Gantt chart: misc fixes and documentation (bids-standard#363)

* misc fixes and start doc

* manage black exclude via gitignore

* switch precommit large file check back on, license year

* add documentation

* fix link

* adjust linkcheck settings

* Update LICENSE

* fix bids dashboard links

.gitignore

@@ -7,3 +7,5 @@ __pycache__
 .sass-cache
 tools/inputs
 tools/*.html
+env/
+_pages/bids_timeline.html

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
-      # - id: check-added-large-files
+      - id: check-added-large-files
       - id: check-case-conflict
 
   - repo: https://github.com/codespell-project/codespell

LICENSE

@@ -1,6 +1,6 @@
 Attribution 4.0 International
 
-Copyright (c) 2020-2023, BIDS Contributors.
+Copyright (c) 2020, BIDS Contributors.
 
 =======================================================================
 

_layouts/default.html

@@ -14,7 +14,7 @@
       "url": "http://bids.neuroimaging.io",
       "sameAs": [
         "https://en.wikipedia.org/wiki/Brain_Imaging_Data_Structure",
-        "https://twitter.com/BIDSstandard"
+        "https://x.com/BIDSstandard"
       ]
     }
   </script>

_layouts/index.html

@@ -14,7 +14,7 @@
       "url": "http://bids.neuroimaging.io",
       "sameAs": [
         "https://en.wikipedia.org/wiki/Brain_Imaging_Data_Structure",
-        "https://twitter.com/BIDSstandard"
+        "https://x.com/BIDSstandard"
       ]
     }
   </script>
@@ -106,7 +106,7 @@
   {% if site.show_footer %}
   <footer class="site-footer">
     <div class="container">
-      <a href="https://x.com/BIDSstandard?ref_src=twsrc%5Etfw" target="_blank">X</a>
+      <a href="https://x.com/BIDSstandard" target="_blank">X</a>
       <a href="https://fosstodon.org/@bidsstandard/" target="_blank">Mastodon</a>
       <a href="https://bsky.app/profile/bidsstandard.bsky.social/" target="_blank">Bluesky</a>
     </div>
@@ -127,7 +127,7 @@
     anchors.add('h6');
   </script>
 
-  <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+  <script async src="https://platform.x.com/widgets.js" charset="utf-8"></script>
 
   {% include tracking.html %}
 

_pages/governance.md

@@ -210,7 +210,7 @@ Past members of the Maintainers group are:
 If you need to contact the maintainers on a specific topic you can use the following emails:
 
 - bids-website and domain ( [Stefan Appelhoff](mailto:bids.maintenance+website@gmail.com) )
-- [Twitter account](https://twitter.com/bidsstandard){:target="_blank"} ( [Stefan Appelhoff](mailto:bids.maintenance+twitter@gmail.com) )
+- [Twitter account](https://x.com/bidsstandard){:target="_blank"} ( [Stefan Appelhoff](mailto:bids.maintenance+twitter@gmail.com) )
 - [Mastodon account](https://fosstodon.org/@bidsstandard){:target="_blank"} ( [Rémi Gau](mailto:bids.maintenance+youtube@gmail.com) )
 - [Youtube account](https://www.youtube.com/@brainimagingdatastructure6721){:target="_blank"} ( [Rémi Gau](mailto:bids.maintenance+youtube@gmail.com) )
 
@@ -272,7 +272,7 @@ letter via a "read-only" Google Document addressed to the BIDS Steering
 Group. The open letter will be posted on: the [BIDS-Specification
 GitHub](https://github.com/bids-standard/bids-specification){:target="_blank"}, [Google
 Group](https://groups.google.com/forum/#!forum/bids-discussion){:target="_blank"}, and
-[Twitter](https://twitter.com/BIDSstandard){:target="_blank"}. This proposal will state
+[Twitter](https://x.com/BIDSstandard){:target="_blank"}. This proposal will state
 what their group aims and goals are.
 
 ### BIDS Community

_pages/index.md

@@ -48,7 +48,7 @@ If you are interested in receiving occasional updates around BIDS, feel free to
 
 - The `bids-discussions` Google Group for [updates via email](https://groups.google.com/g/bids-discussion){:target="_blank"}
 - Follow BIDS on:
-  - [x](https://x.com/BIDSstandard?ref_src=twsrc%5Etfw){:target="_blank"}
+  - [x](https://x.com/BIDSstandard){:target="_blank"}
   - [Mastodon](https://fosstodon.org/@bidsstandard/){:target="_blank"}
   - [Bluesky](https://bsky.app/profile/bidsstandard.bsky.social/){:target="_blank"}
 - Join the [Brainhack Mattermost](https://mattermost.brainhack.org/) for a number of BIDS-related channels

_posts/2022-10-29-BIDS-Version-1.8.0-Release.md

@@ -20,6 +20,6 @@ along with the complete changelog:
 [https://bids-specification.readthedocs.io/en/v1.8.0/CHANGES.html](https://bids-specification.readthedocs.io/en/v1.8.0/CHANGES.html){:target="_blank"}
 
 See also the corresponding tweet-thread:
-[https://twitter.com/BIDSstandard/status/1586327298608955392](https://twitter.com/BIDSstandard/status/1586327298608955392){:target="_blank"}
+[https://x.com/BIDSstandard/status/1586327298608955392](https://x.com/BIDSstandard/status/1586327298608955392){:target="_blank"}
 
 A huge thanks to all contributors involved!

