diff --git a/.github/workflows/pr_tests.yml b/.github/workflows/pr_tests.yml index 4dda062fa..addfd5bb8 100644 --- a/.github/workflows/pr_tests.yml +++ b/.github/workflows/pr_tests.yml @@ -33,6 +33,9 @@ jobs: - name: Compile Cython components run: | make clean compile + - name: Set PYTHONPATH + run: | + echo "PYTHONPATH=." >> $GITHUB_ENV - name: Test ParCa reproducibility run: | python runscripts/parca.py -c 3 -o out/parca_1 @@ -67,10 +70,13 @@ jobs: pip install -r requirements.txt - name: Install nextflow run: | - curl -s https://get.sdkman.io | bash + curl -s https://get.nextflow.io | bash - name: Compile Cython components run: | make clean compile + - name: Set PYTHONPATH + run: | + echo "PYTHONPATH=." >> $GITHUB_ENV - name: Two generations run: | python runscripts/workflow.py --config ecoli/composites/ecoli_configs/two_generations.json diff --git a/doc/index.rst b/doc/index.rst index 59c3d5503..2b1cb609f 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -2,7 +2,12 @@ Welcome to Vivarium *E. coli*'s documentation! ============================================== Vivarium *E. coli* is a port of the |text|_ to the `Vivarium framework `_. -We recommend new users read through the sections below in order. +For more scientific details about the model, refer to the +`documentation `_ +for the model as well its corresponding publication +(`10.1126/science.aav3751 `_). +This website covers how the model was implemented using Vivarium and describes the user interface +for developing and running the model. We recommend new users read through the sections below in order. .. Comment: We need to use text substitution because ReST does not