diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 96627f8f..3f0d1b3a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -57,11 +57,6 @@ repos: hooks: - id: isort -- repo: https://github.com/codespell-project/codespell - rev: v2.2.6 - hooks: - - id: codespell - - repo: https://github.com/PyCQA/flake8 rev: 7.0.0 hooks: diff --git a/.vscode/settings.json b/.vscode/settings.json index 9d2618cd..9c3b312e 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -6,5 +6,9 @@ "tag:yaml.org,2002:python/name:material.extensions.emoji.twemoji", "tag:yaml.org,2002:python/name:pymdownx.superfences.fence_code_format" ], - "restructuredtext.pythonRecommendation.disabled": true + "restructuredtext.pythonRecommendation.disabled": true, + "circleci.persistedProjectSelection": [ + "gh/bids-standard/in_darkness_bind_them", + "gh/bids-standard/bids-website" + ] } diff --git a/docs/blog/posts/2024-02-22-steering-group-minutes.md b/docs/blog/posts/2024-02-22-steering-group-minutes.md index 1352afa7..d3559d7d 100644 --- a/docs/blog/posts/2024-02-22-steering-group-minutes.md +++ b/docs/blog/posts/2024-02-22-steering-group-minutes.md @@ -110,15 +110,11 @@ Online Presence Working Group: Working Document - Eric is chairing the BIDS Online Presence Working Group - Eric owes the open letter to the Steering Group -- May use google season of docs (need to sign up for the program, - starts April 2nd for applications) -- Will reach out to INCF to reconnect as the admin for google - season of docs -- Mentors identified: Eric, Christine, and Remi (outlined in doc - linked in agenda) +- May use google season of docs (need to sign up for the program, starts April 2nd for applications) +- Will reach out to INCF to reconnect as the admin for google season of docs +- Mentors identified: Eric, Christine, and Remi (outlined in doc linked in agenda) - Eric will reach out to the group to schedule a follow up meeting. -- Yaroslav reminded the group that he has \$5k CAD to compensate for - work on this project +- Yaroslav reminded the group that he has \$5k CAD to compensate for work on this project BEP39 for dimensionality reduction-based networks diff --git a/docs/blog/posts/2024-03-21-steering-group-minutes.md b/docs/blog/posts/2024-03-21-steering-group-minutes.md new file mode 100644 index 00000000..88413a6f --- /dev/null +++ b/docs/blog/posts/2024-03-21-steering-group-minutes.md @@ -0,0 +1,290 @@ +--- +date: 2024-03-21 +slug: "Steering Group minutes #69" +author: anonymous +categories: +- steering group minutes +--- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links and to do + +
+ + + Guest + + Franco Pestilli + + +
+ Cooperation with DICOM standard + +

+ YOH pointed David Clunie to our + + + DICOMs deficits table + + + , he forwarded to WG-16 to consider at the next meeting March Wed 13th, 2024. +

+ +
+ BIDS 2.0 going forward! + + +
+ BEP guidelines updating (Camille & Rémi) + +

+ + + https://github.com/bids-standard/bids-extensions/pull/28 + + +

+

+ See Oscar’s vision of having BEP leads as core experts of BIDS and other domain expert be contributors (i.e. not lead BEPs) + + + https://github.com/bids-standard/bids-extensions/pull/28#discussion_r1528721354 + + +

+
+ BEP guidelines PR on technical committee + + + + https://github.com/bids-standard/bids-extensions/pull/29 + + +
+

