Chore: Move to Github (#1)

Author: adrien-berchet

.auto-changelog

@@ -1,12 +1,11 @@
 {
     "output": "CHANGELOG.md",
     "template": ".auto-changelog-template.hbs",
-    "tagPrefix": "bluepyparallel-v",
     "commitLimit": false,
     "backfillLimit": false,
-    "ignoreCommitPattern": "^Release:? [0-9]+\\.[0-9]+\\.[0-9]+$|^Update CHANGELOG.*|.*\\[skip-changelog\\].*|^\\[pre-commit.ci\\]|^\\(dependabot\\) .*",
-    "commitUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/commit/{id}",
-    "issueUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/issues/{id}",
-    "mergeUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/merge_requests/{id}",
-    "compareUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/compare/{from}...{to}"
+    "ignoreCommitPattern": "^Release:? [0-9]+\\.[0-9]+\\.[0-9]+( ?\\(#[0-9]+\\))?$|^Update CHANGELOG.*|.*\\[skip-changelog\\].*|^\\[pre-commit.ci\\]|^\\(dependabot\\) .*",
+    "commitUrl": "https://github.com/BlueBrain/BluePyParallel/commit/{id}",
+    "issueUrl": "https://github.com/BlueBrain/BluePyParallel/issues/{id}",
+    "mergeUrl": "https://github.com/BlueBrain/BluePyParallel/pull/{id}",
+    "compareUrl": "https://github.com/BlueBrain/BluePyParallel/compare/{from}..{to}"
 }

.auto-changelog-template.hbs

@@ -136,7 +136,7 @@ Example Definitions
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[dD]eprecate:|^[dD]eprecate\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild ?\(|^[dD]eprecate:|^[dD]eprecate ?\(|^[fF]eat:|^[fF]eat ?\(|^[fF]ix:|^[fF]ix ?\(|^[cC]hore:|^[cC]hore ?\(|^[cC][iI]:|^[cC][iI] ?\(|^[dD]ocs:|^[dD]ocs ?\(|^[rR]efactor:|^[rR]efactor ?\(|^[tT]est:|^[tT]est ?\(|^[sS]tyle:|^[sS]tyle ?\(|^[pP]erf:|^[pP]erf ?\(|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -190,7 +190,7 @@ Example Definitions
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[dD]eprecate:|^[dD]eprecate\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild ?\(|^[dD]eprecate:|^[dD]eprecate ?\(|^[fF]eat:|^[fF]eat ?\(|^[fF]ix:|^[fF]ix ?\(|^[cC]hore:|^[cC]hore ?\(|^[cC][iI]:|^[cC][iI] ?\(|^[dD]ocs:|^[dD]ocs ?\(|^[rR]efactor:|^[rR]efactor ?\(|^[tT]est:|^[tT]est ?\(|^[sS]tyle:|^[sS]tyle ?\(|^[pP]erf:|^[pP]erf ?\(|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 

.codespellrc

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

.copier-answers.yml

@@ -1,27 +1,25 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.52
+_commit: 0.1.55
 _src_path: [email protected]:neuromath/python-template.git
-author_email: [email protected]
-author_name: bbp-ou-cells
-copyright_license: BBP-internal-confidential
-copyright_year: '2022'
-distribution_name: bluepyparallel
-download_url: https://bbpgitlab.epfl.ch/neuromath/bluepyparallel
+author_name: Blue Brain Project, EPFL
+copyright_license: Apache License 2.0
+copyright_year: '2024'
+distribution_name: BluePyParallel
+download_url: https://github.com/BlueBrain/BluePyParallel
 init_git: false
 maintainer: Adrien Berchet
 package_name: bluepyparallel
-project_description: Provides an embarassingly parallel tool with sql backend.
+project_description: Provides an embarrassingly parallel tool with sql backend.
 project_name: BluePyParallel
-project_url: https://bbpteam.epfl.ch/documentation/projects/bluepyparallel
-repository_name: bluepyparallel
-repository_namespace: neuromath
-repository_provider: gitlab
+project_url: https://BluePyParallel.readthedocs.io
+repository_name: BluePyParallel
+repository_namespace: BlueBrain
+repository_provider: github
 setup_codeql: false
-ssh_url: [email protected]:neuromath/bluepyparallel.git
-team_name: neuromath
-tracker_url: https://bbpteam.epfl.ch/project/issues/projects/CELLS/issues
-use_pyproject_toml: false
+ssh_url: [email protected]:BlueBrain/BluePyParallel.git
+tracker_url: https://github.com/BlueBrain/BluePyParallel/issues
+use_pyproject_toml: true
 version: 0.0.9.dev0
 
 # End of Copier answers

.coveragerc

@@ -3,4 +3,4 @@ source_paths =
 	bluepyparallel
 	*/site-packages/bluepyparallel
 	*/bluepyparallel/bluepyparallel
-	*/bluepyparallel/bluepyparallel
+	*/BluePyParallel/bluepyparallel

.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 BluePyParallel 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/BluePyParallel/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://BluePyParallel.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: bluepyparallel 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://BluePyParallel.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/BluePyParallel/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 BluePyParallel
+description: Questions about bluepyparallel 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://BluePyParallel.readthedocs.io) carefully.
+If you still have a question, you should search in the [issue list](https://github.com/BlueBrain/BluePyParallel/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: bluepyparallel 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): "