Refactor Github action workflows (#1907)

This PR simplifies the github action workflows. The tox configuration
was removed and where necessary replaced by uv commands. Additionally,
nightly/weekly/health checks are removed and their test coverage is now
executed on every single PR in the pr_test workflow. PRs will now also
go through a merge queue.

**CI/CD Workflow Modernization**

* Updated GitHub Actions workflows to use the `uv` package manager
instead of `tox` for installing dependencies and running documentation
builds, making the process faster and more consistent.
(`.github/workflows/docs_latest.yml`,
`.github/workflows/docs_stable.yml`, `docs/README.md`,
[[1]](diffhunk://#diff-2c9c11d26b09b8afde329980309d967121543a456e4592c76886a20b5cf56c90L1-L3)
[[2]](diffhunk://#diff-2c9c11d26b09b8afde329980309d967121543a456e4592c76886a20b5cf56c90L13-R16)
[[3]](diffhunk://#diff-844e4187f46e808f7df7020885a8a23669e6e65cfca837c81f4abdd1449781edL31-R39)
[[4]](diffhunk://#diff-8c82e9b578b937661bce0dcd204f21acd57e7aac7797bbf41274982f691e8af3L31-R38)
[[5]](diffhunk://#diff-0b5ca119d2be595aa307d34512d9679e49186307ef94201e4b3dfa079aa89938L4-R7)
* Simplified test execution in the PR workflow by merging unit and
integration tests into a single step and using `uv` for dependency
management. (`.github/workflows/pr_check.yml`,
[.github/workflows/pr_check.ymlL71-R63](diffhunk://#diff-420f4a16d0bf9d7626fa0fa302aee0382b72f5fdbf9e55cfcad43a4bbd6dfb9dL71-R63))
* Expanded workflow triggers to include `main` and `release**` branches
for PRs, merges, and pushes, making CI coverage more robust.
(`.github/workflows/linter.yml`, `.github/workflows/pr_check.yml`,
[[1]](diffhunk://#diff-ba16fc050e9c818b8125acc6d33b13f4c427ca91373d286af13d0fc92da90605L2-R15)
[[2]](diffhunk://#diff-420f4a16d0bf9d7626fa0fa302aee0382b72f5fdbf9e55cfcad43a4bbd6dfb9dR3-R15)

**Removal of Legacy and Unused Files**

* Deleted several workflow files related to nightly regression tests,
weekly stability tests, health checks, and Microsoft Teams
notifications, indicating a shift away from these legacy CI steps.
(`.github/workflows/nightly_check.yml`,
`.github/workflows/weekly_check.yml`,
`.github/workflows/health_check.yml`,
`.github/workflows/notify_teams.yml`,
[[1]](diffhunk://#diff-18e182faeed9bfe9da47114d8d1e5b5ba8a885320b1d64730565c1fa79c26a8aL1-L72)
[[2]](diffhunk://#diff-ba9f78b777607d7d59723e085aff0dbae9ac1ef9af63378da939d1b59c565850L1-L64)
[[3]](diffhunk://#diff-bac26813a2033c4d03f4e88f2ffe29044faca4127f5feb9bdf9b4121778f921bL1-L60)
[[4]](diffhunk://#diff-7b96a0448208ff4ff4469eb08644836bbfcbbebab69f4632fe45d9b73e98a306L1-L49)
* Removed fuzzing test scripts and related assets, suggesting these
tests are no longer maintained or required.
(`tests/fuzzing/__init__.py`, `tests/fuzzing/cli_fuzzing.py`,
`tests/fuzzing/helper.py`, `tests/fuzzing/assets/cli_operations.dict`,
[[1]](diffhunk://#diff-48adbbc0cf2f5e5ebce4b883fc903ec94668cbc214de780bbf077f83d8b509d8L1-L3)
[[2]](diffhunk://#diff-7dfda8fa44f953c939cb36267613c1cc0522ca6d3d27d94516b4325ec79591daL1-L44)
[[3]](diffhunk://#diff-8ce93919d3b3598065f01b58bea74b321f7b4464a2caf19f40504b43a29a5d1aL1-L16)
[[4]](diffhunk://#diff-246b8125c745d9a4c6b6bca29e40eb8d3ecea4e04e199d80237a3a036c7d2eb8L1-L16)

**Configuration Cleanup**

* Removed references to `.tox` in `pyproject.toml` and updated Bandit
configuration to exclude `.tox/`, reflecting the migration away from
`tox`.
[[1]](diffhunk://#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711L220)
[[2]](diffhunk://#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711L263)
* Deleted the `tox.ini` file, fully deprecating the use of `tox` for
environment management and testing.

