diff --git a/.github/workflows/generate_phenopackets.yml b/.github/workflows/generate_phenopackets.yml deleted file mode 100644 index 81e2baf6..00000000 --- a/.github/workflows/generate_phenopackets.yml +++ /dev/null @@ -1,65 +0,0 @@ -name: Generate phenopackets - -env: - # We generate the phenopackets from this state - # of the `phenopacket-store` repository. - PHENOPACKET_STORE_TAG: pyphe-ci-wip -# PHENOPACKET_STORE_TAG: c06a52e0 # State from Mar 5th, 2024 - -on: - push: - branches: [ develop ] - pull_request: - branches: [ main, develop ] - -jobs: - build: - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - - name: Initialize Python 3.8 - uses: actions/setup-python@v4.3.1 - with: - python-version: "3.8" - - - name: Install pyphetools & dependencies - run: | - python3 -m pip install --editable . - - - name: Install Jupyter and register current Python as kernel - run: | - python3 -m pip install ipykernel notebook - python3 -m ipykernel install --user --name pp_env --display-name "Pyphetools (Python 3)" - - - name: Check out phenopacket-store - run: | - cd .. - git clone https://github.com/monarch-initiative/phenopacket-store.git - cd phenopacket-store - git checkout $PHENOPACKET_STORE_TAG - - - name: Generate phenopackets - run: | - # phenopacket-store folder - pps_dir=$(dirname $(pwd))/phenopacket-store - - # Prepare the notebooks to run - declare -a fbn1_notebooks=( - "FBN1/Comeglio_isolated_ectopia_lentis.ipynb" - "FBN1/FBN1_lipodystrophy_Lin_2020.ipynb" - "FBN1/Katzke_2002_Marfan.ipynb" - "FBN1/LeGoff_FBN1_acromicric_and_geleophysic_dysplasia.ipynb" - "FBN1/Loeys2010_stiff_skin_syndrome.ipynb" - "FBN1/Palz_Marfan_2000.ipynb" - "FBN1/Tiecke_2001_Marfan.ipynb" - ) - - # Run the notebooks - for nb in ${fbn1_notebooks[@]} - do - nb_path=${pps_dir}/notebooks/${nb} - printf "Running %s\n" ${nb_path} - jupyter execute --kernel_name=pp_env ${nb_path} - done diff --git a/docs/developers/developers.md b/docs/developers/developers.md index ba96e3fb..4e34e893 100644 --- a/docs/developers/developers.md +++ b/docs/developers/developers.md @@ -1,5 +1,35 @@ # For developers +## Local Installation + +We recommend creating a local environment: + +```bash +python3 -m venv venv +source venv/bin/activate +``` + +and updating Python's `pip` tool: + +```bash +python3 -m pip install --upgrade pip +``` + +You can then do a local/editable install: + + +```bash +python3 -m pip install --editable ".[test]" +``` + +After installation you should be able to run the test suite: + +```bash +pytest +``` + + +## Creating Phenopackets pyphetools provides two main ways of creating phenopackets. diff --git a/docs/user-guide/template.md b/docs/user-guide/template.md index cf64b8ba..0404d6b7 100644 --- a/docs/user-guide/template.md +++ b/docs/user-guide/template.md @@ -64,7 +64,7 @@ tc.create_template(disease_id="", disease_label="", gene_symbol="", HGNC_id="", - transcript="" + transcript="") ```