yeast 8.5.0

.github/CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at bensan@chalmers.se. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at eduardk@chalmers.se. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 

.github/issue_template.md

@@ -7,7 +7,7 @@
 
 
 #### Current feature/value/output:
-*How the reaction/metabolite/gene/simulation actually looks in the `master` branch. PLEASE DELETE THIS LINE.*
+*How the reaction/metabolite/gene/simulation actually looks in the `main` branch. PLEASE DELETE THIS LINE.*
 
 
 #### Reproducing these results:
@@ -18,6 +18,6 @@
 
 **I hereby confirm that I have:**
 - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model
-- [ ] Done this analysis in the `master` branch of the repository
+- [ ] Done this analysis in the `main` branch of the repository
 - [ ] Checked that a similar issue does not exist already
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue

.github/pull_request_template.md

@@ -4,5 +4,5 @@
 **I hereby confirm that I have:**
 
 - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---contributor) for running the model
-- [ ] Selected `devel` as a target branch (top left drop-down menu)
+- [ ] Selected `develop` as a target branch (top left drop-down menu)
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about this PR

.github/workflows/memote-history.yml

@@ -0,0 +1,60 @@
+name: memote history
+
+on: push
+
+jobs:
+  memote-history:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install memote
+      run: pip install -r requirements/ci-requirements.txt
+
+    - name: Setup variables
+      id: setup
+      run: |
+        echo "::set-output name=history::history_report.html"
+        echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
+        echo "::set-output name=other-repo::gh-pages-repo"
+
+    - name: Checkout repo for gh-pages branch
+      uses: actions/checkout@v2
+      with:
+        repository: ${{ github.repository }}
+        ref: ${{ steps.setup.outputs.deployment }}
+        path: ${{ steps.setup.outputs.other-repo }}
+
+    # - name: Convert model
+    #   run: |
+    #     touch .env
+    #     python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+
+    - name: Memote short run
+      run: |
+        memote run --ignore-git --skip-unchanged --solver-timeout 30
+
+    - name: Compute Memote history on push
+      run: |
+        # Generate the history report on the deployment branch
+        memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"
+
+    - name: Auto-commit results
+      uses: stefanzweifel/[email protected]
+      with:
+        commit_user_name: memote-bot
+        commit_message: "chore: update memote history report"
+        file_pattern: ${{ steps.setup.outputs.history }}
+        branch: ${{ steps.setup.outputs.deployment }}
+        repository: ${{ steps.setup.outputs.other-repo }}
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/memote-run.yml

@@ -0,0 +1,29 @@
+name: memote run
+
+on: pull_request
+
+jobs:
+  memote-run:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Install memote
+      run: pip install -r requirements/ci-requirements.txt
+
+    - name: Convert model
+      run: |
+        touch .env
+        python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+
+    - name: Memote on PR
+      run: |
+        # Untracked build, skip saving to gh-pages
+        memote run --ignore-git --solver-timeout 30

.github/workflows/yaml-validation.yml

@@ -0,0 +1,39 @@
+name: YAML validation
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ main, develop ]
+
+jobs:
+  yaml-validation:
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+
+    - name: YAML Lint
+      uses: ibiqlik/[email protected]
+      with:
+        ## File(s) or Directory, separate by space if multiple files or folder are specified
+        file_or_dir: model/
+        ## Custom configuration (as YAML source)
+        config_data: "{extends: default, rules: {line-length: disable}}"
+        ## Format for parsing output [parsable,standard,colored,auto]
+        # format: # optional, default is colored
+        ## Return non-zero exit code on warnings as well as errors
+        # strict: # optional, default is false
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Import with cobrapy
+      run: |
+        pip install -r requirements/ci-requirements.txt
+        python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')"