From fbfaf3f378cb6ecb2466e71b16697ecf515fda22 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 22 May 2023 21:25:49 -0400 Subject: [PATCH] [ENH] add steering group minutes 2021 (#302) * add minutes 2021 * fix tables * clean up new pages --- .vscode/settings.json | 3 - _posts/2021-05-20-Steering-Group-minutes.md | 278 +++++++++++ _posts/2021-06-10-Steering-Group-minutes.md | 295 ++++++++++++ _posts/2021-07-01-Steering-Group-minutes.md | 184 ++++++++ _posts/2021-08-12-Steering-Group-minutes.md | 157 +++++++ _posts/2021-09-02-Steering-Group-minutes.md | 200 ++++++++ _posts/2021-11-04-Steering-Group-minutes.md | 258 ++++++++++ _posts/2021-12-14-Steering-Group-minutes.md | 440 ++++++++++++++++++ .../YYYY-MM-DD-Steering-Group-minutes.md | 24 + tools/Makefile | 8 + tools/convert_to_md.py | 139 ++++++ tools/convert_to_md.sh | 26 ++ tools/requirements.txt | 1 + 13 files changed, 2010 insertions(+), 3 deletions(-) delete mode 100644 .vscode/settings.json create mode 100644 _posts/2021-05-20-Steering-Group-minutes.md create mode 100644 _posts/2021-06-10-Steering-Group-minutes.md create mode 100644 _posts/2021-07-01-Steering-Group-minutes.md create mode 100644 _posts/2021-08-12-Steering-Group-minutes.md create mode 100644 _posts/2021-09-02-Steering-Group-minutes.md create mode 100644 _posts/2021-11-04-Steering-Group-minutes.md create mode 100644 _posts/2021-12-14-Steering-Group-minutes.md create mode 100644 templates/YYYY-MM-DD-Steering-Group-minutes.md create mode 100644 tools/Makefile create mode 100644 tools/convert_to_md.py create mode 100644 tools/convert_to_md.sh create mode 100644 tools/requirements.txt diff --git a/.vscode/settings.json b/.vscode/settings.json deleted file mode 100644 index 7c2feb7e..00000000 --- a/.vscode/settings.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "editor.formatOnSave": false -} diff --git a/_posts/2021-05-20-Steering-Group-minutes.md b/_posts/2021-05-20-Steering-Group-minutes.md new file mode 100644 index 00000000..22b5f4b5 --- /dev/null +++ b/_posts/2021-05-20-Steering-Group-minutes.md @@ -0,0 +1,278 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/05/20 + +Date: Thursday, May 20, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+ Meeting guest: BEP30: NIRS leads + + Extension proposal: + + + https://bids.neuroimaging.io/bep030 + + +
+

+ INCF: BIDS training slot at INCF training event +

+
    +
  • +
    +

    + Reserved a 60 minute slot for a live panel +

    +
    +
    • +
  • +
    +

    + Topics: BIDS-Apps, Derivatives, and highlighting the work Maintainers do +

    +
    +
    • +
+ 		+
+

+ New BEP: BIDS-aDWI +

+
    +
  • +
    +

    + Scheduling leads to meet with Maintainers Group +

    +
    +
    • +
  • +
    +

    + Invited Oscar and Franco to that meeting +

    +
    +
    • +
+ 		+ Extension proposal: + + + https://bids.neuroimaging.io/bep033 + + +
+

+ BIDS Steering Group elections in the Fall +

+
    +
  • +
    +

    + Promote during OHBM +

    +
    +
    • +
  • +
    +

    + 1 member to be rotated out? +

    +
    +
    • +
+ 		+
+

+ GN items +

+
    +
  • +
    +

    + GN and RO taking pass at website enhancement +

    +
    +
    • +
  • +
    +

    + BIDS adoption/usage survey +

    +
    +
    • +
  • +
    +

    + BIDS-Protocol bep efforts? +

    +
    +
    • +
+ 		+ BIDS usage survey 2019: https://reproducibility.stanford.edu/bids-usage-survey-results/ +
+

