diff --git a/.github/workflows/r-conda.yml b/.github/workflows/r-conda.yml index 3466a98..0d0a8a5 100644 --- a/.github/workflows/r-conda.yml +++ b/.github/workflows/r-conda.yml @@ -33,43 +33,32 @@ jobs: - name: Create conda environment uses: conda-incubator/setup-miniconda@v2 with: - activate-environment: recetox-aplcms + activate-environment: recetox-aplcms-dev auto-update-conda: true environment-file: conda/environment-dev.yaml auto-activate-base: false - run: | conda init bash conda env list - - name: Fetch adjusted test data - run: wget -P tests/testdata/adjusted -i tests/remote-files/adjusted.txt - - name: Fetch aligned test data - run: wget -P tests/testdata/aligned -i tests/remote-files/aligned.txt - - name: Fetch extracted test data - run: wget -P tests/testdata/extracted -i tests/remote-files/extracted.txt - - name: Fetch input test data - run: wget -P tests/testdata/input -i tests/remote-files/input.txt - - name: Fetch recovered test data - run: wget -P tests/testdata/recovered -i tests/remote-files/recovered.txt - - name: Fetch recovered-extracted test data - run: wget -P tests/testdata/recovered/recovered-extracted -i tests/remote-files/recovered-extracted.txt - - name: Fetch recovered-corrected test data - run: wget -P tests/testdata/recovered/recovered-corrected -i tests/remote-files/recovered-corrected.txt - - name: Fetch filtered test data - run: wget -P tests/testdata/filtered -i tests/remote-files/filtered.txt - - name: Fetch run_filter test data - run: wget -P tests/testdata/filtered/run_filter -i tests/remote-files/run_filter.txt - - name: Fetch features test data - run: wget -P tests/testdata/features -i tests/remote-files/features.txt - - name: Fetch clusters test data - run: wget -P tests/testdata/clusters -i tests/remote-files/clusters.txt - - name: Fetch features test data - run: wget -P tests/testdata/hybrid -i tests/remote-files/hybrid.txt - - name: Fetch template test data - run: wget -P tests/testdata/template -i tests/remote-files/template.txt - - name: Fetch unsupervised test data - run: wget -P tests/testdata/unsupervised -i tests/remote-files/unsupervised.txt + conda list + - name: Fetch test data + run: | + wget -P tests/testdata/adjusted -i tests/remote-files/adjusted.txt + wget -P tests/testdata/aligned -i tests/remote-files/aligned.txt + wget -P tests/testdata/extracted -i tests/remote-files/extracted.txt + wget -P tests/testdata/input -i tests/remote-files/input.txt + wget -P tests/testdata/recovered -i tests/remote-files/recovered.txt + wget -P tests/testdata/recovered/recovered-extracted -i tests/remote-files/recovered-extracted.txt + wget -P tests/testdata/recovered/recovered-corrected -i tests/remote-files/recovered-corrected.txt + wget -P tests/testdata/filtered -i tests/remote-files/filtered.txt + wget -P tests/testdata/filtered/run_filter -i tests/remote-files/run_filter.txt + wget -P tests/testdata/features -i tests/remote-files/features.txt + wget -P tests/testdata/clusters -i tests/remote-files/clusters.txt + wget -P tests/testdata/hybrid -i tests/remote-files/hybrid.txt + wget -P tests/testdata/template -i tests/remote-files/template.txt + wget -P tests/testdata/unsupervised -i tests/remote-files/unsupervised.txt - name: Test coverage run: | - conda activate recetox-aplcms + conda activate recetox-aplcms-dev Rscript -e "covr::codecov(quiet = FALSE)" diff --git a/conda/environment-dev.yaml b/conda/environment-dev.yaml index a0c519b..2e76f77 100644 --- a/conda/environment-dev.yaml +++ b/conda/environment-dev.yaml @@ -5,6 +5,7 @@ channels: - defaults dependencies: - r-base =4.2 + - icu <=70.1 - r-mass - r-rgl - bioconductor-mzR