OS

.auto-changelog

@@ -1,13 +1,11 @@
 {
     "output": "CHANGELOG.md",
     "template": ".auto-changelog-template.hbs",
-    "tagPrefix": "synthesis-workflow-v",
     "commitLimit": false,
     "backfillLimit": false,
     "ignoreCommitPattern": "^Release:? [0-9]+\\.[0-9]+\\.[0-9]+( ?\\(#[0-9]+\\))?$|^Update CHANGELOG.*|.*\\[skip-changelog\\].*|^\\[pre-commit.ci\\]|^\\(dependabot\\) .*",
-    "commitUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/commit/{id}",
-    "issueUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/issues/{id}",
-    "mergeUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/merge_requests/{id}",
-    "compareUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/compare/{from}...{to}",
-    "startingVersion": "0.1.1"
+    "commitUrl": "https://github.com/BlueBrain/synthesis-workflow/commit/{id}",
+    "issueUrl": "https://github.com/BlueBrain/synthesis-workflow/issues/{id}",
+    "mergeUrl": "https://github.com/BlueBrain/synthesis-workflow/pull/{id}",
+    "compareUrl": "https://github.com/BlueBrain/synthesis-workflow/compare/{from}..{to}"
 }

.codespellrc

@@ -1,3 +1,2 @@
 [codespell]
 skip = .git/*
-ignore-regex = @groupes.epfl.ch|hist|INT|INH

.copier-answers.yml

@@ -1,26 +1,26 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.63
+_commit: 0.1.65
 _src_path: [email protected]:neuromath/python-template.git
-author_email: [email protected]
-author_name: bbp-ou-cells
-copyright_license: BBP-internal-confidential
+author_email: ''
+author_name: Blue Brain Project, EPFL
+copyright_license: Apache License 2.0
 copyright_year: '2022'
 distribution_name: synthesis-workflow
-download_url: https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow
+download_url: https://github.com/BlueBrain/synthesis-workflow
 init_git: false
-maintainer: ''
+maintainer: Adrien Berchet
 package_name: synthesis_workflow
 project_description: Workflow used for synthesis and its validation.
 project_name: Synthesis Workflow
-project_url: https://bbpteam.epfl.ch/documentation/projects/synthesis-workflow
+project_url: https://synthesis_workflow.readthedocs.io
 repository_name: synthesis-workflow
-repository_namespace: neuromath
-repository_provider: gitlab
+repository_namespace: BlueBrain
+repository_provider: github
 setup_codeql: false
-ssh_url: git@bbpgitlab.epfl.ch:neuromath/synthesis-workflow.git
-team_name: neuromath
-tracker_url: https://bbpteam.epfl.ch/project/issues/projects/CELLS/issues
+ssh_url: git@github.com:BlueBrain/synthesis-workflow.git
+team_name: ''
+tracker_url: https://github.com/BlueBrain/synthesis-workflow/issues
 use_pyproject_toml: false
 version: 0.1.2.dev1
 

.coveragerc

@@ -1,11 +1,6 @@
 [paths]
 source_paths =
-	src/synthesis_workflow
+	synthesis_workflow
 	*/site-packages/synthesis_workflow
-	*/synthesis_workflow/src/synthesis_workflow
-	*/synthesis-workflow/src/synthesis_workflow
-
-source_morphval =
-	src/morphval
-	*/site-packages/morphval
-	*/synthesis-workflow/src/morphval
+	*/synthesis_workflow/synthesis_workflow
+	*/synthesis-workflow/synthesis_workflow

