From 277bcdfaafcdc2a8ebb44e199f12f41b29adeaa9 Mon Sep 17 00:00:00 2001 From: dilpath Date: Wed, 17 Apr 2024 15:15:47 +0200 Subject: [PATCH] consolidate with old template --- .../new_petab_problem.md | 14 --------- pull_request_template.md | 29 ++++++++++++------- 2 files changed, 19 insertions(+), 24 deletions(-) delete mode 100644 .github/PULL_REQUEST_TEMPLATE/new_petab_problem.md diff --git a/.github/PULL_REQUEST_TEMPLATE/new_petab_problem.md b/.github/PULL_REQUEST_TEMPLATE/new_petab_problem.md deleted file mode 100644 index 19c2a3b..0000000 --- a/.github/PULL_REQUEST_TEMPLATE/new_petab_problem.md +++ /dev/null @@ -1,14 +0,0 @@ -# Checklist -- [ ] Information about the model is in the SBML metadata - - [ ] Reference to the original publication, and any other relevant references - - [ ] A brief model description (one or two sentences) - - [ ] A brief description of the data (one or two sentences) - - [ ] Any differences between the implementation and the original publication -- [ ] Information is in the model's GitHub issue - - [ ] Any differences between the implementation and the original publication - - [ ] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit) - - [ ] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting) -- [ ] PEtab files - - [ ] A "simulated data" measurement table is included, using the nominal parameters - - [ ] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication -- [ ] I am assigned to the GitHub issue diff --git a/pull_request_template.md b/pull_request_template.md index d8e415d..21626d8 100644 --- a/pull_request_template.md +++ b/pull_request_template.md @@ -1,14 +1,23 @@ -# Checklist for the submission of new problems -- [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`) -- The problem is setup to quickly reproduce figures from the original paper, by including - - [ ] A PEtab visualization file - - [ ] Simulated data generated by simulating the PEtab problem with parameters from the original paper -- [ ] The problem name follows the following convention: `{LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}` +**Checklist for the submission of new PEtab problems** +- [ ] The problem ID is in the format `{LAST_NAME_OF_FIRST_AUTHOR}_{ABBREVIATED_JOURNAL_NAME}{YEAR_OF_PUBLICATION}` +- [ ] There is a GitHub issue for this problem + - [ ] The problem ID is in the title + - [ ] A brief model description (one or two sentences) + - [ ] A brief data description (one or two sentences) + - [ ] The issue and PR are linked to each other + - [ ] Differences between the implementation and the original publication are described + - [ ] Experience of fitting / uncertainty analysis (e.g. optimizer used, hyperparameters, reproducibility of best fit) + - [ ] Source of nominal parameters (e.g.: taken from the original publication, or from your own fitting) +- [ ] The SBML file + - [ ] Annotation with reference to the original publication ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L4-L14)) + - [ ] The model ID and model name attributes in the SBML model file match the problem name +- [ ] PEtab files + - [ ] A "simulated data" measurement table is included, using the nominal parameters + - [ ] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication + - [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`) +- [ ] The PEtab problem author(s) are assigned to the GitHub issue - [ ] The PEtab problem is based on a model that is - [ ] peer-reviewed and - [ ] published -- [ ] The model ID and model name attributes in the SBML model file match the problem name -- [ ] Any information related to methods used with the PEtab problem to reproduce work from the original paper is included in the PR, e.g.: - - [ ] Optimization method and hyperparameters -- [ ] There is an identifier tag to contains a reference to the original publication - [ ] The README has been updated with “python scripts/overview.py --update” + - [ ] The new PEtab problem row in the generated table has the correct reference (and other entries)