Setup C/I workflows (#10)

* Bump versions * Update docs * Add comment * Initial version test.yml * WIP * WIP * WIP * Reformat * WIP * WIP * WIP * WIP * WIP * Add analyse.yml * Add badge * WIP * pre-commit fixes * WIP * WIP * WIP * WIP * WIP * WIP * WIP * WIP * Return non-zero value in case of error * WIP * WIP * WIP * WIP * WIP * WIP
Deltares-research · Apr 5, 2024 · 701cc71 · 701cc71
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diff --git a/.github/workflows/analyse.yml b/.github/workflows/analyse.yml
@@ -0,0 +1,37 @@
+name: Analyse
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  build:
+    name: ${{ matrix.platform.os }} / ${{ matrix.platform.arch }} / python-${{ matrix.python_version }}
+    runs-on: ${{ matrix.platform.os }}
+    timeout-minutes: 30
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.12"]
+        platform:
+          - { os: "ubuntu-22.04", arch: x64 }
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python_version }}
+          cache: "pip"
+          cache-dependency-path: "**/requirements*.txt"
+      - name: Install packages
+        run: |
+          pip install -r environment/configuration/requirements.txt -r environment/configuration/requirements-dev.txt
+      - name: Analyse files
+        run: |
+          pre-commit install
+          # TODO For some reason pylint in a GH workflow complains about PySide6...
+          SKIP=pylint pre-commit run --all-files
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,59 @@
+name: Test
+
+on:
+  pull_request:
+  push:
+
+jobs:
+  build:
+    name: ${{ matrix.platform.os }} / ${{ matrix.platform.arch }} / python-${{ matrix.python_version }}
+    runs-on: ${{ matrix.platform.os }}
+    timeout-minutes: 30
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        # min version, max version
+        # 3.11 is the first version supported by darwin / arm64 runner
+        python_version: ["3.11", "3.12"]
+        platform:
+          - { os: "macos-14", arch: arm64 }
+          - { os: "macos-13", arch: x64 }
+          - { os: "ubuntu-22.04", arch: x64 }
+          - { os: "windows-2022", arch: x64 }
+    steps:
+      - name: Setup Linux platform
+        if: ${{ startsWith(matrix.platform.os, 'ubuntu') }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install libegl1
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        id: py
+        with:
+          python-version: ${{ matrix.python_version }}
+          cache: "pip"
+          cache-dependency-path: "**/requirements*.txt"
+      - name: Install packages
+        run: |
+          py_interpreter="${{ steps.py.outputs.python-path }}"
+          $py_interpreter -m pip install \
+            -r environment/configuration/requirements.txt \
+            -r environment/configuration/requirements-dev.txt
+      - name: Run tests
+        run: |
+          mkdir build
+          cd build
+          cmake -S .. -G Ninja
+          ctest --test-dir . --output-on-failure
+      - name: Create documentation
+        run: |
+          cmake --build build --target documentation
+      # - name: Create and verify release
+      #   run: |
+      #     py_interpreter="${{ steps.py.outputs.python-path }}"
+      #     PYTHONPATH=source/package ${py_interpreter} environment/script/create_and_verify_release.py ./build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,23 +1,23 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
 - repo: https://github.com/psf/black
-  rev: 24.1.1
+  rev: 24.3.0
   hooks:
   - id: black
 - repo: https://github.com/pycqa/isort
   rev: 5.13.2
   hooks:
   - id: isort
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.8.0
+  rev: v1.9.0
   hooks:
   - id: mypy
     additional_dependencies: ["types-requests"]
@@ -37,13 +37,14 @@ repos:
       [
         "-rn",  # Only display messages
         "-sn",  # Don't display the score
+        "--extension-pkg-allow-list=PySide6",
       ]
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+  rev: v3.15.2
   hooks:
   - id: pyupgrade
 - repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.5.4
+  rev: v1.5.5
   hooks:
   - id: forbid-tabs
   - id: remove-tabs
@@ -55,11 +56,3 @@ repos:
       (?x)^(
         adaptation_pathways.spec.in|
       )$
-# - repo: https://github.com/cmake-lint/cmake-lint
-#   rev: 1.4.2
-#   hooks:
-#   - id: cmakelint
-#     args:
-#       [
-#         "--filter=-linelength,-convention/filename,-package/stdargs",
-#       ]
diff --git a/README.md b/README.md
@@ -1,3 +1,7 @@
 # Adaptation pathways
+[![Test](https://github.com/Deltares-research/PathwaysGenerator/actions/workflows/test.yml/badge.svg)](https://github.com/Deltares-research/PathwaysGenerator/actions/workflows/test.yml)
+[![Analyse](https://github.com/Deltares-research/PathwaysGenerator/actions/workflows/analyse.yml/badge.svg)](https://github.com/Deltares-research/PathwaysGenerator/actions/workflows/analyse.yml)
 