+ BIDS plans for OHBM +

+
    +
  • +
    +

    + Open Science Room: only Town Hall +

    +
    +
      +
    • +
      +

      + Panel canceled +

      +
      +
      • +
    +
    • +
  • +
    +

    + Will support our own Zoom webinar +

    +
    +
    • +
  • +
    +

    + Special scheduling permission +

    +
    +
      +
    • +
      +

      + Hold it on the first day (Monday)? +

      +
      +
      • +
    +
    • +
+ 		+ + + https://ohbm.github.io/osr2021/ + + +
+ Incorporated initial pass of nudging BEP leads to work more transparently during the BEP paper writing process + + + + https://github.com/bids-standard/bids-specification/wiki/BIDS-Extension-Proposal-(BEP)-submission-process + + +
+

+ Guest scheduling: +

+

+ June 10 - Joint Steering-Maintainers group meeting (prep for OHBM) +

+

+ July 20 - aDWI (BEP33) leads joining BIDS Maintainers Group meeting (Franco Pestilli planning to join: BEP16-DWI derivatives lead) +

+

+ July 22 - MIDS (BEP25) BEP leads joining +

+

+ August 12 - Dave Keator returning to share an update on NIDM-terms +

+ 		+

+ aDWI - BEP33: + + + https://bids.neuroimaging.io/bep033 + + +

+

+ MIDS: + + + https://bids.neuroimaging.io/bep025 + + +

+

+ NIDM-terms update: + + + https://github.com/bids-standard/bids-specification/issues/423#issuecomment-844255673 + + +

+
+ + + + + + + +Executive summary + +Action items + +Minutes diff --git a/_posts/2021-06-10-Steering-Group-minutes.md b/_posts/2021-06-10-Steering-Group-minutes.md new file mode 100644 index 00000000..6a267ce8 --- /dev/null +++ b/_posts/2021-06-10-Steering-Group-minutes.md @@ -0,0 +1,295 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/06/10 + +Date: Thursday, June 10, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+ Joint meeting with BIDS Maintainers + +
+

+ BIDS Steering Group elections in the Fall +

+
    +
  • +
    +

    + Promote during OHBM +

    +
    +
    • +
  • +
    +

    + 1 member to be rotated out? +

    +
    +
    • +
  • +
    +

    + Switch chair???? +

    +
    +
    • +
+

+ From the governing structure: +

+

+ Initially, Steering Group members will be elected for staggered terms of 2/3/4 years, to allow continuity and overlap across years. This will ensure institutional knowledge is preserved within the BIDS Steering Group. In the initial BIDS Steering Group, there will be at least one non-MRI modality represented. -> +

+

+ One person drops after 1 year, 2 more after 2 and 2 more after 4. +

+ 		+ + + https://bids.neuroimaging.io/governance.html#c-Governance-ratification-and-BIDS-Steering-Group-initialization + + +
+

+ BIDS plans for OHBM +

+
    +
  • +
    +

    + Open Science Room: only Town Hall +

    +
    +
      +
    • +
      +

      + Panel canceled +

      +
      +
      • +
    +
    • +
  • +
    +

    + Will support our own Zoom webinar +

    +
    +
    • +
  • +
    +

    + Town Hall process +

    +
    +
    • +
  • +
    +

    + Town Hall will be on Monday June 21 at 10pm CEST/ 4pm ET/ 1pm PT +

    +
    +
    • +
+

+ More OHBM prep? +

+
    +
  • +
    +

    + Prepare survey material for querying community +

    +
    +
    • +
  • +
    +

    + Also advertise maintainer roles, especially the more administrative role? +

    +
    +
    • +
+ 		+

+ + + https://ohbm.github.io/osr2021/ + + +

+
+

+ GN items +

+
    +
  • +
    +

    + GN and RO taking pass at website enhancement +

    +
    +
    • +
  • +
    +

    + BIDS adoption/usage survey +

    +
    +
    • +
  • +
    +

    + BIDS-Protocol bep efforts? +

    +
    +
    • +
+ 		+ BIDS usage survey 2019: + + + https://reproducibility.stanford.edu/bids-usage-survey-results/ + + +
+