**Miscellaneous**

* Updated the pull request template to reference the correct
contributing guide filename. (`.github/pull_request_template.md`,
[.github/pull_request_template.mdL3-R3](diffhunk://#diff-b2496e80299b8c3150b1944450bd81c622e04e13d15c411d291db0927d75fd6bL3-R3))
* Removed the Docsy theme submodule, likely indicating a change in
documentation theming or structure. (`.gitmodules`,
[.gitmodulesL1-L3](diffhunk://#diff-fe7afb5c9c916e521401d3fcfb4277d5071798c3baf83baf11d6071742823584L1-L3))


<!-- Contributing guide:
https://github.com/open-edge-platform/datumaro/blob/develop/CONTRIBUTING.md
-->

<!--
Please add a summary of changes. You may use Copilot to auto-generate
the PR description but please consider including any other relevant
facts which Copilot may be unaware of (such as design choices and
testing procedure).

Add references to the relevant issues and pull requests if any like so:

Resolves #111 and #222.
Depends on #1000 (for series of dependent commits).
-->

### Checklist
<!-- Put an 'x' in all the boxes that apply -->
- [ ] I have added tests to cover my changes or documented any manual
tests.
- [ ] I have updated the
[documentation](https://github.com/open-edge-platform/datumaro/tree/develop/docs)
accordingly

---------

Signed-off-by: Albert van Houten <[email protected]>
Co-authored-by: Copilot <[email protected]>

Author: AlbertvanHouten

.github/pull_request_template.md

@@ -1,6 +1,6 @@
 
 
-<!-- Contributing guide: https://github.com/open-edge-platform/datumaro/blob/develop/CONTRIBUTING.md -->
+<!-- Contributing guide: https://github.com/open-edge-platform/datumaro/blob/develop/contributing.md -->
 
 <!--
 Please add a summary of changes. You may use Copilot to auto-generate the PR description but please consider including any other relevant facts which Copilot may be unaware of (such as design choices and testing procedure).

.github/workflows/docs_latest.yml

@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - develop
+
 # No permissions by default
 permissions: {}
 
@@ -28,11 +29,14 @@ jobs:
           python-version: "3.11"
       - name: Install dependencies
         run: |
-          python -m pip install tox
+          python -m pip install uv
           sudo apt-get install pandoc graphviz
       - name: Build-Docs
         run: |
-          tox -e build-docs
+          uv pip install -r docs/requirements.txt
+          cd docs
+          make clean
+          make html
       - name: Create gh-pages branch
         run: |
           if [[ ${{github.event_name}} == 'workflow_dispatch' ]]; then

.github/workflows/docs_stable.yml

@@ -28,11 +28,14 @@ jobs:
           python-version: "3.11"
       - name: Install dependencies
         run: |
-          python -m pip install tox
+          python -m pip install uv
           sudo apt-get install pandoc graphviz
       - name: Build-Docs
         run: |
-          tox -e build-docs
+          uv pip install -r docs/requirements.txt
+          cd docs
+          make clean
+          make html
       - name: Create gh-pages branch
         env:
           TAG_NAME: ${{ github.event.release.tag_name }}

.github/workflows/health_check.yml

@@ -1,5 +1,18 @@
 name: Linter
-on: pull_request
+on:
+  pull_request:
+    branches:
+      - develop
+      - release**
+  merge_group:
+    branches:
+      - develop
+      - release**
+  push:
+    branches:
+      - develop
+      - release**
+
 # No permissions by default, no specific permissions are required for this workflow
 permissions: {}
 jobs:

.github/workflows/linter.yml

@@ -1,16 +1,18 @@
 name: PR Test
 on:
+  pull_request:
+    branches:
+      - develop
+      - release**
+  merge_group:
+    branches:
+      - develop
+      - release**
   push:
     branches:
-      - "master"
-      - "develop"
-      - "releases/*"
-  pull_request:
-    types:
-      - opened
-      - synchronize
-      - reopened
-      - ready_for_review
+      - develop
+      - release**
+
 permissions:
   # The id-token permission is required by Codecov to use OIDC
   id-token: write
@@ -30,17 +32,6 @@ jobs:
       matrix:
         os: ["ubuntu-24.04", "windows-2022", "macos-15"]
         python-version: ["3.10", "3.13"]
-        include:
-          - python-version: "3.10"
-            tox-env-py: "310"
-          - python-version: "3.13"
-            tox-env-py: "313"
-          - os: "ubuntu-24.04"
-            tox-env-os: "lin"
-          - os: "windows-2022"
-            tox-env-os: "win"
-          - os: "macos-15"
-            tox-env-os: "mac"
     name: pr test (${{ matrix.os }}, Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     steps:
@@ -68,11 +59,8 @@ jobs:
       - name: Installing dependencies
         run: uv sync --locked --all-extras --dev
 
-      - name: Unit testing
-        run: uv run pytest tests/unit --cov --cov-report=xml
-
-      - name: Integration testing
-        run: uv run pytest tests/integration
+      - name: Tests
+        run: uv run pytest --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5.5.1