diff --git a/README.md b/README.md index 432e728a3cae2d779273648df78716792d9bbf86..a54fae77c391966a4db9215b6c5f56f7c168cdff 100644 --- a/README.md +++ b/README.md @@ -189,7 +189,7 @@ cp -r ./examples/concepts/* ./workspace/phen/concepts From the command prompt, copy example phenotype configuration files `/examples/config.json` to the phenotype directory: ```bash -cp -r ./examples/config1.yaml ./workspace/phen/config.yaml +cp -r ./examples/config1.yml ./workspace/phen/config.yml ``` - You can view the configuarion file here [`config.json`](./examples/config.json) diff --git a/docs/index.md b/docs/index.md index 430dfb5dd038853e7420d3139c99f9b281693f2a..c4ec6e027020da1362b579b036f0ef12c5f6a551 100644 --- a/docs/index.md +++ b/docs/index.md @@ -71,13 +71,13 @@ workspace/ # Default workspace directory │ │ ├── omop/ # Processed phenotype concept sets in OMOP CDM database exported as CSV files │ ├── map/ # Process mapping from source to target code types │ │ ├── errors/ # Errors recorded during mapping process -│ ├── config.yaml # Phenotype configuration file -│ ├── vocab_versions.yaml # Versions file for vocabularies used to generate concept sets +│ ├── config.yml # Phenotype configuration file +│ ├── vocab_versions.yml # Versions file for vocabularies used to generate concept sets ``` ### **Configuration File** -Each phenotype is defined by configuration is stored in the root of the phenotype directory in `config.yaml`. The file is yaml format. +Each phenotype is defined by configuration is stored in the root of the phenotype directory in `config.yml`. The file is yaml format. #### **Root Phenotype Element** - `phenotype`: **(object)** The root element containing all phenotype-related concept sets and metadata. diff --git a/pyproject.toml b/pyproject.toml index c1a313cde96ac18f10c79da4f57fa01a3b06f628..438f1f0f26ab7f9baca52c590d48ac5b5d4250d4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "hatchling.build" [project] name = "acmc" -version = "0.1.1" +version = "0.1.2" authors = [ { name = "Jakub Dylag", email = "j.j.dylag@soton.ac.uk" }, { name = "Michael Boniface", email = "m.j.boniface@soton.ac.uk" }