+ BEP guidelines +

+
    +
  • +
    +

    + Advise against graduate students or master’s students to lead BEP efforts +

    +
    +
      +
    • +
      +

      + Part of requirement to graduate from program +

      +
      +
      • +
    +
    • +
+ 		+
+ BIDS Stat Model publishing plan? + +
+

+ Guest scheduling: +

+

+ June 10 - Joint Steering-Maintainers group meeting (prep for OHBM) +

+

+ July 20 - aDWI (BEP33) leads joining BIDS Maintainers Group meeting (Franco Pestilli planning to join: BEP16-DWI derivatives lead) +

+

+ July 22 - MIDS (BEP25) BEP leads joining +

+

+ August 3 - Microscopy (BEP31) leads joining BIDS Maintainers meeting +

+

+ August 12 - Dave Keator returning to share an update on NIDM-terms +

+

+ August 17 - NIRS (BEP30) leads joining BIDS Maintainers meeting +

+ 		+

+ aDWI - BEP33: + + + https://bids.neuroimaging.io/bep033 + + +

+

+ MIDS - BEP25: + + + https://bids.neuroimaging.io/bep025 + + +

+

+ Microscopy - BEP31: +

+

+ + + https://bids.neuroimaging.io/bep031 + + +

+

+ NIDM-terms update: + + + https://github.com/bids-standard/bids-specification/issues/423#issuecomment-844255673 + + +

+

+ NIRS - BEP30: + + + https://bids.neuroimaging.io/bep030 + + +

+
diff --git a/_posts/2021-07-01-Steering-Group-minutes.md b/_posts/2021-07-01-Steering-Group-minutes.md new file mode 100644 index 00000000..49a0513a --- /dev/null +++ b/_posts/2021-07-01-Steering-Group-minutes.md @@ -0,0 +1,184 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/07/01 + +Date: Thursday, July 1, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+

+ BIDS Steering Group elections in the Fall +

+
    +
  • +
    +

    + Promote during OHBM +

    +
    +
    • +
  • +
    +

    + 1 member to be rotated out? +

    +
    +
    • +
  • +
    +

    + Switch chair???? +

    +
    +
    • +
+

+ From the governing structure: +

+

+ Initially, Steering Group members will be elected for staggered terms of 2/3/4 years, to allow continuity and overlap across years. This will ensure institutional knowledge is preserved within the BIDS Steering Group. In the initial BIDS Steering Group, there will be at least one non-MRI modality represented. -> +

+

+ One person drops after 1 year, 2 more after 2 and 2 more after 4. +

+ 		+ + + https://bids.neuroimaging.io/governance.html#c-Governance-ratification-and-BIDS-Steering-Group-initialization + + +
+ OHBM review + +
+ (ongoing) BIDS usage survey + +
+ BEP guidelines - recommend against student leading BEP if it is a requirement for graduation + +
+

+ Guest scheduling: +

+

+ July 20 - aDWI (BEP33) leads joining BIDS Maintainers Group meeting (Franco Pestilli planning to join: BEP16-DWI derivatives lead) +

+

+ July 22 - MIDS (BEP25) BEP leads joining +

+

+ August 3 - Microscopy (BEP31) leads joining BIDS Maintainers meeting +

+

+ August 12 - Dave Keator returning to share an update on NIDM-terms +

+

+ August 17 - NIRS (BEP30) leads joining BIDS Maintainers meeting +

+ 		+

+ aDWI - BEP33: + + + https://bids.neuroimaging.io/bep033 + + +

+

+ MIDS - BEP25: + + + https://bids.neuroimaging.io/bep025 + + +

+

+ Microscopy - BEP31: +

+

+ + + https://bids.neuroimaging.io/bep031 + + +

+

+ NIDM-terms update: + + + https://github.com/bids-standard/bids-specification/issues/423#issuecomment-844255673 + + +