-https://publicwiki.deltares.nl/display/AP/Adaptation+Pathways
+- [Developer manual](documentation/develop/index.rst)
+- [User manual](documentation/use/index.rst)
+- [Tester manual](documentation/test/index.rst)
diff --git a/documentation/develop/index.rst b/documentation/develop/index.rst
@@ -41,19 +41,11 @@ In commands:
    pip3 install -r environment/configuration/requirements.txt -r environment/configuration/requirements-dev.txt
 
    # Install handy tools that will keep our code in good shape:
-   pip3 install pre-commit
    pre-commit install
    # Note: commit .pre-commit-config.yaml if any hooks actually got updated
    pre-commit autoupdate
 
-   # Use a local updated version of pylint instead of the older version possibly installed on
-   # the system and instead of the normal pylint pre-commit hook. pre-commit hooks run in their own
-   # virtual environment that doesn't know about our package, resulting in lots of errors.
-   pip3 install pylint
-
-   pathways_generator.py browser
-   pathways_generator.py window
-   jupyter-lab --notebook-dir=source/notebook/
+   source/script/ap_pathway_generator.py --help
 
 
 The project contains code for generating :ref:`targets <sec-cmake>`, like documentation and the

diff --git a/environment/configuration/requirements-dev.txt b/environment/configuration/requirements-dev.txt
@@ -6,7 +6,12 @@ linkchecker
 ninja
 pre-commit
 pyinstaller
+
+# Use a local updated version of pylint instead of the older version possibly installed on
+# the system and instead of the normal pylint pre-commit hook. pre-commit hooks run in their own
+# virtual environment that doesn't know about our package, resulting in lots of errors.
 pylint
+
 sphinx
 sphinxcontrib-mermaid
 sphinx-gallery
diff --git a/environment/configuration/requirements.txt b/environment/configuration/requirements.txt
@@ -1,4 +1,4 @@
 docopt
 matplotlib
 networkx[default]
-pyside6
+pyside6>=6.6
diff --git a/environment/script/create_and_verify_release.py b/environment/script/create_and_verify_release.py
@@ -11,6 +11,7 @@
 import docopt
 
 import adaptation_pathways as ap
+from adaptation_pathways.cli.main import main_function
 
 
 def verify_build_directory(build_directory_path: Path) -> None:
@@ -129,7 +130,8 @@ def create_and_verify_release(build_directory_path: Path) -> Path:
     return release_zip_path
 
 
-def main() -> None:
+@main_function
+def main() -> int:
     command = os.path.basename(sys.argv[0])
     usage = f"""\
 Create a release and verify the contents seem OK
@@ -152,6 +154,8 @@ def main() -> None:
 
     print(f"\nPackage {release_zip_path} is ready to be released!")
 