+ Unsticking BEPs (may be covered by previous topics). Maintainer suggestions: +

+
    +
  1. +
    +

    + Steering directly mediate conflicts +

    +
    +
    2. +
  2. +
    +

    + "BEP delegates" a la Python +

    +
    +
    3. +
+

+ Rough consensus: Resolve first, formalize process later +

+ 		+
+ +**Present:** Kim Ray, Camille Maumet, Yarik Halchenko, Ariel Rokem, +Chris Markiewicz, Dora Hermes + +**Apologies:** + +**Guest:** Franco Pestilli + +## BIDS Meeting Notes + +Franco is sick, so meeting with him deferred to future meeting (possibly next time, April 4th) + +### Cooperation with DICOM standard + +YOH met with them to discuss issues between BIDS and DICOM + +- Dicom cannot enforce anything, and its difficult for them to suddenly make things mandatory + +- YOH will meet with GE manufacturer this Fri to discover more about "IHE Sharazone", + which is a system that the vendors use to share example data between them to check for compatibility across. + It seems that this is rather closed down, so hard to access and contribute to. + +- Overall, the call useful in the context that DICOM folks are now more aware of incompatibilities between BIDS and DICOM + +### BIDS 2.0 going forward! + +YOH + +- A replacement/substitution of inheritance principles would be useful + (allows you to define common metadata at the top level and more specific metadata at lower levels) + + - Proposed: limit that values cannot be overloaded + + - Related: [[BEP036 - Phenotypic Data]](https://bids.neuroimaging.io/bep036) + + - Does not conflict with Dora\'s use cases where EEG participants often each have different metadata + (e.g. number of electrodes) and would not have many common metadata across subjects + + - [[https://github.com/bids-standard/bids-2-devel/issues/65]](https://github.com/bids-standard/bids-2-devel/issues/65) + +- Discusses formalizing common principles into a standard + + - Eg BIDS like standards: [[bids-2-devel/issues/62]](https://github.com/bids-standard/bids-2-devel/issues/62) + +- Might want to reach out to [[PsychDS]](https://psych-ds.github.io/) to create a migration path + +- For example: Allen institute has a file naming schema that we might want to adopt/incorporate + + - [[bids-2-devel/issues/60]](https://github.com/bids-standard/bids-2-devel/issues/60) + + - Could help Allen institute merge/adopt BIDS + +- Please add examples to this issue for consideration (issue 62?) + +### BEP guidelines updating (Camille & Rémi) + +- Update the process of how people can submit new proposals for BEPS + +- The process of obtaining a BEP number is not clearly outlined + + - Maintainers are discussing what explicit process should be outlined + + - [[https://github.com/bids-standard/bids-extensions/pull/28]](https://github.com/bids-standard/bids-extensions/pull/28) + +- The expectation to 'become familiar' with BIDS before starting a BEP is a 'high bar' to attain + + - Some believe that BEP leads should be BIDS experts and domain experts should be contributors + + - Concerns exist that this approach may limit entrance to BIDS + +- Suggestions - adopt a procedure similar to debian where experts need to pass an exam to obtain an expert status + + - Should a BEP lead already be a BIDS contributor to ensure they have some existing BIDS knowledge + +- Often BEP leads are already BIDS familiar because of the steps that they need to create the BEP + + - Create BIDS examples in a pull request + - Add to schema + - However sometimes this familiarity is a result of going through the BEP creation process + +- CM: Current loose guidelines for establishing a BEP + + - Maintainers have a template that they provide to individuals that are interested in creating a BEP, often the maintainers ensure that the BEP lead has contributed to BIDS previously. + + - There has also been some approval by the steering committee + + - Currently, BIDS maintainers are not comfortable with the new expectation that they help 'solve' many BIDS issues/concerns (instead of the community agree on solutions) + +- The committee returns to the idea of having a BEP mentor for each BEP that has BIDS/BEP experience and