+

+ NIRS - BEP30: + + + https://bids.neuroimaging.io/bep030 + + +

+
+ + +## Executive summary + +After a discussion we decided that Kirstie will rotate out now, but then +Russ should probably rotate out next, maybe together with Melanie, to +ensure the balance of the remaining members. This way it's very likely +that we can keep an MRI representative in the steering group which is a +requirement. + +Wrt election proceedings we may have people put up a 200 word criteria +on how they complement the current steering group in terms of e.g. +modality, gender, geographic location, seniority, etc. Maybe add this to +the governance document by adding something regarding not only ensuring +diversity wrt modality but also diversity. + +Regarding resilience wrt Franklin\'s maintainer job, since he needs to +step out a bit, maybe we can together with the empty steering group slot +advertise for two more communication type of maintainers. Robert +suggests to maybe reach out and go for people to spend their PhD duty +hours on for example being BIDS maintainer. Kirstie proposes writing up +a clear role description, accompanied with suggestions on how to justify +time to supervisors. Promote to the broader community before relying on +steering committee to find maintainers. diff --git a/_posts/2021-08-12-Steering-Group-minutes.md b/_posts/2021-08-12-Steering-Group-minutes.md new file mode 100644 index 00000000..716fa683 --- /dev/null +++ b/_posts/2021-08-12-Steering-Group-minutes.md @@ -0,0 +1,157 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/08/12 + +Date: Thursday, August 12, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+ Dave Keator (NIDM) joining to give an update on NIDM-terms + +

+ NIDM terms: + + + https://nidm-terms.github.io/ + + +

+

+ + + https://github.com/bids-standard/bids-specification/issues/423#issuecomment-844255673 + + +

+
+

+ BIDS Steering Group elections in the Fall +

+
    +
  • +
    +

    + Switch chair? +

    +
    +
    • +
  • +
    +

    + Discuss process +

    +
    +
    • +
+

+ KW will be rotated out - will be invited back to give advice on specific topics (e.g. community development) +

+

+ From the governing structure: +

+

+ Initially, Steering Group members will be elected for staggered terms of 2/3/4 years, to allow continuity and overlap across years. This will ensure institutional knowledge is preserved within the BIDS Steering Group. In the initial BIDS Steering Group, there will be at least one non-MRI modality represented. -> +

+

+ One person drops after 1 year, 2 more after 2 and 2 more after 4. +

+ 		+ + + https://bids.neuroimaging.io/governance.html#c-Governance-ratification-and-BIDS-Steering-Group-initialization + + +
+ (ongoing) BIDS usage survey + +
+

+ BEP guidelines - recommend against student leading BEP if it is a requirement for graduation +

+

+ -> move to next meeting, should maybe be added to governance? +

+ 		+
+

+ Guest scheduling: +

+

+ August 12 - Dave Keator returning to share an update on NIDM-terms +

+

+ August 17 - NIRS (BEP30) leads joining BIDS Maintainers meeting +

+

+ October 14 - MIDS (BEP25) BEP leads joining +

+ 		+

+ MIDS - BEP25: +

+

+ + + https://bids.neuroimaging.io/bep025 + + +

+

+ NIDM-terms update: + + + https://github.com/bids-standard/bids-specification/issues/423#issuecomment-844255673 + + +

+

+ NIRS - BEP30: + + + https://bids.neuroimaging.io/bep030 + + +

+
+ +Items for next time: + +Update from SquishyMedia on the validator refactoring (Mel) diff --git a/_posts/2021-09-02-Steering-Group-minutes.md b/_posts/2021-09-02-Steering-Group-minutes.md new file mode 100644 index 00000000..90d796aa --- /dev/null +++ b/_posts/2021-09-02-Steering-Group-minutes.md @@ -0,0 +1,200 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/09/02 + +Date: Thursday, September 2, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+ New BIDS maintainer - Anthony Galassi + +
+

+ BIDS Steering Group elections in the Fall +

+
    +
  • +
    +

    + Switch chair? +

    +
    +
    • +
  • +
    +

    + Discuss process +

    +
    +
    • +
+

+ Suggestion from previous meeting: +

+
    +
  • +
    +

    + Have candidates make statement about what they add to steering group, including diversity (broadly construed) +

