Merge pull request #32 from OSIPI/poetry

Poetry

.github/workflows/pre-commit.yaml

@@ -0,0 +1,39 @@
+name: Lint and Auto-Fix Code
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.9'  # Specify the Python version you need
+
+      - name: Install Poetry
+        uses: Gr1N/setup-poetry@v8
+        with:
+          poetry-version: '1.8.3'
+
+      - name: Cache Poetry dependencies
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pypoetry
+            ~/.virtualenvs
+          key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-poetry-
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Run pre-commit
+        run: poetry run pre-commit run --all-files

.github/workflows/pytest-actions.yaml

@@ -1,4 +1,3 @@
-# GitHub Actions Configuration for integrated testing using pytest
 name: Test osipi
 
 on: [push]
@@ -15,28 +14,43 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+
       - name: Set up Python 3.10
         uses: actions/setup-python@v4
         with:
           python-version: '3.10'
+
       - name: Set up Java
         uses: actions/setup-java@v3
         with:
           java-version: '11'
           distribution: 'adopt'
           architecture: x64
+
+      - name: Install Poetry
+        uses: Gr1N/setup-poetry@v8
+        with:
+          poetry-version: '1.8.3'  # Specify the Poetry version you need
+
+      - name: Cache Poetry dependencies
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/.cache/pypoetry
+            ~/.virtualenvs
+          key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-poetry-
+
+      - name: Update lock file
+        run: poetry lock --no-update
+
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -r requirements.txt
-      - name: Install osipi
-        run: |
-          python -m pip install -e .[docs]
-          python -m pip install -e .[tests]
+        run: poetry install
+
       - name: Test with pytest
-        run: |
-          python -m pip install pytest pytest-cov
-          pytest --junitxml=junit/test-results.xml --cov=dbdicom tests/
+        run: poetry run pytest --junitxml=junit/test-results.xml --cov=dbdicom tests/
+
       - name: Upload coverage to Codecov
         if: runner.os == 'Windows'
         uses: codecov/codecov-action@v3

.gitignore

@@ -4,3 +4,8 @@ dist
 pytest_cache
 src/osipi/__pycache__
 tests/__pycache__
+.coverage
+junit
+docs/build
+docs/source/generated
+docs/source/sg_execution_times.rst

.pre-commit-config.yaml

@@ -25,8 +25,5 @@ repos:
     rev: v6.1.2  # Use the latest version
     hooks:
       - id: rstcheck
-        entry: rstcheck --ignore-messages="(Hyperlink target .* is not referenced.|No directive entry for
-          .*|Unknown directive type .*|Duplicate explicit target name.*)"
-        args: [
-        "--ignore-roles", "ref",
-        ]
+        args: ["--ignore-directives=autosummary,autofunction,minigallery,image-sg","--ignore-messages=(Hyperlink target *|Duplicate explicit target name*)"]
+        additional_dependencies: [sphinx]

.rstcheck.cfg

@@ -0,0 +1,5 @@
+[rstcheck]
+ignore-directives =
+    autosummary,
+    image-sg,
+    minigallery

docs/build/html/_sphinx_design_static/design-tabs.js

@@ -0,0 +1,101 @@
+// @ts-check
+
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
+/**
+ * @type {Record<string, HTMLElement[]>}
+ */
+let sd_id_to_elements = {};
+const storageKeyPrefix = "sphinx-design-tab-id-";
+
+/**
+ * Create a key for a tab element.
+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
+ */
+function create_key(el) {
+  let syncId = el.getAttribute("data-sync-id");
+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
+function ready() {
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
+            group
+          );
+          if (tabParam) {
+            console.log(
+              "sphinx-design: Selecting tab id for group '" +
+                group +
+                "' from URL parameter: " +
+                tabParam
+            );
+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
+        }
+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
+          storageKeyPrefix + group
+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
+      }
+    }
+  });
+}
+
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
+  let data = create_key(this);
+  if (!data) return;
+  let [group, id, key] = data;
+  for (const label of sd_id_to_elements[key]) {
+    if (label === this) continue;
+    // @ts-ignore
+    label.previousElementSibling.checked = true;
+  }
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);

docs/examples/aif/plot_aif_parker.py

@@ -1,7 +1,9 @@
-"""======================================
+"""
+======================================
+The Parker AIF - a play with variables
+======================================
 
-The Parker AIF - a play with variables ======================================  Simulating a Parker
-AIF with different settings.
+Simulating a Parker AIF with different settings.
 
 """