From 87812321e539dc7e55d7ea7da4b592e596a48892 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:12:27 +0000
Subject: [PATCH 01/16] Try to add badges to a different repo's gh-pages

---
 .github/workflows/tests.yml | 41 ++++++++++++++++++++++++++++++++++---
 .gitignore                  |  2 ++
 setup.cfg                   |  4 +++-
 3 files changed, 43 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2f4f28e..1ce78ee 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -24,9 +24,44 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-        
+
       - name: Install
         run: pip install .[test]
 
-      - name: Run tests
-        run: pytest
+      - name: Run tests and create reports and badges
+        run: |
+          coverage run -m pytest --junitxml=reports/junit/junit.xml --html=reports/junit/report.html
+          coverage xml -o reports/coverage/coverage.xml
+          coverage html -d reports/coverage/
+          genbadge coverage -i reports/coverage/coverage.xml
+          genbadge tests -i reports/junit/junit.xml
+
+      - name: Upload badges and reports to github actions
+        run: |
+          mkdir -p badges
+          mv *badge.svg badges
+          ## todo:
+          ## upload badges and reports to github pages
+          ## link to badges in readme
+          ## test badge links
+
+      - name: Setup Temporary Directory
+        run: |
+          mkdir gh-pages
+          cp -R badges gh-pages/
+          cp -R reports gh-pages/
+
+      - name: Clone Target Repository
+        run: |
+          git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
+          cp -R gh-pages/* target_repo/
+
+      # Push changes to the target repository
+      - name: Deploy to gh-pages
+        run: |
+          cd target_repo
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add .
+          git commit -m "Update badges and reports"
+          git push
diff --git a/.gitignore b/.gitignore
index d226ef3..bb194fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -138,3 +138,5 @@ dmypy.json
 # Generated test images
 *.tif
 *.zarr
+reports
+*.svg
diff --git a/setup.cfg b/setup.cfg
index 603b379..3c2eec2 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -36,7 +36,9 @@ dev =
     jupyter ~= 1.0.0
 test =
     pytest ~= 8.2.2
-openslide =
+    pytest-html ~= 4.1.1
+    coverage ~= 7.6.5
+    genbadge[all] ~= 1.1.1
 doc =
     sphinx ~= 7.4.5
     sphinx-rtd-theme ~= 2.0.0

From 216b9d075e0fe0afa879e3b0ef8580598c912872 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:16:16 +0000
Subject: [PATCH 02/16] mv not cp

---
 .github/workflows/tests.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 1ce78ee..2365503 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -37,6 +37,7 @@ jobs:
           genbadge tests -i reports/junit/junit.xml
 
       - name: Upload badges and reports to github actions
+        if: github.ref_name == 'main'
         run: |
           mkdir -p badges
           mv *badge.svg badges
@@ -46,18 +47,21 @@ jobs:
           ## test badge links
 
       - name: Setup Temporary Directory
+        if: github.ref_name == 'main'
         run: |
           mkdir gh-pages
-          cp -R badges gh-pages/
-          cp -R reports gh-pages/
+          mv badges gh-pages/
+          mv reports gh-pages/
 
       - name: Clone Target Repository
+        if: github.ref_name == 'main'
         run: |
           git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
           cp -R gh-pages/* target_repo/
 
       # Push changes to the target repository
       - name: Deploy to gh-pages
+        if: github.ref_name == 'main'
         run: |
           cd target_repo
           git config user.name "github-actions[bot]"

From 826cb8c733d1b98071654f686f388a1de589c11a Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:25:06 +0000
Subject: [PATCH 03/16] badges

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 2365503..a4c301c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -57,7 +57,7 @@ jobs:
         if: github.ref_name == 'main'
         run: |
           git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
-          cp -R gh-pages/* target_repo/
+          cp -R gh-pages/* badges/
 
       # Push changes to the target repository
       - name: Deploy to gh-pages

From b2cd472be6668eb4d68f192cf72f3f5f296767c2 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:28:13 +0000
Subject: [PATCH 04/16] badges

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index a4c301c..10f81bb 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -63,7 +63,7 @@ jobs:
       - name: Deploy to gh-pages
         if: github.ref_name == 'main'
         run: |
-          cd target_repo
+          cd badges
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git add .

From d2eb38dff3485582e13bc5de1dbf4b2319628eee Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:34:46 +0000
Subject: [PATCH 05/16] Add readme

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 6b7191e..6208650 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,8 @@
+[![Coverage](https://alanocallaghan.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/coverage/index.html?dummy=1234)
+[![Tests](https://alanocallaghan.github.io/badges/badges/test-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
 # QuBaLab
 
+
 This is a Python package for exploring quantitative bioimage analysis... *especially* (but not exclusively) in combination with QuPath (https://qupath.github.io/).
 
