Travel costs will be covered for PhD or post-docs.*
 
 This event aims at showcasing the outcomes of the ETH Domain ORD programme and advocate excellence in ORD practices in Switzerland and beyond.

about.md

@@ -29,7 +29,7 @@ OpenEM will target both researchers producing EM data and consumers of open data
 
 ### Our Goal
 
-Our primary goal is to strengthen co-operation and innovation in the field of electron microscopy. 
+Our primary goal is to strengthen co-operation and innovation in the field of electron microscopy.
 
 OpenEM enables collaboration and data exchange in specific groups by providing a platform for data exchange and streamlining data collection processes. OpenEM ensures integration with globally recognised platforms and closes gaps in functionality and application.
 
@@ -52,4 +52,4 @@ For more information, see
 
 - [OpenEM Poster](https://zenodo.org/record/7845286)
 - [Github organization](https://github.com/SwissOpenEM/)
-- [SciCat](https://scicatproject.github.io/)
+- [SciCat](https://scicatproject.github.io/)