    +
    +
    • +
  • +
    +

    + PR from steering group to clarify candidate filtering process by existing steering group (KW) +

    +
    +
    • +
+

+ KW will be rotated out - will be invited back to give advice on specific topics (e.g. community development) +

+

+ From the governing structure: +

+

+ Initially, Steering Group members will be elected for staggered terms of 2/3/4 years, to allow continuity and overlap across years. This will ensure institutional knowledge is preserved within the BIDS Steering Group. In the initial BIDS Steering Group, there will be at least one non-MRI modality represented. -> +

+

+ One person drops after 1 year, 2 more after 2 and 2 more after 4. +

+ 		+ + + https://bids.neuroimaging.io/governance.html#c-Governance-ratification-and-BIDS-Steering-Group-initialization + + +
+ Writing up BIDS usage survey into blog post + +
+

+ BEP guidelines - recommend against student leading BEP if it is a requirement for graduation +

+

+ -> should maybe be added to governance? +

+

+ -> +1 preparing a BEP is okay, requiring acceptance is not +

+ 		+
+ Stat-model discussion + + + + https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M/edit + + +
+

+ BEP updates: +

+ + 		+
+ MG: Update from SquishyMedia on the validator refactoring + +
+ MG: As modalities get more complicated - converters should be built to ease the forking and enhancing process + + + + https://neurostars.org/t/repetitiontime-parameters-what-are-they-and-where-to-find-them/20020/8 + + +
+

+ Guest scheduling: +

+

+ October 14 - MIDS (BEP25) BEP leads joining +

+ 		+

+ MIDS - BEP25: +

+

+ + + https://bids.neuroimaging.io/bep025 + + +

+
diff --git a/_posts/2021-11-04-Steering-Group-minutes.md b/_posts/2021-11-04-Steering-Group-minutes.md new file mode 100644 index 00000000..837acf38 --- /dev/null +++ b/_posts/2021-11-04-Steering-Group-minutes.md @@ -0,0 +1,258 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/11/04 + +Date: Thursday, November 4, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+

+ Next meeting: December 14 at 8:30am PT / 5:30pm CET +

+
    +
  • +
    +

    + Last meeting of the year +

    +
    +
      +
    • +
      +

      + Canceled November 25 and December 16 +

      +
      +
      • +
    +
    • +
  • +
    +

    + Starting back up on January 6 at 6am PT / 3pm CET +

    +
    +
    • +
+ 		+
+ BEP31: Microscopy community review kicking off on November 8 and closing November 19 + + + + https://github.com/bids-standard/bids-specification/pull/881 + + +
+

+ BIDS Steering Group elections +

+
    +
  • +
    +

    + Update +

    +
    +
      +
    • +
      +

      + Minor irregularities such as ballots that are rank 1 for 1st person rank 2 for 2nd and so on +

      +
      +
      • +
    • +
      +

      + Analyzing for more irregularities +

      +
      +
      • +
    +
    • +
  • +
    +

    + Have surpassed quorum +

    +
    +
    • +
+ 		+
+

+ (continued) Consider modularizing the specification +

+
    +
  • +
    +

    + Components: Raw, derivatives, modeling, and metadata +

    +
    +
    • +
  • +
    +

    + Each have their own common principles to help establish foundation to build upon +

    +
    +
    • +
  • +
    +

    + Ease incorporation process +

    +
    +
    • +
+ 		+
+

+ Clarification of the relationship between BIDS and BIDS-Apps +

+
    +
  • +
    +

    + Description/perspective from Steering Group? +

    +
    +
    • +
+

+ > To be addressed in website improvements. +

+ 		+
+ (continued) Writing up BIDS usage survey into blog post + +
+

+ (continued) BEP guidelines - recommend against student leading BEP if it is a requirement for graduation +

