Merge branch 'master' into baseline_correct_curation

RECETOX · Apr 14, 2023 · 9469163 · 9469163
2 parents 0770b52 + 12522b2
commit 9469163
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diff --git 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/README.md b/README.md
@@ -1,6 +1,7 @@
 # recetox-aplcms
 ![GitHub R package version](https://img.shields.io/github/r-package/v/RECETOX/recetox-aplcms)
 [![Conda](https://img.shields.io/conda/v/bioconda/r-recetox-aplcms)](https://anaconda.org/bioconda/r-recetox-aplcms)
+[![codecov](https://codecov.io/gh/RECETOX/recetox-aplcms/branch/master/graph/badge.svg?token=1B664Z8DHT)](https://codecov.io/gh/RECETOX/recetox-aplcms)
 
 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise. Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
 

diff --git 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