Update the version to 0.14.0 by boulderdaze · Pull Request #708 · NCAR/musica

boulderdaze · 2025-12-10T22:26:38Z

Update the version to 0.14.0

…e mech config update

github-actions · 2025-12-10T22:26:58Z

📄 Documentation for this branch is available at: https://ncar.github.io/musica/branch/update_version/

codecov-commenter · 2025-12-10T23:32:42Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 76.10%. Comparing base (c1e08ad) to head (4ffa582).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #708   +/-   ##
=======================================
  Coverage   76.10%   76.10%           
=======================================
  Files         105      105           
  Lines        7768     7768           
=======================================
  Hits         5912     5912           
  Misses       1856     1856

Flag	Coverage Δ
cpp_fortran	`69.61% <ø> (ø)`
javascript	`90.87% <ø> (ø)`
python	`82.66% <ø> (ø)`

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Copilot

Pull request overview

This PR updates the MUSICA project to version 0.14.0, which includes several breaking changes and dependency updates alongside systematic configuration path updates across all test files and documentation.

Key Changes:

Version bumped from 0.13.0 to 0.14.0 across CMakeLists.txt and CITATION.cff
Configuration paths updated from directory references to explicit config.json file paths throughout all test suites
Dependency updates: MICM to v3.11.0, TUV-x to v0.14.0, and MechanismConfiguration to v1.1.0
Python minimum version raised from 3.9 to 3.10 with corresponding build configuration updates
C++ standard upgraded to C++20
Build infrastructure improvements including macOS Clang compiler override and LCOV error handling

Reviewed changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
CMakeLists.txt	Updated project version to 0.14.0 and set C++ standard to C++20
CITATION.cff	Updated version number to 0.14.0
cmake/dependencies.cmake	Updated dependency versions: MechanismConfiguration to v1.1.0, MICM to v3.11.0, TUV-x to v0.14.0
cmake/CodeCoverage.cmake	Added LCOV error handling flags for mismatch and unused errors
docker/Dockerfile.coverage	Updated base image from Fedora 37 to Fedora 39
pyproject.toml	Raised minimum Python to 3.10, removed cp39 builds, added macOS Clang compiler override
include/musica/micm/parse.hpp	Added v0 and v1 mechanism configuration type includes
src/micm/convert_v0_to_v1.cpp	Added v0 parser include for conversion functionality
src/test/unit/micm/parser.cpp	Updated all config paths to point to config.json files
src/test/unit/micm/micm_wrapper.cpp	Updated config path to point to config.json file
src/test/unit/micm/micm_c_api.cpp	Updated all config paths to point to config.json files
python/test/unit/micm/test_micm.py	Updated all config paths to point to config.json files
python/test/integration/test_chapman.py	Updated config path to point to config.json file
python/test/integration/test_analytical.py	Updated all config paths to point to config.json files, added trailing newline
javascript/tests/unit/micm/state.test.js	Updated config path to point to config.json file
javascript/tests/unit/micm/micm.test.js	Updated config path to point to config.json file
javascript/tests/integration/chapman.test.js	Updated config path to point to config.json file
javascript/tests/integration/analytical.test.js	Updated config path to point to config.json file
fortran/test/fetch_content_integration/test_micm_multiple_grid_cells.F90	Updated config path to point to config.json file
fortran/test/fetch_content_integration/test_micm_box_model.F90	Updated config paths to point to config.json files
fortran/test/fetch_content_integration/test_micm_api.F90	Updated all config paths to point to config.json files
docs/source/user_guide/examples/index.rst	Updated documentation links to point to config.json files
docs/source/tutorials/chapter3.rst	Updated documentation reference (contains error - see comments)

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docs/source/tutorials/chapter3.rst

docs/source/user_guide/examples/index.rst

K20shores · 2025-12-12T19:12:34Z

cmake/CodeCoverage.cmake

    set(LCOV_BASELINE_CMD 
        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -c -i -d . -b 
-        ${BASEDIR} -o ${Coverage_NAME}.base
+        ${BASEDIR} --ignore-errors mismatch -o ${Coverage_NAME}.base


Let's not modify this file. We can pass arguments to the setup command using the LCOV_ARGS. This PR handles this same issue.