+

+ -> + + should maybe be added to governance? + +

+

+ -> + + + BEP Lead Guidelines + + +

+

+ - RO: This should become part of website. +

+

+ -> +1 preparing a BEP is okay, requiring acceptance is not +

+ 		+
+

+ MG: As modalities get more complicated - converters should be built to ease the forking and enhancing process +

+

+ > RO: Examples generated from multiple labs with ad hoc or common converters. +

+

+ > RP: Letters of support? Statement of relation to existing standards? +

+ 		+ + + https://neurostars.org/t/repetitiontime-parameters-what-are-they-and-where-to-find-them/20020/8 + + +
+

+ Franco Pestilli’s BIDS-connectivity grant +

+
    +
  • +
    +

    + MG: I’d be especially interested to hear if we are straining maintainers too much by trying to get 7 BEPs merged within two years +

    +
    +
    • +
+ 		+
+

+ Guest scheduling: +

+

+ January 27 - Franco Pestilli joining to discuss scope of BIDS-connectivity grant +

+

+ February 17 - BEP34 (computational models) joining to discuss their BEP +

+ 		+ BEP34: https://docs.google.com/document/d/1NT1ERdL41oz3NibIFRyVQ2iR8xH-dKY-lRCB4eyVeRo/edit +
+ +(2nd half) diff --git a/_posts/2021-12-14-Steering-Group-minutes.md b/_posts/2021-12-14-Steering-Group-minutes.md new file mode 100644 index 00000000..9e3ee0a4 --- /dev/null +++ b/_posts/2021-12-14-Steering-Group-minutes.md @@ -0,0 +1,440 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2021/12/14 + +Date: Tuesday, December 14, 2021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ Topic + + Relevant Links +
+

+ Welcome Ariel Rokem! +

+

+ Farewell to Kirstie! +

+
    +
  • +
    +

    + New maintainer: Eric Earl +

    +
    +
    • +
+ 		+
+

+ Last meeting of the year +

+
    +
  • +
    +

    + Starting back up on January 6 at 6am PT / 3pm CET +

    +
    +
    • +
+ 		+
+

+ BEP31: Microscopy update +

+
    +
  • +
    +

    + community review completed +

    +
    +
    • +
  • +
    +

    + Final reviews +

    +
    +
    • +
  • +
    +

    + Wrapping up validator and examples +

    +
    +
    • +
  • +
    +

    + Estimated completion and incorporation: early next year +

    +
    +
    • +
+ 		+

+ + + https://github.com/bids-standard/bids-specification/pull/881 + + +

+

+ + + Map bep number to name + + +

+
+

+ (continued) Consider modularizing the specification +

+
    +
  • +
    +

    + Components: Raw, derivatives, modeling, and metadata +

    +
    +
    • +
  • +
    +

    + Each have their own common principles to help establish foundation to build upon +

    +
    +
    • +
  • +
    +

    + Ease incorporation process +

    +
    +
    • +
+ 		+

+ + + https://github.com/bids-standard/bids-specification/issues/255 + + +

+

+ + + https://github.com/bids-standard/bids-specification/issues/401 + + +

+

+ Let’s sort the BEPs here, both upcoming and old: +

+

+ + + https://docs.google.com/spreadsheets/d/1im1AmDfEBRtFOtQlv_atUtOH8xyiEmL_QsstKKQ6_eE/edit?usp=sharing + + +

+
+

+ Clarification of the relationship between BIDS and BIDS-Apps +

+
    +
  • +
    +

    + Description/perspective from Steering Group? +

    +
    +
    • +
+

+ > To be addressed in website improvements. +

+ 		+
+ (continued) Writing up BIDS usage survey into blog post + +
+

+ (continued) BEP guidelines - recommend against student leading BEP if it is a requirement for graduation +

+

+ -> + + should maybe be added to governance? + +

+

+ -> + + + BEP Lead Guidelines + + +

+

+ - RO: This should become part of website. +

+

+ -> +1 preparing a BEP is okay, requiring acceptance is not +

+ 		+
+

+ MG: As modalities get more complicated - converters should be built to ease the forking and enhancing process +

+

+ > RO: Examples generated from multiple labs with ad hoc or common converters. +

