feat: memote

.gitattributes

@@ -0,0 +1,5 @@
+*	text=auto
+*.m	text diff=matlab
+.gitattributes	export-ignore
+.gitignore	export-ignore
+.github	export-ignore

.github/CONTRIBUTING.md

@@ -41,23 +41,26 @@ Here's how to set up yeast-GEM for local development to contribute smaller featu
     ```
     git clone https://github.com/<your Github name>/yeast-GEM.git
     ```
-	
+
 4. Check out the branch that you want to contribute to. Most likely that will be ``devel``:
     ```
     git checkout devel
     ```
-	
+
 5. Create a branch for local development based on the previously checked out branch ([see below](#branching-model) for details on the branching model and how to name your branch):
     ```
     git checkout -b name-of-your-branch
     ```
-	
+
 6. Now you can make your changes locally!
     * Always make your changes in Matlab and never directly editing the model files. For loading the model use `loadYeastModel.m`, and for saving the model use `saveYeastModel.m`. The latter will ensure all 3 versions of the model (`.xml`, `.yml` & `.txt`) get updated in the same way.
     * If your changes are minor (e.g. a single chemical formula you wish to correct), you can do it directly from the command line.
     * If your changes are not so small and require several steps, create a script that loads the model, reads data (if applicable), changes the model accordingly, and saves the model back.
     * Each script should start with a commented section describing the script, explaining the parameters, and indicating your name and the date it was written. Existing functions can clarify what style should be used.
-	* If you add new metabolites and/or rxns to the model, please use `/ComplementaryScripts/otherChanges/getNewIndex.m` for obtaining new ids. If you add a new gene, please use as id the [systematic names from SGD](http://seq.yeastgenome.org/help/community/nomenclature-conventions).
+    * As much as possible follow the model conventions:
+      - For new metabolites and/or reactions, please use `/ComplementaryScripts/otherChanges/getNewIndex.m` for obtaining new ids.
+      - For metabolite and/or reaction names, please avoid any unconventional characters (e.g. Greek letters).
+      - For new genes, please use as id the [systematic names from SGD](http://seq.yeastgenome.org/help/community/nomenclature-conventions).
     * Store scripts in the appropriate folder in `/ComplementaryScripts` and data (as `.tsv` files) in the appropriate folder in `/ComplementaryData`. If you think no folder is adequate for your script/data, feel free to create your own folder. Note that binary data such as `.mat` structures or `.xls` tables cannot be stored in the repo (as they cannot be version-controlled, and they increment too much the size of the repo).
     * When you are done making changes, review locally your changes with `git diff` or any git client, to make sure you are modifying the model as you intended.
 
@@ -86,7 +89,7 @@ Thank you very much for contributing to yeast-GEM!
 * `gh-pages`: Is only touched by the administrator and for maintaining the [landing page](http://sysbiochalmers.github.io/yeast-GEM/) of yeast-GEM.
 
 * `{chore, doc, feat, fix, refactor, style}/descriptive-name`: Any other branch created in the model. If you work on a fix, start the branch name with `fix/`, if you work on a feature, start the branch name with `feat/`. Examples: `fix/format_reactions` or `feat/new_algorithms`. [See below](#semantic-commits) for more details on the possible actions you can use.
-	
+
 #### Semantic commits
 
 Please use concise descriptive commit messages. Ideally, use semantic commit messages to make it easier to show what you are aiming to do:
@@ -95,7 +98,7 @@ Please use concise descriptive commit messages. Ideally, use semantic commit mes
 * `action` = {`feat`, `fix`, `refactor`, `style`, `doc`, `chore`, `test`}
 * `object` (optional field) = {`rxn`, `rxn.annot`, `rxn.prop`, `met`, `met.annot`, `met.prop`, `gene`, `gene.annot`, `comp`, `comp.annot`, `data`}
 
