Merge pull request #2 from DiogoRibeiro7/feat/first_commit

feat: work

Author: DiogoRibeiro7

.github/workflows/bump-version.yml

@@ -0,0 +1,37 @@
+# .github/workflows/bump-version.yml
+name: Bump Version on Merge to Main
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  bump-version:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - run: pip install python-semantic-release
+
+      - name: Configure Git
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Run Semantic Release
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: semantic-release version
+
+      - name: Push changes
+        run: |
+          git push --follow-tags

gen_surv/cmm.py

@@ -0,0 +1,47 @@
+import pandas as pd
+import numpy as np
+from gen_surv.validate import validate_gen_cmm_inputs
+from gen_surv.censoring import runifcens, rexpocens
+from gen_surv.cmm import generate_event_times
+
+def gen_cmm(n, model_cens, cens_par, beta, covar, rate):
+    """
+    Generate survival data using a continuous-time Markov model (CMM).
+
+    Parameters:
+    - n (int): Number of individuals.
+    - model_cens (str): "uniform" or "exponential".
+    - cens_par (float): Parameter for censoring.
+    - beta (list): Regression coefficients (length 3).
+    - covar (float): Covariate range (uniformly sampled from [0, covar]).
+    - rate (list): Transition rates (length 6).
+
+    Returns:
+    - pd.DataFrame with columns: id, start, stop, status, covariate, transition
+    """
+    validate_gen_cmm_inputs(n, model_cens, cens_par, beta, covar, rate)
+
+    rfunc = runifcens if model_cens == "uniform" else rexpocens
+    rows = []
+
+    for k in range(n):
+        z1 = np.random.uniform(0, covar)
+        c = rfunc(1, cens_par)[0]
+        events = generate_event_times(z1, beta, rate)
+
+        t12, t13, t23 = events["t12"], events["t13"], events["t23"]
+        min_event_time = min(t12, t13, c)
+
+        if min_event_time < c:
+            if t12 <= t13:
+                transition = 1  # 1 -> 2
+                rows.append([k + 1, 0, t12, 1, z1, transition])
+            else:
+                transition = 2  # 1 -> 3
+                rows.append([k + 1, 0, t13, 1, z1, transition])
+        else:
+            # Censored before any event
+            rows.append([k + 1, 0, c, 0, z1, np.nan])
+
+    return pd.DataFrame(rows, columns=["id", "start", "stop", "status", "covariate", "transition"])
+

gen_surv/validate.py

@@ -20,3 +20,30 @@ def validate_gen_cphm_inputs(n: int, model_cens: str, cens_par: float, covar: fl
     if covar <= 0:
         raise ValueError("Argument 'covar' must be greater than 0")
 
+def validate_gen_cmm_inputs(n: int, model_cens: str, cens_par: float, beta: list, covar: float, rate: list):
+    """
+    Validate inputs for generating CMM (Continuous-Time Markov Model) data.
+
+    Parameters:
+    - n (int): Number of individuals.
+    - model_cens (str): Censoring model, must be "uniform" or "exponential".
+    - cens_par (float): Parameter for censoring distribution, must be > 0.
+    - beta (list): Regression coefficients, must have length 3.
+    - covar (float): Covariate value, must be > 0.
+    - rate (list): Transition rates, must have length 6.
+
+    Raises:
+    - ValueError: If any parameter is invalid.
+    """
+    if n <= 0:
+        raise ValueError("Argument 'n' must be greater than 0")
+    if model_cens not in {"uniform", "exponential"}:
+        raise ValueError("Argument 'model_cens' must be one of 'uniform' or 'exponential'")
+    if cens_par <= 0:
+        raise ValueError("Argument 'cens_par' must be greater than 0")
+    if len(beta) != 3:
+        raise ValueError("Argument 'beta' must be a list of length 3")
+    if covar <= 0:
+        raise ValueError("Argument 'covar' must be greater than 0")
+    if len(rate) != 6:
+        raise ValueError("Argument 'rate' must be a list of length 6")

pyproject.toml

@@ -14,6 +14,15 @@ numpy = "^1.26"
 [tool.poetry.dev-dependencies]
 pytest = "^8.0"
 
+[tool.semantic_release]
+version_source = "tag"
+version_variable = ["pyproject.toml:project.version"]
+commit_version_number = true
+changelog_file = "CHANGELOG.md"
+upload_to_repository = false
+branch = "main"
+build_command = ""
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"