+

+ > RP: Letters of support? Statement of relation to existing standards? +

+
    +
  • +
    +

    + Focus on sharing in Starter Kit +

    +
    +
    • +
+ 		+ + + https://neurostars.org/t/repetitiontime-parameters-what-are-they-and-where-to-find-them/20020/8 + + +
+

+ Franco Pestilli’s BIDS-connectivity grant +

+
    +
  • +
    +

    + MG: I’d be especially interested to hear if we are straining maintainers too much by trying to get 7 BEPs merged within two years +

    +
    +
    • +
+ 		+
+

+ Starter kit update +

+
    +
  • +
    +

    + Remi and Abrren (new contributor) transferred wiki into repository +

    +
    +
    • +
  • +
    +

    + Pushing into jupyterbook +

    +
    +
    • +
+

+ ––> Try to meet with Remi etc to converge with the website +

+ 		+ + + https://bids-standard.github.io/bids-starter-kit/ + + +
+

+ Moving meeting timeslot? +

+
    +
  • +
    +

    + Perhaps moving from 6am to 8am? +

    +
    +
    • +
  • +
    +

    + Preserve the triweekly schedule +

    +
    +
    • +
+ 		+
+

+ Proposed joint Steering Group - Maintainers Group meeting +

+
    +
  • +
    +

    + March 10? +

    +
    +
    • +
+ 		+
+

+ Performing biannual BEP updates in January 2022 +

+
    +
  • +
    +

    + Provide insights into the status and progress of our BEPs +

    +
    +
    • +
+ 		+
+

+ Guest scheduling: +

+
    +
  • +
    +

    + January 27 - Franco Pestilli joining to discuss scope of BIDS-connectivity grant +

    +
    +
    • +
  • +
    +

    + February 17 - BEP34 (computational models) joining to discuss their BEP +

    +
    +
    • +
+

+ Maintainers Group guests: +

+
    +
  • +
    +

    + January 18 - BEP029: Virtual and physical motion BEP leads joining +

    +
    +
    • +
  • +
    +

    + TBD - BEP020: Eye-tracking +

    +
    +
    • +
+ 		+

+ BEP34 (comp models): + + + https://docs.google.com/document/d/1NT1ERdL41oz3NibIFRyVQ2iR8xH-dKY-lRCB4eyVeRo/edit + + +