-`action` refers to what exactly are you doing in the commit, following a [standard definition](http://karma-runner.github.io/2.0/dev/git-commit-msg.html) in software development: 
+`action` refers to what exactly are you doing in the commit, following a [standard definition](http://karma-runner.github.io/2.0/dev/git-commit-msg.html) in software development:
 * `chore`: updating toolbox, data files, etc.
 * `doc`: updating documentation or explanatory comments in functions.
 * `feat`: new feature added, e.g. new reaction / metabolite / function / etc.
@@ -143,7 +146,7 @@ Follow all other steps in the same way. Also, when creating your pull request (o
 * Choose 1 or more members of the team (ideally with knowledge on the pull request) as reviewers. Note that the person making the pull request and the reviewer _cannot_ be the same person.
 * Assign appropriate [labels](https://github.com/SysBioChalmers/yeast-GEM/issues/labels).
 * Assign the pull request to one of the available [projects](https://github.com/SysBioChalmers/yeast-GEM/projects), if applicable.
-	
+
 ### Reviewing pull requests
 
 Every pull request must be approved by at least one reviewer before it can be merged. When reviewing someone else's pull request, keep in mind the following aspects:
@@ -160,6 +163,7 @@ Every pull request must be approved by at least one reviewer before it can be me
 This section is meant for the administrator of this repo. The main duties of the administrator are:
 * To make sure conventions and standards in the model are kept.
 * To keep the repository clean and organized, i.e. avoid redundancy in functions and/or data, and keep coherency in naming of files.
+* To manage package dependencies and regularly update them.
 * To help in the reviewing process of external pull requests by assigning reviewers, [labels](https://github.com/SysBioChalmers/yeast-GEM/issues/labels) and [projects](https://github.com/SysBioChalmers/yeast-GEM/projects), if applicable.
 * To keep [issues](https://github.com/SysBioChalmers/yeast-GEM/issues) with the proper labels, and to close them once they are fixed in the `master` branch.
 * In cases of disagreement between contributors, to decide how to resolve the issue.
@@ -172,6 +176,21 @@ The following points should be considered when merging branches to `devel`:
 * Wait at least a day before merging, to allow other developers to inspect the pull request.
 * As soon as the branch is merged, check if `devel` is still possible to merge to `master` (this can be checked [here](https://github.com/SysBioChalmers/yeast-GEM/compare/devel)). If conflicts appear (which should rarely happen and only if the `.xml` file was changed in an unexpected way by a toolbox update), fix the conflict _locally_ as soon as possible in `devel` and then push it (note, **DO NOT** pull any other changes from `master` to `devel`, just the single file that is creating the conflict).
 
+### Managing python dependencies
+
+We use [pip-tools](https://github.com/jazzband/pip-tools) for managing dependencies:
+
+* If a new dependency is needed for users/developers:
+  1. Add the dependency to `/requirements/requirements.in` or `/requirements/dev-requirements.in`, respectively (note that by default any requirement in `requirements.in` will also be in `dev-requirements.in`).
+  2. From `/requirements`, run `pip-compile requirements.in` and/or `pip-compile dev-requirements.in` as needed.
+
+* If dependencies need to be upgraded, from `/requirements` run:
+  ```
+  pip-compile --upgrade requirements.in
+  pip-compile --upgrade dev-requirements.in
+  ```
+  Dependencies should be upgraded regularly, but always first tested in separate branches.
+
 ### Releasing a new version
 
