Merge branch 'main' into stable

Author: guillaume-gricourt

.github/workflows/build.yml

@@ -98,20 +98,6 @@ jobs:
           path: ${{ steps.update_version.outputs.version_path }}
           retention-days: 1
 
-  Badge:
-    needs: Tag
-    runs-on: ubuntu-latest
-    steps:
-      - name: 'Badge version'
-        uses: schneegans/[email protected]
-        with:
-          auth: ${{ secrets.GIST }}
-          gistID: dcbec0ab9a7556f091c36e48a58980dd
-          filename: version.json
-          label: Version
-          message: ${{ needs.Tag.outputs.tag }}
-          color: green
-
   Commit:
     needs: [ Tag, Changelog, Version ]
     runs-on: ubuntu-latest
@@ -154,10 +140,7 @@ jobs:
 
   BuildPip:
     needs: Commit
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        os: [ubuntu]
+    runs-on: ubuntu-latest
     env:
       bld_path: /tmp/build
       asset: pip.zip
@@ -176,10 +159,9 @@ jobs:
         with:
           miniconda-version: "latest"
           environment-file: conda.recipes/conda_build_env.yaml
-          activate-environment: build
+          python-version: '3.9'
       - name: 'Build pip package'
         run: |
-          pip install build
           python3 -m build --outdir ${bld_path}
       - name: 'Create asset'
         run: |

.github/workflows/coverage.yml

@@ -1,7 +1,10 @@
-on: ["push", "pull_request"]
-
 name: Coverage
 
+on:
+  push:
+    branches:
+      - main
+
 jobs:
 
   Coveralls:

.github/workflows/test.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu"]
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.9']
     env:
       bld_path: /tmp/build
     defaults:
@@ -41,24 +41,22 @@ jobs:
       - name: 'Deploying miniconda'
         uses: conda-incubator/setup-miniconda@v2
         with:
-          miniconda-version: "latest"
+          miniconda-version: 'latest'
           environment-file: conda.recipes/conda_build_env.yaml
-          activate-environment: build
           python-version: ${{ matrix.python-version }}
       - name: 'Set up output folder'
         run: |
           mkdir -p "${bld_path}"
       - name: 'Build pip package'
         run: |
-          pip install build
           python3 -m build --outdir "${bld_path}"
 
   Pytest:
     needs: [Build]
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
+        python-version: ['3.8', '3.9']
         os: [ubuntu, macos]
     env:
       bld_path: /tmp/build

README.md

@@ -10,6 +10,20 @@
 
 ## Installation
 
+### Conda
+
+```sh
+conda install -c bioconda rpfbagr
+```
+
+### Docker
+
+```sh
+docker pull ghcr.io/brsynth/rpfbagr:<release version>
+```
+
+### Pip
+
 Download asset from the last *Releases*.  
 
 * Unzip asset  

conda.recipes/conda_build_env.yaml

@@ -1,16 +1,15 @@
-name: build
+name: test
 channels:
   - bioconda
   - conda-forge
   - defaults
 dependencies:
   - anaconda-client
   - biopython
+  - build
   - cameo
   - cobra<0.25.0
-  - conda-build
-  - markupsafe==2.0.1
+  - markupsafe=2.0.1
   - pandas
   - pytest
-  - python
   - pyyaml