Merge branch 'main' into stable

brsynth · Jan 5, 2023 · 44bd921 · 44bd921
2 parents 5a70dc0 + 3fd9069
commit 44bd921
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diff --git a/.github/linters/.flake8 b/.github/linters/.flake8
@@ -1,3 +1,3 @@
 [flake8]
 max-line-length = 120
-extend-ignore = E402
+extend-ignore = E203,E402,F401,F403
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -7,13 +7,13 @@ on:
 
 jobs:
 
-  Tag:
+  TagRaw:
     runs-on: ubuntu-latest
     outputs:
      tag: ${{ steps.tag_label.outputs.tag }}
      changelog: ${{ steps.tag_raw.outputs.changelog }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -31,20 +31,12 @@ jobs:
           TAG: ${{ steps.tag_raw.outputs.new_tag }}
         run: |
           TAG=$(echo "$TAG" | cut -f1 -d "-")
-          echo "::set-output name=tag::$TAG"
-      - name: 'Bump version and push tag'
-        id: tag
-        uses: mathieudutour/[email protected]
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          release_branches: stable
-          custom_tag: ${{ steps.tag_label.outputs.tag }}
-          tag_prefix:
+          echo "tag=$TAG" >> "$GITHUB_OUTPUT"
 
   Changelog:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
@@ -72,54 +64,53 @@ jobs:
           retention-days: 1
 
   Version:
-    needs: Tag
+    needs: TagRaw
     runs-on: ubuntu-latest
     outputs:
       version_path: ${{ steps.update_version.outputs.version_path }}
       version_dir: ${{ steps.update_version.outputs.version_dir }}
     steps:
-      - uses: actions/checkout@v2
-        with:
-          ref: stable
+      - uses: actions/checkout@v3
       - name: 'Update _version.py'
         id: update_version
         env:
-          TAG: ${{ needs.Tag.outputs.tag }}
+          TAG: ${{ needs.TagRaw.outputs.tag }}
         run: |
           VERSION_PATH=$(find . -name _version.py | head -n 1)
           VERSION_DIR=$(dirname "$VERSION_PATH")
           sed -i "2s/.*/__version__ = \"$TAG\"/" "$VERSION_PATH"
-          echo "::set-output name=version_path::${VERSION_PATH}"
-          echo "::set-output name=version_dir::${VERSION_DIR}"
+          echo "version_path=$VERSION_PATH" >> "$GITHUB_OUTPUT"
+          echo "version_dir=$VERSION_DIR" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Version'
         uses: actions/upload-artifact@v2
         with:
           name: version-artifact
           path: ${{ steps.update_version.outputs.version_path }}
-          retention-days: 1
 
   Commit:
-    needs: [ Tag, Changelog, Version ]
+    needs: [Changelog, Version]
     runs-on: ubuntu-latest
     steps:
       # Get Data
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           persist-credentials: false
           fetch-depth: 0
       - name: 'Download Artifact Version'
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: version-artifact
           path: ${{ needs.Version.outputs.version_dir }}
       - name: 'Download Artifact Changelog'
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: changelog-artifact
       # Commit
       - name: 'Commit files'
         run: |
+          echo "show version file"
+          cat ${{ needs.Version.outputs.version_path }}
           git config --local user.email "$GITHUB_EMAIL"
           git config --local user.name "$GITHUB_USERNAME"
           git add .
@@ -138,49 +129,72 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           branch: main
 
+  Tag:
+    needs: [Commit, TagRaw]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: 'Bump version and push tag'
+        id: tag
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          release_branches: stable
+          custom_tag: ${{ needs.TagRaw.outputs.tag }}
+          tag_prefix:
+
   BuildConda:
-    needs: [Commit, Tag]
+    needs: [Tag]
     runs-on: ubuntu-latest
     env:
-      asset: straindesign-${{ needs.Tag.outputs.tag }}-py_0.tar.bz2
+      dirbuild: /tmp/build
     outputs:
-      asset: ${{ env.asset }}
+      asset: ${{ steps.identify_asset.outputs.asset }}
     defaults:
       run:
         shell: bash -l {0} # activate env conda
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
-        with:
-          ref: stable
+        uses: actions/checkout@v3
       - name: 'Deploying miniconda'
         uses: conda-incubator/setup-miniconda@v2
         with:
-          miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
           python-version: '3.9'
+          mamba-version: "*"
+          channel-priority: true
+          use-mamba: true
       - name: 'Build conda package'
         run: |
-          conda-build recipes --output-folder . --output "${{ env.asset }}"
+          mkdir -p ${{ env.dirbuild }}
+          conda-build recipes --output-folder ${{ env.dirbuild }}
+      - name: 'Find name package'
+        id: identify_asset
+        run: |
+          filename=$(find ${{ env.dirbuild }} | head -n 1)
+          echo "asset=$filename" >> "$GITHUB_OUTPUT"
       - name: 'Upload Artifact Package'
         uses: actions/upload-artifact@v2
         with:
           name: package-conda-artifact
-          path: ${{ env.asset }}
+          path: ${{ steps.identify_asset.outputs.asset }}
           retention-days: 1
           if-no-files-found: error
 
