Merge pull request #162 from SysBioChalmers/feat/memote

Feat/memote

.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: ${{ steps.setup.outputs.other-repo }}
+
+    # - name: Convert model
+    #   run: |
+    #     touch .env
+    #     python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+
+    - name: Memote short run
+      run: |
+        memote run --skip-unchanged --solver-timeout 30
+
+    - name: Compute Memote history on push
+      run: |
+        # Generate the history report on the deployment branch
+        memote report history --filename="${{ 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

README.md

@@ -1,7 +1,7 @@
  @@ -0,0 +1,94 @@
 # yeast-GEM: The consensus genome-scale metabolic model of _Saccharomyces cerevisiae_
 
-[![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598) [![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem.svg)](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem) [![Join the chat at https://gitter.im/SysBioChalmers/yeast-GEM](https://badges.gitter.im/SysBioChalmers/yeast-GEM.svg)](https://gitter.im/SysBioChalmers/yeast-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598) [![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem.svg)](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem) [![Join the chat at https://gitter.im/SysBioChalmers/yeast-GEM](https://badges.gitter.im/SysBioChalmers/yeast-GEM.svg)](https://gitter.im/SysBioChalmers/yeast-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)[![Memote history](https://github.com/SysBioChalmers/yeast-GEM/workflows/Memote%20history/badge.svg)](https://sysbiochalmers.github.io/yeast-GEM/history_report.html)
 
 ## Description
 
@@ -53,7 +53,14 @@ This repository contains the current consensus genome-scale metabolic model of _
 * The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN).
 * A [git wrapper](https://github.com/manur/MATLAB-git) added to the search path.
 
-### Dependencies - Recommended software:
+**NOTE:** You also require [git lfs](https://git-lfs.github.com/) if you wish to run locally any of the following two [memote](https://github.com/opencobra/memote) commands:
+* `memote run`
+* `memote report history`
+
+This is because `results.db` (the database that stores all memote results) is tracked with git lfs.
+
+### Dependencies - Recommended Software:
+
 * For Matlab, the [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/) (version 5.17.0 is recommended).
 * [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.
 

memote.ini

@@ -0,0 +1,6 @@
+[memote]
+model = model/yeast-GEM.xml
+location = sqlite:///results.db
+github_username = SysBioChalmers
+github_repository = yeast-GEM
+deployment = gh-pages

requirements/ci-requirements.in

@@ -1,3 +1,5 @@
 # Requirements for GitHub Actions:
 cobra
-memote
+memote
+python-dotenv
+symengine