✨ Complete internal rewrite - new result API

.github/CODEOWNERS

@@ -12,55 +12,58 @@
 # This should make it easy to add new rules without breaking existing ones.
 
 # Global rule:
-*                                   @glotaran/admins
+*                                       @glotaran/admins
 
 # tooling
-/.github                            @glotaran/admins @glotaran/maintainers
-/.*                                 @glotaran/admins @glotaran/maintainers
-/*.y*ml                             @glotaran/admins @glotaran/maintainers
-/*.ini                              @glotaran/admins @glotaran/maintainers
-/*.toml                             @glotaran/admins @glotaran/maintainers
-/*.txt                              @glotaran/admins @glotaran/maintainers
-LICENSE                             @glotaran/pyglotaran_creators
+/.github                                @glotaran/admins @glotaran/maintainers
+/.*                                     @glotaran/admins @glotaran/maintainers
+/*.y*ml                                 @glotaran/admins @glotaran/maintainers
+/*.toml                                 @glotaran/admins @glotaran/maintainers
+/*.txt                                  @glotaran/admins @glotaran/maintainers
+LICENSE                                 @glotaran/pyglotaran_creators
 
 # docs
-/docs/**/*.rst                      @glotaran/maintainers @glotaran/pyglotaran_creators
-# /docs/**/*.md                     @glotaran/maintainers @glotaran/pyglotaran_creators
+/docs/**/*.rst                          @glotaran/maintainers @glotaran/pyglotaran_creators
+/docs/**/*.md                           @glotaran/maintainers @glotaran/pyglotaran_creators
 
 # analysis module:
-/glotaran/analysis/                 @jsnel @joernweissenborn
+# /glotaran/analysis/                     @jsnel @joernweissenborn
 
 # builtin module:
-/glotaran/builtin/io/*              @glotaran/admins
-/glotaran/builtin/io/ascii          @jsnel @glotaran/maintainers
-/glotaran/builtin/io/pandas         @glotaran/maintainers
-/glotaran/builtin/io/netCDF         @glotaran/maintainers
-/glotaran/builtin/io/sdt            @glotaran/maintainers
-/glotaran/builtin/megacomplexes/    @jsnel @joernweissenborn
+/glotaran/builtin/io/*                  @glotaran/admins
+/glotaran/builtin/io/ascii              @jsnel @glotaran/maintainers
+/glotaran/builtin/io/pandas             @glotaran/maintainers
+/glotaran/builtin/io/netCDF             @glotaran/maintainers
+/glotaran/builtin/io/sdt                @glotaran/maintainers
 
-# cli
-/glotaran/cli/                      @jsnel @glotaran/admins
+/glotaran/builtin/elements              @jsnel @joernweissenborn
+/glotaran/builtin/items                 @jsnel @joernweissenborn
+/glotaran/optimization                  @jsnel @joernweissenborn
+/glotaran/model                         @jsnel @joernweissenborn
+
+# cli (deprecated)
+# /glotaran/cli/                          @jsnel @glotaran/admins
 
 # examples # Removed in PR #866
-# /glotaran/examples/                 @jsnel @glotaran/maintainers
+# /glotaran/examples/                     @jsnel @glotaran/maintainers
 
 # io
-/glotaran/io/                       @jsnel @glotaran/maintainers
+/glotaran/io/                           @jsnel @glotaran/maintainers
 
 # model
-/glotaran/model/                    @jsnel @glotaran/admins @joernweissenborn
+/glotaran/model/                        @jsnel @glotaran/admins @joernweissenborn
 
 # parameter
-/glotaran/parameter/                @jsnel @glotaran/admins @joernweissenborn
+/glotaran/parameter/                    @jsnel @glotaran/admins @joernweissenborn
 
 # plugin_system
-glotaran/plugin_system              @s-weigand @glotaran/admins
+/glotaran/plugin_system                 @s-weigand @glotaran/admins
 
-# deprecation framework and tests
-glotaran/deprecation                @s-weigand @glotaran/admins
+# deprecation framework
+/glotaran/deprecation                   @s-weigand @glotaran/admins
 
 # utility function
-glotaran/utils                      @s-weigand @glotaran/admins
+/glotaran/utils                         @s-weigand @glotaran/admins
 
 # project
-/glotaran/project/                  @jsnel @glotaran/admins
+/glotaran/project/                      @jsnel @glotaran/admins