   Release:
-    needs: [Tag, BuildConda]
+    needs: [TagRaw, BuildConda]
     runs-on: ubuntu-latest
     steps:
       - name: 'Download Artifact Package - Pip'
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           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 }}
+          tag_name: ${{ needs.TagRaw.outputs.tag }}
+          body: ${{ needs.TagRaw.outputs.changelog }}
           files: ${{ needs.BuildConda.outputs.asset }}
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -18,6 +18,8 @@ jobs:
           VALIDATE_ALL_CODEBASE: false
           VALIDATE_YAML: false
           VALIDATE_XML: false
+          VALIDATE_JSON: false
           VALIDATE_DOCKERFILE_HADOLINT: false
+          VALIDATE_PYTHON_ISORT: false
           DEFAULT_BRANCH: main
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -26,6 +26,9 @@ jobs:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
           python-version: '3.9'
+          mamba-version: "*"
+          channel-priority: true
+          use-mamba: true
       - name: 'Build conda package'
         run: |
           conda-build recipes/
@@ -47,13 +50,16 @@ jobs:
       - name: 'Deploying miniconda'
         uses: conda-incubator/setup-miniconda@v2
         with:
-          miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
           python-version: ${{ matrix.python-version }}
+          mamba-version: "*"
+          channel-priority: true
+          use-mamba: true
       - name: 'Run tests'
         run: |
           pip install --no-deps .
-          python -m pytest tests/unit
+          python -m pytest tests/straindesign/unit
+          python -m pytest tests/cameobrs
 
   Coverage:
     needs: [Build]
@@ -72,10 +78,13 @@ jobs:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
           python-version: '3.9'
+          mamba-version: "*"
+          channel-priority: true
+          use-mamba: true
       - name: 'Run tests'
         run: |
           pip install --no-deps .
-          coverage run -m pytest
+          coverage run -m pytest tests/straindesign/unit
           coverage lcov
       - name: 'Coveralls'
         uses: coverallsapp/github-action@master

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1,8 @@
+include MANIFEST.in
+include LICENSE
+include README
 graft recipes
+graft src/cameobrs/ui/assets
+graft src/cameobrs/data
+graft src/cameobrs/models
+graft tests
diff --git a/README.md b/README.md
@@ -6,7 +6,8 @@
 
 ## Description
 
-*straindesign* provides a cli interface to predict gene knockout targets with an heterologous pathway  
+*straindesign* provides a cli interface to predict gene knockout targets with an heterologous pathway.
+Integrate an hard fork from [cameo](https://github.com/biosustain/cameo) (v0.13.6) named `cameobrs` to add features.
 
 ## Installation
 
@@ -16,7 +17,7 @@ conda install -c bioconda straindesign
 
 ## Usage
 
-### 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 simulate-deletion \
@@ -46,8 +47,10 @@ python -m straindesign reduce-model \
     [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
@@ -79,16 +82,6 @@ cd <repository>
 python -m pytest
 ```
 
-## Built with these main libraries
+## Built with:
 
-* [cameo](https://github.com/biosustain/cameo) - Computer aided metabolic engineering & optimization
 * [cobrapy](https://github.com/opencobra/cobrapy) - Constraint-based modeling of metabolic networks
-* [Pandas](https://github.com/pandas-dev/pandas) - Essential dataframe object
-
-## Authors
-
-* **Guillaume Gricourt**
-
-## Licence
-
-See the LICENCE file for details.
diff --git a/recipes/meta.yaml b/recipes/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "straindesign" %}
-{% set version = "3.0.0" %}
+{% set version = "3.1.0" %}
 
 package:
   name: {{ name }}
@@ -16,21 +16,36 @@ build:
 requirements:
   build:
     - pip
-    - pytest
     - python
     - pyyaml
     - setuptools
   run:
     - biopython
-    - cameo
-    - cobra<0.25.0 # https://github.com/biosustain/cameo/issues/296
-    - markupsafe==2.0.1 # https://github.com/pallets/markupsafe/issues/304
-    - pandas
+    - blessings
+    - click
+    - cobra>=0.24
+    - escher
+    - future
+    - gnomic
+    - inspyred
+    - IProgress
+    - lazy-object-proxy
     - plotly
-    - pytest
-    - python-kaleido
     - python
-    - pyyaml
+    - markupsafe
+    - networkx
+    - numexpr
+    - numpy<1.24 # Related to https://github.com/numpy/numpy/pull/22607
+    - openbabel
+    - openpyxl
+    - optlang
+    - ordered-set
+    - palettable
+    - pandas
+    - redis-py
+    - requests
+    - scipy
+    - seaborn
 
 test:
   imports:
@@ -40,7 +55,7 @@ test:
 
 about:
   home: https://github.com/brsynth/{{ name }}
-  summary: Cli interface to predict gene knockout targets with an heterologous pathway
+  summary: Library to make metabolic engineering
   license: MIT
   license_file: LICENSE