_posts/2023-07-06-Steering-Group-minutes.md

@@ -149,8 +149,7 @@ Zotero collection for tracking BIDS related publications, BEPs, etc:
 
 The BIDS grant writing kit could be updated
 
-There is also a github for this:
-[[https://github.com/Remi-Gau/bids\_citations/blob/main/dashboard.md]{.underline}](https://github.com/Remi-Gau/bids_citations/blob/main/dashboard.md)
+See also this [GitHub repo](https://github.com/bids-standard/grant_writing_kit/blob/main/README.md#dashboards)
 
 This info should also be displayed on the BIDS.io website
 
@@ -163,7 +162,7 @@ Suggested to include grant writing boilerplate info about BIDS stats
 Add rationale at the beginning of both the [[BIDS grant writing
 kit]{.underline}](https://docs.google.com/document/d/1Q7JTOvUqt05YQfnbvGoP1SZQy_CGkNEVcsVZeS4D5_o/edit#heading=h.pb4yuopfe1pt)
 and [[Remi's github
-dashboard]{.underline}](https://github.com/Remi-Gau/bids_citations/blob/main/dashboard.md)
+dashboard]{.underline}](https://github.com/bids-standard/grant_writing_kit/blob/main/README.md#dashboards)
 
 Is the BIDS granting writing kit meant to support building the BIDS
 community or for users to mention BIDS in their grants.

md_link_check_config.json

@@ -10,7 +10,7 @@
       "pattern": "^/get_involved$"
     },
     {
-      "pattern": "^https://twitter.com/[BIDSbids]*standard.*"
+      "pattern": "^https://x.com/[BIDSbids]*standard.*"
     },
     {
       "pattern": "drupal.org\/governance"

pyproject.toml

@@ -1,11 +1,3 @@
 [tool.black]
 line-length = 99
-target-version = ['py39']
-exclude = '''
-(
-  /(
-    \.git
-    | env
-  )/
-)
-'''
+target-version = ["py39"]

tools/README.md

@@ -16,3 +16,15 @@ This README file describes the tools under the `/tools` directory of the bids-we
 1. From the command line, navigate to `tools`, and then run `make all`
 1. Clean up, check the newly added files, commit
 
+## Update the Gantt chart of completed BEPs
+
+There are two ways of creating Gantt charts for a BIDS timeline.
+First install all Python requirements under `tools/requirements.txt`.
+Then, use one of the following two methods:
+
+1. `python -u tools/bep_gantt_html_create` creates a file: `_pages/bids_timeline.html` that you can inspect in your browser.
+   This file depends on the `tools/timeline.csv` data, which you should keep up to date.
+1. `python -u tools/bep_gantt_mermaid_insert` directly inserts code for a "mermaid" Gantt chart into the Get Involved page of the website.
+   You can inspect how that chart looks by building the website using Jekyll and serving locally.
+   This code depends on data from the files `beps_completed.yml` files in the `_data` directory.
+   You should keep that file up to date.

tools/bep_gant_chart.py → tools/bep_gantt_html_create.py

@@ -1,4 +1,4 @@
-"""Creates a gant chart for the completed BEPs.
+"""Creates a Gantt chart for the completed BEPs.
 
 Also include a timeline of the main BIDS events.
 """
@@ -10,7 +10,7 @@
 import pandas as pd
 import plotly.express as px
 import plotly.graph_objects as go
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from pyzotero import zotero
 
 INCLUDE_PATCHES = False
@@ -31,7 +31,8 @@ def create_bep_timeline() -> type[go.Figure]:
     completd_beps = data_dir() / "beps_completed.yml"
 
     with open(completd_beps, "r") as f:
-        data = yaml.safe_load(f)
+        yaml = YAML(typ="safe", pure=True)
+        data = yaml.load(f)
 
     df = []
 
@@ -140,9 +141,9 @@ def add_publications_to_timeline(fig: go.Figure) -> type[go.Figure]:
     dois = []
     dates = []
     for item in items:
-        titles.append(item["data"].get("title"))
-        dois.append(item["data"]["DOI"])
-        dates.append(item["data"]["date"])
+        titles.append(item["data"].get("title", "n/a"))
+        dois.append(item["data"].get("DOI", "n/a"))
+        dates.append(item["data"].get("date", "n/a"))
 
     fig.add_trace(
         go.Scatter(
@@ -191,6 +192,7 @@ def main():
     fig.show()
 
     # save as html
+    # NOTE: This file is ignored in git (see .gitignore)
     fig.write_html(root_dir() / "_pages" / "bids_timeline.html")
 
 

tools/insert_mermaid_bep_gantt.py → tools/bep_gantt_mermaid_insert.py

@@ -1,10 +1,10 @@
-"""Creates a gant chart for the completed BEPs"""
+"""Creates a Gantt chart for the completed BEPs"""
 from __future__ import annotations
 
 from pathlib import Path
 
 import pandas as pd
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from rich import print
 
 
@@ -30,7 +30,8 @@ def get_bep_timeline() -> pd.DataFrame:
     completd_beps = data_dir() / "beps_completed.yml"
 
     with open(completd_beps, "r") as f:
-        data = yaml.safe_load(f)
+        yaml = YAML(typ="safe", pure=True)
+        data = yaml.load(f)
 
     df = []