.github/workflows/CI_CD_actions.yml

@@ -17,26 +17,11 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Run pre-commit
-        uses: pre-commit/action@v3.0.0
-
-  check-manifest:
-    name: Check Manifest
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out repo
-        uses: actions/checkout@v4
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.10"
-      - name: Install check manifest
-        run: python -m pip install check-manifest 'setuptools>=62.4.0'
-      - name: Run check manifest
-        run: check-manifest
+        uses: pre-commit/action@v3.0.1
 
   docs:
     runs-on: ubuntu-latest
@@ -48,15 +33,15 @@ jobs:
           conda-channels: conda-forge
           activate-conda: false
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
         run: |
           conda install -y pandoc
           python -m pip install -U pip wheel
-          python -m pip install .
-          python -m pip install -U -r docs/requirements.txt
+          python -m pip install -U pip wheel
+          python -m pip install .[docs]
       - name: Show installed packages
         run: pip freeze
       - name: Build docs
@@ -73,38 +58,37 @@ jobs:
           conda-channels: conda-forge
           activate-conda: false
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
         run: |
           conda install -y pandoc
           python -m pip install -U pip wheel
-          python -m pip install .
-          python -m pip install -U -r docs/requirements.txt
+          python -m pip install .[docs]
       - name: Show installed packages
         run: pip freeze
       - name: Check doc links
         run: |
-          make --directory=docs clean linkcheck $@ | tee linkcheck-output.txt
-          exit ${PIPESTATUS[0]}
+          make --directory=docs clean linkcheck "$@" | tee linkcheck-output.txt
+          exit "${PIPESTATUS[0]}"
       - name: Linkcheck summary
         if: ${{ always() }}
-        run: cat linkcheck-output.txt | grep -E "(\(line.*\)|writing output)"
+        run: grep -E "(\(line.*\)|writing output)" < linkcheck-output.txt
 
   docs-notebooks:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install -U pip wheel
-          python -m pip install -U -r requirements_dev.txt
-          pip install .
+          python -m pip install -U -r requirements_pinned.txt
+          python -m pip install .[docs]
       - name: Show installed packages
         run: python -m pip freeze
       - name: Build docs
@@ -113,53 +97,55 @@ jobs:
 
   test:
     runs-on: ${{ matrix.os }}
-    needs: [pre-commit, check-manifest]
+    needs: [pre-commit]
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest, macOS-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip wheel
-          python -m pip install -r requirements_dev.txt
-          python -m pip install -e .
+          python -m pip install -U -r requirements_pinned.txt
+          python -m pip install ".[test]"
       - name: Show installed packages
         run: python -m pip freeze
       - name: Run tests
         run: |
-          python -m pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml glotaran
+          python -m pytest --cov=./ --cov-report term --cov-report xml --cov-config pyproject.toml tests
 
       - name: Codecov Upload
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   deploy:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     needs: [test, docs, docs-notebooks]
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
+
       - name: Install dependencies
-        run: |
-          python -m pip install -U pip wheel 'setuptools>=62.4.0'
+        run: python -m pip install -U hatch
+
       - name: Build dist
-        run: |
-          python setup.py sdist bdist_wheel
+        run: hatch build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@v1.9.0
         with:
-          user: __token__
-          password: ${{ secrets.pypi_pyglotaran_token }}
+          print-hash: true

.github/workflows/autoupdate-pre-commit-config.yml

@@ -14,8 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
-      - uses: actions/cache@v3
+        uses: actions/setup-python@v5
+      - uses: actions/cache@v4
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-autoupdate

.github/workflows/binder-on-pr.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: comment on PR with Binder link
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           github-token: ${{secrets.GITHUB_TOKEN}}
           script: |

.github/workflows/codeql.yml

@@ -27,17 +27,17 @@ jobs:
           submodules: recursive
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
           setup-python-dependencies: false
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3
         with:
           upload: False
           output: sarif-results
@@ -51,6 +51,6 @@ jobs:
           output: sarif-results/${{ matrix.language }}.sarif
 
       - name: Upload SARIF
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: sarif-results/${{ matrix.language }}.sarif

.github/workflows/doxygen.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -63,7 +63,7 @@ jobs:
         with:
           doxyfile-path: "docs/Doxyfile.ini"
       - name: Upload Doxygen Docs Artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: doxygen_docs_pyglotaran
           path: doxygen_docs_pyglotaran