 The name comes from **Quantitative Bioimage Analysis Laboratory**. This is chosen to be reminiscent of QuPath (*Quantitative Pathology*), but recognizes that neither is really restricted to pathology.

From 0300ec18bc1e811031ec9b1518d39acc3bf73324 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:39:34 +0000
Subject: [PATCH 06/16] Clean code and use subdir

---
 .github/workflows/tests.yml | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 10f81bb..71e61bd 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -36,32 +36,30 @@ jobs:
           genbadge coverage -i reports/coverage/coverage.xml
           genbadge tests -i reports/junit/junit.xml
 
+  upload:
+    runs-on: ubuntu-latest
+    if: github.ref_name == 'main'
+    needs: test
+    steps:
+
       - name: Upload badges and reports to github actions
-        if: github.ref_name == 'main'
         run: |
           mkdir -p badges
           mv *badge.svg badges
-          ## todo:
-          ## upload badges and reports to github pages
-          ## link to badges in readme
-          ## test badge links
 
       - name: Setup Temporary Directory
-        if: github.ref_name == 'main'
         run: |
-          mkdir gh-pages
-          mv badges gh-pages/
-          mv reports gh-pages/
+          mkdir assets
+          mv badges assets/
+          mv reports assets/
 
       - name: Clone Target Repository
-        if: github.ref_name == 'main'
         run: |
-          git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
-          cp -R gh-pages/* badges/
+            git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
+            mkdir -p badges/${{ github.event.repository.name }}
+            mv assets/* badges/${{github.event.repository.name}}/
 
-      # Push changes to the target repository
       - name: Deploy to gh-pages
-        if: github.ref_name == 'main'
         run: |
           cd badges
           git config user.name "github-actions[bot]"

From d93dbaf800f9a65c7e61df97ec2dc1acc3c80b71 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:40:45 +0000
Subject: [PATCH 07/16] typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6208650..858eafa 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 [![Coverage](https://alanocallaghan.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/coverage/index.html?dummy=1234)
-[![Tests](https://alanocallaghan.github.io/badges/badges/test-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
+[![Tests](https://alanocallaghan.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
 # QuBaLab
 
 

From 2b8476cbc37e80db7e22f6b743474359a3b8098c Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:46:35 +0000
Subject: [PATCH 08/16] Dumb way

---
 .github/workflows/tests.yml | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 71e61bd..f445939 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -28,38 +28,41 @@ jobs:
       - name: Install
         run: pip install .[test]
 
-      - name: Run tests and create reports and badges
+      - name: Run tests
         run: |
           coverage run -m pytest --junitxml=reports/junit/junit.xml --html=reports/junit/report.html
+
+      - name: Create reports and badges
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
           coverage xml -o reports/coverage/coverage.xml
           coverage html -d reports/coverage/
           genbadge coverage -i reports/coverage/coverage.xml
           genbadge tests -i reports/junit/junit.xml
 
-  upload:
-    runs-on: ubuntu-latest
-    if: github.ref_name == 'main'
-    needs: test
-    steps:
 
       - name: Upload badges and reports to github actions
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           mkdir -p badges
           mv *badge.svg badges
 
       - name: Setup Temporary Directory
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           mkdir assets
           mv badges assets/
           mv reports assets/
 
       - name: Clone Target Repository
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
             git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
             mkdir -p badges/${{ github.event.repository.name }}
             mv assets/* badges/${{github.event.repository.name}}/
 
       - name: Deploy to gh-pages
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           cd badges
           git config user.name "github-actions[bot]"

From 54f089d587793313326d80b210c6043ca8efd05b Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:48:21 +0000
Subject: [PATCH 09/16] Add workflow badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 858eafa..abc9234 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 [![Coverage](https://alanocallaghan.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/coverage/index.html?dummy=1234)
 [![Tests](https://alanocallaghan.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
+![Actions](https://github.com/alanocallaghan/qubalab/actions/workflows/main.yml/badge.svg?dummy=1234)
 # QuBaLab
 
 

From c38b52821803403c09e83e61eadee5ab4d446d0f Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:52:32 +0000
Subject: [PATCH 10/16] Typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index abc9234..2bbfe34 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![Coverage](https://alanocallaghan.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/coverage/index.html?dummy=1234)
 [![Tests](https://alanocallaghan.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
-![Actions](https://github.com/alanocallaghan/qubalab/actions/workflows/main.yml/badge.svg?dummy=1234)
+![Actions](https://github.com/alanocallaghan/qubalab/actions/workflows/tests.yml/badge.svg?dummy=1234)
 # QuBaLab
 
