Repository: EIT-ALIVE/eitprocessing (language: python)

Issue:
testing CI
either containterized, dockerized, or from another repo
markdown link check
look whether it is working as intended and either get rid of it or fix broken links


Discussion / hints:
We will go with Zenodo + Github registort, as this appears to be best for various reasons, including that because we go from Github container registry to A Github repo it's will all be on the same internal network (of Azure). Another Github repo is a bad idea, because of the potential with a few changes to explode into Gigabytes in a repo.
The only link that is "broken" is the one to PyPi. I need to figure out how to set up pypi correctly (#56) and see whether it then works as intended.



Fix patch:
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 7d68d5172..0022e62df 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -6,19 +6,25 @@ on:
     - main
     - drcandacemakedamoore/docker
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+    paths-ignore:
+      - "**.md"
+      - "**.rst"
+      - "**.ipynb"
     branches:
     - main
 
 jobs:
 
   build:
+    if: github.event.pull_request.draft == false
     name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10']
     steps:
       - uses: actions/checkout@v3
       - name: Connect to Container Registry
@@ -35,12 +41,13 @@ jobs:
           -e EIT_PROCESSING_TEST_DATA=/eitprocessing
           ghcr.io/eit-alive/eittestdata:latest
           sh -c 'set -xe ;
-                 cd /ci ;
-                 python -m pip install ".[dev,publishing]" ; 
-                 pytest -v ; 
-                 python setup.py sdist bdist_wheel'
+            cd /ci ;
+            python -m pip install ".[dev,publishing]" ; 
+            pytest -v ; 
+            python setup.py sdist bdist_wheel'
 
   lint:
+    if: github.event.pull_request.draft == false
     name: Linting build
     runs-on: ubuntu-latest
     strategy:
@@ -64,3 +71,35 @@ jobs:
         run: prospector
       - name: Check import order
         run: isort --check-only eitprocessing --diff
+
+  coveralls:
+    if: github.event.pull_request.draft == false
+    name: Coveralls build
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+      - name: Connect to Container Registry
+        uses: docker/login-action@v2.1.0
+        with:
+          registry: ghcr.io
+          username: drcandacemakedamoore
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Run Tests in Container
+        run: >
+          docker run
+          --rm
+          -v ${{ github.workspace }}:/ci
+          -e EIT_PROCESSING_TEST_DATA=/eitprocessing
+          -e GITHUB_TOKEN=${{ secrets.GITHUB_TOKEN }}
+          -e COVERALLS_REPO_TOKEN=${{ secrets.COVERALLS_REPO_TOKEN }}
+          -e COVERALLS_FLAG_NAME=python-${{ matrix.version }}
+          ghcr.io/eit-alive/eittestdata:latest
+          sh -c 'set -xe ; 
+            cd /ci ; 
+            python -m pip install --upgrade pip setuptools ; 
+            python -m pip install ".[dev,publishing]" ; 
+            pytest --cov --cov-append --cov-report xml --cov-report term --cov-report html ; 
+            coveralls --service=github ; 
+            python setup.py sdist bdist_wheel'
diff --git a/.github/workflows/markdown-link-check.yml b/.github/workflows/markdown-link-check.yml
deleted file mode 100644
index 3cdbce015..000000000
--- a/.github/workflows/markdown-link-check.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-name: markdown-link-check
-
-on:
-  push:
-    branches:
-    - main
-  pull_request:
-    branches:
-    - main
-
-jobs:
-
-  markdown-link-check:
-    name: Check markdown links
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        config-file: '.mlc-config.json'
diff --git a/.mlc-config.json b/.mlc-config.json
deleted file mode 100644
index d1302eb29..000000000
--- a/.mlc-config.json
+++ /dev/null
@@ -1,33 +0,0 @@
-{
-    "_comment": "Markdown Link Checker configuration, see https://github.com/gaurav-nelson/github-action-markdown-link-check and https://github.com/tcort/markdown-link-check",
-    "ignorePatterns": [
-        {
-            "pattern": "^http://localhost"
-        },
-        {
-          "pattern": "^https://doi.org/<replace-with-created-DOI>"
-        },
-        {
-          "pattern": "^https://github.com/.*/settings/secrets/actions$"
-        },
-        {
-          "pattern": "^https://github.com/organizations/.*/repositories/new"
-        },
-        {
-          "pattern": "^https://test.pypi.org"
-        },
-        {
-          "pattern": "git@github.com:EIT-ALIVE/eitprocessing/*"
-        },
-        {
-          "pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
-        },
-        {
-          "pattern": "^https://readthedocs.org/dashboard/import.*"
-        }
-    ],
-    "replacementPatterns": [
-    ],
-    "retryOn429": true,
-    "timeout": "20s"
-}
diff --git a/README.dev.md b/README.dev.md
index b1f8a3cf7..c58a371d6 100644
--- a/README.dev.md
+++ b/README.dev.md
@@ -125,6 +125,7 @@ source env/bin/activate
 python3 -m pip install --upgrade pip setuptools
 
 # install runtime dependencies and publishing dependencies
+cd eitprocessing
 python3 -m pip install --no-cache-dir .
 python3 -m pip install --no-cache-dir .[publishing]
 
diff --git a/setup.cfg b/setup.cfg
index 6f629d712..435a41f48 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -15,11 +15,11 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
 description = Processing of lung image data from electrical impedance tomography
-keywords:
-  - Mechanical lung ventilation
-  - Electrical impedance tomography
-  - Image/data processing
-  - Advanced respiratory care
+keywords =
+    - Mechanical lung ventilation
+    - Electrical impedance tomography
+    - Image/data processing
+    - Advanced respiratory care
 long_description = file: README.md
 long_description_content_type = text/markdown
 name = eitprocessing
@@ -54,7 +54,8 @@ install_requires =
 [options.extras_require]
 dev =
     bump2version
-    coverage [toml]
+    coverage
+    coveralls
     prospector[with_pyroma]
     isort
     pytest


Test patch:
diff --git a/tests/test_my_module.py b/tests/test_my_module.py
index 33b035a21..c168bccf6 100644
--- a/tests/test_my_module.py
+++ b/tests/test_my_module.py
@@ -16,14 +16,12 @@
 
 sample_data1 = os.path.join(
     data_directory,
-    "tests",
     "test_data",
     "Testdata.bin",
 )
 
 sample_data2 = os.path.join(
     data_directory,
-    "tests",
     "test_data",
     "Testdata2.bin",
 )
diff --git a/tests/test_timpel_sequence.py b/tests/test_timpel_sequence.py
index 344b5e71b..ea5821701 100644
--- a/tests/test_timpel_sequence.py
+++ b/tests/test_timpel_sequence.py
@@ -13,7 +13,7 @@
 
 print(__file__)
 
-sample_data1 = os.path.join(data_directory, "tests", "test_data", "testdata_timpel.txt")
+sample_data1 = os.path.join(data_directory, "test_data", "testdata_timpel.txt")
 
 
 def test_read():