+    return 0
+
 
 if __name__ == "__main__":
-    main()
+    sys.exit(main())
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,7 @@
 [tool.isort]
+known_ap = "adaptation_pathways"
 lines_after_imports = 2
+sections = "FUTURE,STDLIB,THIRDPARTY,AP,FIRSTPARTY,LOCALFOLDER"
 profile = "black"
 
 [tool.pylint]

diff --git a/source/package/adaptation_pathways/__init__.py b/source/package/adaptation_pathways/__init__.py
@@ -1,6 +1,7 @@
 """
 Package containing all code related to the Adaptation Pathways
 """
+
 from .action import Action
 from .action_combination import ActionCombination
 from .version import __version__
diff --git a/source/package/adaptation_pathways/cli/create_logo.py b/source/package/adaptation_pathways/cli/create_logo.py
@@ -5,49 +5,49 @@
 import docopt
 import matplotlib.pyplot as plt
 
-from ..graph.conversion import (
-    sequence_graph_to_pathway_map,
-    sequences_to_sequence_graph,
-)
-from ..graph.io import (
-    action_level_by_first_occurrence,
-    read_sequences,
-    read_tipping_points,
-)
+from ..graph import conversion
+from ..io import text
 from ..plot import init_axes, plot_classic_pathway_map, save_plot
+from ..plot.util import action_level_by_first_occurrence
 from ..version import __version__ as version
 from .main import main_function
 
 
 @main_function
 def create_logo(plot_pathname: str) -> int:
-    sequences = read_sequences(
+    actions, colour_by_action = text.read_actions(
         StringIO(
             """
-a b
-a c
-a d
-c d
-"""
+            a #ffbf616a
+            b #ffd08770
+            c #ffebcb8b
+            d #ffa3be8c
+            """
         )
     )
-    sequence_graph = sequences_to_sequence_graph(sequences)
-    level_by_action = action_level_by_first_occurrence(sequences)
-    pathway_map = sequence_graph_to_pathway_map(sequence_graph)
-    tipping_points = read_tipping_points(
+    sequences, tipping_point_by_action = text.read_sequences(
         StringIO(
             """
-a 2040
-b 2050
-c 2060
-d 2070
-"""
+            a a    2040
+            a b    2050
+            a c    2060
+            a d[1] 2070
+            c d[2] 2070
+    """
         ),
-        pathway_map.actions(),
+        actions,
     )
+    sequence_graph = conversion.sequences_to_sequence_graph(sequences)
+    pathway_map = conversion.sequence_graph_to_pathway_map(sequence_graph)
+
+    level_by_action = action_level_by_first_occurrence(sequences)
+    colour_by_action_name = {
+        action.name: colour for action, colour in colour_by_action.items()
+    }
 
-    pathway_map.assign_tipping_points(tipping_points)
-    pathway_map.set_attribute("level", level_by_action)
+    pathway_map.assign_tipping_points(tipping_point_by_action)
+    pathway_map.set_attribute("level_by_action", level_by_action)
+    pathway_map.set_attribute("colour_by_action_name", colour_by_action_name)
 
     _, axes = plt.subplots(layout="constrained")
     init_axes(axes)

diff --git a/source/package/adaptation_pathways/graph/node/__init__.py b/source/package/adaptation_pathways/graph/node/__init__.py
@@ -6,6 +6,7 @@
 (position in a layout for example), and some information needs to be shared between nodes but
 unique per action (colour in a plot for example).
 """
+
 from .action import Action
 from .action_begin import ActionBegin
 from .action_conversion import ActionConversion

diff --git a/source/package/adaptation_pathways/graph/node/action_conversion.py b/source/package/adaptation_pathways/graph/node/action_conversion.py
@@ -3,6 +3,7 @@
 
 This module contains the implementation of the :py:class:`ActionConversion` class.
 """
+
 from .action_period import ActionPeriod
 from .node import Node
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,7 @@ @@
     This module contains the implementation of the :py:class:`ActionConversion` class.
     """
     from .action_period import ActionPeriod
     from .node import Node
@@ Expand Down @@