Merge branch 'main' into stable

Author: guillaume-gricourt

.github/workflows/build.yml

@@ -138,12 +138,11 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           branch: main
 
-  BuildPip:
-    needs: Commit
+  BuildConda:
+    needs: [Commit, Tag]
     runs-on: ubuntu-latest
     env:
-      bld_path: /tmp/build
-      asset: pip.zip
+      asset: straindesign-${{ needs.Tag.outputs.tag }}-py_0.tar.bz2
     outputs:
       asset: ${{ env.asset }}
     defaults:
@@ -158,74 +157,30 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: "latest"
-          environment-file: conda.recipes/conda_build_env.yaml
+          environment-file: recipes/workflow.yaml
           python-version: '3.9'
-      - name: 'Build pip package'
+      - name: 'Build conda package'
         run: |
-          python3 -m build --outdir ${bld_path}
-      - name: 'Create asset'
-        run: |
-          zip -r -j ${asset} ${bld_path}
+          conda-build recipes --output-folder . --output "${{ env.asset }}"
       - name: 'Upload Artifact Package'
         uses: actions/upload-artifact@v2
         with:
-          name: package-pip-artifact
+          name: package-conda-artifact
           path: ${{ env.asset }}
           retention-days: 1
           if-no-files-found: error
 
   Release:
-    needs: [Tag, BuildPip]
+    needs: [Tag, BuildConda]
     runs-on: ubuntu-latest
     steps:
       - name: 'Download Artifact Package - Pip'
         uses: actions/download-artifact@v2
         with:
-          name: package-pip-artifact
+          name: package-conda-artifact
       - name: 'Create Release'
         uses: softprops/action-gh-release@v1
         with:
           tag_name: ${{ needs.Tag.outputs.tag }}
           body: ${{ needs.Tag.outputs.changelog }}
-          files: ${{ needs.BuildPip.outputs.asset }}
-
-  Docker:
-    needs: [Tag, BuildPip]
-    runs-on: ubuntu-latest
-    permissions:
-      packages: write
-      contents: read
-    steps:
-      - name: 'Checkout'
-        uses: actions/checkout@v2
-        with:
-          ref: stable
-      - name: 'Download Artifact Package - Pip'
-        uses: actions/download-artifact@v2
-        with:
-          name: package-pip-artifact
-      - name: 'Unzip pip artifact'
-        run: |
-          echo "list directory"
-          ls
-          unzip pip.zip
-          echo "list directory"
-          ls
-      - name: 'Define Image name'
-        run: |
-          image_name=${{ github.repository }}
-          image_name=$(echo "$image_name" | cut -f2 -d"/" | tr '[:upper:]' '[:lower:]')
-          echo "image_name=$image_name" >> "$GITHUB_ENV"
-      - name: 'Build image'
-        run: |
-          docker build . --file Dockerfile --tag ${{ env.image_name }} --label "runnumber=${GITHUB_RUN_ID}"
-      - name: 'Log in to registry'
-        run: |
-          echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
-      - name: 'Push image'
-        run: |
-          IMAGE_ID=$(echo ghcr.io/${{ github.repository_owner }}/${{ env.image_name }} | tr '[:upper:]' '[:lower:]')
-          VERSION=${{ needs.Tag.outputs.tag }}
-          echo "IMAGE_ID=$IMAGE_ID | VERSION=$VERSION"
-          docker tag ${{ env.image_name }} "${IMAGE_ID}:${VERSION}"
-          docker push "${IMAGE_ID}:${VERSION}"
+          files: ${{ needs.BuildConda.outputs.asset }}

.github/workflows/coverage.yml

@@ -0,0 +1,23 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+
+  Lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v2
+        with:
+          ref: ${{ github.ref }}
+          fetch-depth: 0
+      - name: Lint Code Base
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          VALIDATE_YAML: false
+          VALIDATE_XML: false
+          VALIDATE_DOCKERFILE_HADOLINT: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/lint.yml

@@ -1,35 +1,41 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
 
 jobs:
 
-  Lint:
+  Build:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: 'Checkout'
         uses: actions/checkout@v2
         with:
           ref: ${{ github.ref }}
-          fetch-depth: 0
-      - name: Lint Code Base
-        uses: github/super-linter@v4
-        env:
-          VALIDATE_ALL_CODEBASE: false
-          VALIDATE_YAML: false
-          VALIDATE_XML: false
-          VALIDATE_DOCKERFILE_HADOLINT: false
-          DEFAULT_BRANCH: main
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: 'Deploying miniconda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          environment-file: recipes/workflow.yaml
+          python-version: '3.9'
+      - name: 'Build conda package'
+        run: |
+          conda-build recipes/
 
