microbiomedata/nmdc-schema

Issues

• Docs: Mermaid diagram of development environment says "Unsupported markdown" in some places

  #2247 opened 20 days ago by eecavanna
  0

• Document process of merging `nmdc-schema/main` into `berkeley-schema-fy24/main` (in local slang: "backmerge")

  #2170 opened 3 months ago by eecavanna
  11

• Add inter-class diagram generated by refscan to schema documentation

  #2242 opened 22 days ago by eecavanna
  0

• post berkeley-schema-fy24 merge issue: review `FileTypeEnum` composition and correlation with other `DataObject` slots/relationships

  #2186 opened 2 months ago by turbomam
  2

• remove PR template

  #2236 opened 21 days ago by mslarae13
  0

• Add inter-collection diagram generated by refscan to schema documentation

  #2240 opened 22 days ago by eecavanna
  1

• `berkeley`: Incorporate `refscan` graphs into schema documentation

  #2188 opened 22 days ago by eecavanna
  8

• make slot usage range match structured syntax patterns

  #2238 opened 22 days ago by aclum
  0

• `direct_infusion_category` and `DirectInfusionEnum` should be removed

  #2234 opened 23 days ago by kheal
  0

• Edit `#` headers in `src/docs/v10-vs-v11-retrospective.md` for better right hand index in GH Pages

  #2233 opened 23 days ago by turbomam
  0

• Sentence in docs starts with lowercase letter and lacks trailing period

  #2232 opened a month ago by eecavanna
  1

• move markdown and images from https://github.com/microbiomedata/berkeley-schema-fy24 into this repo's docs directory

  #2226 opened 23 days ago by turbomam
  0

• Other updates to MagBin modeling

  #2160 opened 25 days ago by aclum
  1

• add genomad file type enumerations

  #2182 opened 25 days ago by aclum
  0

• groom dependencies

  #2217 opened a month ago by turbomam
  5

• Re-instate full MetaProteomics records in validation

  #2231 opened a month ago by kheal
  1

• Change Instrument name from `GC-MS` to `Agilent GC-MS (2009)`

  #2208 opened a month ago by brynnz22
  2

• Add kegg module prefix

  #2169 opened a month ago by aclum
  0

• `MagBin.members_id` should be multivalued

  #2221 opened a month ago by turbomam
  1

• MagBin.members_id should be multivalued

  #2222 opened a month ago by aclum
  3

• add figshare to DoiProviderEnum

  #2192 opened a month ago by aclum
  0

• update documentation of workarounds/collection exclusion in `pure-export` in project.Makefile

  #2219 opened a month ago by turbomam
  0

• Comment in `pyproject.toml` contains a typo ("Turtle")

  #2196 opened a month ago by eecavanna
  0

• do a poetry update?

  #2216 opened a month ago by turbomam
  0

• reinstall poetry and commit poetry.lock to include `date-created-blank-node` script

  #2214 opened a month ago by turbomam
  3

• replace usages of api-berkeley in makefiles with production api

  #2212 opened a month ago by turbomam
  0

• `src/data/invalid/DissolvingProcess-minimal-no-solvent.yaml` implies `solvent` is required (testing fails)

  #2200 opened a month ago by turbomam
  1

• Review "Berkeley Schema Switch-over Day: Plan" document

  #2206 opened a month ago by eecavanna
  2

• Migrations: Revisit requirement of specifying schema versions in migrators

  #2205 opened a month ago by eecavanna
  0

• GitHub Actions `test_pages_build.yaml` workflow fails on cross-fork PRs

  #2199 opened a month ago by eecavanna
  2

• Remove `PeptideQuantification` class, migrate information from `PeptideQuantification` `best_protein` slot to new `razor_protein` slot on `MetaproteomicsAnalysis` class

  #2157 opened 3 months ago by kheal
  0

• GHA uses Python 3.9 for building docs, but Python 3.10 for building package

  #2191 opened 2 months ago by eecavanna
  2

• `berkeley-schema-fy24`: `make squeaky-clean all` output begins with error message about missing file `local/gold-study-ids.yaml`

  #2177 opened 3 months ago by eecavanna
  10

• Make a TSV mapping file for NEON/NMDC instrument names/ids

  #2185 opened 2 months ago by sujaypatil96
  0

• `berkeley-schema-fy24`: Restore missing derived files (e.g. `nmdc_schema/nmdc_materialized_patterns.yaml`)

  #2176 opened 2 months ago by eecavanna
  4

• alternative to hard-coded `___`indentation in environmental context value sets: is_a relations between permissible values

  #2184 opened 2 months ago by turbomam
  0

• Fix WorkflowExecution identifier format in `functional_annotation_agg` invalid example file (berkeley-schema-fy24)

  #2175 opened 2 months ago by bmeluch
  1

• `berkeley`: Generate/update derivative files in preparation for release

  #2181 opened 2 months ago by eecavanna
  0

• Delete `.swp` file from repo or document rationale for including it

  #2168 opened 3 months ago by eecavanna
  2

• novaseq x updates

  #2183 opened 2 months ago by aclum
  0

• Add `aliases` / `mappings` / `annotations` for GOLD platform / model CV

  #2174 opened 2 months ago by sujaypatil96
  15

• backmerge metatranscriptome issues

  #2164 opened 2 months ago by aclum
  3

• `berkeley-schema` - `type` slot requirement on `Protocol` class requires a migrator

  #2180 opened 2 months ago by kheal
  1

• `berkeley` reverse parthood on DataGeneration

  #2179 opened 2 months ago by aclum
  0

• `env_package` should have a range of an Enum

  #2167 opened 3 months ago by sujaypatil96
  4

• `berkeley` check on syntax pattern on metagenome_annotation_id after latest backmerge

  #2172 opened 3 months ago by aclum
  1

• Slot `name` on `PersonValue` class needs to made more granular

  #2166 opened 3 months ago by sujaypatil96
  0

• add pfam clan prefix

  #2162 opened 3 months ago by aclum
  0

• eukaryotic binning results modeling

  #2158 opened 3 months ago by aclum
  0

• Markdown docs contain broken links

  #2156 opened 3 months ago by github-actions
  0