cleaning pass 2

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @DomInvivo

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,7 @@
 Checklist:
 
-- [ ] Added a `news` entry: _copy `news/TEMPLATE.rst` to `news/my-feature-or-branch.rst`) and edit it._
+- [ ] Was this PR discussed in a issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR.
+- [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
+- [ ] Update the API documentation is a new function is added or an existing one is deleted.
 
 ---

.github/workflows/lint.yml → .github/workflows/code-check.yml

@@ -1,26 +1,26 @@
-name: Lint
+name: code-check
 
 on:
   push:
-    branches:
-      - "master"
+    branches: ["main"]
+    tags: ["*"]
   pull_request:
     branches:
       - "*"
+      - "!gh-pages"
 
 jobs:
-  lint-source-code:
-    name: Lint
-    runs-on: "ubuntu-latest"
-
+  python-format-black:
+    name: Python lint [black]
+    runs-on: ubuntu-latest
     steps:
       - name: Checkout the code
         uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install black
         run: |

.github/workflows/doc.yml

@@ -2,8 +2,9 @@ name: doc
 
 on:
   push:
-    branches:
-      - "master"
+    branches: ["main"]
+  release:
+    types: [published]
 
 jobs:
   doc:
@@ -18,22 +19,34 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v3
 
-      - name: Setup Mamba
-        uses: mamba-org/provision-with-micromamba@v14
+      - name: Setup mamba
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: env.yml
-          environment-name: goli
+          environment-name: openfractal
+          cache-environment: true
           cache-downloads: true
-          cache-env: true
-          channel-priority: strict
 
       - name: Install library
         run: python -m pip install --no-deps .
 
       - name: Deploy the doc
         run: |
-          # Get the privpage branch
+          echo "Configure git"
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+
+          echo "Get the gh-pages branch"
           git fetch origin gh-pages
 
-          # Build and serve the doc
-          mkdocs gh-deploy --force
+          TAG_OR_BRANCH_NAME=${GITHUB_REF##*/}
+
+          if [ $TAG_OR_BRANCH_NAME = "main" ]; then
+            echo "Build and deploy the doc on main"
+            mike deploy --push --force main
+          else
+            echo "Build and deploy the doc on $TAG_OR_BRANCH_NAME"
+
+            mike deploy --push --force stable
+            mike deploy --push --force $TAG_OR_BRANCH_NAME
+          fi

.github/workflows/release.yml

@@ -0,0 +1,112 @@
+name: release
+
+on:
+  workflow_dispatch:
+    inputs:
+      release-version:
+        description: "A valid Semver version string"
+        required: true
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  release:
+    # Do not release if not triggered from the default branch
+    if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout the code
+        uses: actions/checkout@v3
+
+      - name: Setup mamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: env.yml
+          environment-name: graphium
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
+            pip
+            semver
+            python-build
+            setuptools_scm
+
+      - name: Check the version is valid semver
+        run: |
+          RELEASE_VERSION="${{ inputs.release-version }}"
+
+          {
+            pysemver check $RELEASE_VERSION
+          } || {
+            echo "The version '$RELEASE_VERSION' is not a valid Semver version string."
+            echo "Please use a valid semver version string. More details at https://semver.org/"
+            echo "The release process is aborted."
+            exit 1
+          }
+
+      - name: Check the version is higher than the latest one
+        run: |
+          # Retrieve the git tags first
+          git fetch --prune --unshallow --tags &> /dev/null
+
+          RELEASE_VERSION="${{ inputs.release-version }}"
+          LATEST_VERSION=$(git describe --abbrev=0 --tags)
+
+          IS_HIGHER_VERSION=$(pysemver compare $RELEASE_VERSION $LATEST_VERSION)
+
+          if [ "$IS_HIGHER_VERSION" != "1" ]; then
+            echo "The version '$RELEASE_VERSION' is not higher than the latest version '$LATEST_VERSION'."
+            echo "The release process is aborted."
+            exit 1
+          fi
+
+      - name: Build Changelog
+        id: github_release
+        uses: mikepenz/release-changelog-builder-action@v4
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Configure git
+        run: |
+          git config --global user.name "${GITHUB_ACTOR}"
+          git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
+
+      - name: Create and push git tag
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # Tag the release
+          git tag -a "${{ inputs.release-version }}" -m "Release version ${{ inputs.release-version }}"
+
+          # Push the modified changelogs
+          git push origin main
+
+          # Push the tags
+          git push origin "${{ inputs.release-version }}"
+
+      - name: Install library
+        run: python -m pip install --no-deps .
+
+      - name: Build the wheel and sdist
+        run: python -m build --no-isolation
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages-dir: dist/
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
+        with:
+          tag_name: ${{ inputs.release-version }}
+          body: ${{steps.github_release.outputs.changelog}}

.github/workflows/test.yml

@@ -2,11 +2,14 @@ name: test
 
 on:
   push:
-    branches:
-      - "master"
+    branches: ["main"]
+    tags: ["*"]
   pull_request:
     branches:
       - "*"
+      - "!gh-pages"
+  schedule:
+    - cron: "0 4 * * MON"
 
 jobs:
   test:
@@ -31,17 +34,16 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v3
 
-      - name: Setup Mamba
-        uses: mamba-org/provision-with-micromamba@v15
+      - name: Setup mamba
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: env.yml
-          environment-name: goli
-          extra-specs: |
+          environment-name: graphium
+          cache-environment: true
+          cache-downloads: true
+          create-args: >-
             python=${{ matrix.python-version }}
             pytorch=${{ matrix.pytorch-version }}
-          cache-downloads: true
-          cache-env: true
-          channel-priority: strict
 
       - name: Install library
         run: python -m pip install --no-deps .
@@ -50,7 +52,7 @@ jobs:
         run: pytest
 
       - name: Test CLI
-        run: goli --help
+        run: graphium --help
 
       - name: Test building the doc
         run: mkdocs build