Merged devel branch (2bee3b9) into this branch. Fixed some type annotations and added comments. Fixed issues that came forward when running tox. Updated pickle files due to renaming of custompairs.py.

Author: pascalaldo

.editorconfig

@@ -10,7 +10,7 @@ insert_final_newline = true
 trim_trailing_whitespace = true
 max_line_length = 88
 
-[*.{json,yml}]
+[*.{json,yml,yaml}]
 indent_size = 2
 
 [*.{md,rst}]

.github/CONTRIBUTING.rst

@@ -105,6 +105,15 @@ Ready to contribute? Here's how to set up cobrapy for local development.
 
        tox --parallel
 
+   We also provide some `git pre-commit hooks <https://pre-commit.com/>`_ for
+   your convenience. They run our linting steps and will ensure that your
+   contributions pass linting with every commit that you make.  When you want to
+   use them, run the following commands.
+
+   .. code-block:: console
+
+       pip install pre-commit
+       pre-commit install
 
 7. Push your branch to GitHub.
 

.github/ISSUE_TEMPLATE/01-bug-report.md

@@ -0,0 +1,64 @@
+name: 🐞 Bug report
+description: Report a problem to help improve this project
+title: "[BUG] "
+labels: [bug, triage]
+body:
+    - type: checkboxes
+      attributes:
+          label: Is there an existing issue for this?
+          description: Please search to see if an [issue already exists](https://github.com/opencobra/cobrapy/issues) for the bug you encountered.
+          options:
+              - label: I have searched the existing issues
+                required: true
+    - type: textarea
+      attributes:
+          label: Problem description
+          description: |
+              A concise description of what you're experiencing.
+
+              Please explain:
+
+                * **what** you tried to achieve,
+                * **how** you went about it (referring to the code sample), and
+                * **why** the current behaviour is a problem and what output you expected instead.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Code sample
+          description: >
+              Create a [minimal, complete, verifiable example](https://stackoverflow.com/help/mcve).
+              Please, paste your code between the ``` tickmarks below or link to a [gist](https://gist.github.com/).
+          value: |
+              Code run:
+
+              ```python
+              ```
+
+              Traceback:
+
+              ```text
+              ```
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Environment
+          description: >
+              Please paste the output of running `depinfo --markdown cobra`
+              in your environment between the `details` tags below.
+          value: |
+              <details>
+
+              </details>
+      validations:
+          required: true
+    - type: textarea
+      attributes:
+          label: Anything else?
+          description: |
+              Links? References? Anything that will give us more context about the issue you are encountering!
+
+              Tip: You can attach images or log files by clicking this area to highlight it and then dragging files in.
+      validations:
+          required: false

.github/ISSUE_TEMPLATE/01-bug-report.yaml

@@ -0,0 +1,46 @@
+
+name: Feature request
+description: Suggest an idea for this project
+title: "[Feature] "
+labels: [enhancement]
+body:
+    - type: checkboxes
+      attributes:
+          label: Checklist
+          description: >
+              Please make sure you check all these items before submitting your feature request.
+          options:
+              - label: There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet.
+                required: true
+    - type: textarea
+      attributes:
+          label: Problem
+          description: >
+              A clear and concise description of what you are trying to achieve.
+          placeholder: >
+              "I want to be able to [...] but I can't because [...]".
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Solution
+          description: >
+              A clear and concise description of what you would want to happen.
+              For API changes, try to provide a code snippet of what you would like the new API to look like.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Alternatives
+          description: >
+              Please describe any alternative solutions or features you've considered to solve
+              your problem and why they didn't help.
+      validations:
+          required: false
+    - type: textarea
+      attributes:
+          label: Anything else?
+          description: >
+              Provide any additional context, screenshots, tracebacks, etc. about the feature here.
+      validations:
+          required: false

.github/ISSUE_TEMPLATE/02-feature-request.yaml

@@ -1,11 +1,10 @@
 # Ref: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser
 blank_issues_enabled: true
 contact_links:
-- name: 📧 Google Group
-  url: http://groups.google.com/group/cobra-pie
+- name: Question
+  url: https://github.com/opencobra/cobrapy/discussions
   about: >
-    Please ask typical questions here: General constraint-based modelling problems or
-    issues with genome-scale models in COBRApy.
+    Please ask general questions about constraint-based modeling or COBRApy specifically here.
 - name: 💬 Gitter
   url: https://gitter.im/opencobra/cobrapy
   about: >

.github/ISSUE_TEMPLATE/02-question.md

@@ -9,14 +9,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Get tag
-        id: tag
-        run: echo "::set-output name=version::${GITHUB_REF#refs/tags/}"
       - name: Dispatch new release version to BioSimulators
         uses: benc-uk/workflow-dispatch@v1
         with:
           workflow: Continuous integration
           repo: biosimulators/Biosimulators_COBRApy
           ref: dev
           token: ${{ secrets.BIOSIM_DISPATCH_TOKEN }}
-          inputs: '{ "simulatorVersion": "${{ steps.tag.outputs.version }}", "simulatorVersionLatest": "true" }'
+          inputs: '{ "simulatorVersion": "${{ github.ref_name }}", "simulatorVersionLatest": "true" }'

.github/ISSUE_TEMPLATE/03-feature-request.md

@@ -0,0 +1,11 @@
+name: Cron Test
+
+on:
+  schedule:
+  # Run every Tuesday at 10:30.
+  - cron: '30 10 * * 2'
+
+jobs:
+  prerequisites:
+    uses: ./.github/workflows/test.yml
+