K20shores · 2025-12-12T19:12:46Z

cmake/CodeCoverage.cmake

    set(LCOV_CAPTURE_CMD 
        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --directory . -b 
-        ${BASEDIR} --capture --output-file ${Coverage_NAME}.capture
+        ${BASEDIR} --capture --ignore-errors mismatch --output-file ${Coverage_NAME}.capture


see above comments, I think we can revert this change

K20shores · 2025-12-12T19:12:56Z

cmake/CodeCoverage.cmake

    set(LCOV_FILTER_CMD 
        ${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --remove 
-        ${Coverage_NAME}.total ${LCOV_EXCLUDES} --output-file ${Coverage_NAME}.info
+        ${Coverage_NAME}.total ${LCOV_EXCLUDES} --ignore-errors unused --output-file ${Coverage_NAME}.info


see above comments, I think we can revert this change

K20shores · 2025-12-12T19:13:49Z

fortran/test/fetch_content_integration/test_micm_api.F90

    integer                               :: jO2_index, jO3a_index, jO3b_index

-    config_path = "configs/v0/chapman"
+    config_path = "configs/v0/chapman/config.json"


Why are we adding the path? This isn't how this solver used to work. If we are required to have the file now, this will break downstream things and I'd rather not go through the process of updating music box, music box interactive to be compatible. Can this and the other paths be removed?

Since the version check is done to get the exact parser that matched the version, the function takes the file path instead of a directory. I understand your concerns and will open a PR that allows a directory in mech config

a good path would be to keep the development parser out of the universal parser, I think

K20shores · 2025-12-12T23:08:40Z

CMakeLists.txt

+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+


Do these need to be added? We already have c++20 turned on for all of our targets.

I encountered the errors that format library are not found and adding this worked. Let me remove it and try it again

update the version, add headers, udpate that config path following th…

073b816

…e mech config update

fix the error messages

4dc7133

boulderdaze added 6 commits December 10, 2025 16:48

use clang to workaround macos15 c++ lib header conflict with gcc

a694d55

add config path

03169fd

fix a bug

d95aabf

update the path

1326411

update tha path

acb6ee6

remove python 3.9

3010e01

boulderdaze requested a review from Copilot December 11, 2025 22:09

Copilot started reviewing on behalf of boulderdaze December 11, 2025 22:09 View session

Copilot AI reviewed Dec 11, 2025

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docs/source/tutorials/chapter3.rst Outdated Show resolved Hide resolved

docs/source/user_guide/examples/index.rst Outdated Show resolved Hide resolved

boulderdaze added 5 commits December 11, 2025 15:17

address copilot review

c34bbb0

disable tuvx temporarily

95a4b80

enable tuvx

800075f

test fetch cotent

5ea6928

revert back

608bfe6

boulderdaze requested review from K20shores and dwfncar December 12, 2025 19:00

boulderdaze self-assigned this Dec 12, 2025

K20shores requested changes Dec 12, 2025

View reviewed changes

boulderdaze added 3 commits December 12, 2025 15:16

address the code review

3f02c96

clean up

cfdd702

update lcov

391959e

K20shores reviewed Dec 12, 2025

View reviewed changes

boulderdaze added 3 commits December 12, 2025 16:40

remove specific c++ version

93c0ef4

merge main

e1a25ea

fix the merging error

4ffa582

K20shores approved these changes Dec 16, 2025

View reviewed changes

boulderdaze merged commit b31f130 into main Dec 16, 2025
77 of 81 checks passed

boulderdaze deleted the update_version branch December 16, 2025 16:49

		set(CMAKE_CXX_STANDARD 20)
		set(CMAKE_CXX_STANDARD_REQUIRED ON)

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codecov-commenter commented Dec 10, 2025 •

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