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -0,0 +1,114 @@
+# docs https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-issue-forms
+# https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema
+
+name: Create a bug report regarding Synthesis Workflow runtime behavior
+description: Errors and regression reports with complete reproducing test cases and/or stack traces.
+labels: [bug]
+title: "[Bug report] "
+body:
+  - type: markdown
+    attributes:
+      value: "
+Thanks for taking the time to fill out this bug report!
+
+
+Before submitting, make sure you search in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar issue was not already reported.
+If it is not the case, please read the following guidelines.
+
+### GUIDELINES FOR REPORTING BUGS
+
+Bug reports that are not properly formulated and formatted or without enough details can be very hard for us to understand and fix.
+In order to ensure we can help you fixing your bug, please follow these guidelines.
+
+
+Your reports must include the following features:
+
+1. **succinct description** of the problem - typically a line or two at most.
+
+2. **succinct, dependency-free code** which reproduces the problem, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
+  IF YOU DO NOT HAVE A COMPLETE, RUNNABLE TEST CASE WRITTEN DIRECTLY IN THE TEXTAREA BELOW, YOUR ISSUE MAY BE CLOSED.
+
+3. **complete stack traces for all errors** - please avoid screenshots, use formatted text inside issues.
+
+4. other relevant things as applicable: **dependencies**, **comparative performance timings** for performance issues, etc.
+"
+
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: input
+    id: relevant_documentation
+    attributes:
+      label: Optional link from https://synthesis_workflow.readthedocs.io which documents the behavior that is expected
+      description: "
+Please make sure the behavior you are seeing is definitely in contradiction to what's documented as the correct behavior.
+"
+    validations:
+      required: false
+
+  - type: textarea
+    attributes:
+      label: To Reproduce
+      description: "
+Provide your [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example here."
+      placeholder: "# Insert code here (text area already python formatted)"
+      render: Python
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Error
+      description: "
+Provide the complete text of any errors received **including the complete stack trace**.
+If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
+"
+      placeholder: "# Copy the complete stack trace and error message here (text area already formatted for Python backtrace)"
+      render: Python traceback
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Add any other context about the problem here.
+    validations:
+      required: false
+
+  - type: input
+    id: package_version
+    attributes:
+      label: synthesis_workflow Version in Use
+      description: e.g. 1.4.42, 2.0.2, etc or commit hash
+    validations:
+      required: true
+
+  - type: input
+    id: python_version
+    attributes:
+      label: Python Version
+      description: Assumes cpython unless otherwise stated, e.g. 3.10, 3.11, pypy
+    validations:
+      required: true
+
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating system
+      description: Check all that apply
+      multiple: true
+      options:
+        - Linux
+        - MacOS
+        - Windows
+        - Other
+    validations:
+      required: true
+
+  - type: markdown
+    attributes:
+      value: "### Thanks! Have a nice day!"

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -0,0 +1,56 @@
+# docs https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-issue-forms
+# https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema
+
+name: Request a new use case
+description: Support for new features
+labels: [enhancement]
+title: "[Feature request] "
+body:
+  - type: markdown
+    attributes:
+      value: "
+Thanks for taking the time to fill out this feature request!
+
+
+Before submitting, make sure the feature does not already exist in the [documentation](https://synthesis_workflow.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar feature request has not already been reported.
+If it is not the case, please read the following guidelines.
+
+### GUIDELINES FOR REQUESTING HELP
+
+Feature requests that are not properly formulated and formatted or without enough details can be very hard for us to understand.
+In order to ensure we can help you, please follow these guidelines.
+
+
+Your requests must include the following features:
+
+1. **succinct description** of the feature - typically a line or two at most to describe what the new feature would do.
+
+2. **succinct, dependency-free code** which shows how you would like to use this feature, otherwise known as a [Minimal, Complete, and Verifiable](https://stackoverflow.com/help/mcve) example.
+
+3. Why do you need this feature? What would be the use cases?
+"
+
+  - type: textarea
+    attributes:
+      label: Describe the feature
+      description: A clear and concise description of what the feature would consist in.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Example Use
+      description: Provide a clear example of what the usage of this feature would look like.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Use cases
+      description: Add as much information as possible about the use cases here.
+    validations:
+      required: true
+
+  - type: markdown
+    attributes:
+      value: "### Thanks! Have a nice day!"

