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2575d65
chore: prepare v1.4
Benncs Nov 23, 2025
c4fa6e4
feat: cmtool-assemble for xml reactor descriptor parsing
Benncs Nov 23, 2025
3406d0f
feat(xml): correct feed parsing
Benncs Nov 23, 2025
7f13d20
chore: add spdx header
Benncs Nov 23, 2025
8b7aac0
refractor
Benncs Nov 23, 2025
ba74c61
doc(example): add reactive example
Benncs Nov 26, 2025
79b8a2e
feat(data): use only json case, add method to determine residence_time
Benncs Nov 26, 2025
ac45747
feat(generation/parser): improve parsing exposed function to be used …
Benncs Nov 26, 2025
aa93464
feat(generation): clean and add reactor from file xml descriptor
Benncs Nov 28, 2025
06d6c4f
fix: reactor from file scheme and feed parsing
Benncs Nov 30, 2025
1ab61be
feat(cxx): add has_misc to check if existing key
Benncs Dec 5, 2025
3166c7b
feat(python): improve bindings transition and rawscalar
Benncs Dec 8, 2025
2570a22
feat(example): full two phase flow reactive python example
Benncs Dec 8, 2025
1c83540
feat(example): improve reactive simulation
Benncs Dec 17, 2025
0626bad
Merge branch 'v1.4-cxx' into v1.4
Benncs Dec 17, 2025
c471f96
fix(parser): need by rbiomc, add run_id to domain_data to be compared…
Benncs Jan 19, 2026
ed80431
feat: working flowmap generation
Benncs Jan 20, 2026
63a6337
ci: remove macos-13 runner, change pr template
Benncs Jan 20, 2026
b696f05
chore: fix license for cmtool-asssemble
Benncs Feb 11, 2026
822f80a
chore: readme and cargo-deny
Benncs Feb 12, 2026
afd0386
chore: update project meson version to have uniform versioning
Benncs Feb 16, 2026
bca7df1
chore: prek,clippy,update and clean dependencies, fix docstring tests
Benncs Feb 17, 2026
a9a148e
chore: clippy
Benncs Feb 17, 2026
bce387a
chore: minor
Benncs Feb 17, 2026
e66b4f4
doc: improve crate documentation
Benncs Feb 18, 2026
b20e2bb
fix(assemble): panic if feed/connection id is not known
Benncs Feb 19, 2026
d85fdac
feat(pycmtool): expose neighbors getter for flowmaps
Benncs Feb 20, 2026
dcd235f
feat(core): method to extract mesh boundary as compartment id
Benncs Feb 20, 2026
a29d5d2
chore: add roadmap
Benncs Feb 20, 2026
cb50166
feat: compute total volume from state
Benncs Feb 23, 2026
5c1c95e
chore: add comments
Benncs Feb 23, 2026
b7362c4
feat(vtk): python method to create vtk file
Benncs Mar 16, 2026
d2cc6c3
refractor
Benncs Mar 16, 2026
3966907
fix(cm): work in progress improve flux calculation
Benncs Mar 16, 2026
c2822d2
fix(cm): wip flow calculation
Benncs Mar 18, 2026
959e0ed
feat: try impl divergence free method
Benncs Mar 18, 2026
99a588f
feat(example): add example manip CM
Benncs Mar 18, 2026
7533469
fix(xml): hot fix because of xsd-parser update
Benncs Mar 18, 2026
fa4819b
fix(nix): working flake check
Benncs Mar 18, 2026
d905de2
fix(core): find a new way to calculate flows with null divergence (#8)
Benncs Mar 23, 2026
db2740f
feat(pycmtool): improve example and expose rawdata getter/setters
Benncs Mar 25, 2026
4694a92
feat(core): clean code improve vtk support, add scale/shift operation…
Benncs Mar 25, 2026
f1829fa
fix(data): remove rounding error on flowmap/probability/neighbor calc…
Benncs Mar 25, 2026
fa22fad
fix(states): probability leaving do not trigger assert for 0d flowmap
Benncs Mar 25, 2026
f918b1a
fix(CDF): hot fix, remove assertion in cumulative proba which are not…
Benncs Apr 28, 2026
859c43c
chore: clippy prepare merge
Benncs Apr 28, 2026
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27 changes: 6 additions & 21 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,24 +4,9 @@

## Content

- Scope:
- [ ] Code: if relevant, add affected target
- [ ] Build script: if relevant, add affected target
- [ ] Documentation
- [ ] CI
- [ ] Repository
- [ ] Other: ...
- Type of change:
- [ ] New feature(s)
- [ ] Fix: if relevant, add issue #...
- [ ] Testing
- [ ] Refactor
- [ ] Revert
- [ ] Chore
- Other:
- [ ] Breaking change
- [ ] New dependency
- Necessary follow-up:
- [ ] Needs documentation
- [ ] Needs testing
- [ ] Other: ...
### Main changes


## Issues


2 changes: 0 additions & 2 deletions .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -187,8 +187,6 @@ jobs:
strategy:
matrix:
platform:
- runner: macos-13
target: x86_64
- runner: macos-14
target: aarch64
steps:
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20 changes: 14 additions & 6 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -1,10 +1,18 @@
fail_fast: false
repos:
- repo: https://github.com/doublify/pre-commit-rust
- repo: https://github.com/doublify/pre-commit-rust
rev: v1.0

hooks:
# - id: cargo-check
# args: ["--workspace"]
- id: fmt
- id: cargo-check
args: ["--workspace"]
- id: fmt
args: ["--", "--check"]
# - id: clippy
# args: ["--", "-D", "warnings"]
- id: clippy
args: ["--", "-D", "warnings"]

- repo: https://github.com/EmbarkStudios/cargo-deny
rev: 0.19.0
hooks:
- id: cargo-deny
args: ["--all-features", "check", "ban", "licenses", "sources"]
31 changes: 31 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,36 @@
# CHANGELOG

## 0.1.4
*Date: *

#### Features:

- Assemble flowmaps


#### General Enhancements

- Improve transitioner api and performance
- Improve documentation and examples
- Improve python bindings

#### Build System Changes

- Update and clean dependencies

#### Breaking Changes

#### Deprecations
- C Case Reader

#### Bug Fixes

#### Known Issue

- CFD generated model does not compute flows correctly



## 0.1.3
*Date: 11/23/2025*

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