Fix codecov and test failures

.github/workflows/change-coverage.yml

@@ -27,6 +27,11 @@ jobs:
           python-version: "3.11"
           architecture: x64
 
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin' # See 'Supported distributions' for available options
+          java-version: '21'
+
       - uses: Gr1N/setup-poetry@v8
 
       - name: Check system dependencies

.github/workflows/execute-tests.yml

@@ -11,12 +11,15 @@ on:
       workpath:
         required: true
         type: string
+    secrets:
+      CODECOV_TOKEN:
+        required: true
 
 jobs:
   test:
     runs-on: ${{ inputs.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     name: Python ${{ matrix.python-version }}
@@ -43,6 +46,11 @@ jobs:
           python-version: ${{ matrix.python-version }}
           architecture: x64
 
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin' # See 'Supported distributions' for available options
+          java-version: '21'
+
       - uses: Gr1N/setup-poetry@v8
 
       - name: Check system dependencies
@@ -56,18 +64,9 @@ jobs:
       - name: Install project dependencies
         run: make install
 
-      # Some tests fails intermittently, likely due to the public runners being
-      # very slow. Especially any client/server tests seems to be problematic.
-      # This is a simple attempt to re-run the tests up to three times if they
-      # fail. Does not add any execution time if successful.
-      - uses: Wandalen/wretry.action@v1.4.4
-        name: Run tests
-        with:
-          command: make test
-          current_path: ${{ inputs.workpath }}
-          attempt_limit: 5
-          attempt_delay: 2000
-
+      - name: Run tests
+        run: make test
+
       - name: Upload coverage
         uses: codecov/codecov-action@v4
         if: ${{ inputs.os == 'ubuntu-latest' && matrix.python-version == '3.9' && github.repository == 'doorstop-dev/doorstop' }}

.github/workflows/test-linux.yml

@@ -11,8 +11,11 @@ jobs:
     with:
       os: "ubuntu-latest"
       workpath: "/home/runner/work/doorstop/doorstop"
+
   Test:
     uses: ./.github/workflows/execute-tests.yml
     with:
       os: "ubuntu-latest"
       workpath: "/home/runner/work/doorstop/doorstop"
+    secrets:
+      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}

.github/workflows/test-osx.yml

@@ -11,3 +11,5 @@ jobs:
     with:
       os: "macos-13"
       workpath: "/Users/runner/work/doorstop/doorstop"
+    secrets:
+      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}

.github/workflows/test-windows.yml

@@ -12,3 +12,5 @@ jobs:
       basepath: 'D:\'
       os: "windows-latest"
       workpath: 'C:\a\doorstop\doorstop'
+    secrets:
+      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}

doorstop/core/tests/files/REQ002.yml

@@ -10,7 +10,7 @@ reviewed: 1PvBLmy0xmdK_zLKrLu1au0wlIw_zsD6A8Oc5F4zWxU=
 text: |
   Hello, world!
 
-  ```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
+  ```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
   @startuml
   Author --> (Create Document)
   Author --> (Create Item)

doorstop/core/tests/files/exported.csv

@@ -14,7 +14,7 @@ type:file,path:external/text2.txt",REQ001:35ed54323e3054c33ae5545fffdbbbf5,True,
 REQ004,1.6,"Hello, world!",,,,True,False,,True,
 REQ002,2.1,"Hello, world!
 
-```plantuml format=""svg_inline"" alt=""Use Cases of Doorstop"" title=""Use Cases of Doorstop""
+```plantuml format=""png"" alt=""Use Cases of Doorstop"" title=""Use Cases of Doorstop""
 @startuml
 Author --> (Create Document)
 Author --> (Create Item)

doorstop/core/tests/files/exported.tsv

@@ -14,7 +14,7 @@ type:file,path:external/text2.txt"	REQ001:35ed54323e3054c33ae5545fffdbbbf5	True
 REQ004	1.6	Hello, world!				True	False		True	
 REQ002	2.1	"Hello, world!
 
-```plantuml format=""svg_inline"" alt=""Use Cases of Doorstop"" title=""Use Cases of Doorstop""
+```plantuml format=""png"" alt=""Use Cases of Doorstop"" title=""Use Cases of Doorstop""
 @startuml
 Author --> (Create Document)
 Author --> (Create Item)

doorstop/core/tests/files/exported.yml

@@ -76,7 +76,7 @@ REQ002:
   text: |
     Hello, world!
 
-    ```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
+    ```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
     @startuml
     Author --> (Create Document)
     Author --> (Create Item)

doorstop/core/tests/files/published.md

@@ -36,7 +36,7 @@ Hello, world!
 
 Hello, world!
 