.github/ISSUE_TEMPLATE/how_to_use.yaml

@@ -0,0 +1,91 @@
+# docs https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-issue-forms
+# https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/syntax-for-githubs-form-schema
+
+name: Ask for help about Synthesis Workflow
+description: Questions about synthesis_workflow features.
+labels: [how to use]
+title: "[How to use] "
+body:
+  - type: markdown
+    attributes:
+      value: "
+Thanks for using this package and taking the time to fill out this help request!
+
+
+Before submitting, make sure you read the [documentation](https://synthesis_workflow.readthedocs.io) carefully.
+If you still have a question, you should search in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar issue has not already been reported, you might find your answer there.
+If it is not the case, please read the following guidelines.
+
+### GUIDELINES FOR REQUESTING HELP
+
+Questions that are not properly formulated and formatted or without enough details can be very hard for us to understand.
+In order to ensure we can help you, please follow these guidelines.
+
+
+Your requests must include the following features:
+
+1. **succinct description** of the problem - typically a line or two at most to describe what you want to achieve.
+
+2. **succinct, dependency-free code** which shows what you tried to do, otherwise known as a [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve).
+
+3. **expected results**
+
+4. **complete stack traces for all errors** if you have any - please avoid screenshots, use formatted text inside issues.
+
+5. other relevant things: **dependencies**, **operating system**, **comparative performance timings** for performance issues.
+"
+
+  - type: textarea
+    attributes:
+      label: Describe the problem
+      description: A clear and concise description of what you want to achieve.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Show what you tried to do.
+      description: "
+Provide your [Minimal, Complete, and Verifiable Example](https://stackoverflow.com/help/mcve) here."
+      placeholder: "# Insert code here (text area already python formatted)"
+      render: Python
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Describe what you expected.
+      description: A clear and concise description of what you which result you expected by doing this.
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Error
+      description: "
+If you are facing an arror, provide the complete text of any errors received **including the complete stack trace**.
+If the message is a warning, run your program with the ``-Werror`` flag: ``python -Werror myprogram.py``
+"
+      placeholder: "# Copy the complete stack trace and error message here (text area already formatted for Python backtrace)"
+      render: Python traceback
+    validations:
+      required: false
+
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Add any other context about the problem here.
+    validations:
+      required: false
+
+  - type: input
+    id: package_version
+    attributes:
+      label: synthesis_workflow Version in Use
+      description: e.g. 1.4.42, 2.0.2, etc or commit hash
+    validations:
+      required: true
+
+  - type: markdown
+    attributes:
+      value: "### Thanks! Have a nice day!"

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Configure check for outdated GitHub Actions actions in workflows.
+  # See: https://docs.github.com/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+  - package-ecosystem: "github-actions"
+    directory: "/" # Check the repository's workflows under /.github/workflows/
+    schedule:
+      interval: "weekly"
+    commit-message:
+      # Prefix all commit messages with "CI(dependabot): "
+      prefix: "CI(dependabot): "

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+<!-- Provide a general summary of your proposed changes in the Title field above -->
+<!-- The title should have the following form: 'Type: Subject' with 'type' in [Build,Chore,CI,Reprecate,Docs,Feat,Fix,Perf,Refactor,Revert,Style,Test] -->
+
+### Description
+<!-- Describe your changes in detail and the reasons of these changes -->
+
+### Checklist
+<!-- Go over following points. Check them with an `x` if they do apply (they turn into clickable checkboxes once the PR is submitted, so no need to do everything at once). -->
+
+This pull request is:
+
+- [ ] A documentation / typographical error fix
+	- Good to go, no issue or tests are needed
+- [ ] A short code fix
+	- [ ] Please include: `Fixes: #<issue number>` in the description if it solves an existing issue
+	  (which must include a complete example of the issue).
+	- [ ] Please include tests that fail with the `main` branch and pass with the provided fix.
+- [ ] A new feature implementation or update an existing feature
+	- [ ] Please include: `Fixes: #<issue number>` in the description if it solves an existing issue
+	  (which must include a complete example of the feature).
+	- [ ] Please include tests that cover every lines of the new/updated feature.
+	- [ ] Please update the documentation to describe the new/updated feature.
+
+<!-- **Have a nice day!** -->