can help guide the BEP lead through the BEP process + + - This could reduce zombie BEPs (when a BEP is forgotten or not actively being developed) + - Could also help with junior people contributing and potentially becoming BEP leads + +- Should there be a google doc or pull request first for a BEP? diff --git a/docs/blog/posts/2024-04-04-steering-group-minutes.md b/docs/blog/posts/2024-04-04-steering-group-minutes.md new file mode 100644 index 00000000..1a77f4db --- /dev/null +++ b/docs/blog/posts/2024-04-04-steering-group-minutes.md @@ -0,0 +1,123 @@ +--- +date: 2024-04-04 +slug: "Steering Group minutes #70" +author: anonymous +categories: +- steering group minutes +--- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links and to do + +
+ Is $70 USD acceptable as a cost to acquire the domain + + bids.org + + ? + + + https://www.godaddy.com/domainsearch/find?domainToCheck=bids.org + +
+ Is BIDS steering group moving to mattermost? + +
+ +
+ +
+ +
+ +**Present:** Ross Blair, Ariel Rokem, Kimberly Ray, Camille Maumet, Dora +Hermes, Cyril Pernet + +**Apologies:** Yaraslaw Halchenko + +**Guest:** + +## BIDS Meeting Notes + +### BIDS.org + +- \$70 is the broker fee to negotiate for the BIDS.org domain +- Steering group thinks that 4 letter URLS are likely very costly to acquire and we will not be able to afford +- A quick search on the IP shows that bids.org is owned by "web addresses for businesses inc", so... + +### MATTERmost + +- The BIDS slack group is costly , the maintainers are likely moving mattermost +- The has been a group created for the steering groups, should they utilize this channel? +- Stanford & MIT have enterprise accounts for Slack, which could allow for BIDS to have a slack channel under their license. + + - Yarik/Satra might be able to help with this at MIT + - Russ/Ross at Stanford, (but would prefer to not have BIDS slack within Stanford?) + +### BEPs - stalling (related to the BIDS connectivity BEPS) + +- Franco unable to attend meetings +- Hoping to find a solution for how to keep BEPs moving forward +- Franco, Yarik, and Ariel will be at the upcoming BIDS maintainers meeting in Seattle, they may try to begin a discussion and proposed solutions + + - Meeting facilities have good zoom capabilities, Dora may join this conversation virtually, others might is possible, + +- Proposed solutions should be brought back to the steering group for further discussion + +### BIDS maintenance Infrastructure Award Spending + +- Ariel has a google doc with the BIDS maintainers + (2024 Seattle BIDS maintainers meeting goals) + that lists requests from BIDS maintainers and community on financial needs for BIDS + +BEP BIDS Technical committee (proposal to aid with stalled BEPS) + +[[https://github.com/bids-standard/bids-extensions/pull/29]](https://github.com/bids-standard/bids-extensions/pull/29) + +- Should we invite Oscar for discussion with the BIDS steering group? + +- The complaints are not clear and there have not been alternative solutions proposed to address the issue + +- Dora proposed meeting with Oscar (~~possibly with Ariel?~~ + to better understand the concerns and bring it to the steering committee, + she would like another person to join the conversation if more clarity or context is needed + +- Additional comments: + [[https://github.com/bids-standard/bids-extensions/pull/28]](https://github.com/bids-standard/bids-extensions/pull/28), + [[https://github.com/bids-standard/bids-extensions/pull/28\#discussion\_r1514025385]](https://github.com/bids-standard/bids-extensions/pull/28#discussion_r1514025385) diff --git a/docs/blog/posts/2024-05-02-steering-group-minutes.md b/docs/blog/posts/2024-05-02-steering-group-minutes.md new file mode 100644 index 00000000..c4a66d9e --- /dev/null +++ b/docs/blog/posts/2024-05-02-steering-group-minutes.md @@ -0,0 +1,256 @@ +--- +date: 2024-05-02 +slug: "Steering Group minutes #71" +author: anonymous +categories: +- steering group minutes +--- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links and to do + +
+ potential BEPs being initiated for stimuli and EMG on gitHub + + +
+ BIDS 2.0 + + +
+ OHBM + +
    +
  • +
    +

