👷 Configure ☂️ Codecov reporting (#2224)

Author: shnizzedy

.circleci/main.yml

@@ -2,6 +2,9 @@
 version: 2.1
 # Singularity started failing to set up on Circle circa May 2023, so those tests are currently disabled
 
+orbs:
+  codecov: codecov/codecov@5
+
 parameters:
   branch:
     type: string
@@ -36,7 +39,8 @@ commands:
           name: "Combining and reporting coverage"
           command: |
               coverage combine
-              coverage html --ignore-errors
+              coverage xml -o coverage.xml  # Generate XML report
+      - codecov/upload
   configure-git-user:
     steps:
       - add_ssh_keys:
@@ -185,8 +189,6 @@ jobs:
       #     key: coverage-singularity-lite-{{ .Revision }}
       - set-python-version
       - combine-coverage
-      - store_artifacts:
-          path: htmlcov
   push-branch-to-docker-hub:
     parameters:
       variant:

.codecov.yml

@@ -0,0 +1,21 @@
+codecov:
+  branch: main
+
+comment:
+  layout: "diff, files"
+  behavior: default
+  require_changes: false
+  require_base: false
+  require_head: true
+  hide_project_coverage: false
+
+coverage:
+  precision: 1
+  range: "50..90"
+  round: nearest
+  status:
+    project:
+      default:   # default is the status check's name, not default settings
+        only_pulls: false
+        target: auto
+        threshold: "5"

README.md

@@ -9,8 +9,7 @@ C-PAC is distributed in the hope that it will be useful, but WITHOUT ANY WARRANT
 You should have received a copy of the GNU Lesser General Public License along with C-PAC. If not, see <https://www.gnu.org/licenses/>. -->
 C-PAC: Configurable Pipeline for the Analysis of Connectomes
 ============================================================
-<span title="Moving Beyond Processing and Analysis-Related Variation in Neuroscience">[![DOI for "Moving Beyond Processing and Analysis-Related Variation in Neuroscience"](https://zenodo.org/badge/DOI/10.1101/2021.12.01.470790.svg)](https://doi.org/10.1101/2021.12.01.470790)</span> <span title="FCP-INDI/C-PAC: CPAC Version 1.0.0 Beta">[![DOI for "FCP-INDI/C-PAC: CPAC Version 1.0.0 Beta"](https://zenodo.org/badge/DOI/10.5281/zenodo.164638.svg)](https://doi.org/10.5281/zenodo.164638)</span> [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/FCP-INDI/C-PAC/main.svg)](https://results.pre-commit.ci/latest/github/FCP-INDI/C-PAC/main)
-
+<span title="Moving Beyond Processing and Analysis-Related Variation in Neuroscience">[![DOI for "Moving Beyond Processing and Analysis-Related Variation in Neuroscience"](https://zenodo.org/badge/DOI/10.1101/2021.12.01.470790.svg)](https://doi.org/10.1101/2021.12.01.470790)</span> <span title="FCP-INDI/C-PAC: CPAC Version 1.0.0 Beta">[![DOI for "FCP-INDI/C-PAC: CPAC Version 1.0.0 Beta"](https://zenodo.org/badge/DOI/10.5281/zenodo.164638.svg)](https://doi.org/10.5281/zenodo.164638)</span> [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/FCP-INDI/C-PAC/main.svg)](https://results.pre-commit.ci/latest/github/FCP-INDI/C-PAC/main) [![codecov](https://codecov.io/github/FCP-INDI/C-PAC/graph/badge.svg?token=sWxXoDRf1M)](https://codecov.io/github/FCP-INDI/C-PAC)
 
 [![LGPL](https://www.gnu.org/graphics/lgplv3-88x31.png)](./COPYING.LESSER)
 

pyproject.toml

@@ -18,3 +18,22 @@
 [build-system]
 requires = ["nipype==1.8.6", "numpy==1.25.1", "pyyaml==6.0", "setuptools<60.0", "voluptuous==0.13.1"]
 build-backend = "setuptools.build_meta"
+
+[tool.coverage.paths]
+source = [
+  "/code",
+  "/home/circleci/project"
+]
+
+[tool.coverage.report]
+ignore_errors = true
+include_namespace_packages = true
+skip_empty = true
+
+[tool.coverage.run]
+branch = true
+relative_files = true
+source = [
+  "CPAC",
+  "dev/circleci_data"
+]