From 9f4dbabf20d1d098b58b5af426af835b08613a32 Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:32:31 -0500
Subject: [PATCH 1/9] Attempt to get unit test output

---
 .gitlab-ci.yml       | 3 +++
 tests/test_codecs.py | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 18789e1..18ba834 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -38,6 +38,9 @@ test:
     - pip install -r requirements.txt
     - pip install .
     - python3 tests/test_codecs.py
+  artifacts:
+    reports:
+      junit: 'results.xml'
 
 auto-docs:
   image: ltcodecs-docs:latest
diff --git a/tests/test_codecs.py b/tests/test_codecs.py
index 5df51de..2dcbee9 100755
--- a/tests/test_codecs.py
+++ b/tests/test_codecs.py
@@ -424,4 +424,4 @@ class TestCodecs:
 
 
 if __name__ == "__main__":
-    sys.exit(pytest.main(['--capture=no', __file__]))
+    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', __file__]))
-- 
GitLab


From 92637e3e80c110edc627028f1f7e6216b2f92f2c Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:37:03 -0500
Subject: [PATCH 2/9] Some tweaks to doc generation.

---
 .gitlab-ci.yml            | 2 --
 docs/auto-docs.Dockerfile | 5 +----
 docs/conf.py              | 4 ++--
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 18ba834..3d9e091 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -48,7 +48,6 @@ auto-docs:
   script:
     - pip install -r requirements.txt
     - pip install .
-    - pip install python-docs-theme
     - cd docs
     - make latexpdf
     - mv _build/latex/ltcodecs.pdf ..
@@ -62,7 +61,6 @@ pages:
   script:
     - pip install -r requirements.txt
     - pip install .
-    - pip install python-docs-theme
     - cd docs
     - sphinx-build -b html . ../public
   artifacts:
diff --git a/docs/auto-docs.Dockerfile b/docs/auto-docs.Dockerfile
index 4e908ad..65faa37 100644
--- a/docs/auto-docs.Dockerfile
+++ b/docs/auto-docs.Dockerfile
@@ -24,7 +24,4 @@ RUN apt-get install --no-install-recommends -y \
  && apt-get autoremove \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
-RUN pip install -U sphinx
-RUN pip install -U pytest
-RUN pip install -U sphinxawesome-theme
-RUN pip install -U python-docs-theme
\ No newline at end of file
+RUN pip install -U sphinx sphinx-book-theme myst_parser pytest
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 64c2a84..b03fd58 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -21,7 +21,7 @@ release = "2.0.1"
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 # Napoleon allows using numpy- or Google-style docstrings
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+extensions = ["myst_parser", "sphinx.ext.autodoc", "sphinx.ext.napoleon"]
 
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
@@ -35,7 +35,7 @@ latex_elements = {
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-html_theme = "python_docs_theme"
+html_theme = "sphinx_book_theme"
 
 add_function_parentheses = True
 add_module_names = True
-- 
GitLab


From c2068fa033753666c260e17d259bbf3fdb14d2dc Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:42:33 -0500
Subject: [PATCH 3/9] Attempt at coverage

---
 .gitlab-ci.yml       | 3 +++
 tests/test_codecs.py | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3d9e091..1064245 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,6 +41,9 @@ test:
   artifacts:
     reports:
       junit: 'results.xml'
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
 
 auto-docs:
   image: ltcodecs-docs:latest
diff --git a/tests/test_codecs.py b/tests/test_codecs.py
index 2dcbee9..5d38c21 100755
--- a/tests/test_codecs.py
+++ b/tests/test_codecs.py
@@ -424,4 +424,5 @@ class TestCodecs:
 
 
 if __name__ == "__main__":
-    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', __file__]))
+    ltcodecs_path = os.path.dirname(__file__) + "/../src/ltcodecs"
+    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', '--cov='+ltcodecs_path, '--cov-report=xml', __file__]))
-- 
GitLab


From 0a1ab07a6f1a6cbe35aed9869f8a6b8da7b889d1 Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:43:45 -0500
Subject: [PATCH 4/9] Fix missing pytest-cov requirement.