+

+ BEP029 (motion): + + + https://bids.neuroimaging.io/bep029 + + +

+

+ BEP020 (eye-tracking): + + + https://bids.neuroimaging.io/bep020 + + +

+
diff --git a/templates/YYYY-MM-DD-Steering-Group-minutes.md b/templates/YYYY-MM-DD-Steering-Group-minutes.md new file mode 100644 index 00000000..226d72be --- /dev/null +++ b/templates/YYYY-MM-DD-Steering-Group-minutes.md @@ -0,0 +1,24 @@ +--- +title: Steering Group executive summary, action items, and minutes +author: +display: true +--- + +# Steering Group minutes + +Date: + + + +### Executive Summary + +### Action items + +| Action item | +| ----------- | +| | + +### Minutes + +- +- diff --git a/tools/Makefile b/tools/Makefile new file mode 100644 index 00000000..8513c055 --- /dev/null +++ b/tools/Makefile @@ -0,0 +1,8 @@ +clean: + rm -f *.html + rm -f *.md + +all: clean + bash convert_to_md.sh + python3 convert_to_md.py + mv *.md ../_posts diff --git a/tools/convert_to_md.py b/tools/convert_to_md.py new file mode 100644 index 00000000..77b01cdc --- /dev/null +++ b/tools/convert_to_md.py @@ -0,0 +1,139 @@ +""" +- rename files to YYYY-MM-DD-Steering-Group-minutes.* +- prettifies the html files +- process the markdown files by: + - adding the front matter + - removing the lines that are not relevant + - using the html version of the tables instead of the markdown version + because the pandoc version of the markdown tables is not very good +""" +from rich import print +from pathlib import Path +import datetime + +input_folder = Path(__file__).parent + + +from bs4 import BeautifulSoup + + +def prettify_html(input_folder): + for file in input_folder.glob("*.html"): + # Read the HTML file + with open(file, "r") as f: + html = f.read() + # Create BeautifulSoup object + soup = BeautifulSoup(html, "html.parser") + # Pretty print the HTML + pretty_html = soup.prettify() + with open(file, "w") as f: + f.write(pretty_html) + + +def rename_files(input_folder): + for file in input_folder.glob("*.md"): + with open(file, "r") as f: + text = f.readlines() + + for line in text: + if "Date" in line: + line = line.replace("\n", "") + year = str(file.name).split("_")[0] + if len(year) > 4: + year = str(file.name).split("-")[0] + month, day = line.split(" ")[2:] + mnum = datetime.datetime.strptime(month, "%B").month + new_name = f"{year}-{mnum:02d}-{int(day):02d}-Steering-Group-minutes.md" + print(file) + print(new_name) + file.rename(new_name) + hmtl_file = file.with_suffix(".html") + if hmtl_file.exists(): + hmtl_file.rename(Path(new_name).with_suffix(".html")) + break + + +def sanitize_md(input_folder): + for file in input_folder.glob("*.md"): + year = str(file.name).split("-")[0] + month = str(file.name).split("-")[1] + day = str(file.name).split("-")[2] + + with open(file, "r") as f: + text = f.readlines() + + with open(file, "w") as f: + add_front_matter_and_title(f, year, month, day) + + write_line = False + + for line in text: + # skip lines that are not relevant + if any( + x in line + for x in [ + "Check your local time", + "arewemeetingyet", + "stanford.zoom", + "Password:", + "Time:", + "Room:", + "Attending:", + ] + ): + continue + + # skip lines that are markdown tables + if any(line.startswith(x) for x in ["|", "+-", "+="]): + continue + + if write_line: + f.write(line) + + if "Date" in line: + write_line = True + line = line.replace("\n", "") + f.write(f"{line}, {year}\n") + f.write("\n\n\n\n") + # add the table in html format for better rendering + print_table_from_html(file, f) + + +def add_front_matter_and_title(f, year, month, day): + f.write( + f"""--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes {year}/{month}/{day} + +""" + ) + + +def print_table_from_html(input_file: Path, output_file): + html_file = input_file.with_suffix(".html") + if html_file.exists(): + with open(html_file, "r") as f: + text = f.readlines() + print_line = False + for line in text: + if "" in line: + print_line = True + if "
" in line: + output_file.write(line) + print_line = False + if print_line: + output_file.write(line) + + +def main(): + rename_files(input_folder) + prettify_html(input_folder) + sanitize_md(input_folder) + + +if __name__ == "__main__": + main() diff --git a/tools/convert_to_md.sh b/tools/convert_to_md.sh new file mode 100644 index 00000000..ca904153 --- /dev/null +++ b/tools/convert_to_md.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +# Convert from .docx to markdown. +# - requires to have pandoc installed +# +# from https://github.com/llbbl/scripts/blob/main/util/convert_all_word_files.sh + +YEAR="2021" + +# save current working directory to variable +cwd=$(pwd)/inputs/${YEAR} + +# find all .docx files in current directory +find $cwd -name "*.docx" -type f -print0 | while IFS= read -r -d $'\0' line; do + + # remove spaces in filename + ns_filename=$(echo $line | sed 's/ /_/g') + + # get filename from input + the_filename=$(basename -s .docx $ns_filename) + + # convert word to markdown + echo "pandoc --from docx --to markdown \"$line\" -o ${YEAR}_$the_filename.md" + pandoc --from docx --to markdown "$line" -o ${YEAR}_$the_filename.md + pandoc --from docx --to html "$line" -o ${YEAR}_$the_filename.html +done diff --git a/tools/requirements.txt b/tools/requirements.txt new file mode 100644 index 00000000..c1f5f713 --- /dev/null +++ b/tools/requirements.txt @@ -0,0 +1 @@ +beautifulsoup4