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Fixed CI by restricting icu version #195

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merged 3 commits into from
Apr 14, 2023
Merged

Fixed CI by restricting icu version #195

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6be76a2
Update r-conda.yml to simplify test data download and add printing en…
hechth Apr 14, 2023
407c807
pinned icu to <= 58
hechth Apr 14, 2023
2296f5a
pinned icu to <= 70.1
hechth Apr 14, 2023
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49 changes: 19 additions & 30 deletions .github/workflows/r-conda.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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)"
1 change: 1 addition & 0 deletions conda/environment-dev.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ channels:
- defaults
dependencies:
- r-base =4.2
- icu <=70.1
- r-mass
- r-rgl
- bioconductor-mzR
Expand Down