    + Yarik (CON) and BrainLife will have “exhibit tables” – could schedule some BIDS related demos/discussions etc +

    +
    +
    • +
  • +
    +

    + Round table +

    +
    +
    • +
+
+ INCF + + +
+ BIDS working group on BEP process? + +
+ +**Present:** Ariel Rokem, Kim Ray, Anthony Galassi, Dora Hermes, Camille +Maumet, Yaroslav Halchenko, Cyril Pernet + +**Apologies:** + +**Guest:** + +## BIDS Meeting Notes + +### BIDS Seattle meeting recap + +- Successful, groups worked on various projects, a lot of progress was made on BIDS 2.0, new contributors joined + +- New work on BEP for animal modeling (BEP 32?) + +- The budget/expense summary has not been finalized yet, Ariel will work on this and report back to the steering group + +- Will establish a sub-contract at copenhagen to transfer the BIDS award money there + + - European meeting to be organized in spring 2025? + +### BEPs for stimuli and EMG on gitHub + +- What is the official protocol for this? +- No opposition for the BEP +- Appears to be an extension of EEG/MEG +- We are making the decision in support of a BEP number for this work, based on the support from the maintainers + +### BIDS 2.0 + +github project [[bids-standard/projects/10]](https://github.com/orgs/bids-standard/projects/10) + +- Should this get an official BEP? +- What is the difference between a BEP and a working group? (should this be a working group?) + + - Currently only a single working group for online progress + - This will be paving new directions/definitions of what a working group is and does + - Yarik organized the "GitHub Team" BIDS 2.0: [[bids-standard/teams/bids-2-0]](https://github.com/orgs/bids-standard/teams/bids-2-0) + +- Would like feedback on projects on github, big issues have been better formalized +- Yarik will tackle the hierarchy of file names/inheritances +- Yarik will work on this at the OHBM Brainhack in June 2024, Seoul +- INCF and SfN abstracts for BIDS 2.0 - please join is you would like to contribute + + - Can we get stickers? They are not allowed at SfN + + - A BIDS 'cheat-sheet' could be distributed as an alternative (1 page print out/flyer) + including different modalities in BIDS, ongoing BEPs, etc. + +### OHBM + +- What does BIDS have at OHBM? + +- Round Table (this is replacing the previous 'townhall') + + - We need to prepare documentation for this: a slide deck that includes the current state of BEPs + - Slide deck should focus on large themes (e.g. getting Asai involvement, BIDS 2.0) + - Will there be a hybrid option? Camille will email Beth Slater + +- Cyril will meet Korean/Asian chapter to discuss how to include Asia in BIDS + +- Can we create BIDS stickers for posters that use BIDS + +- Peer has a poster? + +- Round Table/Town hall should have a hybrid option. This should be prioritized for future OHBM meetings, + if its not a possibility for the Round Table, then we should explore moving back to the OSR Round Table + so that it can be broadcasted live. + +### INCF + +- Good opportunity to promote BEP 32 + + - Yariks postdoc might submit an abstract for this + +- Neurobagel has a participants .tsv standardization schema - should this be harmonized with BIDS 2.0. + It should help improve the participant.tsv file content + +### Participants.tsv + +- NIDM, and Neurobagel try to harmonize metadata in this file. + +- CP proposes that neurobagel should be doing their harmonization work in tandem / within BIDS. + +- Has been discussed at previous brainhacks. + +- We need a schema to standardize how metadata in this file should be structured. + +- This effort needs to be driven by Neurobagel, HED, etc (not driven by BIDS efforts). + +- HED is an example of a case where "external" efforts have contributed to BIDS substantially + and where the effort goes hand-in-glove with BIDS. + +- YOH formalized above as an issue: + [[https://github.com/bids-standard/bids-2-devel/issues/74]](https://github.com/bids-standard/bids-2-devel/issues/74) + +### BIDS working group on BEP process? + +- We need to better characterize when and how to determine what constitutes a BEP + +- Our governance documents could/should be improved to describe this process + +- Needs to address: timelines, voting processes, + + - Anthony supports having a BEP timeline proposed and presented to be voted on at the next BIDS elections. + + - Some form of rules to know, regular check-ins + + - Chris has notes from the Seattle meeting discussion on this topic: [[https://docs.google.com/document/d/10oa3rCNMDOdtprc7\_009uctfkOQqDJJVoK8dipgE6S4/edit\#heading=h.hxv1sz2uaf5f]](https://docs.google.com/document/d/10oa3rCNMDOdtprc7_009uctfkOQqDJJVoK8dipgE6S4/edit#heading=h.hxv1sz2uaf5f) + +Next Guest: Franco diff --git a/pyproject.toml b/pyproject.toml index 16e1d3b5..c9825004 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,7 +2,7 @@ line-length = 79 [tool.codespell] -ignore-words-list = "nd,manuel,ALS,TE,Acknowledgements" +ignore-words-list = "nd,manuel,ALS,TE,Acknowledgements,asai" skip = ".git,env,specification,starter_kit,examples,apps,execution,pyproject.toml,data/affiliations.tsv" [tool.isort] diff --git a/tools/convert_to_md.py b/tools/convert_to_md.py index a336974b..16932dff 100644 --- a/tools/convert_to_md.py +++ b/tools/convert_to_md.py @@ -47,14 +47,14 @@ def rename_files(input_folder): for line in text: if "Date" in line: - line = line.replace("\n", "") + line = line.replace("\n", "").replace(",", "") year = str(file.name).split("_")[0] if len(year) > 4: year = str(file.name).split("-")[0] - month, day = line.split(" ")[2:] + month, day = line.split(" ")[2:4] day = ( day.replace("th", "")