-```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
+```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
 @startuml
 Author --> (Create Document)
 Author --> (Create Item)

doorstop/core/tests/files/published.txt

@@ -38,8 +38,8 @@
 
         Hello, world!
 
-        ```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use
-        Cases of Doorstop"
+        ```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases
+        of Doorstop"
         @startuml
         Author --> (Create Document)
         Author --> (Create Item)

doorstop/core/tests/files/published2.md

@@ -36,7 +36,7 @@ Hello, world!
 
 Hello, world!
 
-```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
+```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
 @startuml
 Author --> (Create Document)
 Author --> (Create Item)

doorstop/core/tests/files/published2.txt

@@ -38,8 +38,8 @@
 
         Hello, world!
 
-        ```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use
-        Cases of Doorstop"
+        ```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases
+        of Doorstop"
         @startuml
         Author --> (Create Document)
         Author --> (Create Item)

doorstop/core/tests/test_all.py

@@ -15,10 +15,12 @@
 
 import openpyxl
 import yaml
+from plantuml_markdown import PlantUMLMarkdownExtension
 
 from doorstop import common, core
 from doorstop.common import DoorstopError, DoorstopInfo, DoorstopWarning
 from doorstop.core.builder import _clear_tree, _get_tree
+from doorstop.core.publishers.html import HtmlPublisher
 from doorstop.core.tests import (
     EMPTY,
     ENV,
@@ -172,7 +174,7 @@ def test_issues_count(self):
         issues = self.document.issues
         for issue in self.document.issues:
             logging.info(repr(issue))
-        self.assertEqual(13, len(issues))
+        self.assertEqual(14, len(issues))
 
     @patch("doorstop.settings.REORDER", False)
     @patch("doorstop.settings.REVIEW_NEW_ITEMS", False)
@@ -328,7 +330,7 @@ def test_issues_count(self):
         issues = self.tree.issues
         for issue in self.tree.issues:
             logging.info(repr(issue))
-        self.assertEqual(15, len(issues))
+        self.assertEqual(16, len(issues))
 
     @patch("doorstop.settings.REORDER", False)
     @patch("doorstop.settings.REVIEW_NEW_ITEMS", False)
@@ -575,6 +577,16 @@ def setUp(self):
         self.tree = core.build(cwd=FILES, root=FILES)
         self.document = self.tree.find_document("REQ")
         self.temp = tempfile.mkdtemp()
+        # Use local plantuml of known version
+        plantuml_cmd = "java -Dplantuml.include.path=includes -jar " + os.path.join(
+            FILES, "plantuml-1.2024.7.jar"
+        )
+        plantuml_ext = next(
+            x for x in HtmlPublisher.EXTENSIONS if type(x) is PlantUMLMarkdownExtension
+        )
+        plantuml_ext.setConfigs(
+            {"server": "", "plantuml_cmd": plantuml_cmd, "theme": "bluegray"}
+        )
 
     def tearDown(self):
         if os.path.exists(self.temp):

doorstop/core/tests/test_importer.py

@@ -32,7 +32,7 @@
 Inline Style 2: \\(ax^2 + bx + c = 0\\)
 Multiline: $$x = {-b \\pm \\sqrt{b^2-4ac} \\over 2a}.$$"""
 
-PLANTUML_TXT = """```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
+PLANTUML_TXT = """```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"
 @startuml
 Author --> (Create Document)
 Author --> (Create Item)
@@ -359,7 +359,7 @@ def test_file_xlsx(self, mock_itemize):
             [
                 "REQ002",
                 "2.1",
-                'Hello, world!\n\n```plantuml format="svg_inline" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"\n@startuml\nAuthor --> (Create Document)\nAuthor --> (Create Item)\nAuthor --> (Link Item to Document)\nAuthor --> (Link Item to other Item)\nAuthor --> (Edit Item)\nAuthor --> (Review Item)\nAuthor -> (Delete Item)\nAuthor -> (Delete Document)\n(Export) <- (Author)\n(Import) <- (Author)\nReviewer --> (Review Item)\nSystem --> (Suspect Changes)\nSystem --> (Integrity)\n@enduml\n```',
+                'Hello, world!\n\n```plantuml format="png" alt="Use Cases of Doorstop" title="Use Cases of Doorstop"\n@startuml\nAuthor --> (Create Document)\nAuthor --> (Create Item)\nAuthor --> (Link Item to Document)\nAuthor --> (Link Item to other Item)\nAuthor --> (Edit Item)\nAuthor --> (Review Item)\nAuthor -> (Delete Item)\nAuthor -> (Delete Document)\n(Export) <- (Author)\n(Import) <- (Author)\nReviewer --> (Review Item)\nSystem --> (Suspect Changes)\nSystem --> (Integrity)\n@enduml\n```',
                 None,
                 None,
                 None,