chore: sync version and tidy changelog (#84)

Author: DiogoRibeiro7

.flake8

@@ -1,5 +1,5 @@
 # .github/workflows/bump-version.yml
-name: Tag Version on Merge to Main
+name: Sync Version on Merge to Main
 
 on:
   push:
@@ -21,6 +21,6 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Tag repository from pyproject
-        run: python scripts/check_version_match.py --fix
+      - name: Synchronize tag and pyproject version
+        run: python scripts/check_version_match.py --fix --write
 

.github/workflows/bump-version.yml

@@ -39,7 +39,7 @@ jobs:
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Install dependencies
-        run: poetry install --with dev --no-interaction --no-root
+        run: poetry install --with dev --no-interaction
 
       - name: Check runtime dependencies
         run: |
@@ -90,7 +90,7 @@ jobs:
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Install dependencies
-        run: poetry install --with dev --no-interaction --no-root
+        run: poetry install --with dev --no-interaction
 
       - name: Run pre-commit checks
         run: poetry run pre-commit run --all-files

.github/workflows/ci.yml

@@ -11,6 +11,7 @@ repos:
     rev: 6.1.0
     hooks:
       - id: flake8
+        additional_dependencies: [flake8-pyproject]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0
     hooks:

.pre-commit-config.yaml

@@ -221,9 +221,6 @@
 - Update pyproject
   ([`a4b25e4`](https://github.com/DiogoRibeiro7/genSurvPy/commit/a4b25e470954091254b1384a44a991a47341bf80))
 
-- Work
-  ([`5ac5130`](https://github.com/DiogoRibeiro7/genSurvPy/commit/5ac513098238a8298430d1a95c6fbeed99db4cad))
-
 ### Continuous Integration
 
 - Add GitHub Actions workflow for test automation
@@ -253,6 +250,3 @@
 
 - Implement THMM data generator and finalize full model suite
   ([`1e667ba`](https://github.com/DiogoRibeiro7/genSurvPy/commit/1e667babf28892c3a85c43477562f2de85f07f3c))
-
-- Work
-  ([`45de359`](https://github.com/DiogoRibeiro7/genSurvPy/commit/45de359bbb0d7fbc671e41fa07d3a37b09e68e18))

CHANGELOG.md

@@ -1,13 +1,26 @@
 # Benchmarks
 
-This directory contains performance benchmarks run with `pytest-benchmark`.
-Run them with:
+Performance benchmarks for **genSurvPy** powered by the [`pytest-benchmark`](https://pytest-benchmark.readthedocs.io/en/latest/) plugin.
+
+## Running
+
+Install the optional `pytest-benchmark` dependency and execute:
+
+```bash
+poetry run pytest benchmarks -q --benchmark-only
+```
+
+To run an individual benchmark module:
 
 ```bash
-pytest benchmarks -q --benchmark-only
+poetry run pytest benchmarks/test_cmm_benchmark.py --benchmark-only
 ```
 
 ## Available benchmarks
 
-- validation helpers
-- TDCM generation
+- Validation helpers (`test_validation_benchmark.py`)
+- Time-dependent Cox model generation (`test_tdcm_benchmark.py`)
+- Continuous-time Markov model generation (`test_cmm_benchmark.py`)
+- Piecewise exponential generation (`test_piecewise_benchmark.py`)
+- Cox proportional hazards model generation (`test_cphm_benchmark.py`)
+- Mixture cure model generation (`test_mixture_benchmark.py`)

benchmarks/README.md

@@ -0,0 +1,18 @@
+import pytest
+
+pytest.importorskip("pytest_benchmark")
+
+from gen_surv.cmm import gen_cmm
+
+
+def test_cmm_generation_benchmark(benchmark):
+    benchmark(
+        gen_cmm,
+        n=1000,
+        model_cens="uniform",
+        cens_par=1.0,
+        beta=[0.1, 0.2, 0.3],
+        covariate_range=2.0,
+        rate=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
+        seed=42,
+    )

benchmarks/test_cmm_benchmark.py

@@ -0,0 +1,17 @@
+import pytest
+
+pytest.importorskip("pytest_benchmark")
+
+from gen_surv.cphm import gen_cphm
+
+
+def test_cphm_generation_benchmark(benchmark):
+    benchmark(
+        gen_cphm,
+        n=1000,
+        model_cens="uniform",
+        cens_par=1.0,
+        beta=0.5,
+        covariate_range=2.0,
+        seed=42,
+    )

benchmarks/test_cphm_benchmark.py

@@ -0,0 +1,14 @@
+import pytest
+
+pytest.importorskip("pytest_benchmark")
+
+from gen_surv.mixture import gen_mixture_cure
+
+
+def test_mixture_generation_benchmark(benchmark):
+    benchmark(
+        gen_mixture_cure,
+        n=1000,
+        cure_fraction=0.3,
+        seed=42,
+    )

benchmarks/test_mixture_benchmark.py

@@ -0,0 +1,16 @@
+import pytest
+
+pytest.importorskip("pytest_benchmark")
+
+from gen_surv.piecewise import gen_piecewise_exponential
+
+
+def test_piecewise_generation_benchmark(benchmark):
+    benchmark(
+        gen_piecewise_exponential,
+        n=1000,
+        breakpoints=[1.0, 2.0],
+        hazard_rates=[0.5, 0.3, 0.1],
+        n_covariates=3,
+        seed=42,
+    )