 * A merge of `devel` with `master` invokes a new release.
@@ -190,17 +209,25 @@ yeast-GEM follows [semantic versioning](https://semver.org/), adapted to GEMs:
   * Updating toolboxes.
   * Re-organization of data
   * Refactoring of code.
-  
+
 When releasing, please follow these steps:
   1. Make sure all dependencies in `devel` correspond to the setup from the local computer from which the release will be made. If not, make a single commit in `devel` updating this with a `loadYeastModel`/`saveYeastModel` cycle.
-  2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Fixes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
+  2. Create a pull request from `devel` to `master`, indicating all new features/fixes/etc. and referencing every previous pull request included (examples [here](https://github.com/SysBioChalmers/yeast-GEM/releases)). Tip: if any [issue](https://github.com/SysBioChalmers/yeast-GEM/issues) gets solved in the release, write in the pull request description "Closes #X", where "X" is the issue number. That way the issue will be automatically closed after merge.
   3. Merge at least a day after (having at least one accepted review).
-  4. Switch locally to `master` and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
+  4. Switch locally to `master`, pull changes and update `history.md`, by putting at the top the same description of the corresponding PR from step 2.
   5. Bump version with `increaseVersion.m`. **NOTE:** The function will error if unexpected changes are occurring. If this happens, probably step 1 was done incorrectly. To fix it, commit in `devel` any necessary changes and make a new pull request.
-  6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`.
-  7. Make the new release at GitHub (https://github.com/SysBioChalmers/yeast-GEM/releases/new), using the proper tag "vX.Y.Z" and with the same description as the corresponding PR from step 2.
-  8. Pull from `master` to `gh-pages` to update the landing page.
-
+  6. Commit changes from steps 4 and 5 with the message `chore: version X.Y.Z`, and push to the remote.
+  7. Make the new release at GitHub [here](https://github.com/SysBioChalmers/yeast-GEM/releases/new), using the proper tag "vX.Y.Z" and with the same description as the corresponding PR from step 2.
+  8. Merge locally `master` into `gh-pages` and push to update the landing page.
+  9. Review the [Zenodo](https://zenodo.org) release: Every new release from Github (step 7) automatically triggers a new release in Zenodo. However, so far it is not possible to fully customize this release, and some manual curation is needed. This includes:
+      * Ensuring the title of the release has the format `SysBioChalmers/yeast-GEM: yeast X.Y.Z`.
+      * Correcting author names to include all commit authors and PR reviewers that contributed to the release.
+      * Ensuring the version of the release has the format `vX.Y.Z`.
+      * Setting the language to English.
+      * Adding any grant IDs (if applicable).
+
+     Make sure to both save & publish your edits. You will find the new release at the top of [all Zenodo releases](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%221494182%22&sort=-publication_date&all_versions=True). Note that it might take some minutes for the Zenodo release to appear after you create the release in Github.
+
 ## Acknowledgments
 
 These contribution guidelines were written based on the contribution guidelines of [opencobra/cobrapy](https://github.com/opencobra/cobrapy/blob/devel/.github/CONTRIBUTING.rst) and [SysBioChalmers/RAVEN](https://github.com/SysBioChalmers/RAVEN/wiki/DevGuidelines).

.github/issue_template.md

@@ -21,5 +21,3 @@
 - [ ] Done this analysis in the `master` 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
-
-*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/pull_request_template.md

@@ -6,5 +6,3 @@
 - [ ] 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)
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about this PR
-
-*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE*

.github/workflows/memote-history.yml

@@ -0,0 +1,61 @@
+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 $2}' memote.ini | tr -d ' ')"
+        echo "::set-output name=location::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /location/) 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: ${{ steps.setup.outputs.other-repo }}
+
+    - name: Convert model
+      run: |
+        touch .env
+        python -c \
+          'import ComplementaryScripts.io as io; \
+          model = io.read_yeast_model(make_bigg_compliant=True); \
+          io.write_yeast_model(model)'
+
+    - name: Memote on push
+      run: |
+        memote run --skip-unchanged --solver-timeout 30
+        # Generate the history report on the deployment branch
+        memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}" --solver-timeout 30
+
+    - name: Auto-commit results
+      uses: stefanzweifel/[email protected]
+      with:
+        commit_user_name: memote-bot
+        commit_message: 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 +1,32 @@
+name: Memote history
+
+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 ComplementaryScripts.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 +1,41 @@
+name: YAML validation
+
+on:
+  push:
+    branches: [ devel ]
+  pull_request:
+    branches: [ master, devel ]
+
+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]
+      continue-on-error: true
+      with:
+        ## File(s) or Directory, separate by space if multiple files or folder are specified
+        file_or_dir: ModelFiles/
+        ## 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
+      continue-on-error: true
+      run: |
+        pip install -r requirements/ci-requirements.txt
+        python -c "import cobra ; cobra.io.load_yaml_model('ModelFiles/yml/yeastGEM.yml')"

.gitignore

@@ -41,13 +41,19 @@ Thumbs.db
 *.asv
 *.m~
 *.mex*
-*.mlappinstall 
+*.mlappinstall
 *.mltbx
 *.mat
 helpsearch*/
 
+# Python-related things #
+#########################
+*.ipynb_checkpoints/
+*.pyc
+*.env
+
 # Non-complying tables #
 ########################
 *.xls
 *.xlsx
-*.tab
+*.tab