---
 tests/tests.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/tests.Dockerfile b/tests/tests.Dockerfile
index 3f617c5..e04f2f5 100644
--- a/tests/tests.Dockerfile
+++ b/tests/tests.Dockerfile
@@ -3,4 +3,4 @@ FROM ros:noetic-ros-core
 # install ros package
 RUN apt-get update && apt-get upgrade -y
 RUN apt install python3-pip -y
-RUN pip install pytest
\ No newline at end of file
+RUN pip -U install pytest pytest-cov
\ No newline at end of file
-- 
GitLab


From be99184cd5279b88a560b3d2ac301d2723733902 Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:45:20 -0500
Subject: [PATCH 5/9] Fix pip command.

---
 tests/tests.Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/tests.Dockerfile b/tests/tests.Dockerfile
index e04f2f5..a9a7403 100644
--- a/tests/tests.Dockerfile
+++ b/tests/tests.Dockerfile
@@ -3,4 +3,4 @@ FROM ros:noetic-ros-core
 # install ros package
 RUN apt-get update && apt-get upgrade -y
 RUN apt install python3-pip -y
-RUN pip -U install pytest pytest-cov
\ No newline at end of file
+RUN pip install -U pytest pytest-cov
\ No newline at end of file
-- 
GitLab


From afab0e509affffd68dca311e31858bf08abb07e9 Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:53:02 -0500
Subject: [PATCH 6/9] Add coverage report to terminal output.

---
 tests/test_codecs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_codecs.py b/tests/test_codecs.py
index 5d38c21..f1837f5 100755
--- a/tests/test_codecs.py
+++ b/tests/test_codecs.py
@@ -425,4 +425,4 @@ class TestCodecs:
 
 if __name__ == "__main__":
     ltcodecs_path = os.path.dirname(__file__) + "/../src/ltcodecs"
-    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', '--cov='+ltcodecs_path, '--cov-report=xml', __file__]))
+    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', '--cov='+ltcodecs_path, '--cov-report=xml', '--cov-report=term', __file__]))
-- 
GitLab


From bbdf796381f4654fe624f01b9d4fd9407e35bcc5 Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 13:57:48 -0500
Subject: [PATCH 7/9] Add coverage parsing.

---
 .gitlab-ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1064245..ab521e5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -44,6 +44,7 @@ test:
       coverage_report:
         coverage_format: cobertura
         path: coverage.xml
+  coverage: '/TOTAL\s+\d+\s+\d+\s+(\d+)%/'
 
 auto-docs:
   image: ltcodecs-docs:latest
-- 
GitLab


From 7932f9f4ee4f3fca782fa225b7820973cfac32ab Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 14:00:45 -0500
Subject: [PATCH 8/9] Fix coverage path.

---
 tests/test_codecs.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_codecs.py b/tests/test_codecs.py
index f1837f5..49414fa 100755
--- a/tests/test_codecs.py
+++ b/tests/test_codecs.py
@@ -424,5 +424,4 @@ class TestCodecs:
 
 
 if __name__ == "__main__":
-    ltcodecs_path = os.path.dirname(__file__) + "/../src/ltcodecs"
-    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', '--cov='+ltcodecs_path, '--cov-report=xml', '--cov-report=term', __file__]))
+    sys.exit(pytest.main(['--capture=no', '--junitxml=results.xml', '--cov=ltcodecs', '--cov-report=xml', '--cov-report=term', __file__]))
-- 
GitLab


From cb7abe5e5fd6984e8b9953479101b1c3379d50fd Mon Sep 17 00:00:00 2001
From: Eric Gallimore <egallimore@whoi.edu>
Date: Fri, 12 Jan 2024 14:06:36 -0500
Subject: [PATCH 9/9] Add badges to README.md

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 6fc704a..b8ab8b8 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,9 @@
 # LT Codecs
 
+ [![pipeline status](https://git.whoi.edu/acomms/ltcodec/badges/master/pipeline.svg)](https://git.whoi.edu/acomms/ltcodec/-/commits/master) 
+ [![coverage report](https://git.whoi.edu/acomms/ltcodec/badges/master/coverage.svg)](https://git.whoi.edu/acomms/ltcodec/-/commits/master) 
+ [![Latest Release](https://git.whoi.edu/acomms/ltcodec/-/badges/release.svg)](https://git.whoi.edu/acomms/ltcodec/-/releases) 
+
 Flexible, lightweight codec system for transferring messages over acoustic and other low-throughput links.
 
 See the documentation for more information: https://acomms.pages.whoi.edu/ltcodec/
-- 
GitLab