 

From 37b9bdc12dc7483b17854ee8a8311d3b69872aa0 Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:53:58 +0000
Subject: [PATCH 11/16] Remove before adding

---
 .github/workflows/tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f445939..6375ba8 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -58,6 +58,8 @@ jobs:
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
             git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
+            ## cba handling merging or dealing with stale resources
+            rm -r badges/${{ github.event.repository.name }}
             mkdir -p badges/${{ github.event.repository.name }}
             mv assets/* badges/${{github.event.repository.name}}/
 

From 7e62baa0734a2b677d1c84c6580dd7d8e57851dd Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:56:23 +0000
Subject: [PATCH 12/16] Rename workflow

---
 .github/workflows/tests.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6375ba8..1abb887 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,6 +1,6 @@
 # This workflow will run unit tests on pull requests or when manually activated
 
-name: test
+name: pytest
 
 on:
   push:
@@ -32,6 +32,8 @@ jobs:
         run: |
           coverage run -m pytest --junitxml=reports/junit/junit.xml --html=reports/junit/report.html
 
+
+      ## everything from here deals with generating and uploading reports and badges to a separate "badges" repo.
       - name: Create reports and badges
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
@@ -57,7 +59,7 @@ jobs:
       - name: Clone Target Repository
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
-            git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/alanocallaghan/badges.git badges
+            git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/qupath/badges.git badges
             ## cba handling merging or dealing with stale resources
             rm -r badges/${{ github.event.repository.name }}
             mkdir -p badges/${{ github.event.repository.name }}

From 6606ecd1f39c4af9f97fd855f534f29a806fa53d Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 15:59:42 +0000
Subject: [PATCH 13/16] qupath github links

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 2bbfe34..dea151e 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
-[![Coverage](https://alanocallaghan.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/coverage/index.html?dummy=1234)
-[![Tests](https://alanocallaghan.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://alanocallaghan.github.io/badges/reports/junit/report.html?dummy=1234)
-![Actions](https://github.com/alanocallaghan/qubalab/actions/workflows/tests.yml/badge.svg?dummy=1234)
+[![Coverage](https://qupath.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://qupath.github.io/badges/reports/coverage/index.html?dummy=1234)
+[![Tests](https://qupath.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://qupath.github.io/badges/reports/junit/report.html?dummy=1234)
+![Actions](https://github.com/qupath/qubalab/actions/workflows/tests.yml/badge.svg?dummy=1234)
 # QuBaLab
 
 

From 6a50b6aa9edcc488ecfa820f4d1cd5ee67ca286f Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 16:03:13 +0000
Subject: [PATCH 14/16] force in case not existing

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 1abb887..17d3c6f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -61,7 +61,7 @@ jobs:
         run: |
             git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/qupath/badges.git badges
             ## cba handling merging or dealing with stale resources
-            rm -r badges/${{ github.event.repository.name }}
+            rm -rf badges/${{ github.event.repository.name }}
             mkdir -p badges/${{ github.event.repository.name }}
             mv assets/* badges/${{github.event.repository.name}}/
 

From a131d4a80b907e06550860bae7fcf45214fdd6aa Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 16:07:38 +0000
Subject: [PATCH 15/16] Better step names

---
 .github/workflows/tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 17d3c6f..948eaf5 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -43,20 +43,20 @@ jobs:
           genbadge tests -i reports/junit/junit.xml
 
 
-      - name: Upload badges and reports to github actions
+      - name: Make badge dir
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           mkdir -p badges
           mv *badge.svg badges
 
-      - name: Setup Temporary Directory
+      - name: Setup assets dir
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           mkdir assets
           mv badges assets/
           mv reports assets/
 
-      - name: Clone Target Repository
+      - name: Clone badges repo
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
             git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/qupath/badges.git badges
@@ -65,7 +65,7 @@ jobs:
             mkdir -p badges/${{ github.event.repository.name }}
             mv assets/* badges/${{github.event.repository.name}}/
 
-      - name: Deploy to gh-pages
+      - name: Deploy badges to gh-pages
         if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
         run: |
           cd badges

From 94825ca7ef52aaa0cb1e32bad76f9ed80fc59b6b Mon Sep 17 00:00:00 2001
From: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: Fri, 15 Nov 2024 16:13:33 +0000
Subject: [PATCH 16/16] Accurate comment in yaml

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 948eaf5..c5372fc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,4 +1,4 @@
-# This workflow will run unit tests on pull requests or when manually activated
+# This workflow will run unit tests when main is updated, on pull requests or when manually activated
 
 name: pytest