-  Build:
-    runs-on: ${{ matrix.os }}-latest
+  Pytest:
+    needs: [Build]
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: ["ubuntu"]
-        python-version: ['3.8', '3.9']
-    env:
-      bld_path: /tmp/build
+        python-version: [3.8, 3.9]
     defaults:
       run:
         shell: bash -l {0}
@@ -41,38 +47,38 @@ jobs:
       - name: 'Deploying miniconda'
         uses: conda-incubator/setup-miniconda@v2
         with:
-          miniconda-version: 'latest'
-          environment-file: conda.recipes/conda_build_env.yaml
+          miniconda-version: "latest"
+          environment-file: recipes/workflow.yaml
           python-version: ${{ matrix.python-version }}
-      - name: 'Set up output folder'
-        run: |
-          mkdir -p "${bld_path}"
-      - name: 'Build pip package'
+      - name: 'Run tests'
         run: |
-          python3 -m build --outdir "${bld_path}"
+          pip install --no-deps .
+          python -m pytest tests/unit
 
-  Pytest:
+  Coverage:
     needs: [Build]
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9']
-        os: [ubuntu, macos]
-    env:
-      bld_path: /tmp/build
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: 'Checkout'
         uses: actions/checkout@v2
         with:
           ref: ${{ github.ref }}
-      - name: 'Set up Python'
-        uses: actions/setup-python@v2
+      - name: 'Deploying miniconda'
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: ${{ matrix.python-version }}
-      - name: 'Install'
-        run: |
-          pip install .
-      - name: 'Run pytest'
+          miniconda-version: "latest"
+          environment-file: recipes/workflow.yaml
+          python-version: '3.9'
+      - name: 'Run tests'
         run: |
-          pip install pytest
-          python -m pytest
+          pip install --no-deps .
+          coverage run -m pytest
+          coverage lcov
+      - name: 'Coveralls'
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: ./coverage.lcov

.github/workflows/test.yml

@@ -20,3 +20,4 @@ super-linter.log
 .eggs
 build
 debug
+.tox

.gitignore

@@ -1 +1 @@
-include environment.yml
+graft recipes

MANIFEST.in

@@ -10,68 +10,65 @@
 
 ## Installation
 
-### Conda
-
 ```sh
 conda install -c bioconda straindesign
 ```
 
-### Docker
-
-```sh
-docker pull ghcr.io/brsynth/straindesign:<release version>
-```
-
-### Pip
-
-Download asset from the last *Releases*.  
-
-* Unzip asset  
-
-```sh
-unzip <folder>
-```  
-
-* Install *wheel* with *pip*  
-
-```sh
-pip install <unzipped file>.whl
-```  
-
 ## Usage
 
-Example: Define the best combination of genes deletion to optimize a target.
+### Define the best combination of genes deletion to optimize a target.
 
 ```sh
-python -m straindesign \
+python -m straindesign simulate-deletion \
     [input files]
     --input-model-file <SBML file>
     --input-pathway-file <SBML file>
-    --input-medium-file <CSV file>
-    [input parameters]
+    --input-medium-file <CSV/TSV file>
+    [parameters]
     --biomass-rxn-id <id reaction, str>
     --target-rxn-id <id reaction, str>
     --substrate-rxn-id <id reaction, str>
     [output file]
-    --output-file <CSV file>
+    --output-file <CSV/TSV file>
 ```
 
-Or with docker:  
+### Delete genes in a model
 
 ```sh
-docker run \
-    -it \
-    --rm \
-    -v $PWD:/data \
-    straindesign:latest \
-    --input-model /data/<SBML file> \
-    --input-pathway-file /data/<SBML file> \
-    --input-medium-file /data/<CSV file> \
-    --biomass-rxn-id <id reaction, str> \
-    --target-rxn-id <id reaction, str> \
+python -m straindesign reduce-model \
+    [input files]
+    --input-model-file <SBML file>
+    --input-straindesign-file <CSV file>
+    and/or
+    --input-gene-str <id gene, str>
+    [parameters]
+    --parameter-strategy-str <yield-max, gene-max, gene-min>
+    [output file]
+    --output-file-sbml <SBML file>
+```
+You can provide a list of genes to delete in the model or the file produced by the command `simulate-deletion`.
+If this file is provided, the combination of genes is choosen among three strategies:
+* yield-max: genes are sorted by the best yield
+* gene-max: the combination of the maximum number of genes
+* gene-min: the combination of the minimum number of genes
+
+### Produce a pareto plot
+
+````sh
+python -m straindesign analyzing-model \
+    [input files]
+    --input-model-file <SBML file>
+    --input-medium-file <CSV/TSV file>
+    --input-pathway-file <SBML file>
+    [parameters]
+    --biomass-rxn-id <id reaction, str>
+    --target-rxn-id <id reaction, str>
     --substrate-rxn-id <id reaction, str>
-    --output-file /data/<CSV file>
+    [output file]
+    --output-pareto-png <PNG file>
 ```
+You can provide an heterologous pathway to implement the metabolic pathway producing the targeted compound represented by the `target-rxn-id`, the reaction which produces this compound.  
+The `substrate-rxn-id` argument lets you to choose the main carbon source.
 
 ## Tests